1630 3273 691 http://www.ebi.ac.uk/swo/SWO_0000199 GenePix Pro 4.0 'GenePix Pro 4.0' SubClassOf 'GenePix Pro' http://www.ebi.ac.uk/swo/SWO_0000190 GeneRfold 'GeneRfold' SubClassOf 'software' 'GeneRfold' SubClassOf 'is encoded in' some 'R language' 'GeneRfold' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'PostScript')) 'GeneRfold' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GeneRfold' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000192 GeneSelector 'GeneSelector' SubClassOf 'R software' 'GeneSelector' SubClassOf 'implements' some 'Linear modelling' 'GeneSelector' SubClassOf 'implements' some 'Wilcoxon' 'GeneSelector' SubClassOf 'implements' some 'WilcEbam' 'GeneSelector' SubClassOf 'implements' some 'BaldiLongT' 'GeneSelector' SubClassOf 'software' 'GeneSelector' SubClassOf 'implements' some ''t-test'' 'GeneSelector' SubClassOf 'implements' some 'SAM' 'GeneSelector' SubClassOf 'implements' some 'Bayesian Model' 'GeneSelector' SubClassOf 'is encoded in' some 'R language' 'GeneSelector' SubClassOf 'implements' some 'FoxDimmicT' http://www.ebi.ac.uk/swo/SWO_0000191 GeneSelectMMD 'GeneSelectMMD' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GeneSelectMMD' SubClassOf 'is executed in' some 'differential expression analysis' 'GeneSelectMMD' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GeneSelectMMD' SubClassOf 'is encoded in' some 'R language' 'GeneSelectMMD' SubClassOf 'software' 'GeneSelectMMD' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'GeneSelectMMD' SubClassOf 'implements' some 'MMD' 'GeneSelectMMD' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000194 GeneSpringGX 'GeneSpringGX' SubClassOf 'GeneSpring' http://www.ebi.ac.uk/swo/SWO_0000193 GeneSpring 'GeneSpring' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GeneSpring' SubClassOf 'Agilent Technologies Software' 'GeneSpring' SubClassOf 'output of' some ('software development' and ('has participant' value 'Strand Life Sciences')) 'GeneSpring' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'GeneSpring' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) 'GeneSpring' SubClassOf 'R software' 'GeneSpring' SubClassOf 'is encoded in' some 'R language' 'GeneSpring' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000196 GeneTraffic 'GeneTraffic' SubClassOf 'is encoded in' some 'R language' 'GeneTraffic' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GeneTraffic' SubClassOf 'software' 'GeneTraffic' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000195 GeneTac Analyser 'GeneTac Analyser' SubClassOf 'software' 'GeneTac Analyser' SubClassOf 'output of' some ('software development' and ('has participant' value 'Applied Biosystems')) http://www.ontodm.com/OntoDM-core/OntoDM_000192 pattern discovery algorithm DisjointClasses: 'clustering algorithm', 'predictive modeling algorithm', 'pattern discovery algorithm' 'pattern discovery algorithm' SubClassOf 'single generalization algorithm' http://www.ebi.ac.uk/swo/data/SWO_3000070 tabix file format 'tabix file format' SubClassOf 'sequence feature format' 'tabix file format' SubClassOf 'obsolete sequence feature format' http://www.ebi.ac.uk/swo/data/SWO_3000062 FCS3.0 'FCS3.0' SubClassOf 'has version' value 'FCS Data Standard Version 3.0' http://www.ebi.ac.uk/swo/data/SWO_3000060 Affymetrix-compliant data 'Affymetrix-compliant data' EquivalentTo 'has format specification' some ('data format specification' and ('is published by' value 'Affymetrix')) http://www.ebi.ac.uk/swo/data/SWO_3000069 sequence feature format 'sequence feature format' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/data/SWO_3000068 BLASTN 'BLASTN' SubClassOf 'has specified data input' some ('DNA nucleotide sequence' and ('has format specification' some 'GenBank format')) 'BLASTN' SubClassOf 'BLAST' 'BLASTN' SubClassOf 'has specified data input' some ('DNA nucleotide sequence' and ('has format specification' some 'FASTA format')) 'BLASTN' SubClassOf 'obsolete BLAST' http://www.ebi.ac.uk/swo/data/SWO_3000053 Knowledge representation role 'Knowledge representation role' SubClassOf 'role' 'Knowledge representation role' SubClassOf http://www.ifomis.org/bfo/1.1/snap#Role http://www.ontodm.com/OntoDM-core/OntoDM_000160 predictive modeling algorithm DisjointClasses: 'clustering algorithm', 'predictive modeling algorithm', 'pattern discovery algorithm' 'predictive modeling algorithm' SubClassOf 'single generalization algorithm' http://www.ebi.ac.uk/swo/data/SWO_3000059 CEL ASCII format 'CEL ASCII format' SubClassOf 'is published by' value 'Affymetrix' http://www.ebi.ac.uk/swo/data/SWO_3000058 BAR 'BAR' SubClassOf 'is published by' value 'Affymetrix' http://www.ebi.ac.uk/swo/data/SWO_3000057 CDF ASCII format 'CDF ASCII format' SubClassOf 'is published by' value 'Affymetrix' http://www.ebi.ac.uk/swo/data/SWO_3000056 BioPAX Manchester OWL Syntax format 'BioPAX Manchester OWL Syntax format' SubClassOf 'is alternative format of' some 'BioPAX RDF/XML format' 'BioPAX Manchester OWL Syntax format' SubClassOf 'has_role' some 'Knowledge representation role' http://www.ebi.ac.uk/swo/data/SWO_3000055 BioPAX RDF/XML format 'BioPAX RDF/XML format' SubClassOf 'has_role' some 'Knowledge representation role' http://www.ebi.ac.uk/swo/SWO_0000154 COBRA 'COBRA' SubClassOf 'implements' some 'ODE Algorithm' 'COBRA' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'SBML')) 'COBRA' SubClassOf 'has license' some 'GNU GPL v2' 'COBRA' SubClassOf 'uses platform' some 'Linux' 'COBRA' SubClassOf 'has license' only 'GNU GPL v2' 'COBRA' SubClassOf 'uses platform' some 'Microsoft Windows' 'COBRA' SubClassOf 'uses platform' some 'OS X' 'COBRA' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'SBML')) http://www.ebi.ac.uk/swo/SWO_0000153 VCell 'VCell' SubClassOf 'has license' some 'MIT License' 'VCell' SubClassOf 'implements' some 'DAE Algorithm' 'VCell' SubClassOf 'implements' some 'ODE Algorithm' 'VCell' SubClassOf 'implements' some 'PDE Algorithm' 'VCell' SubClassOf 'uses platform' some 'Linux' 'VCell' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'SBML')) 'VCell' SubClassOf 'uses platform' some 'OS X' 'VCell' SubClassOf 'is executed in' some 'Modelling and simulation' 'VCell' SubClassOf 'uses platform' some 'Microsoft Windows' 'VCell' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'SBML')) http://www.ebi.ac.uk/swo/SWO_0000156 COBRA Toolbox 'COBRA Toolbox' SubClassOf 'is software for' only 'MATLAB' 'COBRA Toolbox' SubClassOf 'is software for' some 'MATLAB' http://www.ebi.ac.uk/swo/SWO_0000155 COBRApy 'COBRApy' SubClassOf 'is encoded in' some 'Python' 'COBRApy' SubClassOf 'is encoded in' only 'Python' http://www.ebi.ac.uk/swo/SWO_0000158 libSBML 'libSBML' SubClassOf 'is encoded in' some 'Java' 'libSBML' SubClassOf 'is encoded in' some 'R language' 'libSBML' SubClassOf 'is encoded in' some 'Perl' 'libSBML' SubClassOf 'uses platform' some 'OS X' 'libSBML' SubClassOf 'has interface' some 'application programming interface' 'libSBML' SubClassOf 'software' 'libSBML' SubClassOf 'is encoded in' some 'C++' 'libSBML' SubClassOf 'is encoded in' some 'Python' 'libSBML' SubClassOf 'is software for' some 'MATLAB' 'libSBML' SubClassOf 'is encoded in' some 'C Sharp' 'libSBML' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'SBML')) 'libSBML' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'SBML')) 'libSBML' SubClassOf 'is encoded in' some 'C' 'libSBML' SubClassOf 'R software' 'libSBML' SubClassOf 'has license' only 'GNU LGPL' 'libSBML' SubClassOf 'uses platform' some 'Linux' 'libSBML' SubClassOf 'uses platform' some 'Microsoft Windows' 'libSBML' SubClassOf 'is encoded in' some 'GNU Octave' 'libSBML' SubClassOf 'is encoded in' some 'Ruby' 'libSBML' SubClassOf 'has license' some 'GNU LGPL' 'libSBML' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000152 iBioSim 'iBioSim' SubClassOf 'has license' only 'MIT License' 'iBioSim' SubClassOf 'uses platform' some 'Linux' 'iBioSim' SubClassOf 'is executed in' some 'simulation and analysis of biochemical networks' 'iBioSim' SubClassOf 'implements' some 'ODE Algorithm' 'iBioSim' SubClassOf 'implements' some 'Monte Carlo' 'iBioSim' SubClassOf 'uses platform' some 'OS X' 'iBioSim' SubClassOf 'has license' some 'MIT License' 'iBioSim' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'SBML')) 'iBioSim' SubClassOf 'implements' some 'Markov Chain Monte Carlo' 'iBioSim' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'SBML')) 'iBioSim' SubClassOf 'uses platform' some 'Microsoft Windows' http://purl.obolibrary.org/obo/OBI_0000011 planned process 'planned process' SubClassOf 'process' http://www.ebi.ac.uk/swo/SWO_0000165 Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA) 'Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000164 GLAD 'GLAD' SubClassOf 'implements' some 'Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)' 'GLAD' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GLAD' SubClassOf 'is encoded in' some 'R language' 'GLAD' SubClassOf 'software' 'GLAD' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'GLAD' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000167 GMS 'GMS' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000166 GLEAMS software 'GLEAMS software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Molecular Neuroscience Core, Center for Behavioral Neuroscience, Atlanta')) 'GLEAMS software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000169 Gene Recommender algorithm 'Gene Recommender algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000168 GOstats 'GOstats' SubClassOf 'implements' some 'Hypergeometric probability' 'GOstats' SubClassOf 'is encoded in' some 'R language' 'GOstats' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GOstats' SubClassOf 'software' 'GOstats' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) 'GOstats' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'GOstats' SubClassOf 'implements' some ''t-test'' 'GOstats' SubClassOf 'is executed in' some 'differential expression analysis' 'GOstats' SubClassOf 'has specified data output' some ('Gene expression data' and ('has format specification' some 'data format specification')) 'GOstats' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000163 GGtools 'GGtools' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'GGtools' SubClassOf 'R software' 'GGtools' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'rda')) 'GGtools' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GGtools' SubClassOf 'is encoded in' some 'R language' 'GGtools' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GGtools' SubClassOf 'software' http://purl.obolibrary.org/obo/BFO_0000040 material entity 'material entity' SubClassOf 'independent continuant' http://www.ebi.ac.uk/swo/SWO_0000176 Gene Pix 'Gene Pix' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Molecular Devices')) 'Gene Pix' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000175 GeneData Expressionist Analyst v4.0.5 'GeneData Expressionist Analyst v4.0.5' SubClassOf 'software' 'GeneData Expressionist Analyst v4.0.5' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Genedata')) http://www.ebi.ac.uk/swo/SWO_0000178 GenePix 4.1 'GenePix 4.1' SubClassOf 'Gene Pix' http://www.ebi.ac.uk/swo/SWO_0000177 GenePix 3.0.6 'GenePix 3.0.6' SubClassOf 'Gene Pix' http://www.ebi.ac.uk/swo/SWO_0000179 GenePix 4100A 'GenePix 4100A' SubClassOf 'GenePix' http://www.ebi.ac.uk/swo/SWO_0000170 GSEABase 'GSEABase' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'XML')) 'GSEABase' SubClassOf 'software' 'GSEABase' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GSEABase' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GSEABase' SubClassOf 'is encoded in' some 'R language' 'GSEABase' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000172 Gamma-Gamma hierarchical model 'Gamma-Gamma hierarchical model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000171 GSEAlm 'GSEAlm' SubClassOf 'software' 'GSEAlm' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'GSEAlm' SubClassOf 'R software' 'GSEAlm' SubClassOf 'implements' some 'Gene-Set Enrichment Analysis' 'GSEAlm' SubClassOf 'implements' some 'Linear modelling' 'GSEAlm' SubClassOf 'is executed in' some 'gene expression analysis' 'GSEAlm' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) 'GSEAlm' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GSEAlm' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000174 Gene-Set Enrichment Analysis 'Gene-Set Enrichment Analysis' SubClassOf 'algorithm' http://edamontology.org/operation_0362 Genome annotation 'Genome annotation' SubClassOf 'data transformation' 'Genome annotation' SubClassOf http://edamontology.org/operation_0361 http://www.ebi.ac.uk/swo/SWO_0000173 Gaussian locally weighted regression 'Gaussian locally weighted regression' SubClassOf 'algorithm' http://purl.obolibrary.org/obo/IAO_0000033 directive information entity 'directive information entity' SubClassOf 'information content entity' http://purl.obolibrary.org/obo/IAO_0000030 information content entity 'information content entity' SubClassOf 'generically dependent continuant' http://www.ebi.ac.uk/swo/SWO_0000187 GenePix Pro [Axon Instruments] 'GenePix Pro [Axon Instruments]' SubClassOf 'GenePix Pro' http://www.ebi.ac.uk/swo/SWO_0000186 GenePix Pro 6 [Axon Instruments] 'GenePix Pro 6 [Axon Instruments]' SubClassOf 'GenePix Pro [Axon Instruments]' http://www.ebi.ac.uk/swo/SWO_0000189 GeneRegionScan 'GeneRegionScan' SubClassOf 'software' 'GeneRegionScan' SubClassOf 'R software' 'GeneRegionScan' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'GeneRegionScan' SubClassOf 'is encoded in' some 'R language' 'GeneRegionScan' SubClassOf 'has specified data input' some ('Image' and ('has format specification' some 'CEL binary format')) http://www.ebi.ac.uk/swo/SWO_0000188 GeneR 'GeneR' SubClassOf 'R software' 'GeneR' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GeneR' SubClassOf 'is encoded in' some 'R language' 'GeneR' SubClassOf 'software' 'GeneR' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'GeneR' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'FASTA format')) http://www.ebi.ac.uk/swo/SWO_0000181 GenePix 'GenePix' SubClassOf 'Gene Pix' http://www.ebi.ac.uk/swo/SWO_0000180 GenePix 5.0.1 'GenePix 5.0.1' SubClassOf 'Gene Pix' http://www.ebi.ac.uk/swo/SWO_0000183 GenePix Pro 3 'GenePix Pro 3' SubClassOf 'GenePix Pro' http://www.ebi.ac.uk/swo/SWO_0000182 GenePix Pro 'GenePix Pro' SubClassOf 'Gene Pix' http://www.ebi.ac.uk/swo/SWO_0000185 GenePix Pro 6.0 'GenePix Pro 6.0' SubClassOf 'GenePix Pro' http://www.ebi.ac.uk/swo/SWO_0000184 GenePix Pro 5.0 'GenePix Pro 5.0' SubClassOf 'GenePix Pro' http://purl.obolibrary.org/obo/IAO_0000027 data item 'data item' SubClassOf 'is encoded in' some 'data format specification' http://purl.obolibrary.org/obo/IAO_0000028 symbol 'symbol' SubClassOf 'information content entity' http://www.ebi.ac.uk/swo/SWO_0000594 limmaGUI 'limmaGUI' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' only 'TIFF')) 'limmaGUI' SubClassOf 'software' 'limmaGUI' SubClassOf 'is published by' value 'Bioconductor' 'limmaGUI' SubClassOf 'BioConductor Software' 'limmaGUI' SubClassOf 'is encoded in' some 'R language' 'limmaGUI' SubClassOf 'R software' 'limmaGUI' SubClassOf 'implements' some 'Linear modelling' 'limmaGUI' SubClassOf 'has specified data input' some 'Text data set' http://www.ebi.ac.uk/swo/SWO_0000593 limma 'limma' SubClassOf 'BioConductor Software' 'limma' SubClassOf 'R software' 'limma' SubClassOf 'is published by' value 'Bioconductor' 'limma' SubClassOf 'is encoded in' some 'R language' 'limma' SubClassOf 'software' 'limma' SubClassOf 'has specified data input' some 'Text data set' 'limma' SubClassOf 'implements' some 'Linear modelling' 'limma' SubClassOf 'is developed by' value 'Walter and Eliza Hall Institute' 'limma' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' only 'TIFF')) http://www.ebi.ac.uk/swo/SWO_0000596 lma 'lma' SubClassOf 'binary format' http://www.ebi.ac.uk/swo/SWO_0000595 Linear modelling 'Linear modelling' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000598 log file 'log file' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000597 Local-pooled-error 'Local-pooled-error' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000599 logicFS 'logicFS' SubClassOf 'R software' 'logicFS' SubClassOf 'BioConductor Software' 'logicFS' SubClassOf 'is encoded in' some 'R language' 'logicFS' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'logicFS' SubClassOf 'implements' some 'Logic regression' 'logicFS' SubClassOf 'has specified data input' some ('has format specification' only 'logicFS dataset') 'logicFS' SubClassOf 'is published by' value 'Bioconductor' 'logicFS' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000590 keggorth 'keggorth' SubClassOf 'software' 'keggorth' SubClassOf 'BioConductor Software' 'keggorth' SubClassOf 'has specified data input' some 'Gene expression dataset' 'keggorth' SubClassOf 'is encoded in' some 'R language' 'keggorth' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'keggorth' SubClassOf 'is published by' value 'Bioconductor' 'keggorth' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000592 Likelihood method 'Likelihood method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000591 lapmix 'lapmix' SubClassOf 'has specified data input' some 'Gene expression dataset' 'lapmix' SubClassOf 'BioConductor Software' 'lapmix' SubClassOf 'is encoded in' some 'R language' 'lapmix' SubClassOf 'is published by' value 'Bioconductor' 'lapmix' SubClassOf 'R software' 'lapmix' SubClassOf 'implements' some 'Laplace mixture model' 'lapmix' SubClassOf 'software' 'lapmix' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'lapmix' SubClassOf 'is executed in' some 'differential expression analysis' http://edamontology.org/format_3162 MAGE-TAB 'MAGE-TAB' SubClassOf http://edamontology.org/format_2058 http://edamontology.org/format_3161 MAGE-ML 'MAGE-ML' SubClassOf http://edamontology.org/format_2058 http://edamontology.org/format_3158 http://edamontology.org/format_3158 SubClassOf http://edamontology.org/format_2054 http://www.ebi.ac.uk/efo/swo/SWO_0000408 obsolete Clustered data set 'obsolete Clustered data set' SubClassOf 'obsolete SWO class' 'obsolete Clustered data set' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000409 obsolete R data frame 'obsolete R data frame' SubClassOf 'obsolete SWO class' 'obsolete R data frame' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/efo/swo/SWO_0000406 obsolete Gene list 'obsolete Gene list' SubClassOf 'obsolete SWO class' 'obsolete Gene list' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000405 obsolete ArrayExpress Bioconductor 'obsolete ArrayExpress Bioconductor' SubClassOf 'obsolete SWO class' 'obsolete ArrayExpress Bioconductor' SubClassOf 'obsolete MAGE-TAB inputting software' 'obsolete ArrayExpress Bioconductor' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000133 DAVID 'DAVID' SubClassOf 'has interface' some 'web service' 'DAVID' SubClassOf 'has website homepage' value "http://david.abcc.ncifcrf.gov/" 'DAVID' SubClassOf 'is executed in' some 'Gene-Set Enrichment Analysis' 'DAVID' SubClassOf 'has interface' some 'web user interface' http://www.ebi.ac.uk/swo/SWO_0000135 PSI-BLAST 'PSI-BLAST' SubClassOf 'has license' some 'free to use license' 'PSI-BLAST' SubClassOf 'software' 'PSI-BLAST' SubClassOf 'has interface' some 'graphical user interface' 'PSI-BLAST' SubClassOf 'has specified data input' some ('amino acid protein sequence data' and ('has format specification' some 'GenBank format')) 'PSI-BLAST' SubClassOf 'has specified data input' some ('amino acid protein sequence data' and ('has format specification' some 'FASTA format')) 'PSI-BLAST' SubClassOf 'BLAST' 'PSI-BLAST' SubClassOf 'obsolete BLAST' http://www.ebi.ac.uk/swo/SWO_0000138 Entrez 'Entrez' SubClassOf 'has interface' some 'web user interface' 'Entrez' SubClassOf 'software' 'Entrez' SubClassOf 'is executed in' some 'web content search' http://www.ebi.ac.uk/swo/SWO_0000137 NONMEM 'NONMEM' SubClassOf 'is encoded in' some 'NMTRAN' 'NONMEM' SubClassOf 'implements' some 'SAEM' 'NONMEM' SubClassOf 'has interface' some 'command-line interface' 'NONMEM' SubClassOf 'has license' some 'Proprietary commercial software license' 'NONMEM' SubClassOf 'software' 'NONMEM' SubClassOf 'has version' value '7.2.0' http://www.ebi.ac.uk/efo/swo/SWO_0000419 obsolete ScanArray v3.1 software 'obsolete ScanArray v3.1 software' SubClassOf 'obsolete SWO class' 'obsolete ScanArray v3.1 software' SubClassOf 'obsolete ScanArray' http://www.ebi.ac.uk/efo/swo/SWO_0000417 obsolete ScanAlyze 'obsolete ScanAlyze' SubClassOf 'obsolete SWO class' 'obsolete ScanAlyze' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000418 obsolete ScanArray 'obsolete ScanArray' SubClassOf 'obsolete SWO class' 'obsolete ScanArray' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000415 obsolete R language 'obsolete R language' SubClassOf 'obsolete SWO class' 'obsolete R language' SubClassOf 'programming language' http://www.ebi.ac.uk/efo/swo/SWO_0000416 obsolete ScISI 'obsolete ScISI' SubClassOf 'obsolete SWO class' 'obsolete ScISI' SubClassOf 'obsolete R software' 'obsolete ScISI' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000422 obsolete ShortRead 'obsolete ShortRead' SubClassOf 'obsolete SWO class' 'obsolete ShortRead' SubClassOf 'obsolete R software' 'obsolete ShortRead' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000143 data storage 'data storage' SubClassOf 'data transformation' 'data storage' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000423 obsolete Signaling Pathway Impact Analysis (SPIA) algorithm 'obsolete Signaling Pathway Impact Analysis (SPIA) algorithm' SubClassOf 'obsolete SWO class' 'obsolete Signaling Pathway Impact Analysis (SPIA) algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000142 PostgreSQL 'PostgreSQL' SubClassOf 'is executed in' some 'data storage' 'PostgreSQL' SubClassOf 'has website homepage' value "http://www.postgresql.org/" http://www.ebi.ac.uk/efo/swo/SWO_0000420 obsolete scanning software 'obsolete scanning software' SubClassOf 'obsolete SWO class' 'obsolete scanning software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000145 Segway 1.2 'Segway 1.2' SubClassOf 'has version' value 'Segway version 1.2' 'Segway 1.2' SubClassOf 'has license' some 'GNU GPL v2' 'Segway 1.2' SubClassOf 'is executed in' some 'Genome annotation' 'Segway 1.2' SubClassOf 'has specified data output' some 'GMTK parameter data' 'Segway 1.2' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'BED format')) 'Segway 1.2' SubClassOf 'implements' some 'dynamic Bayesian network model' 'Segway 1.2' SubClassOf 'is encoded in' some ('Python 2.6' or 'Python 2.7') 'Segway 1.2' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'genomedata format')) http://www.ebi.ac.uk/efo/swo/SWO_0000421 obsolete Scanning software G2565AA version A6.3.1 'obsolete Scanning software G2565AA version A6.3.1' SubClassOf 'obsolete SWO class' 'obsolete Scanning software G2565AA version A6.3.1' SubClassOf 'obsolete scanning software' http://www.ebi.ac.uk/swo/SWO_0000147 Python 2.7 'Python 2.7' SubClassOf 'has version' value 'Python version 2.7' http://www.ebi.ac.uk/swo/SWO_0000146 Python 2.6 'Python 2.6' SubClassOf 'has version' value 'Python version 2.6' http://www.ebi.ac.uk/swo/SWO_0000149 Mac OS 'Mac OS' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Apple Inc.')) 'Mac OS' SubClassOf 'is executed in' some 'manage computer operations' 'Mac OS' SubClassOf 'output of' some ('software development' and ('has participant' value 'Apple Inc.')) 'Mac OS' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000148 Firth's bias reduction procedure 'Firth's bias reduction procedure' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000141 Weka 'Weka' SubClassOf 'has website homepage' value "http://www.cs.waikato.ac.nz/~ml/weka/" 'Weka' SubClassOf 'has license' some 'GNU GPL' 'Weka' SubClassOf 'has interface' some 'graphical user interface' 'Weka' SubClassOf 'is encoded in' some 'Java' http://www.ebi.ac.uk/swo/SWO_0000140 search engine 'search engine' EquivalentTo 'software' and ('is executed in' some 'web content search') http://www.ebi.ac.uk/efo/swo/SWO_0000428 obsolete Spot quantification 'obsolete Spot quantification' SubClassOf 'obsolete SWO class' 'obsolete Spot quantification' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000429 obsolete Spotfinder [TIGR] 'obsolete Spotfinder [TIGR]' SubClassOf 'obsolete SWO class' 'obsolete Spotfinder [TIGR]' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000426 obsolete 'Smith-Waterman' 'obsolete 'Smith-Waterman'' SubClassOf 'obsolete SWO class' 'obsolete 'Smith-Waterman'' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000424 obsolete Silicon Genetics Genespring 'obsolete Silicon Genetics Genespring' SubClassOf 'obsolete SWO class' 'obsolete Silicon Genetics Genespring' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000425 obsolete Similarity score 'obsolete Similarity score' SubClassOf 'obsolete SWO class' 'obsolete Similarity score' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000550 gene2pathway 'gene2pathway' SubClassOf 'has specified data input' some 'Gene list' 'gene2pathway' SubClassOf 'is published by' value 'Bioconductor' 'gene2pathway' SubClassOf 'R software' 'gene2pathway' SubClassOf 'is encoded in' some 'R language' 'gene2pathway' SubClassOf 'software' 'gene2pathway' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'gene2pathway' SubClassOf 'BioConductor Software' 'gene2pathway' SubClassOf 'implements' some 'Hierarchical clustering' http://www.ebi.ac.uk/swo/SWO_0000552 Gene array analysis algorithm 'Gene array analysis algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000432 obsolete TAS Software 'obsolete TAS Software' SubClassOf 'obsolete SWO class' 'obsolete TAS Software' SubClassOf 'obsolete Affymetrix Software' http://www.ebi.ac.uk/swo/SWO_0000551 geneRecommender 'geneRecommender' SubClassOf 'software' 'geneRecommender' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'geneRecommender' SubClassOf 'has specified data input' some 'Gene list' 'geneRecommender' SubClassOf 'implements' some 'Gene Recommender algorithm' 'geneRecommender' SubClassOf 'BioConductor Software' 'geneRecommender' SubClassOf 'is executed in' some ('data normalization' and 'differential expression analysis') 'geneRecommender' SubClassOf 'is published by' value 'Bioconductor' 'geneRecommender' SubClassOf 'R software' 'geneRecommender' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000554 Gene expression dataset 'Gene expression dataset' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000430 obsolete Spotfire 'obsolete Spotfire' SubClassOf 'obsolete SWO class' 'obsolete Spotfire' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000553 gene expression analysis 'gene expression analysis' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_0000556 genemeta 'genemeta' SubClassOf 'is encoded in' some 'R language' 'genemeta' SubClassOf 'R software' 'genemeta' SubClassOf 'has specified data output' some 'Graph plot' 'genemeta' SubClassOf 'software' 'genemeta' SubClassOf 'has specified data input' some 'Gene expression data' 'genemeta' SubClassOf 'implements' some (''t-test'' and ''FDR'' and ('Random effects model' or 'Fixed effect model')) http://www.ebi.ac.uk/swo/SWO_0000555 genefilter 'genefilter' SubClassOf 'is encoded in' some 'R language' 'genefilter' SubClassOf 'R software' 'genefilter' SubClassOf 'is executed in' some 'differential expression analysis' 'genefilter' SubClassOf 'is published by' value 'Bioconductor' 'genefilter' SubClassOf 'has specified data input' some 'Gene expression dataset' 'genefilter' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'genefilter' SubClassOf 'BioConductor Software' 'genefilter' SubClassOf 'implements' some 'k-nearest neighbour classification' 'genefilter' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000558 genomeIntervals 'genomeIntervals' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'genomeIntervals' SubClassOf 'is published by' value 'Bioconductor' 'genomeIntervals' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'genomeIntervals' SubClassOf 'has specified data input' some ('has format specification' only ('GFF' and 'R data frame')) 'genomeIntervals' SubClassOf 'BioConductor Software' 'genomeIntervals' SubClassOf 'R software' 'genomeIntervals' SubClassOf 'is encoded in' some 'R language' 'genomeIntervals' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000557 geneplotter 'geneplotter' SubClassOf 'R software' 'geneplotter' SubClassOf 'has specified data input' some 'Gene expression dataset' 'geneplotter' SubClassOf 'software' 'geneplotter' SubClassOf 'is encoded in' some 'R language' 'geneplotter' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/efo/swo/SWO_0000437 obsolete Theodore Ts’o’s 'obsolete Theodore Ts’o’s' SubClassOf 'obsolete SWO class' 'obsolete Theodore Ts’o’s' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000438 obsolete TypeInfo 'obsolete TypeInfo' SubClassOf 'obsolete SWO class' 'obsolete TypeInfo' SubClassOf 'obsolete BioConductor Software' 'obsolete TypeInfo' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000435 obsolete TargetSearch 'obsolete TargetSearch' SubClassOf 'obsolete SWO class' 'obsolete TargetSearch' SubClassOf 'obsolete BioConductor Software' 'obsolete TargetSearch' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000444 obsolete WilcEbam 'obsolete WilcEbam' SubClassOf 'obsolete SWO class' 'obsolete WilcEbam' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000561 globaltest 'globaltest' SubClassOf 'implements' some 'globaltest' 'globaltest' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'globaltest' SubClassOf 'is encoded in' some 'R language' 'globaltest' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'globaltest' SubClassOf 'R software' 'globaltest' SubClassOf 'has specified data input' some 'Gene expression dataset' 'globaltest' SubClassOf 'software' 'globaltest' SubClassOf 'is published by' value 'Bioconductor' 'globaltest' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000445 obsolete Wilcoxon 'obsolete Wilcoxon' SubClassOf 'obsolete SWO class' 'obsolete Wilcoxon' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000560 Global test 'Global test' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000442 obsolete VanillaICE 'obsolete VanillaICE' SubClassOf 'obsolete SWO class' 'obsolete VanillaICE' SubClassOf 'obsolete R software' 'obsolete VanillaICE' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000563 goProfiles 'goProfiles' SubClassOf 'is encoded in' some 'R language' 'goProfiles' SubClassOf 'implements' some 'Gene-Set Enrichment Analysis' 'goProfiles' SubClassOf 'has specified data output' some 'Image' 'goProfiles' SubClassOf 'has specified data input' some 'Gene list' 'goProfiles' SubClassOf 'is executed in' some ('data visualization' and 'descriptive statistical calculation' and 'differential expression analysis') 'goProfiles' SubClassOf 'R software' 'goProfiles' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000562 gmt format 'gmt format' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000565 gpls 'gpls' SubClassOf 'BioConductor Software' 'gpls' SubClassOf 'R software' 'gpls' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'gpls' SubClassOf 'is published by' value 'Bioconductor' 'gpls' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'gpls' SubClassOf 'is encoded in' some 'R language' 'gpls' SubClassOf 'software' 'gpls' SubClassOf 'implements' some 'Iteratively ReWeighted Least Squares' http://www.ebi.ac.uk/efo/swo/SWO_0000441 obsolete Variance-stabilizing transformation (VST) algorithm 'obsolete Variance-stabilizing transformation (VST) algorithm' SubClassOf 'obsolete SWO class' 'obsolete Variance-stabilizing transformation (VST) algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000564 goTools 'goTools' SubClassOf 'is executed in' some 'dataset comparison' 'goTools' SubClassOf 'is encoded in' some 'R language' 'goTools' SubClassOf 'software' 'goTools' SubClassOf 'R software' 'goTools' SubClassOf 'is published by' value 'Bioconductor' 'goTools' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'goTools' SubClassOf 'BioConductor Software' 'goTools' SubClassOf 'has specified data input' some 'Gene list' http://www.ebi.ac.uk/swo/SWO_0000567 graph 'graph' SubClassOf 'R software' 'graph' SubClassOf 'implements' some 'R interface to boost graph library algorithm (RBGL)' 'graph' SubClassOf 'has specified data output' some 'Graph plot' 'graph' SubClassOf 'software' 'graph' SubClassOf 'is executed in' some ('distance calculation' and 'descriptive statistical calculation') 'graph' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'graph' SubClassOf 'is published by' value 'Bioconductor' 'graph' SubClassOf 'is encoded in' some 'R language' 'graph' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000566 gpr format 'gpr format' SubClassOf 'tab delimited file format' http://www.ebi.ac.uk/swo/SWO_0000569 gtr 'gtr' SubClassOf 'tab delimited file format' http://www.ebi.ac.uk/swo/data/SWO_3000036 obsolete CopasiML 'obsolete CopasiML' SubClassOf 'obsolete SWO class' 'obsolete CopasiML' SubClassOf 'XML' http://www.ebi.ac.uk/efo/swo/SWO_0000449 obsolete Xba.CQV and Xba.regions 'obsolete Xba.CQV and Xba.regions' SubClassOf 'obsolete SWO class' 'obsolete Xba.CQV and Xba.regions' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000446 obsolete XDE 'obsolete XDE' SubClassOf 'obsolete SWO class' 'obsolete XDE' SubClassOf 'obsolete R software' 'obsolete XDE' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000447 obsolete XDotsReader 'obsolete XDotsReader' SubClassOf 'obsolete SWO class' 'obsolete XDotsReader' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000455 obsolete 'affyPLM' 'obsolete 'affyPLM'' SubClassOf 'obsolete SWO class' 'obsolete 'affyPLM'' SubClassOf 'obsolete affypdnn' http://www.ebi.ac.uk/swo/SWO_0000572 hexbin 'hexbin' SubClassOf 'implements' some 'Hexagon binning algorithm' 'hexbin' SubClassOf 'is executed in' some ('data visualization' and 'data normalization') 'hexbin' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'hexbin' SubClassOf 'software' 'hexbin' SubClassOf 'BioConductor Software' 'hexbin' SubClassOf 'R software' 'hexbin' SubClassOf 'has specified data output' some 'Graph plot' 'hexbin' SubClassOf 'is encoded in' some 'R language' 'hexbin' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/efo/swo/SWO_0000456 obsolete affyPara 'obsolete affyPara' SubClassOf 'obsolete SWO class' 'obsolete affyPara' SubClassOf 'obsolete BioConductor Software' 'obsolete affyPara' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000453 obsolete affyContam 'obsolete affyContam' SubClassOf 'obsolete SWO class' 'obsolete affyContam' SubClassOf 'obsolete BioConductor Software' 'obsolete affyContam' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000574 hopach 'hopach' SubClassOf 'has specified data output' some ('Image' and 'Graph plot') 'hopach' SubClassOf 'implements' some 'Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm' 'hopach' SubClassOf 'is encoded in' some 'R language' 'hopach' SubClassOf 'R software' 'hopach' SubClassOf 'software' 'hopach' SubClassOf 'has specified data input' some 'Gene expression data' 'hopach' SubClassOf 'is executed in' some ('data visualization' and 'distance calculation' and 'averaging' and 'decision tree induction' and 'differential expression analysis') http://www.ebi.ac.uk/efo/swo/SWO_0000454 obsolete affyImGUI 'obsolete affyImGUI' SubClassOf 'obsolete SWO class' 'obsolete affyImGUI' SubClassOf 'obsolete BioConductor Software' 'obsolete affyImGUI' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000573 Hierarchical clustering 'Hierarchical clustering' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000451 obsolete Acuity 'obsolete Acuity' SubClassOf 'obsolete SWO class' 'obsolete Acuity' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000576 Hypergeometric enrichment 'Hypergeometric enrichment' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000452 obsolete affxparser 'obsolete affxparser' SubClassOf 'obsolete SWO class' 'obsolete affxparser' SubClassOf 'obsolete BioConductor Software' 'obsolete affxparser' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000575 HTML report 'HTML report' SubClassOf 'data item' 'HTML report' SubClassOf 'is encoded in' some 'HTML' http://www.ebi.ac.uk/swo/SWO_0000578 Icens 'Icens' SubClassOf 'R software' 'Icens' SubClassOf 'is encoded in' some 'R language' 'Icens' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'Icens' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'Icens' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000450 obsolete Array Comparative Genomic Hybridization 'obsolete Array Comparative Genomic Hybridization' SubClassOf 'obsolete SWO class' 'obsolete Array Comparative Genomic Hybridization' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000577 hypergraph 'hypergraph' SubClassOf 'is published by' value 'Bioconductor' 'hypergraph' SubClassOf 'is encoded in' some 'R language' 'hypergraph' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'hypergraph' SubClassOf 'R software' 'hypergraph' SubClassOf 'implements' some 'k-cores' 'hypergraph' SubClassOf 'BioConductor Software' 'hypergraph' SubClassOf 'software' 'hypergraph' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000570 gxl format 'gxl format' SubClassOf 'XML' http://www.ebi.ac.uk/swo/SWO_0000579 idiogram 'idiogram' SubClassOf 'BioConductor Software' 'idiogram' SubClassOf 'R software' 'idiogram' SubClassOf 'is encoded in' some 'R language' 'idiogram' SubClassOf 'is published by' value 'Bioconductor' 'idiogram' SubClassOf 'has specified data output' some ('Image' and 'Graph plot') 'idiogram' SubClassOf 'software' 'idiogram' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') http://www.ebi.ac.uk/efo/swo/SWO_0000459 obsolete 'affycoretools' 'obsolete 'affycoretools'' SubClassOf 'obsolete SWO class' 'obsolete 'affycoretools'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000457 obsolete affyQCReport 'obsolete affyQCReport' SubClassOf 'obsolete SWO class' 'obsolete affyQCReport' SubClassOf 'obsolete BioConductor Software' 'obsolete affyQCReport' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000458 obsolete affyTiling 'obsolete affyTiling' SubClassOf 'obsolete SWO class' 'obsolete affyTiling' SubClassOf 'obsolete R software' 'obsolete affyTiling' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000466 obsolete 'annotate' 'obsolete 'annotate'' SubClassOf 'obsolete SWO class' 'obsolete 'annotate'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000583 iterativeBMAsurv 'iterativeBMAsurv' SubClassOf 'is published by' value 'Bioconductor' 'iterativeBMAsurv' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'iterativeBMAsurv' SubClassOf 'implements' some 'Iterative Bayesian Model Averaging (BMA)' 'iterativeBMAsurv' SubClassOf 'BioConductor Software' 'iterativeBMAsurv' SubClassOf 'has specified data output' some 'Graph plot' 'iterativeBMAsurv' SubClassOf 'software' 'iterativeBMAsurv' SubClassOf 'is encoded in' some 'R language' 'iterativeBMAsurv' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000467 obsolete data annotation 'obsolete data annotation' SubClassOf 'obsolete SWO class' 'obsolete data annotation' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/SWO_0000582 iterativeBMA 'iterativeBMA' SubClassOf 'has specified data output' some ('Image' and 'Graph plot') 'iterativeBMA' SubClassOf 'implements' some 'Iterative Bayesian Model Averaging (BMA)' 'iterativeBMA' SubClassOf 'R software' 'iterativeBMA' SubClassOf 'software' 'iterativeBMA' SubClassOf 'has specified data input' some 'Gene expression dataset' 'iterativeBMA' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/efo/swo/SWO_0000465 obsolete annaffy 'obsolete annaffy' SubClassOf 'obsolete SWO class' 'obsolete annaffy' SubClassOf 'obsolete R software' 'obsolete annaffy' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000584 Iterative local regression and model selection 'Iterative local regression and model selection' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000587 k-cores 'k-cores' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000463 obsolete altcdfenvs 'obsolete altcdfenvs' SubClassOf 'obsolete SWO class' 'obsolete altcdfenvs' SubClassOf 'obsolete BioConductor Software' 'obsolete altcdfenvs' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000460 obsolete affyio 'obsolete affyio' SubClassOf 'obsolete SWO class' 'obsolete affyio' SubClassOf 'obsolete R software' 'obsolete affyio' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000589 k-nearest neighbour classification 'k-nearest neighbour classification' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000461 obsolete affypdnn 'obsolete affypdnn' SubClassOf 'obsolete SWO class' 'obsolete affypdnn' SubClassOf 'obsolete BioConductor Software' 'obsolete affypdnn' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000588 k-means 'k-means' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000581 impute 'impute' SubClassOf 'R software' 'impute' SubClassOf 'software' 'impute' SubClassOf 'has specified data input' some 'Gene expression dataset' 'impute' SubClassOf 'implements' some 'k-nearest neighbour classification' 'impute' SubClassOf 'has specified data output' some 'Gene expression dataset' 'impute' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/efo/swo/SWO_0000468 obsolete annotationTools 'obsolete annotationTools' SubClassOf 'obsolete SWO class' 'obsolete annotationTools' SubClassOf 'obsolete R software' 'obsolete annotationTools' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000469 obsolete Annotation data packages 'obsolete Annotation data packages' SubClassOf 'obsolete SWO class' 'obsolete Annotation data packages' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000356 obsolete RefPlus 'obsolete RefPlus' SubClassOf 'obsolete SWO class' 'obsolete RefPlus' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000354 obsolete RdbiPgSQL 'obsolete RdbiPgSQL' SubClassOf 'obsolete SWO class' 'obsolete RdbiPgSQL' SubClassOf 'obsolete BioConductor Software' 'obsolete RdbiPgSQL' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000355 obsolete Rdisop 'obsolete Rdisop' SubClassOf 'obsolete SWO class' 'obsolete Rdisop' SubClassOf 'obsolete BioConductor Software' 'obsolete Rdisop' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000352 obsolete RbcBook1 'obsolete RbcBook1' SubClassOf 'obsolete SWO class' 'obsolete RbcBook1' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000510 crlmm 'crlmm' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'crlmm' SubClassOf 'is executed in' some 'data normalization' 'crlmm' SubClassOf 'BioConductor Software' 'crlmm' SubClassOf 'implements' some 'CRLMM algorithm' 'crlmm' SubClassOf 'is published by' value 'Bioconductor' 'crlmm' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'rda')) 'crlmm' SubClassOf 'software' 'crlmm' SubClassOf 'R software' 'crlmm' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/efo/swo/SWO_0000353 obsolete Rdbi 'obsolete Rdbi' SubClassOf 'obsolete SWO class' 'obsolete Rdbi' SubClassOf 'obsolete BioConductor Software' 'obsolete Rdbi' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000350 obsolete RankProd 'obsolete RankProd' SubClassOf 'obsolete SWO class' 'obsolete RankProd' SubClassOf 'obsolete BioConductor Software' 'obsolete RankProd' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000512 ctc 'ctc' SubClassOf 'is encoded in' some 'R language' 'ctc' SubClassOf 'software' 'ctc' SubClassOf 'BioConductor Software' 'ctc' SubClassOf 'R software' 'ctc' SubClassOf 'has specified data input' some 'Text data set' 'ctc' SubClassOf 'has specified data output' some ('Heat map' and ('has format specification' only ('newick' or 'cdt' or 'gtr'))) 'ctc' SubClassOf 'implements' some 'Hierarchical clustering' 'ctc' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000514 daMA 'daMA' SubClassOf 'R software' 'daMA' SubClassOf 'BioConductor Software' 'daMA' SubClassOf 'software' 'daMA' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'daMA' SubClassOf 'is executed in' some 'differential expression analysis' 'daMA' SubClassOf 'is published by' value 'Bioconductor' 'daMA' SubClassOf 'implements' some ('f-test' and ''FDR'') 'daMA' SubClassOf 'is encoded in' some 'R language' 'daMA' SubClassOf 'has specified data input' some 'Gene expression data' http://www.ebi.ac.uk/swo/SWO_0000513 dChip 'dChip' SubClassOf 'is published by' value 'Havard School of Public Health' 'dChip' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000516 .data '.data' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000518 dcf 'dcf' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/efo/swo/SWO_0000358 obsolete Resourcerer 'obsolete Resourcerer' SubClassOf 'obsolete SWO class' 'obsolete Resourcerer' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000359 obsolete Rgraphviz 'obsolete Rgraphviz' SubClassOf 'obsolete SWO class' 'obsolete Rgraphviz' SubClassOf 'obsolete BioConductor Software' 'obsolete Rgraphviz' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000519 design file 'design file' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000367 obsolete RpsiXML 'obsolete RpsiXML' SubClassOf 'obsolete SWO class' 'obsolete RpsiXML' SubClassOf 'obsolete R software' 'obsolete RpsiXML' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000368 obsolete Rredland 'obsolete Rredland' SubClassOf 'obsolete SWO class' 'obsolete Rredland' SubClassOf 'obsolete R software' 'obsolete Rredland' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000365 obsolete Rosetta Resolver 'obsolete Rosetta Resolver' SubClassOf 'obsolete SWO class' 'obsolete Rosetta Resolver' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000363 obsolete Rnw 'obsolete Rnw' SubClassOf 'obsolete SWO class' 'obsolete Rnw' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_0000521 'domainsignatures' ''domainsignatures'' SubClassOf 'has specified data input' some 'Gene list' ''domainsignatures'' SubClassOf 'is executed in' some 'descriptive statistical calculation' ''domainsignatures'' SubClassOf 'R software' ''domainsignatures'' SubClassOf 'has specified data output' some 'Graph plot' ''domainsignatures'' SubClassOf 'implements' some 'Gene-Set Enrichment Analysis' ''domainsignatures'' SubClassOf 'is encoded in' some 'R language' ''domainsignatures'' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000364 obsolete Robust likelihood-based survival modeling 'obsolete Robust likelihood-based survival modeling' SubClassOf 'obsolete SWO class' 'obsolete Robust likelihood-based survival modeling' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000520 'diffGeneAnalysis' ''diffGeneAnalysis'' SubClassOf 'has specified data output' some ('Graph plot' and 'CSV data set') ''diffGeneAnalysis'' SubClassOf 'software' ''diffGeneAnalysis'' SubClassOf 'implements' some 'Associative T method' ''diffGeneAnalysis'' SubClassOf 'is encoded in' some 'R language' ''diffGeneAnalysis'' SubClassOf 'has specified data input' some 'CSV data set' ''diffGeneAnalysis'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000361 obsolete Rintact 'obsolete Rintact' SubClassOf 'obsolete SWO class' 'obsolete Rintact' SubClassOf 'obsolete BioConductor Software' 'obsolete Rintact' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000523 dyebias 'dyebias' SubClassOf 'is executed in' some ('averaging' and 'correction' and 'data normalization') 'dyebias' SubClassOf 'implements' some 'GASSCO method' 'dyebias' SubClassOf 'is encoded in' some 'R language' 'dyebias' SubClassOf 'has specified data input' some (('Text data set' and ('has format specification' only 'MAGE-TAB')) or ('has format specification' only 'R data frame')) 'dyebias' SubClassOf 'R software' 'dyebias' SubClassOf 'is published by' value 'Bioconductor' 'dyebias' SubClassOf 'software' 'dyebias' SubClassOf 'has specified data output' some 'Text data set' 'dyebias' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000362 obsolete Rmagpie 'obsolete Rmagpie' SubClassOf 'obsolete SWO class' 'obsolete Rmagpie' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000522 'dualKS' ''dualKS'' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') ''dualKS'' SubClassOf 'has specified data input' some 'Gene expression dataset' ''dualKS'' SubClassOf 'R software' ''dualKS'' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') ''dualKS'' SubClassOf 'is encoded in' some 'R language' ''dualKS'' SubClassOf 'implements' some ('Kolmogorov Smirnov rank-sum based algorithm' and 'Bootstrap') ''dualKS'' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000360 obsolete Ringo 'obsolete Ringo' SubClassOf 'obsolete SWO class' 'obsolete Ringo' SubClassOf 'data item' 'obsolete Ringo' SubClassOf 'obsolete BioConductor Software' 'obsolete Ringo' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000525 ecolitk 'ecolitk' SubClassOf 'is encoded in' some 'R language' 'ecolitk' SubClassOf 'BioConductor Software' 'ecolitk' SubClassOf 'software' 'ecolitk' SubClassOf 'R software' 'ecolitk' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'ecolitk' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'ecolitk' SubClassOf 'is published by' value 'Bioconductor' 'ecolitk' SubClassOf 'has specified data input' some 'Meta data' http://www.ebi.ac.uk/swo/SWO_0000524 Dynamic programming algorithm 'Dynamic programming algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000527 'edgeR' ''edgeR'' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') ''edgeR'' SubClassOf 'R software' ''edgeR'' SubClassOf 'has specified data input' some 'Digital gene expression (DGE) datasets' ''edgeR'' SubClassOf 'is encoded in' some 'R language' ''edgeR'' SubClassOf 'is executed in' some 'differential expression analysis' ''edgeR'' SubClassOf 'software' ''edgeR'' SubClassOf 'implements' some ('Negative binomial distribution' and 'Empirical Bayes rule') http://www.ebi.ac.uk/swo/SWO_0000526 edd 'edd' SubClassOf 'is encoded in' some 'R language' 'edd' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'edd' SubClassOf 'BioConductor Software' 'edd' SubClassOf 'R software' 'edd' SubClassOf 'software' 'edd' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'edd' SubClassOf 'is published by' value 'Bioconductor' 'edd' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') http://www.ebi.ac.uk/swo/SWO_0000529 'explorase' ''explorase'' SubClassOf 'has specified data input' some 'CSV data set' ''explorase'' SubClassOf 'is encoded in' some 'R language' ''explorase'' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') ''explorase'' SubClassOf 'implements' some 'Linear modelling' ''explorase'' SubClassOf 'software' ''explorase'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000528 exonmap 'exonmap' SubClassOf 'BioConductor Software' 'exonmap' SubClassOf 'is encoded in' some 'R language' 'exonmap' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'exonmap' SubClassOf 'is executed in' some 'differential expression analysis' 'exonmap' SubClassOf 'implements' some ('RMA' and ''FDR'') 'exonmap' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CDF binary format' or 'CDF ASCII format' or 'CEL ASCII format')) 'exonmap' SubClassOf 'R software' 'exonmap' SubClassOf 'software' 'exonmap' SubClassOf 'is published by' value 'Bioconductor' 'exonmap' SubClassOf 'has specified data input' some ('has format specification' only 'covdesc file') http://www.ebi.ac.uk/efo/swo/SWO_0000369 obsolete Rtreemix 'obsolete Rtreemix' SubClassOf 'obsolete SWO class' 'obsolete Rtreemix' SubClassOf 'obsolete BioConductor Software' 'obsolete Rtreemix' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000378 obsolete SBMLR format 'obsolete SBMLR format' SubClassOf 'obsolete SWO class' 'obsolete SBMLR format' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_0000530 'externalVector' ''externalVector'' SubClassOf 'software' ''externalVector'' SubClassOf 'R software' ''externalVector'' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/efo/swo/SWO_0000377 obsolete SBMLR 'obsolete SBMLR' SubClassOf 'obsolete SWO class' 'obsolete SBMLR' SubClassOf 'obsolete BioConductor Software' 'obsolete SBMLR' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000374 obsolete SAM 'obsolete SAM' SubClassOf 'obsolete SWO class' 'obsolete SAM' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000532 factDesign 'factDesign' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'factDesign' SubClassOf 'software' 'factDesign' SubClassOf 'is encoded in' some 'R language' 'factDesign' SubClassOf 'BioConductor Software' 'factDesign' SubClassOf 'implements' some ('RMA' and 'Linear modelling' and ''ANOVA'' and ''FDR'') 'factDesign' SubClassOf 'has specified data output' some ('Heat map' and 'Graph plot' and 'Text data set') 'factDesign' SubClassOf 'R software' 'factDesign' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/efo/swo/SWO_0000375 obsolete SAS/STAT Software, Version 8 'obsolete SAS/STAT Software, Version 8' SubClassOf 'obsolete SWO class' 'obsolete SAS/STAT Software, Version 8' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000531 f-test 'f-test' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000372 obsolete Serial Analysis of Gene Expression (SAGE) 'obsolete Serial Analysis of Gene Expression (SAGE)' SubClassOf 'obsolete SWO class' 'obsolete Serial Analysis of Gene Expression (SAGE)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000534 fdrame 'fdrame' SubClassOf 'BioConductor Software' 'fdrame' SubClassOf 'is encoded in' some 'R language' 'fdrame' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'fdrame' SubClassOf 'is executed in' some 'gene expression analysis' 'fdrame' SubClassOf 'is published by' value 'Bioconductor' 'fdrame' SubClassOf 'implements' some (''ANOVA'' and ''FDR'') 'fdrame' SubClassOf 'software' 'fdrame' SubClassOf 'has specified data output' some 'Graph plot' 'fdrame' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000373 obsolete SAGx 'obsolete SAGx' SubClassOf 'obsolete SWO class' 'obsolete SAGx' SubClassOf 'obsolete R software' 'obsolete SAGx' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000533 fbat 'fbat' SubClassOf 'R software' 'fbat' SubClassOf 'BioConductor Software' 'fbat' SubClassOf 'software' 'fbat' SubClassOf 'is encoded in' some 'R language' 'fbat' SubClassOf 'implements' some ('Hardy-Weinberg equilibrium' and 'Markov Chain Monte Carlo') 'fbat' SubClassOf 'has specified data input' some ('has format specification' only 'pedigree data file') 'fbat' SubClassOf 'is published by' value 'Bioconductor' 'fbat' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') http://www.ebi.ac.uk/efo/swo/SWO_0000370 obsolete Ruuid 'obsolete Ruuid' SubClassOf 'obsolete SWO class' 'obsolete Ruuid' SubClassOf 'obsolete R software' 'obsolete Ruuid' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000371 obsolete S-Score algorithm 'obsolete S-Score algorithm' SubClassOf 'obsolete SWO class' 'obsolete S-Score algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000536 flagme 'flagme' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'flagme' SubClassOf 'is executed in' some 'data normalization' 'flagme' SubClassOf 'has specified data input' some ('has format specification' only ('CDF binary format' or 'CDF ASCII format')) 'flagme' SubClassOf 'is encoded in' some 'R language' 'flagme' SubClassOf 'is published by' value 'Bioconductor' 'flagme' SubClassOf 'BioConductor Software' 'flagme' SubClassOf 'implements' some ('Dynamic programming algorithm' and 'AMDIS') 'flagme' SubClassOf 'software' 'flagme' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000538 flowCore 'flowCore' SubClassOf 'R software' 'flowCore' SubClassOf 'is encoded in' some 'R language' 'flowCore' SubClassOf 'BioConductor Software' 'flowCore' SubClassOf 'software' 'flowCore' SubClassOf 'has specified data input' some ('has format specification' only ('R data frame' or 'Data File Standard for Flow Cytometry')) 'flowCore' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'flowCore' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000537 flowClust 'flowClust' SubClassOf 'is encoded in' some 'R language' 'flowClust' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'flowClust' SubClassOf 'is published by' value 'Bioconductor' 'flowClust' SubClassOf 'implements' some ('Multivariate t mixture models' and 'Bayesian Model' and 'Expectation-Maximization(EM) algorithm') 'flowClust' SubClassOf 'has specified data input' some ('has format specification' only ('R data frame' or 'Data File Standard for Flow Cytometry')) 'flowClust' SubClassOf 'software' 'flowClust' SubClassOf 'R software' 'flowClust' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000539 flowFlowJo 'flowFlowJo' SubClassOf 'has specified data output' some ('has format specification' only 'Data File Standard for Flow Cytometry') 'flowFlowJo' SubClassOf 'is published by' value 'Bioconductor' 'flowFlowJo' SubClassOf 'has specified data input' some ('has format specification' only 'XML') 'flowFlowJo' SubClassOf 'is executed in' some ('parse' and 'descriptive statistical calculation') 'flowFlowJo' SubClassOf 'R software' 'flowFlowJo' SubClassOf 'is encoded in' some 'R language' 'flowFlowJo' SubClassOf 'software' 'flowFlowJo' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000389 obsolete Semantic Similarity Measures 'obsolete Semantic Similarity Measures' SubClassOf 'obsolete SWO class' 'obsolete Semantic Similarity Measures' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000387 obsolete SNPchip 'obsolete SNPchip' SubClassOf 'obsolete SWO class' 'obsolete SNPchip' SubClassOf 'obsolete BioConductor Software' 'obsolete SNPchip' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000541 flowStats 'flowStats' SubClassOf 'is published by' value 'Bioconductor' 'flowStats' SubClassOf 'is executed in' some 'data normalization' 'flowStats' SubClassOf 'has specified data input' some ('has format specification' only 'Data File Standard for Flow Cytometry') 'flowStats' SubClassOf 'software' 'flowStats' SubClassOf 'BioConductor Software' 'flowStats' SubClassOf 'R software' 'flowStats' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'flowStats' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/efo/swo/SWO_0000388 obsolete SPIA 'obsolete SPIA' SubClassOf 'obsolete SWO class' 'obsolete SPIA' SubClassOf 'obsolete BioConductor Software' 'obsolete SPIA' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000540 flowQ 'flowQ' SubClassOf 'is published by' value 'Bioconductor' 'flowQ' SubClassOf 'has specified data input' some ('has format specification' only 'Data File Standard for Flow Cytometry') 'flowQ' SubClassOf 'is encoded in' some 'R language' 'flowQ' SubClassOf 'BioConductor Software' 'flowQ' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'flowQ' SubClassOf 'R software' 'flowQ' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000385 obsolete SMAP 'obsolete SMAP' SubClassOf 'obsolete SWO class' 'obsolete SMAP' SubClassOf 'obsolete R software' 'obsolete SMAP' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000543 flowViz 'flowViz' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'flowViz' SubClassOf 'software' 'flowViz' SubClassOf 'is published by' value 'Bioconductor' 'flowViz' SubClassOf 'R software' 'flowViz' SubClassOf 'is encoded in' some 'R language' 'flowViz' SubClassOf 'BioConductor Software' 'flowViz' SubClassOf 'has specified data input' some ('has format specification' only 'Data File Standard for Flow Cytometry') http://www.ebi.ac.uk/efo/swo/SWO_0000386 obsolete SNPRMA algorithm 'obsolete SNPRMA algorithm' SubClassOf 'obsolete SWO class' 'obsolete SNPRMA algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000542 flowUtils 'flowUtils' SubClassOf 'has specified data input' some ('has format specification' only 'Data File Standard for Flow Cytometry') 'flowUtils' SubClassOf 'R software' 'flowUtils' SubClassOf 'BioConductor Software' 'flowUtils' SubClassOf 'is executed in' some 'parse' 'flowUtils' SubClassOf 'has specified data output' some ('has format specification' only 'XML') 'flowUtils' SubClassOf 'is published by' value 'Bioconductor' 'flowUtils' SubClassOf 'is encoded in' some 'R language' 'flowUtils' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000383 obsolete SLGI 'obsolete SLGI' SubClassOf 'obsolete SWO class' 'obsolete SLGI' SubClassOf 'obsolete BioConductor Software' 'obsolete SLGI' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000545 'gaggle' ''gaggle'' SubClassOf 'R software' ''gaggle'' SubClassOf 'is encoded in' some 'R language' ''gaggle'' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000384 obsolete SLqPCR 'obsolete SLqPCR' SubClassOf 'obsolete SWO class' 'obsolete SLqPCR' SubClassOf 'obsolete BioConductor Software' 'obsolete SLqPCR' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000544 gaga 'gaga' SubClassOf 'software' 'gaga' SubClassOf 'is published by' value 'Bioconductor' 'gaga' SubClassOf 'BioConductor Software' 'gaga' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'gaga' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'gaga' SubClassOf 'is encoded in' some 'R language' 'gaga' SubClassOf 'R software' 'gaga' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'gaga' SubClassOf 'implements' some ('Gamma-Gamma hierarchical model' and ''FDR'') http://www.ebi.ac.uk/efo/swo/SWO_0000381 obsolete SDF format 'obsolete SDF format' SubClassOf 'obsolete SWO class' 'obsolete SDF format' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/efo/swo/SWO_0000382 obsolete SIM 'obsolete SIM' SubClassOf 'obsolete SWO class' 'obsolete SIM' SubClassOf 'obsolete R software' http://www.ontodm.com/OntoDM-core/OntoDM_530819 ensemble algorithm 'ensemble algorithm' DisjointWith 'single generalization algorithm' 'ensemble algorithm' SubClassOf 'data mining algorithm' http://www.ebi.ac.uk/swo/SWO_0000547 gcrma 'gcrma' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'gcrma' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'gcrma' SubClassOf 'is encoded in' some 'R language' 'gcrma' SubClassOf 'is published by' value 'Bioconductor' 'gcrma' SubClassOf 'BioConductor Software' 'gcrma' SubClassOf 'R software' 'gcrma' SubClassOf 'implements' some 'RMA' 'gcrma' SubClassOf 'software' 'gcrma' SubClassOf 'is executed in' some ('correction' and 'data normalization') http://www.ebi.ac.uk/swo/SWO_0000546 gcRMA quantification 'gcRMA quantification' SubClassOf 'software' 'gcRMA quantification' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Bioconductor')) http://www.ebi.ac.uk/swo/SWO_0000549 'genArise' ''genArise'' SubClassOf 'has specified data output' some 'Graph plot' ''genArise'' SubClassOf 'software' ''genArise'' SubClassOf 'is encoded in' some 'R language' ''genArise'' SubClassOf 'has specified data input' some 'Text data set' ''genArise'' SubClassOf 'R software' ''genArise'' SubClassOf 'is executed in' some ('correction' and 'data normalization' and 'differential expression analysis') http://www.ebi.ac.uk/swo/SWO_0000548 gct 'gct' SubClassOf 'tab delimited file format' http://www.ebi.ac.uk/swo/license/SWO_10000037 Distribution unrestricted 'Distribution restricted' DisjointWith 'Distribution unrestricted' http://www.ebi.ac.uk/swo/license/SWO_10000038 Derivatives allowed 'Derivatives not allowed' DisjointWith 'Derivatives allowed' http://www.ebi.ac.uk/efo/swo/SWO_0000398 obsolete 50-50 MANOVA algorithm 'obsolete 50-50 MANOVA algorithm' SubClassOf 'obsolete SWO class' 'obsolete 50-50 MANOVA algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/license/SWO_10000036 Distribution restricted 'Distribution restricted' DisjointWith 'Distribution unrestricted' http://www.ebi.ac.uk/efo/swo/SWO_0000396 obsolete software developer organization 'obsolete software developer organization' SubClassOf 'obsolete SWO class' 'obsolete software developer organization' SubClassOf 'organization' http://www.ebi.ac.uk/efo/swo/SWO_0000397 obsolete software publisher organization 'obsolete software publisher organization' SubClassOf 'obsolete SWO class' 'obsolete software publisher organization' SubClassOf 'organization' http://www.ebi.ac.uk/efo/swo/SWO_0000392 obsolete software developer role 'obsolete software developer role' SubClassOf 'obsolete SWO class' 'obsolete software developer role' SubClassOf http://www.ifomis.org/bfo/1.1/snap#Role http://www.ebi.ac.uk/efo/swo/SWO_0000390 obsolete SSPA 'obsolete SSPA' SubClassOf 'obsolete SWO class' 'obsolete SSPA' SubClassOf 'obsolete BioConductor Software' 'obsolete SSPA' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000391 obsolete SVDimpute algorithm 'obsolete SVDimpute algorithm' SubClassOf 'obsolete SWO class' 'obsolete SVDimpute algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/algorithm/SWO_4000005 dynamic Bayesian network model 'dynamic Bayesian network model' SubClassOf 'Bayesian Model' 'dynamic Bayesian network model' SubClassOf 'obsolete Bayesian Model' http://www.ebi.ac.uk/swo/SWO_0000501 'codelink' ''codelink'' SubClassOf 'is encoded in' some 'R language' ''codelink'' SubClassOf 'has specified data input' some ('XML' or 'Text data set') ''codelink'' SubClassOf 'software' ''codelink'' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') ''codelink'' SubClassOf 'R software' ''codelink'' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'descriptive statistical calculation' and 'differential expression analysis') http://purl.obolibrary.org/obo/OBI_0200111 data visualization 'data visualization' SubClassOf 'planned process' http://www.ebi.ac.uk/swo/SWO_0000503 Concordance 'Concordance' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000502 dataset comparison 'dataset comparison' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_0000505 copa 'copa' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'copa' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'copa' SubClassOf 'is encoded in' some 'R language' 'copa' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'copa' SubClassOf 'software' 'copa' SubClassOf 'R software' 'copa' SubClassOf 'BioConductor Software' 'copa' SubClassOf 'implements' some ('Median Average Difference Algorithm' and ''FDR'') 'copa' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000504 convert 'convert' SubClassOf 'software' 'convert' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'convert' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'convert' SubClassOf 'is encoded in' some 'R language' 'convert' SubClassOf 'BioConductor Software' 'convert' SubClassOf 'is published by' value 'Bioconductor' 'convert' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000507 cosmoGUI 'cosmoGUI' SubClassOf 'is executed in' some 'gene expression analysis' 'cosmoGUI' SubClassOf 'is encoded in' some 'R language' 'cosmoGUI' SubClassOf 'BioConductor Software' 'cosmoGUI' SubClassOf 'software' 'cosmoGUI' SubClassOf 'R software' 'cosmoGUI' SubClassOf 'implements' some 'cosmo' 'cosmoGUI' SubClassOf 'has specified data output' some ('Image' and ('HTML report' or ('has format specification' only 'R data frame'))) 'cosmoGUI' SubClassOf 'has specified data input' some ('has format specification' only ('FASTA format' or 'R data frame')) 'cosmoGUI' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000506 cosmo 'cosmo' SubClassOf 'BioConductor Software' 'cosmo' SubClassOf 'implements' some 'Cosmo' 'cosmo' SubClassOf 'is encoded in' some 'R language' 'cosmo' SubClassOf 'software' 'cosmo' SubClassOf 'is published by' value 'Bioconductor' 'cosmo' SubClassOf 'is executed in' some 'gene expression analysis' 'cosmo' SubClassOf 'R software' 'cosmo' SubClassOf 'has specified data input' some ('has format specification' only ('FASTA format' or 'R data frame')) 'cosmo' SubClassOf 'has specified data output' some ('Image' and ('HTML report' or ('has format specification' only 'R data frame'))) http://www.ebi.ac.uk/swo/SWO_0000509 database creation 'database creation' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_0000508 covdesc file 'covdesc file' SubClassOf 'data format specification' http://www.ontodm.com/OntoDM-core/OntoDM_000228 predictive model specification 'predictive model specification' SubClassOf 'single generalization specification' http://purl.obolibrary.org/obo/IAO_0000098 data format specification 'data format specification' SubClassOf 'directive information entity' http://purl.obolibrary.org/obo/IAO_0000064 algorithm 'algorithm' SubClassOf 'plan specification' http://www.ontodm.com/OntoDM-core/OntoDM_000264 clustering task DisjointClasses: 'probability distribution estimation task', 'pattern discovery task', 'predictive modeling task', 'clustering task' 'clustering task' SubClassOf 'data mining task' http://kt.ijs.si/panovp/OntoDM#OntoDM_000034 generalization specification 'generalization specification' SubClassOf 'directive information entity' 'generalization specification' SubClassOf 'information content entity' http://www.ontodm.com/OntoDM-core/OntoDM_000253 probability distribution estimation algorithm 'probability distribution estimation algorithm' SubClassOf 'single generalization algorithm' http://edamontology.org/data_0582 Ontology 'Ontology' SubClassOf http://edamontology.org/data_2353 http://www.ontodm.com/OntoDM-core/OntoDM_000235 predictive modeling task DisjointClasses: 'probability distribution estimation task', 'pattern discovery task', 'predictive modeling task', 'clustering task' 'predictive modeling task' SubClassOf 'data mining task' http://www.ontodm.com/OntoDM-core/OntoDM_000072 clustering algorithm DisjointClasses: 'clustering algorithm', 'predictive modeling algorithm', 'pattern discovery algorithm' 'clustering algorithm' SubClassOf 'single generalization algorithm' http://www.ebi.ac.uk/swo/maturity/SWO_9000073 Maintained 'Obsolete' DisjointWith 'Maintained' http://purl.obolibrary.org/obo/IAO_0000129 version number version name 'version name' SubClassOf 'is version of' only ('programming language' or 'algorithm' or 'data format specification' or 'software') 'version name' SubClassOf 'symbol' http://edamontology.org/format_2585 SBML 'SBML' SubClassOf http://edamontology.org/format_2013 http://www.ontodm.com/OntoDM-core/OntoDM_000038 data mining algorithm 'data mining algorithm' SubClassOf 'algorithm' http://www.ontodm.com/OntoDM-core/OntoDM_000037 ensemble specification 'ensemble specification' SubClassOf 'generalization specification' http://purl.obolibrary.org/obo/IAO_0000104 plan specification 'plan specification' SubClassOf 'directive information entity' http://www.ebi.ac.uk/efo/swo/SWO_0000709 obsolete sqlite 'obsolete sqlite' SubClassOf 'obsolete SWO class' 'obsolete sqlite' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000707 obsolete spotSegmentation 'obsolete spotSegmentation' SubClassOf 'obsolete SWO class' 'obsolete spotSegmentation' SubClassOf 'obsolete R software' 'obsolete spotSegmentation' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000708 obsolete sproc 'obsolete sproc' SubClassOf 'obsolete SWO class' 'obsolete sproc' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/maturity/SWO_9000066 Obsolete DisjointClasses: 'alpha', 'beta', 'Release candidate', 'Live', 'Obsolete' 'Obsolete' DisjointWith 'Maintained' http://www.ebi.ac.uk/efo/swo/SWO_0000705 obsolete splicegear 'obsolete splicegear' SubClassOf 'obsolete SWO class' 'obsolete splicegear' SubClassOf 'obsolete R software' 'obsolete splicegear' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/maturity/SWO_9000065 Live DisjointClasses: 'alpha', 'beta', 'Release candidate', 'Live', 'Obsolete' http://www.ebi.ac.uk/efo/swo/SWO_0000706 obsolete splots 'obsolete splots' SubClassOf 'obsolete SWO class' 'obsolete splots' SubClassOf 'obsolete BioConductor Software' 'obsolete splots' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/maturity/SWO_9000064 Release candidate DisjointClasses: 'alpha', 'beta', 'Release candidate', 'Live', 'Obsolete' http://www.ebi.ac.uk/efo/swo/SWO_0000703 obsolete spikeLI 'obsolete spikeLI' SubClassOf 'obsolete SWO class' 'obsolete spikeLI' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/maturity/SWO_9000063 beta DisjointClasses: 'alpha', 'beta', 'Release candidate', 'Live', 'Obsolete' http://www.ebi.ac.uk/efo/swo/SWO_0000704 obsolete spkTools 'obsolete spkTools' SubClassOf 'obsolete SWO class' 'obsolete spkTools' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/maturity/SWO_9000062 alpha DisjointClasses: 'alpha', 'beta', 'Release candidate', 'Live', 'Obsolete' http://www.ebi.ac.uk/efo/swo/SWO_0000701 obsolete snpMatrix 'obsolete snpMatrix' SubClassOf 'obsolete SWO class' 'obsolete snpMatrix' SubClassOf 'obsolete R software' 'obsolete snpMatrix' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000700 obsolete snapCGH 'obsolete snapCGH' SubClassOf 'obsolete SWO class' 'obsolete snapCGH' SubClassOf 'obsolete BioConductor Software' 'obsolete snapCGH' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000275 MAVI Pro 'MAVI Pro' SubClassOf 'software' 'MAVI Pro' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'MWG Biotech')) http://www.ebi.ac.uk/swo/SWO_0000274 MATLAB language 'MATLAB language' SubClassOf 'programming language' http://www.ebi.ac.uk/swo/SWO_0000277 Markov Chain Monte Carlo 'Markov Chain Monte Carlo' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000276 Multivariate correlation estimator 'Multivariate correlation estimator' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000279 MCRestimate 'MCRestimate' SubClassOf 'software' 'MCRestimate' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'R data frame')) 'MCRestimate' SubClassOf 'is encoded in' some 'R language' 'MCRestimate' SubClassOf 'has specified data input' some ('ALL/AML data set' and ('has format specification' some 'data format specification')) 'MCRestimate' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000278 MCR algorithm 'MCR algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000271 MIcroarray Analysis Suite 'MIcroarray Analysis Suite' SubClassOf 'output of' some ('software development' and ('has participant' value 'Affymetrix')) 'MIcroarray Analysis Suite' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000270 MAQC data 'MAQC data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000272 MicroArraySuite 5.0 'MicroArraySuite 5.0' SubClassOf 'MIcroarray Analysis Suite' http://www.ebi.ac.uk/efo/swo/SWO_0000718 obsolete tkWidgets 'obsolete tkWidgets' SubClassOf 'obsolete SWO class' 'obsolete tkWidgets' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000719 obsolete topGO 'obsolete topGO' SubClassOf 'obsolete SWO class' 'obsolete topGO' SubClassOf 'obsolete BioConductor Software' 'obsolete topGO' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000716 obsolete tilingArray 'obsolete tilingArray' SubClassOf 'obsolete SWO class' 'obsolete tilingArray' SubClassOf 'obsolete R software' 'obsolete tilingArray' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000717 obsolete timecourse 'obsolete timecourse' SubClassOf 'obsolete SWO class' 'obsolete timecourse' SubClassOf 'obsolete R software' 'obsolete timecourse' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000714 obsolete stepNorm 'obsolete stepNorm' SubClassOf 'obsolete SWO class' 'obsolete stepNorm' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000715 obsolete 't-test' 'obsolete 't-test'' SubClassOf 'obsolete SWO class' 'obsolete 't-test'' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000712 obsolete stam 'obsolete stam' SubClassOf 'obsolete SWO class' 'obsolete stam' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000713 obsolete Statistical tests 'obsolete Statistical tests' SubClassOf 'obsolete SWO class' 'obsolete Statistical tests' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000710 obsolete sscore 'obsolete sscore' SubClassOf 'obsolete SWO class' 'obsolete sscore' SubClassOf 'obsolete BioConductor Software' 'obsolete sscore' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000711 obsolete ssize 'obsolete ssize' SubClassOf 'obsolete SWO class' 'obsolete ssize' SubClassOf 'obsolete R software' 'obsolete ssize' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000720 obsolete tspair 'obsolete tspair' SubClassOf 'obsolete SWO class' 'obsolete tspair' SubClassOf 'obsolete BioConductor Software' 'obsolete tspair' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000285 MVCClass 'MVCClass' SubClassOf 'is executed in' some 'data visualization' 'MVCClass' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'MVCClass' SubClassOf 'is encoded in' some 'R language' 'MVCClass' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'MVCClass' SubClassOf 'R software' 'MVCClass' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000288 MantelCorr 'MantelCorr' SubClassOf 'R software' 'MantelCorr' SubClassOf 'is encoded in' some 'R language' 'MantelCorr' SubClassOf 'implements' some 'k-means' 'MantelCorr' SubClassOf 'software' 'MantelCorr' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'MantelCorr' SubClassOf 'has specified data output' some ('Clustered data set' and ('has format specification' some 'data format specification')) 'MantelCorr' SubClassOf 'is executed in' some 'differential expression analysis' http://www.ebi.ac.uk/swo/SWO_0000287 Mahalanobis distance 'Mahalanobis distance' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000289 MassSpecWavelet 'MassSpecWavelet' SubClassOf 'software' 'MassSpecWavelet' SubClassOf 'implements' some 'Continuous Wavelet Transform (CWT)-based peak detection algorithm' 'MassSpecWavelet' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'MassSpecWavelet' SubClassOf 'is encoded in' some 'R language' 'MassSpecWavelet' SubClassOf 'R software' 'MassSpecWavelet' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) http://www.ebi.ac.uk/swo/SWO_0000280 MEDME 'MEDME' SubClassOf 'software' 'MEDME' SubClassOf 'is encoded in' some 'R language' 'MEDME' SubClassOf 'R software' 'MEDME' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'MEDME' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'GFF')) http://www.ontodm.com/OntoDM-core/OntoDM_000098 data mining task 'data mining task' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_0000282 Mutual information matrix (MIM) 'Mutual information matrix (MIM)' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000281 'MI' ''MI'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000284 MMD 'MMD' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000283 MLInterfaces 'MLInterfaces' SubClassOf 'has specified data output' some ('ALL/AML data set' and ('has format specification' some 'data format specification')) 'MLInterfaces' SubClassOf 'is encoded in' some 'R language' 'MLInterfaces' SubClassOf 'R software' 'MLInterfaces' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'MLInterfaces' SubClassOf 'software' 'MLInterfaces' SubClassOf 'implements' some 'k-nearest neighbour classification' http://www.ebi.ac.uk/efo/swo/SWO_0000729 obsolete xcms 'obsolete xcms' SubClassOf 'obsolete SWO class' 'obsolete xcms' SubClassOf 'obsolete R software' 'obsolete xcms' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000727 obsolete webbioc 'obsolete webbioc' SubClassOf 'obsolete SWO class' 'obsolete webbioc' SubClassOf 'obsolete R software' 'obsolete webbioc' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000728 obsolete widgetTools 'obsolete widgetTools' SubClassOf 'obsolete SWO class' 'obsolete widgetTools' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000725 obsolete vsn 'obsolete vsn' SubClassOf 'obsolete SWO class' 'obsolete vsn' SubClassOf 'obsolete R software' http://edamontology.org/format_2549 OBO Flat File Format 'OBO Flat File Format' SubClassOf http://edamontology.org/format_2196 http://www.ebi.ac.uk/efo/swo/SWO_0000726 obsolete weaver 'obsolete weaver' SubClassOf 'obsolete SWO class' 'obsolete weaver' SubClassOf 'obsolete R software' 'obsolete weaver' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000723 obsolete vbmp 'obsolete vbmp' SubClassOf 'obsolete SWO class' 'obsolete vbmp' SubClassOf 'obsolete BioConductor Software' 'obsolete vbmp' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000724 obsolete data visualization 'obsolete data visualization' SubClassOf 'obsolete SWO class' 'obsolete data visualization' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000721 obsolete twilight 'obsolete twilight' SubClassOf 'obsolete SWO class' 'obsolete twilight' SubClassOf 'obsolete R software' 'obsolete twilight' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000722 obsolete Two-stage measurement error model 'obsolete Two-stage measurement error model' SubClassOf 'obsolete SWO class' 'obsolete Two-stage measurement error model' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000730 obsolete xps 'obsolete xps' SubClassOf 'obsolete SWO class' 'obsolete xps' SubClassOf 'obsolete BioConductor Software' 'obsolete xps' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000297 MicroArraySuite 4.0 'MicroArraySuite 4.0' SubClassOf 'MIcroarray Analysis Suite' http://www.ebi.ac.uk/efo/swo/SWO_0000731 obsolete yaqcaffy 'obsolete yaqcaffy' SubClassOf 'obsolete SWO class' 'obsolete yaqcaffy' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000296 Misclassification-Penalized Posteriors (MiPP) 'Misclassification-Penalized Posteriors (MiPP)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000298 Mixed model equations 'Mixed model equations' SubClassOf 'algorithm' http://www.ontodm.com/OntoDM-core/OntoDM_000087 probability distribution estimation task DisjointClasses: 'probability distribution estimation task', 'pattern discovery task', 'predictive modeling task', 'clustering task' 'probability distribution estimation task' SubClassOf 'data mining task' http://www.ebi.ac.uk/swo/SWO_0000293 MergeMaid 'MergeMaid' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'MergeMaid' SubClassOf 'software' 'MergeMaid' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'MergeMaid' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'MergeMaid' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'MergeMaid' SubClassOf 'R software' 'MergeMaid' SubClassOf 'is encoded in' some 'R language' 'MergeMaid' SubClassOf 'implements' some 'Regression model' 'MergeMaid' SubClassOf 'implements' some 'Logic regression' http://www.ebi.ac.uk/swo/SWO_0000292 MeasurementError.cor 'MeasurementError.cor' SubClassOf 'is encoded in' some 'R language' 'MeasurementError.cor' SubClassOf 'R software' 'MeasurementError.cor' SubClassOf 'implements' some 'Two-stage measurement error model' 'MeasurementError.cor' SubClassOf 'software' 'MeasurementError.cor' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'MeasurementError.cor' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'MeasurementError.cor' SubClassOf 'is executed in' some 'descriptive statistical calculation' http://www.ebi.ac.uk/swo/SWO_0000295 MiPP 'MiPP' SubClassOf 'is executed in' some 'data normalization' 'MiPP' SubClassOf 'has specified data input' some ('ALL/AML data set' and ('has format specification' some 'data format specification')) 'MiPP' SubClassOf 'R software' 'MiPP' SubClassOf 'implements' some 'Misclassification-Penalized Posteriors (MiPP)' 'MiPP' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'MiPP' SubClassOf 'is encoded in' some 'R language' 'MiPP' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000294 Mfuzz 'Mfuzz' SubClassOf 'implements' some 'clustering algorithm' 'Mfuzz' SubClassOf 'is encoded in' some 'R language' 'Mfuzz' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'Mfuzz' SubClassOf 'R software' 'Mfuzz' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'Mfuzz' SubClassOf 'software' 'Mfuzz' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) http://www.ontodm.com/OntoDM-core/OntoDM_000092 pattern discovery task DisjointClasses: 'probability distribution estimation task', 'pattern discovery task', 'predictive modeling task', 'clustering task' 'pattern discovery task' SubClassOf 'data mining task' http://www.ontodm.com/OntoDM-core/OntoDM_000078 pattern specification 'pattern specification' SubClassOf 'single generalization specification' http://www.ebi.ac.uk/swo/SWO_0000231 ITALICS 'ITALICS' SubClassOf 'has specified data input' some ('Image' and ('has format specification' some 'CEL binary format')) 'ITALICS' SubClassOf 'is executed in' some 'data normalization' 'ITALICS' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'ITALICS' SubClassOf 'is encoded in' some 'R language' 'ITALICS' SubClassOf 'R software' 'ITALICS' SubClassOf 'software' 'ITALICS' SubClassOf 'implements' some 'AWS algorithm' 'ITALICS' SubClassOf 'implements' some 'HaarSeg algorithm' 'ITALICS' SubClassOf 'implements' some 'Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)' http://www.ebi.ac.uk/swo/SWO_0000230 IRanges 'IRanges' SubClassOf 'is executed in' some 'data normalization' 'IRanges' SubClassOf 'R software' 'IRanges' SubClassOf 'software' 'IRanges' SubClassOf 'is executed in' some 'decision tree induction' 'IRanges' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'IRanges' SubClassOf 'is encoded in' some 'R language' 'IRanges' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) http://www.ebi.ac.uk/swo/SWO_0000233 ILLUMINA data 'ILLUMINA data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000235 ImaGene 3.0 'ImaGene 3.0' SubClassOf 'ImaGene' http://www.ebi.ac.uk/swo/SWO_0000234 ImaGene4.1 software 'ImaGene4.1 software' SubClassOf 'ImaGene' http://www.ebi.ac.uk/swo/SWO_0000237 ImageReader 'ImageReader' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000236 ImageQuant 'ImageQuant' SubClassOf 'output of' some ('software development' and ('has participant' value 'Molecular Dynamics')) 'ImageQuant' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000239 Imagene v4.0 'Imagene v4.0' SubClassOf 'ImaGene' http://www.ebi.ac.uk/swo/SWO_0000238 ImaGene 'ImaGene' SubClassOf 'output of' some ('software development' and ('has participant' value 'Bio Discovery')) 'ImaGene' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000241 Initial microarray data processing (data filtering, local normalisation and quality control) 'Initial microarray data processing (data filtering, local normalisation and quality control)' SubClassOf 'output of' some ('software development' and ('has participant' value 'Bahler Lab')) 'Initial microarray data processing (data filtering, local normalisation and quality control)' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000243 Jaccard’s index 'Jaccard’s index' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000246 KCsmart 'KCsmart' SubClassOf 'software with image input' 'KCsmart' SubClassOf 'R software' 'KCsmart' SubClassOf 'software' 'KCsmart' SubClassOf 'is executed in' some 'background correction' 'KCsmart' SubClassOf 'has specified data input' some ('Graph plot' and ('has format specification' some 'image format')) 'KCsmart' SubClassOf 'implements' some 'Gaussian locally weighted regression' 'KCsmart' SubClassOf 'is executed in' some 'data normalization' 'KCsmart' SubClassOf 'is encoded in' some 'R language' 'KCsmart' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'KCsmart' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) http://www.ebi.ac.uk/swo/SWO_0000245 Jaguar 'Jaguar' SubClassOf 'software' 'Jaguar' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Affymetrix')) http://www.ebi.ac.uk/swo/SWO_0000248 KEGGgraph 'KEGGgraph' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'KEGGgraph' SubClassOf 'is encoded in' some 'R language' 'KEGGgraph' SubClassOf 'R software' 'KEGGgraph' SubClassOf 'software' 'KEGGgraph' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'KGML')) 'KEGGgraph' SubClassOf 'implements' some 'R interface to boost graph library algorithm (RBGL)' http://www.ebi.ac.uk/swo/SWO_0000247 KEGGSOAP 'KEGGSOAP' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'KEGGSOAP' SubClassOf 'software' 'KEGGSOAP' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'KEGGSOAP' SubClassOf 'R software' 'KEGGSOAP' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000249 KGML 'KGML' SubClassOf 'XML' http://www.ebi.ac.uk/swo/SWO_0000253 LC-MS data 'LC-MS data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000252 LBE 'LBE' SubClassOf 'is executed in' some 'differential expression analysis' 'LBE' SubClassOf 'R software' 'LBE' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'LBE' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'LBE' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'LBE' SubClassOf 'software' 'LBE' SubClassOf 'implements' some ''FDR'' 'LBE' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000255 Locally Moderated Weighted-t (LMW) method 'Locally Moderated Weighted-t (LMW) method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000254 LMGene 'LMGene' SubClassOf 'is encoded in' some 'R language' 'LMGene' SubClassOf 'is executed in' some 'Linear modelling' 'LMGene' SubClassOf 'software' 'LMGene' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'LMGene' SubClassOf 'R software' 'LMGene' SubClassOf 'is executed in' some 'data normalization' 'LMGene' SubClassOf 'implements' some 'Linear modelling' 'LMGene' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) http://www.ebi.ac.uk/swo/SWO_0000257 Lognormal Normal with Modied Variance Model 'Lognormal Normal with Modied Variance Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000256 Lognormal Normal Model 'Lognormal Normal Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000259 LPEadj 'LPEadj' SubClassOf 'is executed in' some 'data normalization' 'LPEadj' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'LPEadj' SubClassOf 'is encoded in' some 'R language' 'LPEadj' SubClassOf 'is executed in' some 'differential expression analysis' 'LPEadj' SubClassOf 'software' 'LPEadj' SubClassOf 'R software' 'LPEadj' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'LPEadj' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'LPEadj' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'LPEadj' SubClassOf 'implements' some 'Local-pooled-error' 'LPEadj' SubClassOf 'implements' some ''FDR'' http://www.ebi.ac.uk/swo/SWO_0000258 LPE 'LPE' SubClassOf 'software' 'LPE' SubClassOf 'is encoded in' some 'R language' 'LPE' SubClassOf 'is executed in' some 'data normalization' 'LPE' SubClassOf 'implements' some 'Local-pooled-error' 'LPE' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'LPE' SubClassOf 'is executed in' some 'differential expression analysis' 'LPE' SubClassOf 'implements' some ''FDR'' 'LPE' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'LPE' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'LPE' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000251 Kolmogorov Smirnov rank-sum based algorithm 'Kolmogorov Smirnov rank-sum based algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000250 'KLD' ''KLD'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000264 Loess algorithm 'Loess algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000263 Library Search Algorithm 'Library Search Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000266 MAANOVA v1.2 package for MATLAB 'MAANOVA v1.2 package for MATLAB' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000265 Logic regression 'Logic regression' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000267 Median Average Difference Algorithm 'Median Average Difference Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000269 MANOR 'MANOR' SubClassOf 'implements' some 'HaarSeg algorithm' 'MANOR' SubClassOf 'is executed in' some ('data visualization' and 'data normalization') 'MANOR' SubClassOf 'implements' some 'AWS algorithm' 'MANOR' SubClassOf 'software' 'MANOR' SubClassOf 'is encoded in' some 'R language' 'MANOR' SubClassOf 'implements' some 'Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)' 'MANOR' SubClassOf 'R software' 'MANOR' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000260 publisher role 'publisher role' SubClassOf 'role' http://www.ebi.ac.uk/swo/SWO_0000262 Laplace mixture model 'Laplace mixture model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000261 Langmuir Isotherm 'Langmuir Isotherm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000309 obsolete OLINgui 'obsolete OLINgui' SubClassOf 'obsolete SWO class' 'obsolete OLINgui' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000307 obsolete OCplus 'obsolete OCplus' SubClassOf 'obsolete SWO class' 'obsolete OCplus' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000308 obsolete OLIN 'obsolete OLIN' SubClassOf 'obsolete SWO class' 'obsolete OLIN' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000305 obsolete Nested Effects Models 'obsolete Nested Effects Models' SubClassOf 'obsolete SWO class' 'obsolete Nested Effects Models' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000306 obsolete Nonlinear Estimation by Iterative Partial Least Squares 'obsolete Nonlinear Estimation by Iterative Partial Least Squares' SubClassOf 'obsolete SWO class' 'obsolete Nonlinear Estimation by Iterative Partial Least Squares' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000304 obsolete 'Needleman-Wunsch' 'obsolete 'Needleman-Wunsch'' SubClassOf 'obsolete SWO class' 'obsolete 'Needleman-Wunsch'' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000312 obsolete OutlierD 'obsolete OutlierD' SubClassOf 'obsolete SWO class' 'obsolete OutlierD' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000671 qpcrNorm 'qpcrNorm' SubClassOf 'implements' some ('Quantile normalization' and 'Rank-invariant set normalization') 'qpcrNorm' SubClassOf 'R software' 'qpcrNorm' SubClassOf 'is executed in' some 'data normalization' 'qpcrNorm' SubClassOf 'is encoded in' some 'R language' 'qpcrNorm' SubClassOf 'has specified data input' some 'qPCR data' 'qpcrNorm' SubClassOf 'has specified data output' some 'Graph plot' 'qpcrNorm' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000313 obsolete Presence-Absence calls with Negative Probesets (PANP) 'obsolete Presence-Absence calls with Negative Probesets (PANP)' SubClassOf 'obsolete SWO class' 'obsolete Presence-Absence calls with Negative Probesets (PANP)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000670 qPCR data 'qPCR data' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000310 obsolete Optiquant 'obsolete Optiquant' SubClassOf 'obsolete SWO class' 'obsolete Optiquant' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000673 Quantile normalization 'Quantile normalization' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000311 obsolete OrderedList 'obsolete OrderedList' SubClassOf 'obsolete SWO class' 'obsolete OrderedList' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000672 qpgraph 'qpgraph' SubClassOf 'is encoded in' some 'R language' 'qpgraph' SubClassOf 'has specified data input' some 'Gene expression data' 'qpgraph' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'qpgraph' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'qpgraph' SubClassOf 'is published by' value 'Bioconductor' 'qpgraph' SubClassOf 'BioConductor Software' 'qpgraph' SubClassOf 'R software' 'qpgraph' SubClassOf 'software' 'qpgraph' SubClassOf 'implements' some ('Pearson correlation estimator' and 'AvgNRRs') http://www.ebi.ac.uk/swo/SWO_0000675 quantsmooth 'quantsmooth' SubClassOf 'R software' 'quantsmooth' SubClassOf 'has specified data input' some ('ILLUMINA data' or 'Gene expression dataset') 'quantsmooth' SubClassOf 'is executed in' some 'data visualization' 'quantsmooth' SubClassOf 'software' 'quantsmooth' SubClassOf 'is encoded in' some 'R language' 'quantsmooth' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000674 Quantile regression techniques 'Quantile regression techniques' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000677 rHVDM 'rHVDM' SubClassOf 'software' 'rHVDM' SubClassOf 'is encoded in' some 'R language' 'rHVDM' SubClassOf 'implements' some 'Hidden Variable Dynamic Modelling HVDM)' 'rHVDM' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'rHVDM' SubClassOf 'R software' 'rHVDM' SubClassOf 'has specified data input' some 'Gene expression dataset' 'rHVDM' SubClassOf 'has specified data output' some 'HTML report' http://www.ebi.ac.uk/swo/SWO_0000676 qvalue 'qvalue' SubClassOf 'has specified data input' some 'Gene expression dataset' 'qvalue' SubClassOf 'R software' 'qvalue' SubClassOf 'implements' some ''FDR'' 'qvalue' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'qvalue' SubClassOf 'is encoded in' some 'R language' 'qvalue' SubClassOf 'software' http://edamontology.org/format_3003 BED format 'BED format' SubClassOf http://edamontology.org/format_2919 http://www.ebi.ac.uk/swo/SWO_0000679 rama 'rama' SubClassOf 'software' 'rama' SubClassOf 'has specified data input' some 'Gene expression dataset' 'rama' SubClassOf 'implements' some ('Markov Chain Monte Carlo' and 'Bayesian Model') 'rama' SubClassOf 'is encoded in' some 'R language' 'rama' SubClassOf 'is published by' value 'Bioconductor' 'rama' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'rama' SubClassOf 'is specified data input of' exactly 2 'Gene expression dataset' 'rama' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'rama' SubClassOf 'BioConductor Software' 'rama' SubClassOf 'data item' 'rama' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000678 rMAT 'rMAT' SubClassOf 'is executed in' some ('gene expression analysis' and 'parse' and 'data normalization') 'rMAT' SubClassOf 'is encoded in' some 'R language' 'rMAT' SubClassOf 'has specified data output' some ('has format specification' only ('CEL binary format' or 'BPMAP')) 'rMAT' SubClassOf 'software' 'rMAT' SubClassOf 'R software' 'rMAT' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'BPMAP')) 'rMAT' SubClassOf 'BioConductor Software' 'rMAT' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/efo/swo/SWO_0000318 obsolete 'PLM' 'obsolete 'PLM'' SubClassOf 'obsolete SWO class' 'obsolete 'PLM'' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000319 obsolete PLPE 'obsolete PLPE' SubClassOf 'obsolete SWO class' 'obsolete PLPE' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000316 obsolete PCpheno 'obsolete PCpheno' SubClassOf 'obsolete SWO class' 'obsolete PCpheno' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000317 obsolete PGSEA 'obsolete PGSEA' SubClassOf 'obsolete SWO class' 'obsolete PGSEA' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000314 obsolete PAnnBuilder 'obsolete PAnnBuilder' SubClassOf 'obsolete SWO class' 'obsolete PAnnBuilder' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000315 obsolete Pearson correlation estimator 'obsolete Pearson correlation estimator' SubClassOf 'obsolete SWO class' 'obsolete Pearson correlation estimator' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000323 obsolete Propagation of uncertainty in microarray analysis 'obsolete Propagation of uncertainty in microarray analysis' SubClassOf 'obsolete SWO class' 'obsolete Propagation of uncertainty in microarray analysis' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000682 .raw files '.raw files' SubClassOf 'ASCII format' http://www.ebi.ac.uk/efo/swo/SWO_0000324 obsolete Pathways 2.01 software 'obsolete Pathways 2.01 software' SubClassOf 'obsolete SWO class' 'obsolete Pathways 2.01 software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000681 Rank product non-parametric method 'Rank product non-parametric method' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000321 obsolete PPC algorithm 'obsolete PPC algorithm' SubClassOf 'obsolete SWO class' 'obsolete PPC algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000200 GenePix Pro 3.0 'GenePix Pro 3.0' SubClassOf 'GenePix Pro' http://www.ebi.ac.uk/swo/SWO_0000684 rda 'rda' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/efo/swo/SWO_0000322 obsolete PROcess 'obsolete PROcess' SubClassOf 'obsolete SWO class' 'obsolete PROcess' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000683 rbsurv 'rbsurv' SubClassOf 'has specified data input' some 'Gene expression data' 'rbsurv' SubClassOf 'is published by' value 'Bioconductor' 'rbsurv' SubClassOf 'R software' 'rbsurv' SubClassOf 'software' 'rbsurv' SubClassOf 'BioConductor Software' 'rbsurv' SubClassOf 'is encoded in' some 'R language' 'rbsurv' SubClassOf 'implements' some 'Robust likelihood-based survival modeling' 'rbsurv' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') http://www.ebi.ac.uk/swo/SWO_0000202 GeneticsDesign 'GeneticsDesign' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'GeneticsDesign' SubClassOf 'software' 'GeneticsDesign' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GeneticsDesign' SubClassOf 'is encoded in' some 'R language' 'GeneticsDesign' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000686 rflowcyt 'rflowcyt' SubClassOf 'software' 'rflowcyt' SubClassOf 'is published by' value 'Bioconductor' 'rflowcyt' SubClassOf 'R software' 'rflowcyt' SubClassOf 'has specified data input' some ('has format specification' only 'Data File Standard for Flow Cytometry') 'rflowcyt' SubClassOf 'BioConductor Software' 'rflowcyt' SubClassOf 'is encoded in' some 'R language' 'rflowcyt' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') http://www.ebi.ac.uk/efo/swo/SWO_0000320 obsolete Probe level Locally moderated Weighted median-t (PLW) method 'obsolete Probe level Locally moderated Weighted median-t (PLW) method' SubClassOf 'obsolete SWO class' 'obsolete Probe level Locally moderated Weighted median-t (PLW) method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000201 GeneticsBase 'GeneticsBase' SubClassOf 'software' 'GeneticsBase' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'GeneticsBase' SubClassOf 'BioConductor Software' 'GeneticsBase' SubClassOf 'has specified data input' some 'CSV data set' 'GeneticsBase' SubClassOf 'is encoded in' some 'R language' 'GeneticsBase' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'GeneticsBase' SubClassOf 'has specified data input' some ('has format specification' only 'pedigree data file') 'GeneticsBase' SubClassOf 'is published by' value 'Bioconductor' 'GeneticsBase' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000685 reb 'reb' SubClassOf 'software' 'reb' SubClassOf 'has specified data output' some ('Heat map' and 'Image') 'reb' SubClassOf 'is encoded in' some 'R language' 'reb' SubClassOf 'R software' 'reb' SubClassOf 'has specified data input' some 'Gene expression dataset' http://www.ebi.ac.uk/swo/SWO_0000688 rsbml 'rsbml' SubClassOf 'R software' 'rsbml' SubClassOf 'is published by' value 'Bioconductor' 'rsbml' SubClassOf 'software' 'rsbml' SubClassOf 'has specified data input' some ('has format specification' only 'SBML') 'rsbml' SubClassOf 'is executed in' some ('parse' and 'cross validation') 'rsbml' SubClassOf 'BioConductor Software' 'rsbml' SubClassOf 'is encoded in' some 'R language' 'rsbml' SubClassOf 'has specified data output' some ('has format specification' only 'XML') http://www.ebi.ac.uk/swo/SWO_0000203 GeneticsPed 'GeneticsPed' SubClassOf 'BioConductor Software' 'GeneticsPed' SubClassOf 'implements' some 'Mixed model equations' 'GeneticsPed' SubClassOf 'is encoded in' some 'R language' 'GeneticsPed' SubClassOf 'is published by' value 'Bioconductor' 'GeneticsPed' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GeneticsPed' SubClassOf 'has specified data input' some ('has format specification' only 'pedigree data file') 'GeneticsPed' SubClassOf 'R software' 'GeneticsPed' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000687 .rma format '.rma format' SubClassOf 'audio format' http://www.ebi.ac.uk/swo/SWO_0000680 Rank-invariant set normalization 'Rank-invariant set normalization' SubClassOf 'algorithm' http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD_778151 data processing task 'data processing task' SubClassOf 'data transformation' 'data processing task' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/SWO_0000206 GlobalAncova 'GlobalAncova' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GlobalAncova' SubClassOf 'software' 'GlobalAncova' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'GlobalAncova' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'GlobalAncova' SubClassOf 'is executed in' some 'differential expression analysis' 'GlobalAncova' SubClassOf 'R software' 'GlobalAncova' SubClassOf 'implements' some 'ANCOVA' 'GlobalAncova' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000205 GenomeGraphs 'GenomeGraphs' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GenomeGraphs' SubClassOf 'is encoded in' some 'R language' 'GenomeGraphs' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'GenomeGraphs' SubClassOf 'R software' 'GenomeGraphs' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000689 rtracklayer 'rtracklayer' SubClassOf 'is encoded in' some 'R language' 'rtracklayer' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'rtracklayer' SubClassOf 'is published by' value 'Bioconductor' 'rtracklayer' SubClassOf 'software' 'rtracklayer' SubClassOf 'R software' 'rtracklayer' SubClassOf 'is executed in' some 'data visualization' 'rtracklayer' SubClassOf 'BioConductor Software' 'rtracklayer' SubClassOf 'has specified data input' some ('has format specification' only ('GFF' or 'BED format')) http://www.ebi.ac.uk/efo/swo/SWO_0000329 obsolete QuantArray scanner software 'obsolete QuantArray scanner software' SubClassOf 'obsolete SWO class' 'obsolete QuantArray scanner software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000208 GraphAT 'GraphAT' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'GraphAT' SubClassOf 'R software' 'GraphAT' SubClassOf 'has specified data input' some ('Clustered data set' and ('has format specification' some 'data format specification')) 'GraphAT' SubClassOf 'implements' some 'k-means' 'GraphAT' SubClassOf 'software' 'GraphAT' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000207 GOSemSim 'GOSemSim' SubClassOf 'software' 'GOSemSim' SubClassOf 'has specified data output' some ('Clustered data set' and ('has format specification' some 'R data frame')) 'GOSemSim' SubClassOf 'R software' 'GOSemSim' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'GOSemSim' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'GOSemSim' SubClassOf 'is encoded in' some 'R language' 'GOSemSim' SubClassOf 'implements' some 'Semantic Similarity Measures' http://www.ebi.ac.uk/efo/swo/SWO_0000327 obsolete Probe Cell Analysis 'obsolete Probe Cell Analysis' SubClassOf 'obsolete SWO class' 'obsolete Probe Cell Analysis' SubClassOf 'obsolete MicroArraySuite 5.0' http://www.ebi.ac.uk/efo/swo/SWO_0000328 obsolete PLIER (Probe Logarithmic Error Intensity Estimate) method 'obsolete PLIER (Probe Logarithmic Error Intensity Estimate) method' SubClassOf 'obsolete SWO class' 'obsolete PLIER (Probe Logarithmic Error Intensity Estimate) method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000209 GraphAlignment 'GraphAlignment' SubClassOf 'is encoded in' some 'R language' 'GraphAlignment' SubClassOf 'R software' 'GraphAlignment' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GraphAlignment' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GraphAlignment' SubClassOf 'software' 'GraphAlignment' SubClassOf 'implements' some 'Bayesian Model' http://www.ebi.ac.uk/efo/swo/SWO_0000326 obsolete Power Law Global Error Model (PLGEM) analysis method 'obsolete Power Law Global Error Model (PLGEM) analysis method' SubClassOf 'obsolete SWO class' 'obsolete Power Law Global Error Model (PLGEM) analysis method' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000334 obsolete R interface to boost graph library algorithm (RBGL) 'obsolete R interface to boost graph library algorithm (RBGL)' SubClassOf 'obsolete SWO class' 'obsolete R interface to boost graph library algorithm (RBGL)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000693 sigPathway 'sigPathway' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'sigPathway' SubClassOf 'software' 'sigPathway' SubClassOf 'has specified data input' some 'Gene expression data' 'sigPathway' SubClassOf 'is encoded in' some 'R language' 'sigPathway' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000335 obsolete RBioinf 'obsolete RBioinf' SubClassOf 'obsolete SWO class' 'obsolete RBioinf' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000692 seqLogo 'seqLogo' SubClassOf 'R software' 'seqLogo' SubClassOf 'software' 'seqLogo' SubClassOf 'BioConductor Software' 'seqLogo' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'seqLogo' SubClassOf 'is published by' value 'Bioconductor' 'seqLogo' SubClassOf 'implements' some 'Position weight matrix (PWM )' 'seqLogo' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'seqLogo' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/efo/swo/SWO_0000332 obsolete Radial basis function 'obsolete Radial basis function' SubClassOf 'obsolete SWO class' 'obsolete Radial basis function' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000695 Sim method 'Sim method' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000333 obsolete RBGL 'obsolete RBGL' SubClassOf 'obsolete SWO class' 'obsolete RBGL' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000210 GridGrinder 'GridGrinder' SubClassOf 'software' 'GridGrinder' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Grid grinder')) http://www.ebi.ac.uk/swo/SWO_0000694 siggenes 'siggenes' SubClassOf 'software' 'siggenes' SubClassOf 'is encoded in' some 'R language' 'siggenes' SubClassOf 'has specified data input' some 'Text data set' 'siggenes' SubClassOf 'is executed in' some 'differential expression analysis' 'siggenes' SubClassOf 'R software' 'siggenes' SubClassOf 'has specified data output' some 'HTML report' 'siggenes' SubClassOf 'implements' some ('SAM' and 'Empirical Bayes rule' and ''FDR'') http://www.ebi.ac.uk/efo/swo/SWO_0000330 obsolete QuantArray, PackaardBiochip technologies 'obsolete QuantArray, PackaardBiochip technologies' SubClassOf 'obsolete SWO class' 'obsolete QuantArray, PackaardBiochip technologies' SubClassOf 'obsolete QuantArray scanner software' http://www.ebi.ac.uk/swo/SWO_0000213 HELP 'HELP' SubClassOf 'is executed in' some 'data normalization' 'HELP' SubClassOf 'implements' some ('RMA' and 'k-nearest neighbour classification') 'HELP' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'pair file')) 'HELP' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'HELP' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'design file')) 'HELP' SubClassOf 'is executed in' some 'data visualization' 'HELP' SubClassOf 'R software' 'HELP' SubClassOf 'software' 'HELP' SubClassOf 'is encoded in' some 'R language' 'HELP' SubClassOf 'is executed in' some 'background correction' 'HELP' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) http://www.ebi.ac.uk/swo/SWO_0000697 simulatorAPMS 'simulatorAPMS' SubClassOf 'software' 'simulatorAPMS' SubClassOf 'has specified data input' some 'AP-MS data' 'simulatorAPMS' SubClassOf 'implements' some 'Complex Estimation Algorithm' 'simulatorAPMS' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'simulatorAPMS' SubClassOf 'is encoded in' some 'R language' 'simulatorAPMS' SubClassOf 'R software' 'simulatorAPMS' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') http://www.ebi.ac.uk/efo/swo/SWO_0000331 obsolete QuantArray version 2 'obsolete QuantArray version 2' SubClassOf 'obsolete SWO class' 'obsolete QuantArray version 2' SubClassOf 'obsolete QuantArray scanner software' http://www.ebi.ac.uk/swo/SWO_0000212 Hexagon binning algorithm 'Hexagon binning algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000696 simpleaffy 'simpleaffy' SubClassOf 'is encoded in' some 'R language' 'simpleaffy' SubClassOf 'BioConductor Software' 'simpleaffy' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' and 'covdesc file')) 'simpleaffy' SubClassOf 'R software' 'simpleaffy' SubClassOf 'has specified data output' some ('Heat map' and 'Graph plot' and 'Text data set') 'simpleaffy' SubClassOf 'software' 'simpleaffy' SubClassOf 'implements' some ('RMA' and ''MAS5'') 'simpleaffy' SubClassOf 'is published by' value 'Bioconductor' 'simpleaffy' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'descriptive statistical calculation') http://www.ebi.ac.uk/swo/SWO_0000215 Heterogeneous Error Model (HEM) 'Heterogeneous Error Model (HEM)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000699 xmapbridge 'xmapbridge' SubClassOf 'BioConductor Software' 'xmapbridge' SubClassOf 'software' 'xmapbridge' SubClassOf 'R software' 'xmapbridge' SubClassOf 'is published by' value 'Bioconductor' 'xmapbridge' SubClassOf 'is encoded in' some 'R language' 'xmapbridge' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'xmapbridge' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000214 HEM 'HEM' SubClassOf 'software' 'HEM' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'HEM' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'HEM' SubClassOf 'implements' some 'Empirical Bayes rule' 'HEM' SubClassOf 'is encoded in' some 'R language' 'HEM' SubClassOf 'implements' some 'Heterogeneous Error Model (HEM)' 'HEM' SubClassOf 'R software' 'HEM' SubClassOf 'implements' some ''FDR'' 'HEM' SubClassOf 'implements' some 'Markov Chain Monte Carlo' http://www.ebi.ac.uk/swo/SWO_0000698 sizepower 'sizepower' SubClassOf 'software' 'sizepower' SubClassOf 'BioConductor Software' 'sizepower' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'sizepower' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'sizepower' SubClassOf 'is published by' value 'Bioconductor' 'sizepower' SubClassOf 'R software' 'sizepower' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'differential expression analysis') 'sizepower' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000691 sagenhaft 'sagenhaft' SubClassOf 'is published by' value 'Bioconductor' 'sagenhaft' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'sagenhaft' SubClassOf 'implements' some 'Serial Analysis of Gene Expression (SAGE)' 'sagenhaft' SubClassOf 'software' 'sagenhaft' SubClassOf 'has specified data output' some 'Text data set' 'sagenhaft' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'sagenhaft' SubClassOf 'BioConductor Software' 'sagenhaft' SubClassOf 'R software' 'sagenhaft' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000690 safe 'safe' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'safe' SubClassOf 'implements' some ('Bootstrap' and 'Global test' and ''t-test'' and ''ANOVA'') 'safe' SubClassOf 'has specified data input' some 'ALL/AML data set' 'safe' SubClassOf 'BioConductor Software' 'safe' SubClassOf 'is specified data input of' exactly 3 'Text data set' 'safe' SubClassOf 'is published by' value 'Bioconductor' 'safe' SubClassOf 'is encoded in' some 'R language' 'safe' SubClassOf 'software' 'safe' SubClassOf 'data item' 'safe' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000217 Hidden Markov Model 'Hidden Markov Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000216 Hubert’s gamma 'Hubert’s gamma' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000219 Hidden Variable Dynamic Modelling HVDM) 'Hidden Variable Dynamic Modelling HVDM)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000218 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm 'Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000338 obsolete RLMM 'obsolete RLMM' SubClassOf 'obsolete SWO class' 'obsolete RLMM' SubClassOf 'obsolete BioConductor Software' 'obsolete RLMM' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000339 obsolete Regression model 'obsolete Regression model' SubClassOf 'obsolete SWO class' 'obsolete Regression model' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000336 obsolete Random effects model 'obsolete Random effects model' SubClassOf 'obsolete SWO class' 'obsolete Random effects model' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000337 obsolete Recursive Feature Elimination (RFE) 'obsolete Recursive Feature Elimination (RFE)' SubClassOf 'obsolete SWO class' 'obsolete Recursive Feature Elimination (RFE)' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000345 obsolete RMAExpress quantification 'obsolete RMAExpress quantification' SubClassOf 'obsolete SWO class' 'obsolete RMAExpress quantification' SubClassOf 'obsolete RMAExpress' http://www.ebi.ac.uk/swo/SWO_0000220 HaarSeg algorithm 'HaarSeg algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000346 obsolete RMAGEML 'obsolete RMAGEML' SubClassOf 'obsolete SWO class' 'obsolete RMAGEML' SubClassOf 'obsolete BioConductor Software' 'obsolete RMAGEML' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000343 obsolete RMAExpress 'obsolete RMAExpress' SubClassOf 'obsolete SWO class' 'obsolete RMAExpress' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000222 Harshlight 'Harshlight' SubClassOf 'R software' 'Harshlight' SubClassOf 'is encoded in' some 'R language' 'Harshlight' SubClassOf 'implements' some 'RMA' 'Harshlight' SubClassOf 'implements' some ''MAS5'' 'Harshlight' SubClassOf 'software' 'Harshlight' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'PostScript')) 'Harshlight' SubClassOf 'has specified data input' some ('Image' and ('has format specification' some 'CEL binary format')) http://www.ebi.ac.uk/efo/swo/SWO_0000344 obsolete RMAExpress 2.0 'obsolete RMAExpress 2.0' SubClassOf 'obsolete SWO class' 'obsolete RMAExpress 2.0' SubClassOf 'obsolete RMAExpress' http://www.ebi.ac.uk/swo/SWO_0000221 Hardy-Weinberg equilibrium 'Hardy-Weinberg equilibrium' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000341 obsolete RMA+ 'obsolete RMA+' SubClassOf 'obsolete SWO class' 'obsolete RMA+' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000224 Heatplus 'Heatplus' SubClassOf 'R software' 'Heatplus' SubClassOf 'has specified data output' some ('Heat map' and ('has format specification' some 'image format')) 'Heatplus' SubClassOf 'is encoded in' some 'R language' 'Heatplus' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'Heatplus' SubClassOf 'is executed in' some 'data visualization' 'Heatplus' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000342 obsolete RMA++ 'obsolete RMA++' SubClassOf 'obsolete SWO class' 'obsolete RMA++' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000226 HilbertVisGUI 'HilbertVisGUI' SubClassOf 'R software' 'HilbertVisGUI' SubClassOf 'software' 'HilbertVisGUI' SubClassOf 'is encoded in' some 'R language' 'HilbertVisGUI' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'BED format')) 'HilbertVisGUI' SubClassOf 'is executed in' some 'data visualization' 'HilbertVisGUI' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'HilbertVisGUI' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'GFF')) http://www.ebi.ac.uk/efo/swo/SWO_0000340 obsolete RMA 'obsolete RMA' SubClassOf 'obsolete SWO class' 'obsolete RMA' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000225 HilbertVis 'HilbertVis' SubClassOf 'software' 'HilbertVis' SubClassOf 'is encoded in' some 'R language' 'HilbertVis' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'BED format')) 'HilbertVis' SubClassOf 'is executed in' some 'data normalization' 'HilbertVis' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'HilbertVis' SubClassOf 'R software' 'HilbertVis' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'GFF')) 'HilbertVis' SubClassOf 'is executed in' some 'data visualization' http://www.ebi.ac.uk/swo/SWO_0000228 ICS-501 (version 2.3) Image Capture System 'ICS-501 (version 2.3) Image Capture System' SubClassOf 'output of' some ('software development' and ('has participant' value 'Genicon Sciences')) 'ICS-501 (version 2.3) Image Capture System' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000227 Hypergeometric probability 'Hypergeometric probability' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000229 Iteratively ReWeighted Least Squares 'Iteratively ReWeighted Least Squares' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000349 obsolete RWebServices 'obsolete RWebServices' SubClassOf 'obsolete SWO class' 'obsolete RWebServices' SubClassOf 'obsolete BioConductor Software' 'obsolete RWebServices' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000347 obsolete RNAither 'obsolete RNAither' SubClassOf 'obsolete SWO class' 'obsolete RNAither' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000348 obsolete ROC 'obsolete ROC' SubClassOf 'obsolete SWO class' 'obsolete ROC' SubClassOf 'obsolete R software' 'obsolete ROC' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000235 obsolete ImaGene 3.0 'obsolete ImaGene 3.0' SubClassOf 'obsolete SWO class' 'obsolete ImaGene 3.0' SubClassOf 'obsolete ImaGene' http://www.ebi.ac.uk/efo/swo/SWO_0000236 obsolete ImageQuant 'obsolete ImageQuant' SubClassOf 'obsolete SWO class' 'obsolete ImageQuant' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000233 obsolete ILLUMINA data 'obsolete ILLUMINA data' SubClassOf 'obsolete SWO class' 'obsolete ILLUMINA data' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000234 obsolete ImaGene4.1 software 'obsolete ImaGene4.1 software' SubClassOf 'obsolete SWO class' 'obsolete ImaGene4.1 software' SubClassOf 'obsolete ImaGene' http://www.ebi.ac.uk/efo/swo/SWO_0000231 obsolete ITALICS 'obsolete ITALICS' SubClassOf 'obsolete SWO class' 'obsolete ITALICS' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000631 Negative binomial distribution 'Negative binomial distribution' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000630 multtest 'multtest' SubClassOf 'BioConductor Software' 'multtest' SubClassOf 'is executed in' some 'differential expression analysis' 'multtest' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'multtest' SubClassOf 'is published by' value 'Bioconductor' 'multtest' SubClassOf 'is encoded in' some 'R language' 'multtest' SubClassOf 'software' 'multtest' SubClassOf 'implements' some 'Multiple testing' 'multtest' SubClassOf 'has specified data input' some 'ALL/AML data set' 'multtest' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000633 Neural networks models 'Neural networks models' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000230 obsolete IRanges 'obsolete IRanges' SubClassOf 'obsolete SWO class' 'obsolete IRanges' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000632 nem 'nem' SubClassOf 'R software' 'nem' SubClassOf 'is executed in' some ('data normalization' and 'decision tree induction' and 'differential expression analysis') 'nem' SubClassOf 'software' 'nem' SubClassOf 'implements' some 'Nested Effects Models' 'nem' SubClassOf 'is encoded in' some 'R language' 'nem' SubClassOf 'has specified data input' some 'Gene expression dataset' 'nem' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/organization/SWO_9000055 software publishing process 'software publishing process' SubClassOf 'process' 'software publishing process' SubClassOf http://purl.obolibrary.org/obo/BFO_0000007 http://www.ebi.ac.uk/swo/organization/SWO_9000056 software development 'software development' SubClassOf 'data transformation' 'software development' SubClassOf http://purl.obolibrary.org/obo/BFO_0000007 http://www.ebi.ac.uk/swo/SWO_0000635 nnNorm 'nnNorm' SubClassOf 'is published by' value 'Bioconductor' 'nnNorm' SubClassOf 'R software' 'nnNorm' SubClassOf 'has specified data input' some 'Gene expression dataset' 'nnNorm' SubClassOf 'is executed in' some 'data normalization' 'nnNorm' SubClassOf 'implements' some 'Neural networks models' 'nnNorm' SubClassOf 'BioConductor Software' 'nnNorm' SubClassOf 'has specified data output' some ('Image' or 'Graph plot' or ('has format specification' only 'R data frame')) 'nnNorm' SubClassOf 'is encoded in' some 'R language' 'nnNorm' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000637 occugene 'occugene' SubClassOf 'BioConductor Software' 'occugene' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'occugene' SubClassOf 'implements' some 'Markov Chain Monte Carlo' 'occugene' SubClassOf 'software' 'occugene' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'occugene' SubClassOf 'is encoded in' some 'R language' 'occugene' SubClassOf 'is published by' value 'Bioconductor' 'occugene' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000636 nudge 'nudge' SubClassOf 'software' 'nudge' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'nudge' SubClassOf 'is encoded in' some 'R language' 'nudge' SubClassOf 'implements' some 'Expectation-Maximization(EM) algorithm' 'nudge' SubClassOf 'BioConductor Software' 'nudge' SubClassOf 'R software' 'nudge' SubClassOf 'is published by' value 'Bioconductor' 'nudge' SubClassOf 'is executed in' some 'differential expression analysis' 'nudge' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') http://www.ebi.ac.uk/efo/swo/SWO_0000239 obsolete Imagene v4.0 'obsolete Imagene v4.0' SubClassOf 'obsolete SWO class' 'obsolete Imagene v4.0' SubClassOf 'obsolete ImaGene' http://www.ebi.ac.uk/swo/SWO_0000639 oligoClasses 'oligoClasses' SubClassOf 'R software' 'oligoClasses' SubClassOf 'is encoded in' some 'R language' 'oligoClasses' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000638 oligo 'oligo' SubClassOf 'is encoded in' some 'R language' 'oligo' SubClassOf 'R software' 'oligo' SubClassOf 'implements' some ('SNPRMA algorithm' and 'CRLMM algorithm') 'oligo' SubClassOf 'BioConductor Software' 'oligo' SubClassOf 'is published by' value 'Bioconductor' 'oligo' SubClassOf 'software' 'oligo' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'oligo' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) http://www.ebi.ac.uk/efo/swo/SWO_0000237 obsolete ImageReader 'obsolete ImageReader' SubClassOf 'obsolete SWO class' 'obsolete ImageReader' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000238 obsolete ImaGene 'obsolete ImaGene' SubClassOf 'obsolete SWO class' 'obsolete ImaGene' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000246 obsolete KCsmart 'obsolete KCsmart' SubClassOf 'obsolete SWO class' 'obsolete KCsmart' SubClassOf 'software with image input' 'obsolete KCsmart' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000247 obsolete KEGGSOAP 'obsolete KEGGSOAP' SubClassOf 'obsolete SWO class' 'obsolete KEGGSOAP' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000640 OMICS data 'OMICS data' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000245 obsolete Jaguar 'obsolete Jaguar' SubClassOf 'obsolete SWO class' 'obsolete Jaguar' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000642 ontoTools 'ontoTools' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'ontoTools' SubClassOf 'is published by' value 'Bioconductor' 'ontoTools' SubClassOf 'software' 'ontoTools' SubClassOf 'R software' 'ontoTools' SubClassOf 'has specified data output' some 'Graph plot' 'ontoTools' SubClassOf 'BioConductor Software' 'ontoTools' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/efo/swo/SWO_0000243 obsolete Jaccard’s index 'obsolete Jaccard’s index' SubClassOf 'obsolete SWO class' 'obsolete Jaccard’s index' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000641 oneChannelGUI 'oneChannelGUI' SubClassOf 'BioConductor Software' 'oneChannelGUI' SubClassOf 'R software' 'oneChannelGUI' SubClassOf 'is encoded in' some 'R language' 'oneChannelGUI' SubClassOf 'has specified data input' some ('ILLUMINA data' or 'Gene expression dataset' or ('has format specification' only ('CEL binary format' or 'GEO Matrix Series format' or 'CEL ASCII format'))) 'oneChannelGUI' SubClassOf 'implements' some ('Regression model' and 'RMA' and 'SAM' and ''FDR'') 'oneChannelGUI' SubClassOf 'software' 'oneChannelGUI' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set' and ('has format specification' only 'pdf')) 'oneChannelGUI' SubClassOf 'is executed in' some ('data visualization' and 'background correction' and 'data normalization' and 'decision tree induction' and 'descriptive statistical calculation' and 'differential expression analysis') 'oneChannelGUI' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000644 pair file 'pair file' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000241 obsolete Initial microarray data processing (data filtering, local normalisation and quality control) 'obsolete Initial microarray data processing (data filtering, local normalisation and quality control)' SubClassOf 'obsolete SWO class' 'obsolete Initial microarray data processing (data filtering, local normalisation and quality control)' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000646 panp 'panp' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' only ('CEL binary format' or 'CEL ASCII format'))) 'panp' SubClassOf 'has specified data output' some ('Graph plot' and 'CSV data set') 'panp' SubClassOf 'is published by' value 'Bioconductor' 'panp' SubClassOf 'implements' some 'Presence-Absence calls with Negative Probesets (PANP)' 'panp' SubClassOf 'is encoded in' some 'R language' 'panp' SubClassOf 'BioConductor Software' 'panp' SubClassOf 'R software' 'panp' SubClassOf 'is executed in' some ('gene expression analysis' and 'descriptive statistical calculation') 'panp' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000645 pamr 'pamr' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'pamr' SubClassOf 'R software' 'pamr' SubClassOf 'BioConductor Software' 'pamr' SubClassOf 'implements' some ''ANOVA'' 'pamr' SubClassOf 'is published by' value 'Bioconductor' 'pamr' SubClassOf 'has specified data input' some 'Text data set' 'pamr' SubClassOf 'software' 'pamr' SubClassOf 'is encoded in' some 'R language' 'pamr' SubClassOf 'is executed in' some 'descriptive statistical calculation' http://www.ebi.ac.uk/swo/SWO_0000648 parse 'parse' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_0000647 parody 'parody' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'parody' SubClassOf 'R software' 'parody' SubClassOf 'is published by' value 'Bioconductor' 'parody' SubClassOf 'BioConductor Software' 'parody' SubClassOf 'is encoded in' some 'R language' 'parody' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'parody' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000649 pathRender 'pathRender' SubClassOf 'is encoded in' some 'R language' 'pathRender' SubClassOf 'is executed in' some ('data visualization' and 'differential expression analysis') 'pathRender' SubClassOf 'software' 'pathRender' SubClassOf 'has specified data input' some 'Gene expression dataset' 'pathRender' SubClassOf 'has specified data output' some 'Graph plot' 'pathRender' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000248 obsolete KEGGgraph 'obsolete KEGGgraph' SubClassOf 'obsolete SWO class' 'obsolete KEGGgraph' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000249 obsolete KGML 'obsolete KGML' SubClassOf 'obsolete SWO class' 'obsolete KGML' SubClassOf 'XML' http://www.ebi.ac.uk/efo/swo/SWO_0000257 obsolete Lognormal Normal with Modied Variance Model 'obsolete Lognormal Normal with Modied Variance Model' SubClassOf 'obsolete SWO class' 'obsolete Lognormal Normal with Modied Variance Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000258 obsolete LPE 'obsolete LPE' SubClassOf 'obsolete SWO class' 'obsolete LPE' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000255 obsolete Locally Moderated Weighted-t (LMW) method 'obsolete Locally Moderated Weighted-t (LMW) method' SubClassOf 'obsolete SWO class' 'obsolete Locally Moderated Weighted-t (LMW) method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000651 pcot2 'pcot2' SubClassOf 'has specified data input' some 'ALL/AML data set' 'pcot2' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'JPEG')) 'pcot2' SubClassOf 'software' 'pcot2' SubClassOf 'is encoded in' some 'R language' 'pcot2' SubClassOf 'is published by' value 'Bioconductor' 'pcot2' SubClassOf 'R software' 'pcot2' SubClassOf 'BioConductor Software' 'pcot2' SubClassOf 'implements' some ''FDR'' http://www.ebi.ac.uk/efo/swo/SWO_0000256 obsolete Lognormal Normal Model 'obsolete Lognormal Normal Model' SubClassOf 'obsolete SWO class' 'obsolete Lognormal Normal Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000650 pcaMethods 'pcaMethods' SubClassOf 'has specified data output' some 'Graph plot' 'pcaMethods' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'pcaMethods' SubClassOf 'R software' 'pcaMethods' SubClassOf 'is published by' value 'Bioconductor' 'pcaMethods' SubClassOf 'is executed in' some ('data visualization' and 'cross validation') 'pcaMethods' SubClassOf 'BioConductor Software' 'pcaMethods' SubClassOf 'software' 'pcaMethods' SubClassOf 'is encoded in' some 'R language' 'pcaMethods' SubClassOf 'implements' some ('Nonlinear Estimation by Iterative Partial Least Squares' and 'SVDimpute algorithm' and 'Bayesian Model' and 'Expectation-Maximization(EM) algorithm') http://www.ebi.ac.uk/efo/swo/SWO_0000253 obsolete LC-MS data 'obsolete LC-MS data' SubClassOf 'obsolete SWO class' 'obsolete LC-MS data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000653 pdInfoBuilder 'pdInfoBuilder' SubClassOf 'is published by' value 'Bioconductor' 'pdInfoBuilder' SubClassOf 'software' 'pdInfoBuilder' SubClassOf 'has specified data input' some ('Text data set' and 'CSV data set' and ('has format specification' only ('CDF binary format' or 'CDF ASCII format'))) 'pdInfoBuilder' SubClassOf 'is encoded in' some 'R language' 'pdInfoBuilder' SubClassOf 'BioConductor Software' 'pdInfoBuilder' SubClassOf 'has specified data output' some 'Text data set' 'pdInfoBuilder' SubClassOf 'is executed in' some 'data annotation' 'pdInfoBuilder' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000254 obsolete LMGene 'obsolete LMGene' SubClassOf 'obsolete SWO class' 'obsolete LMGene' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000251 obsolete Kolmogorov Smirnov rank-sum based algorithm 'obsolete Kolmogorov Smirnov rank-sum based algorithm' SubClassOf 'obsolete SWO class' 'obsolete Kolmogorov Smirnov rank-sum based algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000655 pedigree data file 'pedigree data file' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000252 obsolete LBE 'obsolete LBE' SubClassOf 'obsolete SWO class' 'obsolete LBE' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000654 pdmclass 'pdmclass' SubClassOf 'R software' 'pdmclass' SubClassOf 'implements' some 'Regression model' 'pdmclass' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'pdmclass' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'pdmclass' SubClassOf 'software' 'pdmclass' SubClassOf 'is encoded in' some 'R language' 'pdmclass' SubClassOf 'has specified data input' some 'Gene expression dataset' 'pdmclass' SubClassOf 'is published by' value 'Bioconductor' 'pdmclass' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000250 obsolete 'KLD' 'obsolete 'KLD'' SubClassOf 'obsolete SWO class' 'obsolete 'KLD'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000657 pickgene 'pickgene' SubClassOf 'software' 'pickgene' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'pickgene' SubClassOf 'is published by' value 'Bioconductor' 'pickgene' SubClassOf 'BioConductor Software' 'pickgene' SubClassOf 'implements' some ('Median Average Difference Algorithm' and 'Gene array analysis algorithm') 'pickgene' SubClassOf 'is executed in' some ('background correction' and 'descriptive statistical calculation' and 'differential expression analysis') 'pickgene' SubClassOf 'is encoded in' some 'R language' 'pickgene' SubClassOf 'has specified data input' some 'Gene expression data' 'pickgene' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000656 pgUtils 'pgUtils' SubClassOf 'has specified data output' some ('has format specification' only 'log file') 'pgUtils' SubClassOf 'is published by' value 'Bioconductor' 'pgUtils' SubClassOf 'has specified data input' some 'Text data set' 'pgUtils' SubClassOf 'BioConductor Software' 'pgUtils' SubClassOf 'is executed in' some 'database creation' 'pgUtils' SubClassOf 'software' 'pgUtils' SubClassOf 'is encoded in' some 'R language' 'pgUtils' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000659 plgem 'plgem' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'plgem' SubClassOf 'BioConductor Software' 'plgem' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'plgem' SubClassOf 'is encoded in' some 'R language' 'plgem' SubClassOf 'software' 'plgem' SubClassOf 'implements' some 'Power Law Global Error Model (PLGEM) analysis method' 'plgem' SubClassOf 'has specified data input' some 'Gene expression dataset' 'plgem' SubClassOf 'R software' 'plgem' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000658 pkgDepTools 'pkgDepTools' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'pkgDepTools' SubClassOf 'is encoded in' some 'R language' 'pkgDepTools' SubClassOf 'software' 'pkgDepTools' SubClassOf 'has specified data output' some 'Graph plot' 'pkgDepTools' SubClassOf 'is published by' value 'Bioconductor' 'pkgDepTools' SubClassOf 'BioConductor Software' 'pkgDepTools' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000259 obsolete LPEadj 'obsolete LPEadj' SubClassOf 'obsolete SWO class' 'obsolete LPEadj' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000660 plier 'plier' SubClassOf 'is encoded in' some 'R language' 'plier' SubClassOf 'has specified data input' some 'Gene expression dataset' 'plier' SubClassOf 'software' 'plier' SubClassOf 'R software' 'plier' SubClassOf 'implements' some 'PLIER (Probe Logarithmic Error Intensity Estimate) method' 'plier' SubClassOf 'has specified data output' some 'Gene expression dataset' http://www.ebi.ac.uk/efo/swo/SWO_0000269 obsolete MANOR 'obsolete MANOR' SubClassOf 'obsolete SWO class' 'obsolete MANOR' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000266 obsolete MAANOVA v1.2 package for MATLAB 'obsolete MAANOVA v1.2 package for MATLAB' SubClassOf 'obsolete SWO class' 'obsolete MAANOVA v1.2 package for MATLAB' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000662 plw 'plw' SubClassOf 'R software' 'plw' SubClassOf 'BioConductor Software' 'plw' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'plw' SubClassOf 'software' 'plw' SubClassOf 'implements' some ('Locally Moderated Weighted-t (LMW) method' and 'Probe level Locally moderated Weighted median-t (PLW) method') 'plw' SubClassOf 'is published by' value 'Bioconductor' 'plw' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'plw' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'differential expression analysis') 'plw' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/efo/swo/SWO_0000267 obsolete Median Average Difference Algorithm 'obsolete Median Average Difference Algorithm' SubClassOf 'obsolete SWO class' 'obsolete Median Average Difference Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000661 Graph plot 'Graph plot' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000264 obsolete Loess algorithm 'obsolete Loess algorithm' SubClassOf 'obsolete SWO class' 'obsolete Loess algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000664 Position weight matrix (PWM ) 'Position weight matrix (PWM )' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000265 obsolete Logic regression 'obsolete Logic regression' SubClassOf 'obsolete SWO class' 'obsolete Logic regression' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000262 obsolete Laplace mixture model 'obsolete Laplace mixture model' SubClassOf 'obsolete SWO class' 'obsolete Laplace mixture model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000666 prada 'prada' SubClassOf 'is published by' value 'Bioconductor' 'prada' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'prada' SubClassOf 'software' 'prada' SubClassOf 'BioConductor Software' 'prada' SubClassOf 'is encoded in' some 'R language' 'prada' SubClassOf 'has specified data input' some ('FACS data' and ('has format specification' some 'FCS3.0') and ('has format specification' only 'FCS3.0')) 'prada' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000263 obsolete Library Search Algorithm 'obsolete Library Search Algorithm' SubClassOf 'obsolete SWO class' 'obsolete Library Search Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000665 ppiStats 'ppiStats' SubClassOf 'has specified data input' some 'AP-MS data' 'ppiStats' SubClassOf 'is published by' value 'Bioconductor' 'ppiStats' SubClassOf 'R software' 'ppiStats' SubClassOf 'software' 'ppiStats' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'ppiStats' SubClassOf 'is encoded in' some 'R language' 'ppiStats' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000260 obsolete publisher role 'obsolete publisher role' SubClassOf 'obsolete SWO class' 'obsolete publisher role' SubClassOf http://www.ifomis.org/bfo/1.1/snap#Role http://www.ebi.ac.uk/efo/swo/SWO_0000261 obsolete Langmuir Isotherm 'obsolete Langmuir Isotherm' SubClassOf 'obsolete SWO class' 'obsolete Langmuir Isotherm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000667 preprocessCore 'preprocessCore' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'preprocessCore' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'preprocessCore' SubClassOf 'R software' 'preprocessCore' SubClassOf 'BioConductor Software' 'preprocessCore' SubClassOf 'is encoded in' some 'R language' 'preprocessCore' SubClassOf 'implements' some ''PLM'' 'preprocessCore' SubClassOf 'is published by' value 'Bioconductor' 'preprocessCore' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000669 puma 'puma' SubClassOf 'is published by' value 'Bioconductor' 'puma' SubClassOf 'BioConductor Software' 'puma' SubClassOf 'implements' some ('Propagation of uncertainty in microarray analysis' and 'RMA') 'puma' SubClassOf 'is encoded in' some 'R language' 'puma' SubClassOf 'R software' 'puma' SubClassOf 'is executed in' some ('data normalization' and 'differential expression analysis') 'puma' SubClassOf 'software' 'puma' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'puma' SubClassOf 'has specified data output' some ('Graph plot' and 'CSV data set') http://www.ebi.ac.uk/efo/swo/SWO_0000279 obsolete MCRestimate 'obsolete MCRestimate' SubClassOf 'obsolete SWO class' 'obsolete MCRestimate' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000277 obsolete Markov Chain Monte Carlo 'obsolete Markov Chain Monte Carlo' SubClassOf 'obsolete SWO class' 'obsolete Markov Chain Monte Carlo' SubClassOf 'algorithm' http://kt.ijs.si/panovp/OntoDM#OntoDM_953101 data visualization task 'data visualization task' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 'data visualization task' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000278 obsolete MCR algorithm 'obsolete MCR algorithm' SubClassOf 'obsolete SWO class' 'obsolete MCR algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000275 obsolete MAVI Pro 'obsolete MAVI Pro' SubClassOf 'obsolete SWO class' 'obsolete MAVI Pro' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000276 obsolete Multivariate correlation estimator 'obsolete Multivariate correlation estimator' SubClassOf 'obsolete SWO class' 'obsolete Multivariate correlation estimator' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000274 obsolete MATLAB language 'obsolete MATLAB language' SubClassOf 'obsolete SWO class' 'obsolete MATLAB language' SubClassOf 'programming language' http://www.ebi.ac.uk/efo/swo/SWO_0000271 obsolete MIcroarray Analysis Suite 'obsolete MIcroarray Analysis Suite' SubClassOf 'obsolete SWO class' 'obsolete MIcroarray Analysis Suite' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000272 obsolete MicroArraySuite 5.0 'obsolete MicroArraySuite 5.0' SubClassOf 'obsolete SWO class' 'obsolete MicroArraySuite 5.0' SubClassOf 'obsolete MIcroarray Analysis Suite' http://www.ebi.ac.uk/efo/swo/SWO_0000270 obsolete MAQC data 'obsolete MAQC data' SubClassOf 'obsolete SWO class' 'obsolete MAQC data' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000288 obsolete MantelCorr 'obsolete MantelCorr' SubClassOf 'obsolete SWO class' 'obsolete MantelCorr' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000289 obsolete MassSpecWavelet 'obsolete MassSpecWavelet' SubClassOf 'obsolete SWO class' 'obsolete MassSpecWavelet' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000287 obsolete Mahalanobis distance 'obsolete Mahalanobis distance' SubClassOf 'obsolete SWO class' 'obsolete Mahalanobis distance' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000284 obsolete MMD 'obsolete MMD' SubClassOf 'obsolete SWO class' 'obsolete MMD' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000600 logicFS dataset 'logicFS dataset' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000285 obsolete MVCClass 'obsolete MVCClass' SubClassOf 'obsolete SWO class' 'obsolete MVCClass' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000282 obsolete Mutual information matrix (MIM) 'obsolete Mutual information matrix (MIM)' SubClassOf 'obsolete SWO class' 'obsolete Mutual information matrix (MIM)' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000283 obsolete MLInterfaces 'obsolete MLInterfaces' SubClassOf 'obsolete SWO class' 'obsolete MLInterfaces' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000280 obsolete MEDME 'obsolete MEDME' SubClassOf 'obsolete SWO class' 'obsolete MEDME' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000281 obsolete 'MI' 'obsolete 'MI'' SubClassOf 'obsolete SWO class' 'obsolete 'MI'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000609 made4 'made4' SubClassOf 'has specified data output' some ('Hierarchical clustering' and 'Graph plot') 'made4' SubClassOf 'software' 'made4' SubClassOf 'has specified data input' some 'Gene expression dataset' 'made4' SubClassOf 'is encoded in' some 'R language' 'made4' SubClassOf 'R software' 'made4' SubClassOf 'implements' some 'clustering algorithm' http://www.ebi.ac.uk/swo/SWO_0000602 Logit-t algorithm 'Logit-t algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000601 logitT 'logitT' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'logitT' SubClassOf 'is encoded in' some 'R language' 'logitT' SubClassOf 'implements' some ('Logit-t algorithm' and ''t-test'') 'logitT' SubClassOf 'is executed in' some 'differential expression analysis' 'logitT' SubClassOf 'is published by' value 'Bioconductor' 'logitT' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'logitT' SubClassOf 'R software' 'logitT' SubClassOf 'software' 'logitT' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000604 maCorrPlot 'maCorrPlot' SubClassOf 'software' 'maCorrPlot' SubClassOf 'is encoded in' some 'R language' 'maCorrPlot' SubClassOf 'R software' 'maCorrPlot' SubClassOf 'BioConductor Software' 'maCorrPlot' SubClassOf 'has specified data input' some ('has format specification' only ('mas5 format' or '.rma format')) 'maCorrPlot' SubClassOf 'is published by' value 'Bioconductor' 'maCorrPlot' SubClassOf 'is executed in' some ('data visualization' and 'background correction' and 'data normalization') 'maCorrPlot' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000603 lumi 'lumi' SubClassOf 'software' 'lumi' SubClassOf 'R software' 'lumi' SubClassOf 'is published by' value 'Bioconductor' 'lumi' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'lumi' SubClassOf 'has specified data input' some 'Text data set' 'lumi' SubClassOf 'implements' some 'Variance-stabilizing transformation (VST) algorithm' 'lumi' SubClassOf 'BioConductor Software' 'lumi' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000606 maSigPro 'maSigPro' SubClassOf 'is encoded in' some 'R language' 'maSigPro' SubClassOf 'is executed in' some 'differential expression analysis' 'maSigPro' SubClassOf 'has specified data input' some 'Gene expression dataset' 'maSigPro' SubClassOf 'has specified data output' some ('Heat map' and 'Gene list' and 'Graph plot') 'maSigPro' SubClassOf 'R software' 'maSigPro' SubClassOf 'software' 'maSigPro' SubClassOf 'implements' some ('Regression model' and ''FDR'') http://www.ebi.ac.uk/swo/SWO_0000605 maDB 'maDB' SubClassOf 'R software' 'maDB' SubClassOf 'is published by' value 'Bioconductor' 'maDB' SubClassOf 'BioConductor Software' 'maDB' SubClassOf 'has specified data input' some 'Gene expression data' 'maDB' SubClassOf 'is encoded in' some 'R language' 'maDB' SubClassOf 'is executed in' some ('data visualization' and 'differential expression analysis') 'maDB' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'maDB' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000608 macat 'macat' SubClassOf 'has specified data input' some 'Text data set' 'macat' SubClassOf 'R software' 'macat' SubClassOf 'software' 'macat' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'macat' SubClassOf 'is executed in' some ('data visualization' and 'distance calculation' and 'descriptive statistical calculation' and 'differential expression analysis') 'macat' SubClassOf 'is encoded in' some 'R language' 'macat' SubClassOf 'implements' some ('Radial basis function' and 'k-nearest neighbour classification' and 'Base-Pair-Distance Kernel') http://www.ebi.ac.uk/swo/SWO_0000607 maanova 'maanova' SubClassOf 'is encoded in' some 'R language' 'maanova' SubClassOf 'has specified data input' some ('R data frame' or 'Text data set') 'maanova' SubClassOf 'R software' 'maanova' SubClassOf 'software' 'maanova' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'maanova' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'maanova' SubClassOf 'implements' some ('Bootstrap' and ''ANOVA'' and 'F test' and ''FDR'') http://www.ebi.ac.uk/swo/objective/SWO_7000002 sequence alignment 'sequence alignment' SubClassOf 'pattern discovery task' 'sequence alignment' SubClassOf http://kt.ijs.si/panovp/OntoDM#OntoDM_000092 http://www.ebi.ac.uk/swo/objective/SWO_7000005 averaging 'averaging' SubClassOf 'data transformation' 'averaging' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000297 obsolete MicroArraySuite 4.0 'obsolete MicroArraySuite 4.0' SubClassOf 'obsolete SWO class' 'obsolete MicroArraySuite 4.0' SubClassOf 'obsolete MIcroarray Analysis Suite' http://www.ebi.ac.uk/swo/objective/SWO_7000006 center calculation 'center calculation' SubClassOf 'data transformation' 'center calculation' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000298 obsolete Mixed model equations 'obsolete Mixed model equations' SubClassOf 'obsolete SWO class' 'obsolete Mixed model equations' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/objective/SWO_7000007 class discovery 'class discovery' SubClassOf 'data transformation' 'class discovery' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000295 obsolete MiPP 'obsolete MiPP' SubClassOf 'obsolete SWO class' 'obsolete MiPP' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000611 makePlatformDesign 'makePlatformDesign' SubClassOf 'BioConductor Software' 'makePlatformDesign' SubClassOf 'is published by' value 'Bioconductor' 'makePlatformDesign' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'makePlatformDesign' SubClassOf 'software' 'makePlatformDesign' SubClassOf 'R software' 'makePlatformDesign' SubClassOf 'is encoded in' some 'R language' 'makePlatformDesign' SubClassOf 'has specified data input' some ('has format specification' only ('FASTA format' or 'CDF binary format' or 'CDF ASCII format')) http://www.ebi.ac.uk/swo/objective/SWO_7000008 class prediction 'class prediction' SubClassOf 'data transformation' 'class prediction' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000296 obsolete Misclassification-Penalized Posteriors (MiPP) 'obsolete Misclassification-Penalized Posteriors (MiPP)' SubClassOf 'obsolete SWO class' 'obsolete Misclassification-Penalized Posteriors (MiPP)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000610 maigesPack 'maigesPack' SubClassOf 'R software' 'maigesPack' SubClassOf 'is executed in' some ('data normalization' and 'descriptive statistical calculation' and 'differential expression analysis') 'maigesPack' SubClassOf 'is encoded in' some 'R language' 'maigesPack' SubClassOf 'implements' some (''t-test'' and ''ANOVA'') 'maigesPack' SubClassOf 'has specified data output' some ('Image' and 'Clustered data set' and 'HTML report' and 'Graph plot') 'maigesPack' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000293 obsolete MergeMaid 'obsolete MergeMaid' SubClassOf 'obsolete SWO class' 'obsolete MergeMaid' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000294 obsolete Mfuzz 'obsolete Mfuzz' SubClassOf 'obsolete SWO class' 'obsolete Mfuzz' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000292 obsolete MeasurementError.cor 'obsolete MeasurementError.cor' SubClassOf 'obsolete SWO class' 'obsolete MeasurementError.cor' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/software_before_Microsoft_2007 obsolete software before Microsoft 2007 'obsolete software before Microsoft 2007' SubClassOf 'obsolete SWO class' 'obsolete software before Microsoft 2007' SubClassOf 'software' http://purl.obolibrary.org/obo/OBI_0200000 data transformation 'data transformation' SubClassOf 'planned process' http://www.ebi.ac.uk/swo/SWO_0000613 marray 'marray' SubClassOf 'implements' some 'Linear modelling' 'marray' SubClassOf 'has specified data input' some ('Gene expression dataset' and 'Text data set') 'marray' SubClassOf 'is encoded in' some 'R language' 'marray' SubClassOf 'R software' 'marray' SubClassOf 'is published by' value 'Bioconductor' 'marray' SubClassOf 'is executed in' some 'data normalization' 'marray' SubClassOf 'has specified data output' some ('Graph plot' or ('Text data set' and ('has format specification' only 'gpr format'))) 'marray' SubClassOf 'software' 'marray' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000612 makecdfenv 'makecdfenv' SubClassOf 'R software' 'makecdfenv' SubClassOf 'has specified data input' some ('has format specification' only ('CDF binary format' or 'CDF ASCII format')) 'makecdfenv' SubClassOf 'is published by' value 'Bioconductor' 'makecdfenv' SubClassOf 'software' 'makecdfenv' SubClassOf 'is encoded in' some 'R language' 'makecdfenv' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'makecdfenv' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000615 mas5 format 'mas5 format' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_0000614 'MAS5' ''MAS5'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000617 mdqc 'mdqc' SubClassOf 'has specified data output' some 'Graph plot' 'mdqc' SubClassOf 'software' 'mdqc' SubClassOf 'R software' 'mdqc' SubClassOf 'implements' some ('Multivariate correlation estimator' and 'clustering algorithm') 'mdqc' SubClassOf 'is encoded in' some 'R language' 'mdqc' SubClassOf 'has specified data input' some ('Gene expression dataset' and 'Text data set') http://www.ebi.ac.uk/swo/SWO_0000616 matchprobes 'matchprobes' SubClassOf 'has specified data output' some ('has format specification' only 'CDF binary format') 'matchprobes' SubClassOf 'is published by' value 'Bioconductor' 'matchprobes' SubClassOf 'software' 'matchprobes' SubClassOf 'R software' 'matchprobes' SubClassOf 'is encoded in' some 'R language' 'matchprobes' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'R data frame' or 'CEL ASCII format')) 'matchprobes' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000619 metaArray 'metaArray' SubClassOf 'is encoded in' some 'R language' 'metaArray' SubClassOf 'is published by' value 'Bioconductor' 'metaArray' SubClassOf 'software' 'metaArray' SubClassOf 'R software' 'metaArray' SubClassOf 'has specified data input' some 'Gene expression dataset' 'metaArray' SubClassOf 'implements' some 'Markov Chain Monte Carlo' 'metaArray' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'metaArray' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000618 M-estimation regression 'M-estimation regression' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/objective/SWO_7000013 cross validation 'cross validation' SubClassOf 'data transformation' 'cross validation' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/objective/SWO_7000014 curve fitting 'curve fitting' SubClassOf 'data transformation' 'curve fitting' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/objective/SWO_7000015 data normalization 'data normalization' SubClassOf 'data transformation' 'data normalization' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/objective/SWO_7000016 decision tree induction 'decision tree induction' SubClassOf 'data transformation' 'decision tree induction' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/SWO_0000620 Meta data 'Meta data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/objective/SWO_7000017 descriptive statistical calculation 'descriptive statistical calculation' SubClassOf 'data transformation' 'descriptive statistical calculation' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/objective/SWO_7000018 differential expression analysis 'differential expression analysis' SubClassOf 'data transformation' 'differential expression analysis' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/SWO_0000622 miRNApath 'miRNApath' SubClassOf 'is published by' value 'Bioconductor' 'miRNApath' SubClassOf 'has specified data output' some ('Heat map' and ('has format specification' only 'R data frame')) 'miRNApath' SubClassOf 'BioConductor Software' 'miRNApath' SubClassOf 'is executed in' some 'gene expression analysis' 'miRNApath' SubClassOf 'is encoded in' some 'R language' 'miRNApath' SubClassOf 'has specified data input' some 'Text data set' 'miRNApath' SubClassOf 'implements' some 'Hypergeometric enrichment' 'miRNApath' SubClassOf 'software' 'miRNApath' SubClassOf 'R software' http://www.ebi.ac.uk/swo/objective/SWO_7000019 feature extraction 'feature extraction' SubClassOf 'data transformation' 'feature extraction' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/SWO_0000621 metahdep 'metahdep' SubClassOf 'is published by' value 'Bioconductor' 'metahdep' SubClassOf 'has specified data input' some 'Gene expression dataset' 'metahdep' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'metahdep' SubClassOf 'R software' 'metahdep' SubClassOf 'BioConductor Software' 'metahdep' SubClassOf 'implements' some 'Bayesian Model' 'metahdep' SubClassOf 'software' 'metahdep' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/objective/SWO_7000010 correction 'correction' SubClassOf 'data transformation' 'correction' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/SWO_0000623 microRNA 'microRNA' SubClassOf 'is encoded in' some 'R language' 'microRNA' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'microRNA' SubClassOf 'is published by' value 'Bioconductor' 'microRNA' SubClassOf 'R software' 'microRNA' SubClassOf 'BioConductor Software' 'microRNA' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'microRNA' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000626 mrnet algorithm 'mrnet algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000625 minet 'minet' SubClassOf 'is encoded in' some 'R language' 'minet' SubClassOf 'R software' 'minet' SubClassOf 'software' 'minet' SubClassOf 'implements' some ('mrnet algorithm' and 'ARACNE algorithm' and 'CLR algorithm') 'minet' SubClassOf 'has specified data input' some 'Gene expression data' 'minet' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'minet' SubClassOf 'has specified data output' some ('Mutual information matrix (MIM)' and 'Graph plot') http://www.ebi.ac.uk/swo/SWO_0000628 Multiple testing 'Multiple testing' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000627 Multinomial probit regression with Gaussian Process priors 'Multinomial probit regression with Gaussian Process priors' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000629 Multivariate t mixture models 'Multivariate t mixture models' SubClassOf 'algorithm' http://purl.obolibrary.org/obo/BFO_0000003 occurrent 'occurrent' SubClassOf 'entity' http://purl.obolibrary.org/obo/BFO_0000004 independent continuant 'independent continuant' SubClassOf 'continuant' http://edamontology.org/format_1665 Taverna workflow format 'Taverna workflow format' SubClassOf http://edamontology.org/format_2032 http://purl.obolibrary.org/obo/BFO_0000002 continuant 'continuant' SubClassOf 'entity' http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant 'generically dependent continuant' SubClassOf 'continuant' http://purl.obolibrary.org/obo/BFO_0000017 realizable entity 'realizable entity' SubClassOf 'specifically dependent continuant' http://purl.obolibrary.org/obo/BFO_0000015 process 'process' SubClassOf 'occurrent' http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant 'specifically dependent continuant' SubClassOf 'continuant' http://purl.obolibrary.org/obo/BFO_0000023 role 'role' SubClassOf 'realizable entity' http://www.ontodm.com/OntoDM-core/OntoDM_000112 clustering specification 'clustering specification' SubClassOf 'single generalization specification' http://www.ebi.ac.uk/swo/SWO_0000396 software developer organization 'software developer organization' EquivalentTo 'has_role' some 'software developer role' 'software developer organization' SubClassOf 'organization' http://www.ebi.ac.uk/swo/SWO_0000398 50-50 MANOVA algorithm '50-50 MANOVA algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000397 software publisher organization 'software publisher organization' SubClassOf 'organization' 'software publisher organization' EquivalentTo 'has_role' some 'publisher role' http://www.ebi.ac.uk/swo/SWO_1100014 ARR 'ARR' SubClassOf 'XML' http://www.ebi.ac.uk/swo/SWO_1100015 AWS algorithm 'AWS algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000390 SSPA 'SSPA' SubClassOf 'has specified data input' some 'ALL/AML data set' 'SSPA' SubClassOf 'BioConductor Software' 'SSPA' SubClassOf 'is encoded in' some 'R language' 'SSPA' SubClassOf 'R software' 'SSPA' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'SSPA' SubClassOf 'is published by' value 'Bioconductor' 'SSPA' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100016 Absolute Expression Analysis 'Absolute Expression Analysis' SubClassOf 'MicroArraySuite 4.0' http://www.ebi.ac.uk/swo/SWO_1100017 Absolute Expression Analysis 'Absolute Expression Analysis' SubClassOf 'MicroArraySuite 5.0' http://www.ebi.ac.uk/swo/SWO_0000392 software developer role 'software developer role' SubClassOf 'role' http://www.ebi.ac.uk/swo/SWO_1100010 ANCOVA 'ANCOVA' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000391 SVDimpute algorithm 'SVDimpute algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100011 'ANOVA' ''ANOVA'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100012 AP-MS data 'AP-MS data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_1100013 ARACNE algorithm 'ARACNE algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100018 'AffyCompatible' ''AffyCompatible'' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'MAGE-TAB')) ''AffyCompatible'' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some 'data format specification')) ''AffyCompatible'' SubClassOf 'software' ''AffyCompatible'' SubClassOf 'R software' ''AffyCompatible'' SubClassOf 'is encoded in' some 'R language' ''AffyCompatible'' SubClassOf 'is executed in' some 'parse' http://www.ebi.ac.uk/swo/SWO_1100019 'AffyExpress' ''AffyExpress'' SubClassOf 'is executed in' some 'correction' ''AffyExpress'' SubClassOf 'implements' some ''ANOVA'' ''AffyExpress'' SubClassOf 'is executed in' some 'data normalization' ''AffyExpress'' SubClassOf 'is executed in' some 'differential expression analysis' ''AffyExpress'' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''AffyExpress'' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) ''AffyExpress'' SubClassOf 'is encoded in' some 'R language' ''AffyExpress'' SubClassOf 'R software' ''AffyExpress'' SubClassOf 'has specified data input' some ('Image' and ('has format specification' some 'CEL binary format')) ''AffyExpress'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'data format specification')) ''AffyExpress'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100003 'ACME' ''ACME'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100004 Algorithms for Calculating Microarray Enrichment 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'has specified data output' some 'Graph plot' 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'implements' some ('Algorithms for Calculating Microarray Enrichment' and 'Chi-square') 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'R software' 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'is encoded in' some 'R language' 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100005 Affymetrix Expression Console 'Affymetrix Expression Console' SubClassOf 'has specified data input' some ('Image' and ('has format specification' some 'CEL binary format')) 'Affymetrix Expression Console' SubClassOf 'implements' some 'RMA' 'Affymetrix Expression Console' SubClassOf 'implements' some 'PLIER (Probe Logarithmic Error Intensity Estimate) method' 'Affymetrix Expression Console' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Affymetrix')) 'Affymetrix Expression Console' SubClassOf 'implements' some ''MAS5'' 'Affymetrix Expression Console' SubClassOf 'software' 'Affymetrix Expression Console' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'CHP binary format')) 'Affymetrix Expression Console' SubClassOf 'output of' some ('software development' and ('has participant' value 'Affymetrix')) http://www.ebi.ac.uk/swo/SWO_1100006 AIDA 'AIDA' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Raytest')) 'AIDA' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100000 2-sample pooled t-test '2-sample pooled t-test' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100001 50-50 MANOVA '50-50 MANOVA' SubClassOf 'is encoded in' some 'MATLAB language' '50-50 MANOVA' SubClassOf 'R software' '50-50 MANOVA' SubClassOf 'is encoded in' some 'R language' '50-50 MANOVA' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Matforsk')) '50-50 MANOVA' SubClassOf 'implements' some '50-50 MANOVA algorithm' '50-50 MANOVA' SubClassOf 'software' '50-50 MANOVA' SubClassOf 'matlab software' http://www.ebi.ac.uk/swo/SWO_1100002 ABarray 'ABarray' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) 'ABarray' SubClassOf 'implements' some 'Local-pooled-error' 'ABarray' SubClassOf 'has specified data output' some ('CSV data set' and ('has format specification' some 'data format specification')) 'ABarray' SubClassOf 'is executed in' some 'gene expression analysis' 'ABarray' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some 'data format specification')) 'ABarray' SubClassOf 'is encoded in' some 'R language' 'ABarray' SubClassOf 'implements' some ''FDR'' 'ABarray' SubClassOf 'software' 'ABarray' SubClassOf 'R software' 'ABarray' SubClassOf 'implements' some ''t-test'' 'ABarray' SubClassOf 'implements' some ''ANOVA'' 'ABarray' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some 'data format specification')) http://www.ebi.ac.uk/swo/SWO_1100007 Average log expression across arrays (ALE) 'Average log expression across arrays (ALE)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100008 ALL/AML data set 'ALL/AML data set' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000608 obsolete macat 'obsolete macat' SubClassOf 'obsolete SWO class' 'obsolete macat' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_1100009 AMDIS 'AMDIS' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000609 obsolete made4 'obsolete made4' SubClassOf 'obsolete SWO class' 'obsolete made4' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000606 obsolete maSigPro 'obsolete maSigPro' SubClassOf 'obsolete SWO class' 'obsolete maSigPro' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000607 obsolete maanova 'obsolete maanova' SubClassOf 'obsolete SWO class' 'obsolete maanova' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000604 obsolete maCorrPlot 'obsolete maCorrPlot' SubClassOf 'obsolete SWO class' 'obsolete maCorrPlot' SubClassOf 'obsolete BioConductor Software' 'obsolete maCorrPlot' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000605 obsolete maDB 'obsolete maDB' SubClassOf 'obsolete SWO class' 'obsolete maDB' SubClassOf 'obsolete BioConductor Software' 'obsolete maDB' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000602 obsolete Logit-t algorithm 'obsolete Logit-t algorithm' SubClassOf 'obsolete SWO class' 'obsolete Logit-t algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000603 obsolete lumi 'obsolete lumi' SubClassOf 'obsolete SWO class' 'obsolete lumi' SubClassOf 'obsolete R software' 'obsolete lumi' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000600 obsolete logicFS dataset 'obsolete logicFS dataset' SubClassOf 'obsolete SWO class' 'obsolete logicFS dataset' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000601 obsolete logitT 'obsolete logitT' SubClassOf 'obsolete SWO class' 'obsolete logitT' SubClassOf 'obsolete BioConductor Software' 'obsolete logitT' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000610 obsolete maigesPack 'obsolete maigesPack' SubClassOf 'obsolete SWO class' 'obsolete maigesPack' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_1100030 BGL 'BGL' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100031 'BGmix' ''BGmix'' SubClassOf 'software' ''BGmix'' SubClassOf 'is encoded in' some 'R language' ''BGmix'' SubClassOf 'implements' some 'Markov Chain Monte Carlo' ''BGmix'' SubClassOf 'implements' some 'Bayesian Model' ''BGmix'' SubClassOf 'R software' ''BGmix'' SubClassOf 'is executed in' some 'differential expression analysis' http://www.ebi.ac.uk/swo/SWO_1100036 BRB-ArrayTools 'BRB-ArrayTools' SubClassOf 'software' 'BRB-ArrayTools' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Biometric Research Branch')) http://www.ebi.ac.uk/swo/SWO_1100037 'BSgenome' ''BSgenome'' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'dcf')) ''BSgenome'' SubClassOf 'software' ''BSgenome'' SubClassOf 'is encoded in' some 'R language' ''BSgenome'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'FASTA format')) ''BSgenome'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100038 BZScan 'BZScan' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Technological Advances for Genomics and Clinics, France')) 'BZScan' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100039 BaldiLongT 'BaldiLongT' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100032 BLAST 'BLAST' SubClassOf 'has specified data input' some ('biological sequence data' and ('has format specification' some 'GenBank format')) 'BLAST' SubClassOf 'is executed in' some 'pairwise sequence alignment' 'BLAST' SubClassOf 'output of' some ('software development' and ('has participant' value 'NIH')) 'BLAST' SubClassOf 'has specified data input' some ('biological sequence data' and ('has format specification' some 'FASTA format')) 'BLAST' SubClassOf 'is executed in' some 'multiple sequence alignment' 'BLAST' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'NIH')) 'BLAST' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100033 Iterative Bayesian Model Averaging (BMA) 'Iterative Bayesian Model Averaging (BMA)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100034 Base-Pair-Distance Kernel 'Base-Pair-Distance Kernel' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100035 BPMAP 'BPMAP' SubClassOf 'is published by' value 'Affymetrix' 'BPMAP' SubClassOf 'binary format' http://www.ebi.ac.uk/efo/swo/SWO_0000619 obsolete metaArray 'obsolete metaArray' SubClassOf 'obsolete SWO class' 'obsolete metaArray' SubClassOf 'obsolete BioConductor Software' 'obsolete metaArray' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000617 obsolete mdqc 'obsolete mdqc' SubClassOf 'obsolete SWO class' 'obsolete mdqc' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000618 obsolete M-estimation regression 'obsolete M-estimation regression' SubClassOf 'obsolete SWO class' 'obsolete M-estimation regression' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000615 obsolete mas5 format 'obsolete mas5 format' SubClassOf 'obsolete SWO class' 'obsolete mas5 format' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/efo/swo/SWO_0000616 obsolete matchprobes 'obsolete matchprobes' SubClassOf 'obsolete SWO class' 'obsolete matchprobes' SubClassOf 'obsolete R software' 'obsolete matchprobes' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000613 obsolete marray 'obsolete marray' SubClassOf 'obsolete SWO class' 'obsolete marray' SubClassOf 'obsolete BioConductor Software' 'obsolete marray' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000614 obsolete 'MAS5' 'obsolete 'MAS5'' SubClassOf 'obsolete SWO class' 'obsolete 'MAS5'' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000611 obsolete makePlatformDesign 'obsolete makePlatformDesign' SubClassOf 'obsolete SWO class' 'obsolete makePlatformDesign' SubClassOf 'obsolete R software' 'obsolete makePlatformDesign' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000612 obsolete makecdfenv 'obsolete makecdfenv' SubClassOf 'obsolete SWO class' 'obsolete makecdfenv' SubClassOf 'obsolete R software' 'obsolete makecdfenv' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000620 obsolete Meta data 'obsolete Meta data' SubClassOf 'obsolete SWO class' 'obsolete Meta data' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000621 obsolete metahdep 'obsolete metahdep' SubClassOf 'obsolete SWO class' 'obsolete metahdep' SubClassOf 'obsolete BioConductor Software' 'obsolete metahdep' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_1100020 Affymetrix GCOS v1.2 'Affymetrix GCOS v1.2' SubClassOf 'Affymetrix GeneChip Operating Software' http://www.ebi.ac.uk/swo/SWO_1100025 Agilent Feature Extraction software version 7.1 'Agilent Feature Extraction software version 7.1' SubClassOf 'Agilent Feature Extraction Software' http://www.ebi.ac.uk/swo/SWO_1100026 Agilent Feature Extraction software version 7.5 'Agilent Feature Extraction software version 7.5' SubClassOf 'Agilent Feature Extraction Software' http://www.ebi.ac.uk/swo/SWO_1100027 Agilent Feature Extraction software version A.5.1.1 'Agilent Feature Extraction software version A.5.1.1' SubClassOf 'Agilent Feature Extraction Software' http://www.ebi.ac.uk/swo/SWO_1100028 ArrayVision 6.0 (Imaging Research Inc.) 'ArrayVision 6.0 (Imaging Research Inc.)' SubClassOf 'ArrayVision' http://www.ebi.ac.uk/swo/SWO_1100021 Affymetrix GeneChip Operating Software 'Affymetrix GeneChip Operating Software' SubClassOf 'software' 'Affymetrix GeneChip Operating Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Affymetrix')) http://www.ebi.ac.uk/swo/SWO_1100022 Affymetrix Software 'Affymetrix Software' SubClassOf 'software' 'Affymetrix Software' EquivalentTo 'software' and ('is published by' value 'Affymetrix') http://www.ebi.ac.uk/swo/SWO_1100023 Agi4x44PreProcess 'Agi4x44PreProcess' SubClassOf 'has specified data input' some ('Heat map' and ('has format specification' some 'image format')) 'Agi4x44PreProcess' SubClassOf 'software with image input' 'Agi4x44PreProcess' SubClassOf 'software' 'Agi4x44PreProcess' SubClassOf 'implements' some 'Loess algorithm' 'Agi4x44PreProcess' SubClassOf 'is executed in' some 'differential expression analysis' 'Agi4x44PreProcess' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'cls')) 'Agi4x44PreProcess' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'gct')) 'Agi4x44PreProcess' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'data format specification')) 'Agi4x44PreProcess' SubClassOf 'is executed in' some 'correction' 'Agi4x44PreProcess' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'Agi4x44PreProcess' SubClassOf 'is encoded in' some 'R language' 'Agi4x44PreProcess' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) 'Agi4x44PreProcess' SubClassOf 'R software' 'Agi4x44PreProcess' SubClassOf 'is executed in' some 'data normalization' http://www.ebi.ac.uk/swo/SWO_1100024 Agilent Feature Extraction 5.1.1 'Agilent Feature Extraction 5.1.1' SubClassOf 'Agilent Feature Extraction Software' http://www.ebi.ac.uk/swo/SWO_1100029 'BCRANK' ''BCRANK'' SubClassOf 'R software' ''BCRANK'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'FASTA format')) ''BCRANK'' SubClassOf 'software' ''BCRANK'' SubClassOf 'is encoded in' some 'R language' ''BCRANK'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''BCRANK'' SubClassOf 'implements' some ''BCRANK'' http://www.ebi.ac.uk/efo/swo/SWO_0000628 obsolete Multiple testing 'obsolete Multiple testing' SubClassOf 'obsolete SWO class' 'obsolete Multiple testing' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000629 obsolete Multivariate t mixture models 'obsolete Multivariate t mixture models' SubClassOf 'obsolete SWO class' 'obsolete Multivariate t mixture models' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000626 obsolete mrnet algorithm 'obsolete mrnet algorithm' SubClassOf 'obsolete SWO class' 'obsolete mrnet algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000627 obsolete Multinomial probit regression with Gaussian Process priors 'obsolete Multinomial probit regression with Gaussian Process priors' SubClassOf 'obsolete SWO class' 'obsolete Multinomial probit regression with Gaussian Process priors' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000625 obsolete minet 'obsolete minet' SubClassOf 'obsolete SWO class' 'obsolete minet' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000622 obsolete miRNApath 'obsolete miRNApath' SubClassOf 'obsolete SWO class' 'obsolete miRNApath' SubClassOf 'obsolete R software' 'obsolete miRNApath' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000623 obsolete microRNA 'obsolete microRNA' SubClassOf 'obsolete SWO class' 'obsolete microRNA' SubClassOf 'obsolete R software' 'obsolete microRNA' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000631 obsolete Negative binomial distribution 'obsolete Negative binomial distribution' SubClassOf 'obsolete SWO class' 'obsolete Negative binomial distribution' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000352 RbcBook1 'RbcBook1' SubClassOf 'is encoded in' some 'R language' 'RbcBook1' SubClassOf 'software' 'RbcBook1' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100050 'BufferedMatrix' ''BufferedMatrix'' SubClassOf 'R software' ''BufferedMatrix'' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) ''BufferedMatrix'' SubClassOf 'is encoded in' some 'R language' ''BufferedMatrix'' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''BufferedMatrix'' SubClassOf 'software' ''BufferedMatrix'' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''BufferedMatrix'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'pdf')) http://www.ebi.ac.uk/efo/swo/SWO_0000632 obsolete nem 'obsolete nem' SubClassOf 'obsolete SWO class' 'obsolete nem' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_1100051 'BufferedMatrixMethods' ''BufferedMatrixMethods'' SubClassOf 'has specified data input' some ('Gene expression data' and ('has format specification' some 'CEL binary format')) ''BufferedMatrixMethods'' SubClassOf 'software' ''BufferedMatrixMethods'' SubClassOf 'R software' ''BufferedMatrixMethods'' SubClassOf 'is encoded in' some 'R language' ''BufferedMatrixMethods'' SubClassOf 'has specified data output' some ('Gene expression data' and ('has format specification' some 'CEL binary format')) http://www.ebi.ac.uk/swo/SWO_0000354 RdbiPgSQL 'RdbiPgSQL' SubClassOf 'BioConductor Software' 'RdbiPgSQL' SubClassOf 'has specified data output' some 'Graph plot' 'RdbiPgSQL' SubClassOf 'R software' 'RdbiPgSQL' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'RdbiPgSQL' SubClassOf 'is encoded in' some 'R language' 'RdbiPgSQL' SubClassOf 'software' 'RdbiPgSQL' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_1100052 'CALIB' ''CALIB'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) ''CALIB'' SubClassOf 'R software' ''CALIB'' SubClassOf 'is executed in' some 'differential expression analysis' ''CALIB'' SubClassOf 'is encoded in' some 'R language' ''CALIB'' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''CALIB'' SubClassOf 'software' ''CALIB'' SubClassOf 'is executed in' some 'data normalization' http://www.ebi.ac.uk/efo/swo/SWO_0000630 obsolete multtest 'obsolete multtest' SubClassOf 'obsolete SWO class' 'obsolete multtest' SubClassOf 'obsolete BioConductor Software' 'obsolete multtest' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000353 Rdbi 'Rdbi' SubClassOf 'BioConductor Software' 'Rdbi' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'Rdbi' SubClassOf 'is published by' value 'Bioconductor' 'Rdbi' SubClassOf 'software' 'Rdbi' SubClassOf 'has specified data output' some 'Graph plot' 'Rdbi' SubClassOf 'is encoded in' some 'R language' 'Rdbi' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100053 'CAMERA' ''CAMERA'' SubClassOf 'R software' ''CAMERA'' SubClassOf 'is encoded in' some 'R language' ''CAMERA'' SubClassOf 'has specified data output' some ('CSV data set' and ('has format specification' some http://edamontology.org/format_2330)) ''CAMERA'' SubClassOf 'has specified data input' some ('LC-MS data' and ('has format specification' some 'data format specification')) ''CAMERA'' SubClassOf 'software' ''CAMERA'' SubClassOf 'is executed in' some 'data annotation' http://www.ebi.ac.uk/swo/SWO_0000356 RefPlus 'RefPlus' SubClassOf 'R software' 'RefPlus' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'differential expression analysis') 'RefPlus' SubClassOf 'software' 'RefPlus' SubClassOf 'has specified data output' some 'Graph plot' 'RefPlus' SubClassOf 'has specified data input' some 'Gene expression dataset' 'RefPlus' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000355 Rdisop 'Rdisop' SubClassOf 'is published by' value 'Bioconductor' 'Rdisop' SubClassOf 'software' 'Rdisop' SubClassOf 'BioConductor Software' 'Rdisop' SubClassOf 'R software' 'Rdisop' SubClassOf 'is encoded in' some 'R language' 'Rdisop' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'Rdisop' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000358 Resourcerer 'Resourcerer' SubClassOf 'has specified data output' some 'Text data set' 'Resourcerer' SubClassOf 'software' 'Resourcerer' SubClassOf 'has specified data input' some 'Annotation data packages' 'Resourcerer' SubClassOf 'is encoded in' some 'R language' 'Resourcerer' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100058 CRLMM algorithm 'CRLMM algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100059 Continuous Wavelet Transform (CWT)-based peak detection algorithm 'Continuous Wavelet Transform (CWT)-based peak detection algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100054 CDF binary format 'CDF binary format' SubClassOf 'binary format' 'CDF binary format' SubClassOf 'is published by' value 'Affymetrix' http://www.ebi.ac.uk/swo/SWO_1100055 'CMA' ''CMA'' SubClassOf 'R software' ''CMA'' SubClassOf 'is executed in' some 'descriptive statistical calculation' ''CMA'' SubClassOf 'implements' some ''CMA'' ''CMA'' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) ''CMA'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''CMA'' SubClassOf 'is encoded in' some 'R language' ''CMA'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000350 RankProd 'RankProd' SubClassOf 'implements' some 'Rank product non-parametric method' 'RankProd' SubClassOf 'software' 'RankProd' SubClassOf 'is published by' value 'Bioconductor' 'RankProd' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'RankProd' SubClassOf 'BioConductor Software' 'RankProd' SubClassOf 'has specified data input' some 'Gene expression dataset' 'RankProd' SubClassOf 'is executed in' some 'differential expression analysis' 'RankProd' SubClassOf 'is encoded in' some 'R language' 'RankProd' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100056 CMA 'CMA' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100057 'CORREP' ''CORREP'' SubClassOf 'is executed in' some 'descriptive statistical calculation' ''CORREP'' SubClassOf 'has specified data input' some ('OMICS data' and ('has format specification' some 'R data frame')) ''CORREP'' SubClassOf 'is executed in' some 'differential expression analysis' ''CORREP'' SubClassOf 'is encoded in' some 'R language' ''CORREP'' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) ''CORREP'' SubClassOf 'software' ''CORREP'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000639 obsolete oligoClasses 'obsolete oligoClasses' SubClassOf 'obsolete SWO class' 'obsolete oligoClasses' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000359 Rgraphviz 'Rgraphviz' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'Rgraphviz' SubClassOf 'R software' 'Rgraphviz' SubClassOf 'BioConductor Software' 'Rgraphviz' SubClassOf 'is encoded in' some 'R language' 'Rgraphviz' SubClassOf 'is published by' value 'Bioconductor' 'Rgraphviz' SubClassOf 'has specified data output' some 'Graph plot' 'Rgraphviz' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000637 obsolete occugene 'obsolete occugene' SubClassOf 'obsolete SWO class' 'obsolete occugene' SubClassOf 'obsolete BioConductor Software' 'obsolete occugene' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000638 obsolete oligo 'obsolete oligo' SubClassOf 'obsolete SWO class' 'obsolete oligo' SubClassOf 'obsolete R software' 'obsolete oligo' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000635 obsolete nnNorm 'obsolete nnNorm' SubClassOf 'obsolete SWO class' 'obsolete nnNorm' SubClassOf 'obsolete R software' 'obsolete nnNorm' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000636 obsolete nudge 'obsolete nudge' SubClassOf 'obsolete SWO class' 'obsolete nudge' SubClassOf 'obsolete R software' 'obsolete nudge' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000633 obsolete Neural networks models 'obsolete Neural networks models' SubClassOf 'obsolete SWO class' 'obsolete Neural networks models' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000642 obsolete ontoTools 'obsolete ontoTools' SubClassOf 'obsolete SWO class' 'obsolete ontoTools' SubClassOf 'obsolete BioConductor Software' 'obsolete ontoTools' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000363 Rnw 'Rnw' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_0000362 Rmagpie 'Rmagpie' SubClassOf 'is executed in' some 'cross validation' 'Rmagpie' SubClassOf 'software' 'Rmagpie' SubClassOf 'has specified data input' some 'Gene expression dataset' 'Rmagpie' SubClassOf 'has specified data output' some 'Text data set' 'Rmagpie' SubClassOf 'R software' 'Rmagpie' SubClassOf 'implements' some 'Recursive Feature Elimination (RFE)' 'Rmagpie' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_1100040 BasReader 3.01 'BasReader 3.01' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Raytest')) 'BasReader 3.01' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000640 obsolete OMICS data 'obsolete OMICS data' SubClassOf 'obsolete SWO class' 'obsolete OMICS data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000365 Rosetta Resolver 'Rosetta Resolver' SubClassOf 'software' 'Rosetta Resolver' SubClassOf 'is developed by' value 'Rosetta Biosoftware' http://www.ebi.ac.uk/swo/SWO_1100041 Bayesian Model 'Bayesian Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000641 obsolete oneChannelGUI 'obsolete oneChannelGUI' SubClassOf 'obsolete SWO class' 'obsolete oneChannelGUI' SubClassOf 'obsolete R software' 'obsolete oneChannelGUI' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000364 Robust likelihood-based survival modeling 'Robust likelihood-based survival modeling' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100042 Beadstudio 'Beadstudio' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Illumina')) 'Beadstudio' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000367 RpsiXML 'RpsiXML' SubClassOf 'software' 'RpsiXML' SubClassOf 'R software' 'RpsiXML' SubClassOf 'is published by' value 'Bioconductor' 'RpsiXML' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'RpsiXML' SubClassOf 'has specified data input' some ('has format specification' only 'XML') 'RpsiXML' SubClassOf 'is executed in' some 'parse' 'RpsiXML' SubClassOf 'is encoded in' some 'R language' 'RpsiXML' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000369 Rtreemix 'Rtreemix' SubClassOf 'implements' some ('Likelihood method' or 'Sim method') 'Rtreemix' SubClassOf 'is encoded in' some 'R language' 'Rtreemix' SubClassOf 'is executed in' some 'decision tree induction' 'Rtreemix' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'Rtreemix' SubClassOf 'has specified data input' some 'Text data set' 'Rtreemix' SubClassOf 'software' 'Rtreemix' SubClassOf 'BioConductor Software' 'Rtreemix' SubClassOf 'is published by' value 'Bioconductor' 'Rtreemix' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000368 Rredland 'Rredland' SubClassOf 'BioConductor Software' 'Rredland' SubClassOf 'is encoded in' some 'R language' 'Rredland' SubClassOf 'software' 'Rredland' SubClassOf 'is published by' value 'Bioconductor' 'Rredland' SubClassOf 'has specified data input' some 'Text data set' 'Rredland' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'Rredland' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100047 BioConductor Software 'BioConductor Software' SubClassOf 'is executed in' some 'biological data processing' 'BioConductor Software' SubClassOf 'software' 'BioConductor Software' EquivalentTo 'software' and ('is published by' value 'Bioconductor') http://www.ebi.ac.uk/swo/SWO_1100048 'Biostrings' ''Biostrings'' SubClassOf 'is encoded in' some 'R language' ''Biostrings'' SubClassOf 'implements' some ''Needleman-Wunsch'' ''Biostrings'' SubClassOf 'software' ''Biostrings'' SubClassOf 'implements' some ''Smith-Waterman'' ''Biostrings'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100049 BlueFuse 'BlueFuse' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Cambridge Bluegnome')) 'BlueFuse' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100043 'BicARE' ''BicARE'' SubClassOf 'is encoded in' some 'R language' ''BicARE'' SubClassOf 'software' ''BicARE'' SubClassOf 'R software' ''BicARE'' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) http://www.ebi.ac.uk/swo/SWO_1100044 'BioMVCClass' ''BioMVCClass'' SubClassOf 'is encoded in' some 'R language' ''BioMVCClass'' SubClassOf 'R software' ''BioMVCClass'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000361 Rintact 'Rintact' SubClassOf 'has specified data input' some ('has format specification' only 'XML') 'Rintact' SubClassOf 'is executed in' some 'parse' 'Rintact' SubClassOf 'is published by' value 'Bioconductor' 'Rintact' SubClassOf 'software' 'Rintact' SubClassOf 'BioConductor Software' 'Rintact' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'Rintact' SubClassOf 'R software' 'Rintact' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_1100045 'Biobase' ''Biobase'' SubClassOf 'R software' ''Biobase'' SubClassOf 'is encoded in' some 'R language' ''Biobase'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000360 Ringo 'Ringo' SubClassOf 'has specified data input' some 'Text data set' 'Ringo' SubClassOf 'data item' 'Ringo' SubClassOf 'R software' 'Ringo' SubClassOf 'BioConductor Software' 'Ringo' SubClassOf 'is specified data input of' exactly 2 'Text data set' 'Ringo' SubClassOf 'is encoded in' some 'R language' 'Ringo' SubClassOf 'software' 'Ringo' SubClassOf 'is executed in' some ('data visualization' and 'data normalization') 'Ringo' SubClassOf 'is published by' value 'Bioconductor' 'Ringo' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'GFF')) http://www.ebi.ac.uk/swo/SWO_1100046 'BiocCaseStudies' ''BiocCaseStudies'' SubClassOf 'software' ''BiocCaseStudies'' SubClassOf 'is encoded in' some 'R language' ''BiocCaseStudies'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000648 obsolete parse 'obsolete parse' SubClassOf 'obsolete SWO class' 'obsolete parse' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000649 obsolete pathRender 'obsolete pathRender' SubClassOf 'obsolete SWO class' 'obsolete pathRender' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000646 obsolete panp 'obsolete panp' SubClassOf 'obsolete SWO class' 'obsolete panp' SubClassOf 'obsolete BioConductor Software' 'obsolete panp' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000647 obsolete parody 'obsolete parody' SubClassOf 'obsolete SWO class' 'obsolete parody' SubClassOf 'obsolete R software' 'obsolete parody' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000644 obsolete pair file 'obsolete pair file' SubClassOf 'obsolete SWO class' 'obsolete pair file' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000645 obsolete pamr 'obsolete pamr' SubClassOf 'obsolete SWO class' 'obsolete pamr' SubClassOf 'obsolete BioConductor Software' 'obsolete pamr' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000653 obsolete pdInfoBuilder 'obsolete pdInfoBuilder' SubClassOf 'obsolete SWO class' 'obsolete pdInfoBuilder' SubClassOf 'obsolete R software' 'obsolete pdInfoBuilder' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000374 SAM 'SAM' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100072 Chi-square 'Chi-square' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000654 obsolete pdmclass 'obsolete pdmclass' SubClassOf 'obsolete SWO class' 'obsolete pdmclass' SubClassOf 'obsolete R software' 'obsolete pdmclass' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000373 SAGx 'SAGx' SubClassOf 'is encoded in' some 'R language' 'SAGx' SubClassOf 'BioConductor Software' 'SAGx' SubClassOf 'is published by' value 'Bioconductor' 'SAGx' SubClassOf 'software' 'SAGx' SubClassOf 'R software' 'SAGx' SubClassOf 'implements' some ('Linear modelling' and ''t-test'') 'SAGx' SubClassOf 'has specified data input' some ('Graph plot' and ('has format specification' only 'R data frame')) http://www.ebi.ac.uk/swo/SWO_1100073 Annotation-Driven Clustering 'Annotation-Driven Clustering' SubClassOf 'implements' some 'k-means' 'Annotation-Driven Clustering' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'Annotation-Driven Clustering' SubClassOf 'is encoded in' some 'R language' 'Annotation-Driven Clustering' SubClassOf 'R software' 'Annotation-Driven Clustering' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'Annotation-Driven Clustering' SubClassOf 'implements' some ''FDR'' 'Annotation-Driven Clustering' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) 'Annotation-Driven Clustering' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000651 obsolete pcot2 'obsolete pcot2' SubClassOf 'obsolete SWO class' 'obsolete pcot2' SubClassOf 'obsolete R software' 'obsolete pcot2' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_1100074 distance calculation 'distance calculation' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_1100075 R software 'R software' EquivalentTo 'is encoded in' some 'R language' 'R software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000375 SAS/STAT Software, Version 8 'SAS/STAT Software, Version 8' SubClassOf 'is developed by' value 'SAS Institute Inc.' 'SAS/STAT Software, Version 8' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000378 SBMLR format 'SBMLR format' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/efo/swo/SWO_0000650 obsolete pcaMethods 'obsolete pcaMethods' SubClassOf 'obsolete SWO class' 'obsolete pcaMethods' SubClassOf 'obsolete BioConductor Software' 'obsolete pcaMethods' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000377 SBMLR 'SBMLR' SubClassOf 'is encoded in' some 'R language' 'SBMLR' SubClassOf 'has specified data output' some ('has format specification' only ('SBML' or 'SBMLR format')) 'SBMLR' SubClassOf 'has specified data input' some ('has format specification' only ('SBML' or 'SBMLR format')) 'SBMLR' SubClassOf 'BioConductor Software' 'SBMLR' SubClassOf 'R software' 'SBMLR' SubClassOf 'is published by' value 'Bioconductor' 'SBMLR' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100070 PCMG 'PCMG' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100071 Feature Extraction Software 'Feature Extraction Software' SubClassOf 'is executed in' some 'feature extraction' 'Feature Extraction Software' SubClassOf 'Affymetrix GeneChip Operating Software' http://www.ebi.ac.uk/swo/SWO_0000370 Ruuid 'Ruuid' SubClassOf 'R software' 'Ruuid' SubClassOf 'software' 'Ruuid' SubClassOf 'BioConductor Software' 'Ruuid' SubClassOf 'is published by' value 'Bioconductor' 'Ruuid' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'Ruuid' SubClassOf 'has specified data input' some 'Text data set' 'Ruuid' SubClassOf 'is encoded in' some 'R language' 'Ruuid' SubClassOf 'implements' some 'Theodore Ts’o’s' http://www.ebi.ac.uk/swo/SWO_1100076 BCRANK 'BCRANK' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100077 Cosmo 'Cosmo' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000372 Serial Analysis of Gene Expression (SAGE) 'Serial Analysis of Gene Expression (SAGE)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100078 F test 'F test' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000371 S-Score algorithm 'S-Score algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100079 MAGE-TAB inputting software 'MAGE-TAB inputting software' EquivalentTo 'has specified data input' some ('data item' and ('has format specification' some 'MAGE-TAB')) 'MAGE-TAB inputting software' SubClassOf 'software' http://www.ebi.ac.uk/swo/objective/SWO_4000003 document outlining 'document outlining' SubClassOf 'data transformation' 'document outlining' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/objective/SWO_4000004 image compression 'image compression' SubClassOf 'data transformation' 'image compression' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/Class_6 obsolete matlab software 'obsolete matlab software' SubClassOf 'obsolete SWO class' 'obsolete matlab software' SubClassOf 'software' http://www.ebi.ac.uk/swo/objective/SWO_4000001 spreadsheet editing 'spreadsheet editing' SubClassOf 'data transformation' 'spreadsheet editing' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000659 obsolete plgem 'obsolete plgem' SubClassOf 'obsolete SWO class' 'obsolete plgem' SubClassOf 'obsolete R software' 'obsolete plgem' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/objective/SWO_4000009 laboratory information management 'laboratory information management' SubClassOf 'data transformation' 'laboratory information management' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000657 obsolete pickgene 'obsolete pickgene' SubClassOf 'obsolete SWO class' 'obsolete pickgene' SubClassOf 'obsolete R software' 'obsolete pickgene' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/objective/SWO_4000007 obsolete software development 'obsolete software development' SubClassOf 'obsolete SWO class' 'obsolete software development' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000658 obsolete pkgDepTools 'obsolete pkgDepTools' SubClassOf 'obsolete SWO class' 'obsolete pkgDepTools' SubClassOf 'obsolete R software' 'obsolete pkgDepTools' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/objective/SWO_4000008 simulation and analysis of biochemical networks 'simulation and analysis of biochemical networks' SubClassOf 'data transformation' 'simulation and analysis of biochemical networks' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000655 obsolete pedigree data file 'obsolete pedigree data file' SubClassOf 'obsolete SWO class' 'obsolete pedigree data file' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/objective/SWO_4000005 ontology engineering 'ontology engineering' SubClassOf 'data transformation' 'ontology engineering' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000656 obsolete pgUtils 'obsolete pgUtils' SubClassOf 'obsolete SWO class' 'obsolete pgUtils' SubClassOf 'obsolete R software' 'obsolete pgUtils' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/objective/SWO_4000006 word processing 'word processing' SubClassOf 'data transformation' 'word processing' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000664 obsolete Position weight matrix (PWM ) 'obsolete Position weight matrix (PWM )' SubClassOf 'obsolete SWO class' 'obsolete Position weight matrix (PWM )' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000385 SMAP 'SMAP' SubClassOf 'software' 'SMAP' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'SMAP' SubClassOf 'BioConductor Software' 'SMAP' SubClassOf 'R software' 'SMAP' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'SMAP' SubClassOf 'is published by' value 'Bioconductor' 'SMAP' SubClassOf 'is executed in' some ('data visualization' and 'descriptive statistical calculation') 'SMAP' SubClassOf 'implements' some 'Hidden Markov Model' 'SMAP' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_1100061 Category analysis 'Category analysis' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000665 obsolete ppiStats 'obsolete ppiStats' SubClassOf 'obsolete SWO class' 'obsolete ppiStats' SubClassOf 'obsolete R software' 'obsolete ppiStats' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000384 SLqPCR 'SLqPCR' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'SLqPCR' SubClassOf 'R software' 'SLqPCR' SubClassOf 'is encoded in' some 'R language' 'SLqPCR' SubClassOf 'is published by' value 'Bioconductor' 'SLqPCR' SubClassOf 'is executed in' some ('data normalization' and 'descriptive statistical calculation') 'SLqPCR' SubClassOf 'BioConductor Software' 'SLqPCR' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'SLqPCR' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100062 Category 'Category' SubClassOf 'R software' 'Category' SubClassOf 'BioConductor Software' 'Category' SubClassOf 'has specified data output' some ('Heat map' and ('has format specification' some 'image format')) 'Category' SubClassOf 'has specified data output' some 'Graph plot' 'Category' SubClassOf 'software' 'Category' SubClassOf 'is encoded in' some 'R language' 'Category' SubClassOf 'is executed in' some 'differential expression analysis' 'Category' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'Category' SubClassOf 'implements' some 'Category analysis' 'Category' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/efo/swo/SWO_0000662 obsolete plw 'obsolete plw' SubClassOf 'obsolete SWO class' 'obsolete plw' SubClassOf 'obsolete BioConductor Software' 'obsolete plw' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000387 SNPchip 'SNPchip' SubClassOf 'is published by' value 'Bioconductor' 'SNPchip' SubClassOf 'R software' 'SNPchip' SubClassOf 'is encoded in' some 'R language' 'SNPchip' SubClassOf 'BioConductor Software' 'SNPchip' SubClassOf 'software' 'SNPchip' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'SNPchip' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'SNPchip' SubClassOf 'implements' some ('data visualization' and 'data annotation' and 'descriptive statistical calculation') 'SNPchip' SubClassOf 'implements' some 'Hidden Markov Model' http://www.ebi.ac.uk/swo/SWO_1100063 'ChemmineR' ''ChemmineR'' SubClassOf 'is executed in' some 'distance calculation' ''ChemmineR'' SubClassOf 'is encoded in' some 'R language' ''ChemmineR'' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) ''ChemmineR'' SubClassOf 'software' ''ChemmineR'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'SDF format')) ''ChemmineR'' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) ''ChemmineR'' SubClassOf 'implements' some 'Binning clustering method' ''ChemmineR'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000386 SNPRMA algorithm 'SNPRMA algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100064 ChipReader 3.1 'ChipReader 3.1' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Bio-Rad Laboratories, Inc.')) 'ChipReader 3.1' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000660 obsolete plier 'obsolete plier' SubClassOf 'obsolete SWO class' 'obsolete plier' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000389 Semantic Similarity Measures 'Semantic Similarity Measures' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000661 obsolete Graph plot 'obsolete Graph plot' SubClassOf 'obsolete SWO class' 'obsolete Graph plot' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000388 SPIA 'SPIA' SubClassOf 'R software' 'SPIA' SubClassOf 'is encoded in' some 'R language' 'SPIA' SubClassOf 'is published by' value 'Bioconductor' 'SPIA' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'SPIA' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'SPIA' SubClassOf 'has specified data input' some 'Gene expression dataset' 'SPIA' SubClassOf 'BioConductor Software' 'SPIA' SubClassOf 'implements' some 'Signaling Pathway Impact Analysis (SPIA) algorithm' 'SPIA' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100060 CARMAweb 'CARMAweb' SubClassOf 'software' 'CARMAweb' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Institute for Genomics and Bioinformatics Graz University of Technology')) http://www.ebi.ac.uk/swo/SWO_1100069 affycomp 'affycomp' SubClassOf 'implements' some ('RMA' and ''MAS5'') 'affycomp' SubClassOf 'software' 'affycomp' SubClassOf 'is encoded in' some 'R language' 'affycomp' SubClassOf 'is executed in' some ('dataset comparison' and 'correction') 'affycomp' SubClassOf 'R software' 'affycomp' SubClassOf 'has specified data input' some 'CSV data set' 'affycomp' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') http://www.ebi.ac.uk/swo/SWO_0000381 SDF format 'SDF format' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_1100065 ChipSkipper 'ChipSkipper' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'EMBL')) 'ChipSkipper' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100066 ChipSkipper V0.99 'ChipSkipper V0.99' SubClassOf 'ChipSkipper' http://www.ebi.ac.uk/swo/SWO_0000383 SLGI 'SLGI' SubClassOf 'software' 'SLGI' SubClassOf 'is encoded in' some 'R language' 'SLGI' SubClassOf 'BioConductor Software' 'SLGI' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'SLGI' SubClassOf 'is published by' value 'Bioconductor' 'SLGI' SubClassOf 'R software' 'SLGI' SubClassOf 'has specified data input' some 'Annotation data packages' http://www.ebi.ac.uk/swo/SWO_1100067 multiscan 'multiscan' SubClassOf 'has specified data output' some 'Graph plot' 'multiscan' SubClassOf 'R software' 'multiscan' SubClassOf 'software' 'multiscan' SubClassOf 'implements' some 'Non-linear functional regression model' 'multiscan' SubClassOf 'is encoded in' some 'R language' 'multiscan' SubClassOf 'has specified data input' some ('Text data set' or 'CSV data set') 'multiscan' SubClassOf 'is executed in' some 'differential expression analysis' http://www.ebi.ac.uk/swo/SWO_0000382 SIM 'SIM' SubClassOf 'software' 'SIM' SubClassOf 'R software' 'SIM' SubClassOf 'has specified data input' some 'Gene expression data' 'SIM' SubClassOf 'is encoded in' some 'R language' 'SIM' SubClassOf 'implements' some 'Global test' 'SIM' SubClassOf 'has specified data output' some ('Heat map' and 'Graph plot' and 'Text data set') http://www.ebi.ac.uk/swo/SWO_1100068 affy 'affy' SubClassOf 'implements' some ('RMA' and ''MAS5'') 'affy' SubClassOf 'R software' 'affy' SubClassOf 'has specified data input' some ('has format specification' some ('CEL binary format' or 'CDF binary format' or 'CDF ASCII format' or 'CEL ASCII format')) 'affy' SubClassOf 'is published by' value 'Bioconductor' 'affy' SubClassOf 'software' 'affy' SubClassOf 'has specified data output' some ('Image' and 'Graph plot' and 'Text data set') 'affy' SubClassOf 'BioConductor Software' 'affy' SubClassOf 'is encoded in' some 'R language' 'affy' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'differential expression analysis') http://www.ebi.ac.uk/swo/objective/SWO_4000014 biological data processing 'biological data processing' SubClassOf 'data transformation' 'biological data processing' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/objective/SWO_4000015 obsolete modelling 'obsolete modelling' SubClassOf 'obsolete SWO class' 'obsolete modelling' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/objective/SWO_4000012 file rendering 'file rendering' SubClassOf 'data transformation' 'file rendering' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/objective/SWO_4000013 annotation editing 'annotation editing' SubClassOf 'data transformation' 'annotation editing' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/objective/SWO_4000010 manage computer operations 'manage computer operations' SubClassOf 'data transformation' 'manage computer operations' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/objective/SWO_4000011 text editing 'text editing' SubClassOf 'data transformation' 'text editing' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000669 obsolete puma 'obsolete puma' SubClassOf 'obsolete SWO class' 'obsolete puma' SubClassOf 'obsolete BioConductor Software' 'obsolete puma' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000666 obsolete prada 'obsolete prada' SubClassOf 'obsolete SWO class' 'obsolete prada' SubClassOf 'obsolete BioConductor Software' 'obsolete prada' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/objective/SWO_4000016 molecular sequence analysis 'molecular sequence analysis' SubClassOf 'data transformation' 'molecular sequence analysis' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000667 obsolete preprocessCore 'obsolete preprocessCore' SubClassOf 'obsolete SWO class' 'obsolete preprocessCore' SubClassOf 'obsolete R software' 'obsolete preprocessCore' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/objective/SWO_4000017 citation management 'citation management' SubClassOf 'data transformation' 'citation management' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000675 obsolete quantsmooth 'obsolete quantsmooth' SubClassOf 'obsolete SWO class' 'obsolete quantsmooth' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_1100094 'EBImage' ''EBImage'' SubClassOf 'software' ''EBImage'' SubClassOf 'is encoded in' some 'R language' ''EBImage'' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''EBImage'' SubClassOf 'R software' ''EBImage'' SubClassOf 'has specified data input' some ('Image' and ('has format specification' some 'CEL binary format')) ''EBImage'' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) http://www.ebi.ac.uk/efo/swo/SWO_0000676 obsolete qvalue 'obsolete qvalue' SubClassOf 'obsolete SWO class' 'obsolete qvalue' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_1100095 'EBarrays' ''EBarrays'' SubClassOf 'implements' some 'Lognormal Normal with Modied Variance Model' ''EBarrays'' SubClassOf 'software' ''EBarrays'' SubClassOf 'implements' some 'Empirical Bayes rule' ''EBarrays'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''EBarrays'' SubClassOf 'implements' some 'Gamma Gamma Model' ''EBarrays'' SubClassOf 'is encoded in' some 'R language' ''EBarrays'' SubClassOf 'R software' ''EBarrays'' SubClassOf 'has specified data input' some ('Gene expression data' and ('has format specification' some 'R data frame')) ''EBarrays'' SubClassOf 'implements' some 'Lognormal Normal Model' ''EBarrays'' SubClassOf 'is executed in' some 'differential expression analysis' ''EBarrays'' SubClassOf 'has specified data output' some ('Clustered data set' and ('has format specification' some 'data format specification')) http://www.ebi.ac.uk/efo/swo/SWO_0000673 obsolete Quantile normalization 'obsolete Quantile normalization' SubClassOf 'obsolete SWO class' 'obsolete Quantile normalization' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000310 Optiquant 'Optiquant' SubClassOf 'output of' some ('software development' and ('has participant' value 'PerkinElmer')) 'Optiquant' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100096 Expectation-Maximization(EM) algorithm 'Expectation-Maximization(EM) algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000674 obsolete Quantile regression techniques 'obsolete Quantile regression techniques' SubClassOf 'obsolete SWO class' 'obsolete Quantile regression techniques' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100097 Empirical Bayes rule 'Empirical Bayes rule' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000671 obsolete qpcrNorm 'obsolete qpcrNorm' SubClassOf 'obsolete SWO class' 'obsolete qpcrNorm' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000312 OutlierD 'OutlierD' SubClassOf 'has specified data input' some ('LC-MS data' and ('has format specification' some 'data format specification')) 'OutlierD' SubClassOf 'software' 'OutlierD' SubClassOf 'is encoded in' some 'R language' 'OutlierD' SubClassOf 'is executed in' some 'data normalization' 'OutlierD' SubClassOf 'R software' 'OutlierD' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'OutlierD' SubClassOf 'implements' some 'Quantile regression techniques' http://www.ebi.ac.uk/swo/SWO_1100090 Discriminant Fuzzy Pattern Algorithm 'Discriminant Fuzzy Pattern Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000672 obsolete qpgraph 'obsolete qpgraph' SubClassOf 'obsolete SWO class' 'obsolete qpgraph' SubClassOf 'obsolete R software' 'obsolete qpgraph' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000311 OrderedList 'OrderedList' SubClassOf 'is encoded in' some 'R language' 'OrderedList' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'OrderedList' SubClassOf 'has specified data output' some ('Gene list' and ('has format specification' some 'data format specification')) 'OrderedList' SubClassOf 'software' 'OrderedList' SubClassOf 'is executed in' some 'differential expression analysis' 'OrderedList' SubClassOf 'R software' 'OrderedList' SubClassOf 'implements' some 'Similarity score' http://www.ebi.ac.uk/swo/SWO_1100091 DFW 'DFW' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000314 PAnnBuilder 'PAnnBuilder' SubClassOf 'software' 'PAnnBuilder' SubClassOf 'has specified data input' some ('Annotation data packages' and ('has format specification' some 'data format specification')) 'PAnnBuilder' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'PAnnBuilder' SubClassOf 'is encoded in' some 'R language' 'PAnnBuilder' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100092 Digital gene expression (DGE) datasets 'Digital gene expression (DGE) datasets' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000670 obsolete qPCR data 'obsolete qPCR data' SubClassOf 'obsolete SWO class' 'obsolete qPCR data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000313 Presence-Absence calls with Negative Probesets (PANP) 'Presence-Absence calls with Negative Probesets (PANP)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100093 'DNAcopy' ''DNAcopy'' SubClassOf 'software' ''DNAcopy'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) ''DNAcopy'' SubClassOf 'is encoded in' some 'R language' ''DNAcopy'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''DNAcopy'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100098 Expert 2100 'Expert 2100' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) 'Expert 2100' SubClassOf 'Agilent Technologies Software' 'Expert 2100' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100099 FACS data 'FACS data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/license/SWO_1000145 Xenbase Academic Conditions of Use 'Xenbase Academic Conditions of Use' SubClassOf 'has website homepage' value "http://www.xenbase.org/other/static/aboutXenbase.jsp" 'Xenbase Academic Conditions of Use' SubClassOf 'has clause' some 'Non-commercial use only' 'Xenbase Academic Conditions of Use' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/swo/license/SWO_1000146 RIKEN Copyright 'RIKEN Copyright' SubClassOf 'has clause' some 'Permission required for derivative work' 'RIKEN Copyright' SubClassOf 'has website homepage' value "http://www.riken.jp/en/terms/" http://www.ebi.ac.uk/swo/license/SWO_1000147 Design Science License 'Design Science License' SubClassOf 'has clause' some 'Usage unrestricted' 'Design Science License' SubClassOf 'has clause' some 'Distribution unrestricted' 'Design Science License' SubClassOf 'has clause' some 'Platform unrestricted' 'Design Science License' SubClassOf 'is compatible license of' some (not ('GNU GPL v3' or 'GNU GPL v2')) 'Design Science License' SubClassOf 'has clause' some 'Copyleft' 'Design Science License' SubClassOf 'has clause' some 'Source code available' 'Design Science License' SubClassOf 'software license' 'Design Science License' SubClassOf 'has website homepage' value "https://www.gnu.org/licenses/dsl.html" 'Design Science License' SubClassOf 'has clause' some 'Number of users unrestricted' 'Design Science License' SubClassOf 'has clause' some 'Attribution required' 'Design Science License' SubClassOf 'has clause' some 'Number of installations unrestricted' 'Design Science License' SubClassOf 'has clause' some 'Time for use unrestricted' http://www.ebi.ac.uk/swo/license/SWO_1000148 University of Concordia Terms of Use 'University of Concordia Terms of Use' SubClassOf 'has website homepage' value "http://www.concordia.ca/web/terms.html" 'University of Concordia Terms of Use' SubClassOf 'has clause' some 'Non-commercial use only' http://www.ebi.ac.uk/swo/license/SWO_1000149 OME Software Conditons of Use 'OME Software Conditons of Use' SubClassOf 'has clause' some 'Copyleft' 'OME Software Conditons of Use' SubClassOf 'has clause' some 'Number of installations unrestricted' 'OME Software Conditons of Use' SubClassOf 'has clause' some 'Distribution with notices' 'OME Software Conditons of Use' SubClassOf 'has clause' some 'Free' 'OME Software Conditons of Use' SubClassOf 'has clause' some 'Source code available' 'OME Software Conditons of Use' SubClassOf 'has clause' some 'Attribution required' 'OME Software Conditons of Use' SubClassOf 'has clause' some 'Time for use unrestricted' 'OME Software Conditons of Use' SubClassOf 'has clause' some 'Number of users unrestricted' 'OME Software Conditons of Use' SubClassOf 'has clause' some 'Usage unrestricted' http://www.ebi.ac.uk/swo/SWO_0000316 PCpheno 'PCpheno' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'PCpheno' SubClassOf 'implements' some 'Global test' 'PCpheno' SubClassOf 'R software' 'PCpheno' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'PCpheno' SubClassOf 'is executed in' some 'differential expression analysis' 'PCpheno' SubClassOf 'software' 'PCpheno' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'PCpheno' SubClassOf 'is encoded in' some 'R language' 'PCpheno' SubClassOf 'implements' some 'Hypergeometric enrichment' 'PCpheno' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) http://www.ebi.ac.uk/swo/SWO_0000315 Pearson correlation estimator 'Pearson correlation estimator' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000318 'PLM' ''PLM'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000317 PGSEA 'PGSEA' SubClassOf 'is encoded in' some 'R language' 'PGSEA' SubClassOf 'R software' 'PGSEA' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'PGSEA' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'data format specification')) 'PGSEA' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'PGSEA' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000679 obsolete rama 'obsolete rama' SubClassOf 'obsolete SWO class' 'obsolete rama' SubClassOf 'obsolete R software' 'obsolete rama' SubClassOf 'data item' 'obsolete rama' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000319 PLPE 'PLPE' SubClassOf 'software' 'PLPE' SubClassOf 'is executed in' some 'differential expression analysis' 'PLPE' SubClassOf 'implements' some 'Statistical tests' 'PLPE' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'PLPE' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'PLPE' SubClassOf 'R software' 'PLPE' SubClassOf 'is encoded in' some 'R language' 'PLPE' SubClassOf 'has specified data input' some ('LC-MS data' and ('has format specification' some 'data format specification')) http://www.ebi.ac.uk/swo/license/SWO_1000140 Non-Commercial No-Fee License 'Non-Commercial No-Fee License' EquivalentTo ('has clause' some 'Non-commercial use only') and ('has clause' some 'Free') http://www.ebi.ac.uk/efo/swo/SWO_0000677 obsolete rHVDM 'obsolete rHVDM' SubClassOf 'obsolete SWO class' 'obsolete rHVDM' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/license/SWO_1000141 DrugBank Academic License 'DrugBank Academic License' SubClassOf 'has clause' some 'Attribution required' 'DrugBank Academic License' SubClassOf 'has clause' some 'Non-commercial use only' 'DrugBank Academic License' SubClassOf 'has clause' some 'Distribution unrestricted' 'DrugBank Academic License' SubClassOf 'has website homepage' value "http://www.drugbank.ca/about" http://www.ebi.ac.uk/efo/swo/SWO_0000678 obsolete rMAT 'obsolete rMAT' SubClassOf 'obsolete SWO class' 'obsolete rMAT' SubClassOf 'obsolete BioConductor Software' 'obsolete rMAT' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/license/SWO_1000142 UCSC Genome Browser Commercial Software License 'UCSC Genome Browser Commercial Software License' SubClassOf 'has clause' some 'Derivatives not allowed' 'UCSC Genome Browser Commercial Software License' SubClassOf 'has clause' some 'Distribution restricted' 'UCSC Genome Browser Commercial Software License' SubClassOf 'has clause' some 'Not Free' 'UCSC Genome Browser Commercial Software License' SubClassOf 'has website homepage' value "http://genome.cse.ucsc.edu/license/" 'UCSC Genome Browser Commercial Software License' SubClassOf 'has clause' some 'Commercial use only' http://www.ebi.ac.uk/efo/swo/SWO_0000202 obsolete GeneticsDesign 'obsolete GeneticsDesign' SubClassOf 'obsolete SWO class' 'obsolete GeneticsDesign' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000686 obsolete rflowcyt 'obsolete rflowcyt' SubClassOf 'obsolete SWO class' 'obsolete rflowcyt' SubClassOf 'obsolete BioConductor Software' 'obsolete rflowcyt' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_1100083 'CoCiteStats' ''CoCiteStats'' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) ''CoCiteStats'' SubClassOf 'R software' ''CoCiteStats'' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''CoCiteStats'' SubClassOf 'is executed in' some 'descriptive statistical calculation' ''CoCiteStats'' SubClassOf 'is encoded in' some 'R language' ''CoCiteStats'' SubClassOf 'software' ''CoCiteStats'' SubClassOf 'implements' some 'Concordance' ''CoCiteStats'' SubClassOf 'implements' some 'Hubert’s gamma' ''CoCiteStats'' SubClassOf 'implements' some 'Jaccard’s index' http://www.ebi.ac.uk/efo/swo/SWO_0000203 obsolete GeneticsPed 'obsolete GeneticsPed' SubClassOf 'obsolete SWO class' 'obsolete GeneticsPed' SubClassOf 'obsolete BioConductor Software' 'obsolete GeneticsPed' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000687 obsolete .rma format 'obsolete .rma format' SubClassOf 'obsolete SWO class' 'obsolete .rma format' SubClassOf 'audio format' http://www.ebi.ac.uk/swo/SWO_1100084 CodeLink Expression Analysis Software 'CodeLink Expression Analysis Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Motorola Life Sciences')) 'CodeLink Expression Analysis Software' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000200 obsolete GenePix Pro 3.0 'obsolete GenePix Pro 3.0' SubClassOf 'obsolete SWO class' 'obsolete GenePix Pro 3.0' SubClassOf 'obsolete GenePix Pro' http://www.ebi.ac.uk/efo/swo/SWO_0000684 obsolete rda 'obsolete rda' SubClassOf 'obsolete SWO class' 'obsolete rda' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_0000321 PPC algorithm 'PPC algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100085 CodeLink Expression Scanning Software 'CodeLink Expression Scanning Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Motorola Life Sciences')) 'CodeLink Expression Scanning Software' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000201 obsolete GeneticsBase 'obsolete GeneticsBase' SubClassOf 'obsolete SWO class' 'obsolete GeneticsBase' SubClassOf 'obsolete R software' 'obsolete GeneticsBase' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000685 obsolete reb 'obsolete reb' SubClassOf 'obsolete SWO class' 'obsolete reb' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000320 Probe level Locally moderated Weighted median-t (PLW) method 'Probe level Locally moderated Weighted median-t (PLW) method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100086 Complex Estimation Algorithm 'Complex Estimation Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000682 obsolete .raw files 'obsolete .raw files' SubClassOf 'obsolete SWO class' 'obsolete .raw files' SubClassOf 'ASCII format' http://www.ebi.ac.uk/swo/SWO_0000323 Propagation of uncertainty in microarray analysis 'Propagation of uncertainty in microarray analysis' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000683 obsolete rbsurv 'obsolete rbsurv' SubClassOf 'obsolete SWO class' 'obsolete rbsurv' SubClassOf 'obsolete R software' 'obsolete rbsurv' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000322 PROcess 'PROcess' SubClassOf 'implements' some 'k-nearest neighbour classification' 'PROcess' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'PROcess' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'PROcess' SubClassOf 'is executed in' some 'background correction' 'PROcess' SubClassOf 'is encoded in' some 'R language' 'PROcess' SubClassOf 'R software' 'PROcess' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some 'data format specification')) 'PROcess' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100080 Text data set 'Text data set' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000680 obsolete Rank-invariant set normalization 'obsolete Rank-invariant set normalization' SubClassOf 'obsolete SWO class' 'obsolete Rank-invariant set normalization' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100081 CSV data set 'CSV data set' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000681 obsolete Rank product non-parametric method 'obsolete Rank product non-parametric method' SubClassOf 'obsolete SWO class' 'obsolete Rank product non-parametric method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000324 Pathways 2.01 software 'Pathways 2.01 software' SubClassOf 'output of' some ('software development' and ('has participant' value 'Research Genetics')) 'Pathways 2.01 software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100082 Non-linear functional regression model 'Non-linear functional regression model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/license/SWO_1000129 RegenBase Terms of Use 'RegenBase Terms of Use' SubClassOf 'has clause' some 'Attribution required' 'RegenBase Terms of Use' SubClassOf 'has website homepage' value "http://regenbase.org/terms-of-use.html" http://www.ebi.ac.uk/swo/SWO_1100087 Cyber-T 'Cyber-T' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'UC Irvine')) 'Cyber-T' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100088 'DEDS' ''DEDS'' SubClassOf 'is encoded in' some 'R language' ''DEDS'' SubClassOf 'is executed in' some 'differential expression analysis' ''DEDS'' SubClassOf 'implements' some ''FDR'' ''DEDS'' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) ''DEDS'' SubClassOf 'software' ''DEDS'' SubClassOf 'implements' some ''t-test'' ''DEDS'' SubClassOf 'implements' some 'SAM' ''DEDS'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''DEDS'' SubClassOf 'R software' ''DEDS'' SubClassOf 'is executed in' some 'descriptive statistical calculation' ''DEDS'' SubClassOf 'implements' some 'FC' http://www.ebi.ac.uk/swo/SWO_1100089 'DFP' ''DFP'' SubClassOf 'R software' ''DFP'' SubClassOf 'is executed in' some 'differential expression analysis' ''DFP'' SubClassOf 'is encoded in' some 'R language' ''DFP'' SubClassOf 'software' ''DFP'' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some http://edamontology.org/format_2330)) ''DFP'' SubClassOf 'implements' some 'Discriminant Fuzzy Pattern Algorithm' ''DFP'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) http://www.ebi.ac.uk/swo/license/SWO_1000132 UCUM Terms of Use 'UCUM Terms of Use' SubClassOf 'has clause' some 'Distribution with notices' 'UCUM Terms of Use' SubClassOf 'has clause' some 'Number of installations unrestricted' 'UCUM Terms of Use' SubClassOf 'has clause' some 'Derivatives not allowed' 'UCUM Terms of Use' SubClassOf 'has clause' some 'Usage unrestricted' 'UCUM Terms of Use' SubClassOf 'has website homepage' value "http://unitsofmeasure.org/trac/wiki/TermsOfUse" 'UCUM Terms of Use' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/swo/license/SWO_1000133 UMLS Metathesaurus License 'UMLS Metathesaurus License' SubClassOf 'has clause' some 'Free' 'UMLS Metathesaurus License' SubClassOf 'has clause' some 'Attribution required' 'UMLS Metathesaurus License' SubClassOf 'has clause' some 'Usage unrestricted' 'UMLS Metathesaurus License' SubClassOf 'has clause' some 'Derivatives not allowed' 'UMLS Metathesaurus License' SubClassOf 'has clause' some 'Distribution restricted' 'UMLS Metathesaurus License' SubClassOf 'has website homepage' value "https://uts.nlm.nih.gov/license.html" http://www.ebi.ac.uk/swo/license/SWO_1000134 MHAS Data Policy 'MHAS Data Policy' SubClassOf 'has clause' some 'Attribution required' 'MHAS Data Policy' SubClassOf 'has clause' some 'Free' 'MHAS Data Policy' SubClassOf 'has website homepage' value "http://www.mhasweb.org/Data.aspx" 'MHAS Data Policy' SubClassOf 'has clause' some 'Usage unrestricted' 'MHAS Data Policy' SubClassOf 'has clause' some 'Distribution restricted' http://www.ebi.ac.uk/swo/license/SWO_1000135 ALFRED Copyright 'ALFRED Copyright' SubClassOf 'has clause' some 'Time for use unrestricted' 'ALFRED Copyright' SubClassOf 'has clause' some 'Number of users unrestricted' 'ALFRED Copyright' SubClassOf 'has website homepage' value "hhttps://alfred.med.yale.edu/alfred/fullcopyrightpage.asp" 'ALFRED Copyright' SubClassOf 'has clause' some 'Number of installations unrestricted' 'ALFRED Copyright' SubClassOf 'has clause' some 'Attribution required' 'ALFRED Copyright' SubClassOf 'has clause' some 'Usage unrestricted' 'ALFRED Copyright' SubClassOf 'has clause' some 'Distribution unrestricted' 'ALFRED Copyright' SubClassOf 'has clause' some 'Source code available' 'ALFRED Copyright' SubClassOf 'has clause' some 'Platform unrestricted' 'ALFRED Copyright' SubClassOf 'has clause' some 'No restrictions on derivatives' http://www.ebi.ac.uk/swo/license/SWO_1000137 Fee-Based Commercial License 'Fee-Based Commercial License' EquivalentTo ('has clause' some 'Not Free') and ('has clause' some 'Commercial use only') http://www.ebi.ac.uk/swo/license/SWO_1000138 BRENDA License 'BRENDA License' SubClassOf 'has clause' some 'Derivatives not allowed' 'BRENDA License' SubClassOf 'has clause' some 'Distribution restricted' 'BRENDA License' SubClassOf 'has clause' some 'Usage unrestricted' 'BRENDA License' SubClassOf 'has website homepage' value "http://www.brenda-enzymes.org/copy.php" 'BRENDA License' SubClassOf 'has clause' some 'Free' http://www.ebi.ac.uk/swo/license/SWO_1000139 TCGA Data Use Certification 'TCGA Data Use Certification' SubClassOf 'has website homepage' value "http://cancergenome.nih.gov/pdfs/Data_Use_Certv082014" 'TCGA Data Use Certification' SubClassOf 'has clause' some 'Distribution restricted' 'TCGA Data Use Certification' SubClassOf 'has clause' some 'Usage unrestricted' 'TCGA Data Use Certification' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/swo/SWO_0000327 Probe Cell Analysis 'Probe Cell Analysis' SubClassOf 'MicroArraySuite 5.0' http://www.ebi.ac.uk/swo/SWO_0000326 Power Law Global Error Model (PLGEM) analysis method 'Power Law Global Error Model (PLGEM) analysis method' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000208 obsolete GraphAT 'obsolete GraphAT' SubClassOf 'obsolete SWO class' 'obsolete GraphAT' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000329 QuantArray scanner software 'QuantArray scanner software' SubClassOf 'output of' some ('software development' and ('has participant' value 'PerkinElmer')) 'QuantArray scanner software' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000209 obsolete GraphAlignment 'obsolete GraphAlignment' SubClassOf 'obsolete SWO class' 'obsolete GraphAlignment' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000328 PLIER (Probe Logarithmic Error Intensity Estimate) method 'PLIER (Probe Logarithmic Error Intensity Estimate) method' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000206 obsolete GlobalAncova 'obsolete GlobalAncova' SubClassOf 'obsolete SWO class' 'obsolete GlobalAncova' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000207 obsolete GOSemSim 'obsolete GOSemSim' SubClassOf 'obsolete SWO class' 'obsolete GOSemSim' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000688 obsolete rsbml 'obsolete rsbml' SubClassOf 'obsolete SWO class' 'obsolete rsbml' SubClassOf 'obsolete BioConductor Software' 'obsolete rsbml' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/license/SWO_1000130 SABIO-RK Non-Commercial Purpose License 'SABIO-RK Non-Commercial Purpose License' SubClassOf 'has clause' some 'Attribution required' 'SABIO-RK Non-Commercial Purpose License' SubClassOf 'has website homepage' value "http://sabiork.h-its.org/layouts/content/termscondition.gsp" 'SABIO-RK Non-Commercial Purpose License' SubClassOf 'has clause' some 'Non-commercial use only' http://www.ebi.ac.uk/efo/swo/SWO_0000205 obsolete GenomeGraphs 'obsolete GenomeGraphs' SubClassOf 'obsolete SWO class' 'obsolete GenomeGraphs' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000689 obsolete rtracklayer 'obsolete rtracklayer' SubClassOf 'obsolete SWO class' 'obsolete rtracklayer' SubClassOf 'obsolete R software' 'obsolete rtracklayer' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/license/SWO_1000131 Terms of Use for EMBL-EBI Services 'Terms of Use for EMBL-EBI Services' SubClassOf 'has clause' some 'No restrictions on derivatives' 'Terms of Use for EMBL-EBI Services' SubClassOf 'has clause' some 'Platform unrestricted' 'Terms of Use for EMBL-EBI Services' SubClassOf 'has clause' some 'Source code available' 'Terms of Use for EMBL-EBI Services' SubClassOf 'has clause' some 'Distribution unrestricted' 'Terms of Use for EMBL-EBI Services' SubClassOf 'has clause' some 'Time for use unrestricted' 'Terms of Use for EMBL-EBI Services' SubClassOf 'has clause' some 'Number of installations unrestricted' 'Terms of Use for EMBL-EBI Services' SubClassOf 'has clause' some 'Number of users unrestricted' 'Terms of Use for EMBL-EBI Services' SubClassOf 'has clause' some 'Usage unrestricted' 'Terms of Use for EMBL-EBI Services' SubClassOf 'has website homepage' value "http://www.ebi.ac.uk/about/terms-of-use" 'Terms of Use for EMBL-EBI Services' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/efo/swo/SWO_0000213 obsolete HELP 'obsolete HELP' SubClassOf 'obsolete SWO class' 'obsolete HELP' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000697 obsolete simulatorAPMS 'obsolete simulatorAPMS' SubClassOf 'obsolete SWO class' 'obsolete simulatorAPMS' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000330 QuantArray, PackaardBiochip technologies 'QuantArray, PackaardBiochip technologies' SubClassOf 'QuantArray scanner software' http://www.ebi.ac.uk/efo/swo/SWO_0000214 obsolete HEM 'obsolete HEM' SubClassOf 'obsolete SWO class' 'obsolete HEM' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000698 obsolete sizepower 'obsolete sizepower' SubClassOf 'obsolete SWO class' 'obsolete sizepower' SubClassOf 'obsolete R software' 'obsolete sizepower' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000695 obsolete Sim method 'obsolete Sim method' SubClassOf 'obsolete SWO class' 'obsolete Sim method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000332 Radial basis function 'Radial basis function' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000212 obsolete Hexagon binning algorithm 'obsolete Hexagon binning algorithm' SubClassOf 'obsolete SWO class' 'obsolete Hexagon binning algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000696 obsolete simpleaffy 'obsolete simpleaffy' SubClassOf 'obsolete SWO class' 'obsolete simpleaffy' SubClassOf 'obsolete R software' 'obsolete simpleaffy' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000331 QuantArray version 2 'QuantArray version 2' SubClassOf 'QuantArray scanner software' http://www.ebi.ac.uk/efo/swo/SWO_0000693 obsolete sigPathway 'obsolete sigPathway' SubClassOf 'obsolete SWO class' 'obsolete sigPathway' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000334 R interface to boost graph library algorithm (RBGL) 'R interface to boost graph library algorithm (RBGL)' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000210 obsolete GridGrinder 'obsolete GridGrinder' SubClassOf 'obsolete SWO class' 'obsolete GridGrinder' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000694 obsolete siggenes 'obsolete siggenes' SubClassOf 'obsolete SWO class' 'obsolete siggenes' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000333 RBGL 'RBGL' SubClassOf 'software' 'RBGL' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'RBGL' SubClassOf 'implements' some 'BGL' 'RBGL' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'gxl format')) 'RBGL' SubClassOf 'is executed in' some 'data visualization' 'RBGL' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'XML')) 'RBGL' SubClassOf 'R software' 'RBGL' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'RBGL' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/efo/swo/SWO_0000691 obsolete sagenhaft 'obsolete sagenhaft' SubClassOf 'obsolete SWO class' 'obsolete sagenhaft' SubClassOf 'obsolete BioConductor Software' 'obsolete sagenhaft' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000336 Random effects model 'Random effects model' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000692 obsolete seqLogo 'obsolete seqLogo' SubClassOf 'obsolete SWO class' 'obsolete seqLogo' SubClassOf 'obsolete R software' 'obsolete seqLogo' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000335 RBioinf 'RBioinf' SubClassOf 'implements' some 'Linear modelling' 'RBioinf' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) 'RBioinf' SubClassOf 'R software' 'RBioinf' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'RBioinf' SubClassOf 'software' 'RBioinf' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/efo/swo/SWO_0000690 obsolete safe 'obsolete safe' SubClassOf 'obsolete SWO class' 'obsolete safe' SubClassOf 'obsolete BioConductor Software' 'obsolete safe' SubClassOf 'obsolete R software' 'obsolete safe' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000338 RLMM 'RLMM' SubClassOf 'is published by' value 'Bioconductor' 'RLMM' SubClassOf 'R software' 'RLMM' SubClassOf 'has specified data input' some ('has format specification' only ('Xba.CQV and Xba.regions' and '.raw files')) 'RLMM' SubClassOf 'software' 'RLMM' SubClassOf 'implements' some 'Mahalanobis distance' 'RLMM' SubClassOf 'has specified data output' some 'Graph plot' 'RLMM' SubClassOf 'is executed in' some 'data normalization' 'RLMM' SubClassOf 'BioConductor Software' 'RLMM' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000337 Recursive Feature Elimination (RFE) 'Recursive Feature Elimination (RFE)' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000219 obsolete Hidden Variable Dynamic Modelling HVDM) 'obsolete Hidden Variable Dynamic Modelling HVDM)' SubClassOf 'obsolete SWO class' 'obsolete Hidden Variable Dynamic Modelling HVDM)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000339 Regression model 'Regression model' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000217 obsolete Hidden Markov Model 'obsolete Hidden Markov Model' SubClassOf 'obsolete SWO class' 'obsolete Hidden Markov Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000218 obsolete Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm 'obsolete Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm' SubClassOf 'obsolete SWO class' 'obsolete Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000215 obsolete Heterogeneous Error Model (HEM) 'obsolete Heterogeneous Error Model (HEM)' SubClassOf 'obsolete SWO class' 'obsolete Heterogeneous Error Model (HEM)' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000699 obsolete xmapbridge 'obsolete xmapbridge' SubClassOf 'obsolete SWO class' 'obsolete xmapbridge' SubClassOf 'obsolete BioConductor Software' 'obsolete xmapbridge' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000216 obsolete Hubert’s gamma 'obsolete Hubert’s gamma' SubClassOf 'obsolete SWO class' 'obsolete Hubert’s gamma' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000224 obsolete Heatplus 'obsolete Heatplus' SubClassOf 'obsolete SWO class' 'obsolete Heatplus' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000341 RMA+ 'RMA+' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000225 obsolete HilbertVis 'obsolete HilbertVis' SubClassOf 'obsolete SWO class' 'obsolete HilbertVis' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000340 RMA 'RMA' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000222 obsolete Harshlight 'obsolete Harshlight' SubClassOf 'obsolete SWO class' 'obsolete Harshlight' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000343 RMAExpress 'RMAExpress' SubClassOf 'is developed by' value 'University Of California, Berkeley' 'RMAExpress' SubClassOf 'has specified data output' some 'Text data set' 'RMAExpress' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' and 'CDF binary format')) 'RMAExpress' SubClassOf 'implements' some ('background correction' and 'data normalization') 'RMAExpress' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000342 RMA++ 'RMA++' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000220 obsolete HaarSeg algorithm 'obsolete HaarSeg algorithm' SubClassOf 'obsolete SWO class' 'obsolete HaarSeg algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000345 RMAExpress quantification 'RMAExpress quantification' SubClassOf 'RMAExpress' http://www.ebi.ac.uk/efo/swo/SWO_0000221 obsolete Hardy-Weinberg equilibrium 'obsolete Hardy-Weinberg equilibrium' SubClassOf 'obsolete SWO class' 'obsolete Hardy-Weinberg equilibrium' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000344 RMAExpress 2.0 'RMAExpress 2.0' SubClassOf 'RMAExpress' http://www.ebi.ac.uk/swo/SWO_0000347 RNAither 'RNAither' SubClassOf 'R software' 'RNAither' SubClassOf 'has specified data input' some 'Text data set' 'RNAither' SubClassOf 'is executed in' some ('data normalization' and 'descriptive statistical calculation') 'RNAither' SubClassOf 'has specified data output' some 'HTML report' 'RNAither' SubClassOf 'software' 'RNAither' SubClassOf 'is encoded in' some 'R language' 'RNAither' SubClassOf 'implements' some 'Gene-Set Enrichment Analysis' http://www.ebi.ac.uk/swo/SWO_0000346 RMAGEML 'RMAGEML' SubClassOf 'BioConductor Software' 'RMAGEML' SubClassOf 'has specified data input' some ('has format specification' only 'MAGE-ML') 'RMAGEML' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' only 'R data frame')) 'RMAGEML' SubClassOf 'is encoded in' some 'R language' 'RMAGEML' SubClassOf 'software' 'RMAGEML' SubClassOf 'is published by' value 'Bioconductor' 'RMAGEML' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000349 RWebServices 'RWebServices' SubClassOf 'has specified data input' some ('has format specification' only ('R data frame' and '.data' and '.java file')) 'RWebServices' SubClassOf 'R software' 'RWebServices' SubClassOf 'BioConductor Software' 'RWebServices' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'RWebServices' SubClassOf 'is encoded in' some 'R language' 'RWebServices' SubClassOf 'is published by' value 'Bioconductor' 'RWebServices' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000348 ROC 'ROC' SubClassOf 'has specified data input' some 'Gene expression dataset' 'ROC' SubClassOf 'is published by' value 'Bioconductor' 'ROC' SubClassOf 'is encoded in' some 'R language' 'ROC' SubClassOf 'software' 'ROC' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'ROC' SubClassOf 'R software' 'ROC' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000228 obsolete ICS-501 (version 2.3) Image Capture System 'obsolete ICS-501 (version 2.3) Image Capture System' SubClassOf 'obsolete SWO class' 'obsolete ICS-501 (version 2.3) Image Capture System' SubClassOf 'software' http://www.ebi.ac.uk/swo/license/SWO_1000150 ImmPort Conditions of Use 'ImmPort Conditions of Use' SubClassOf 'has clause' some 'Attribution not required' 'ImmPort Conditions of Use' SubClassOf 'has website homepage' value "https://aspera-immport.niaid.nih.gov:9443/displayAgreement" 'ImmPort Conditions of Use' SubClassOf 'has clause' some 'Usage unrestricted' http://www.ebi.ac.uk/efo/swo/SWO_0000229 obsolete Iteratively ReWeighted Least Squares 'obsolete Iteratively ReWeighted Least Squares' SubClassOf 'obsolete SWO class' 'obsolete Iteratively ReWeighted Least Squares' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000226 obsolete HilbertVisGUI 'obsolete HilbertVisGUI' SubClassOf 'obsolete SWO class' 'obsolete HilbertVisGUI' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000227 obsolete Hypergeometric probability 'obsolete Hypergeometric probability' SubClassOf 'obsolete SWO class' 'obsolete Hypergeometric probability' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000114 obsolete F test 'obsolete F test' SubClassOf 'obsolete SWO class' 'obsolete F test' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000598 obsolete log file 'obsolete log file' SubClassOf 'obsolete SWO class' 'obsolete log file' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000115 obsolete MAGE-TAB inputting software 'obsolete MAGE-TAB inputting software' SubClassOf 'obsolete SWO class' 'obsolete MAGE-TAB inputting software' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000599 obsolete logicFS 'obsolete logicFS' SubClassOf 'obsolete SWO class' 'obsolete logicFS' SubClassOf 'obsolete BioConductor Software' 'obsolete logicFS' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000112 obsolete BCRANK 'obsolete BCRANK' SubClassOf 'obsolete SWO class' 'obsolete BCRANK' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000596 obsolete lma 'obsolete lma' SubClassOf 'obsolete SWO class' 'obsolete lma' SubClassOf 'binary format' http://www.ebi.ac.uk/efo/swo/SWO_0000113 obsolete Cosmo 'obsolete Cosmo' SubClassOf 'obsolete SWO class' 'obsolete Cosmo' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000597 obsolete Local-pooled-error 'obsolete Local-pooled-error' SubClassOf 'obsolete SWO class' 'obsolete Local-pooled-error' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000110 obsolete distance calculation 'obsolete distance calculation' SubClassOf 'obsolete SWO class' 'obsolete distance calculation' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000594 obsolete limmaGUI 'obsolete limmaGUI' SubClassOf 'obsolete SWO class' 'obsolete limmaGUI' SubClassOf 'obsolete R software' 'obsolete limmaGUI' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000111 obsolete R software 'obsolete R software' SubClassOf 'obsolete SWO class' 'obsolete R software' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000595 obsolete Linear modelling 'obsolete Linear modelling' SubClassOf 'obsolete SWO class' 'obsolete Linear modelling' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000592 obsolete Likelihood method 'obsolete Likelihood method' SubClassOf 'obsolete SWO class' 'obsolete Likelihood method' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000593 obsolete limma 'obsolete limma' SubClassOf 'obsolete SWO class' 'obsolete limma' SubClassOf 'obsolete R software' 'obsolete limma' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/license/SWO_9000074 MIT License 'MIT License' SubClassOf 'software license' 'MIT License' SubClassOf 'has clause' some 'Time for use unrestricted' 'MIT License' SubClassOf 'is compatible license of' some ('GNU GPL v3' and 'GNU GPL v2') 'MIT License' SubClassOf 'has clause' some 'Number of installations unrestricted' 'MIT License' SubClassOf 'has clause' some 'Usage unrestricted' 'MIT License' SubClassOf 'has clause' some 'Source code available' 'MIT License' SubClassOf 'has clause' some 'Distribution with notices' 'MIT License' SubClassOf 'has clause' some 'Derivatives allowed' 'MIT License' SubClassOf 'has clause' some 'Number of users unrestricted' 'MIT License' SubClassOf 'has website homepage' value "https://opensource.org/licenses/MIT" http://www.ebi.ac.uk/efo/swo/SWO_0000590 obsolete keggorth 'obsolete keggorth' SubClassOf 'obsolete SWO class' 'obsolete keggorth' SubClassOf 'obsolete BioConductor Software' 'obsolete keggorth' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000591 obsolete lapmix 'obsolete lapmix' SubClassOf 'obsolete SWO class' 'obsolete lapmix' SubClassOf 'obsolete R software' 'obsolete lapmix' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/license/SWO_1000100 ODC-By v1.0 'ODC-By v1.0' SubClassOf 'has clause' some 'Derivatives allowed' 'ODC-By v1.0' SubClassOf 'has clause' some 'Distribution with notices' 'ODC-By v1.0' SubClassOf 'has website homepage' value "http://opendatacommons.org/licenses/by/1.0/" 'ODC-By v1.0' SubClassOf 'has clause' some 'Source code available' 'ODC-By v1.0' SubClassOf 'has clause' some 'Attribution required' 'ODC-By v1.0' SubClassOf 'has clause' some 'Usage unrestricted' http://www.ebi.ac.uk/swo/license/SWO_1000101 PDDL v1.0 'PDDL v1.0' SubClassOf 'has clause' some 'Distribution unrestricted' 'PDDL v1.0' SubClassOf 'has clause' some 'No restrictions on derivatives' 'PDDL v1.0' SubClassOf 'has clause' some 'Attribution not required' 'PDDL v1.0' SubClassOf 'has clause' some 'Usage unrestricted' 'PDDL v1.0' SubClassOf 'has website homepage' value "https://creativecommons.org/publicdomain/zero/1.0/" 'PDDL v1.0' SubClassOf 'has clause' some 'Number of installations unrestricted' 'PDDL v1.0' SubClassOf 'has clause' some 'Source code available' 'PDDL v1.0' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'PDDL v1.0' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'PDDL v1.0' SubClassOf 'has clause' some 'Time for use unrestricted' 'PDDL v1.0' SubClassOf 'has clause' some 'Number of users unrestricted' http://www.ebi.ac.uk/swo/license/SWO_1000104 NIDA NIH Data Access Policy 'NIDA NIH Data Access Policy' SubClassOf 'has website homepage' value "https://www.drugabuse.gov/researchers/research-resources/genetics-research-resources/distribution-genetic-data-biomaterials-nida-center-gene" 'NIDA NIH Data Access Policy' SubClassOf 'has clause' some 'Distribution restricted' http://www.ebi.ac.uk/swo/license/SWO_1000105 Addgene Terms of Use 'Addgene Terms of Use' SubClassOf 'has clause' some 'Distribution with notices' 'Addgene Terms of Use' SubClassOf 'has clause' some 'Attribution required' 'Addgene Terms of Use' SubClassOf 'has website homepage' value "https://www.addgene.org/terms-of-use/" 'Addgene Terms of Use' SubClassOf 'has clause' some 'Non-commercial use only' http://urigen_local_uri/963a1b3b-49f2-4ef9-8f37-5e9cd5403b2a/http://www.ebi.ac.uk/swo/data/SWO_3000069 obsolete sequence feature format 'obsolete sequence feature format' SubClassOf 'obsolete SWO class' 'obsolete sequence feature format' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/license/SWO_1000106 CAS Information Use Policy 'CAS Information Use Policy' SubClassOf 'has clause' some 'Attribution required' 'CAS Information Use Policy' SubClassOf 'has website homepage' value "http://www.cas.org/legal/infopolicy" 'CAS Information Use Policy' SubClassOf 'has clause' some 'Distribution restricted' 'CAS Information Use Policy' SubClassOf 'has clause' some 'Distribution with notices' http://www.ebi.ac.uk/efo/swo/SWO_0000118 obsolete Non-linear functional regression model 'obsolete Non-linear functional regression model' SubClassOf 'obsolete SWO class' 'obsolete Non-linear functional regression model' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000116 obsolete Text data set 'obsolete Text data set' SubClassOf 'obsolete SWO class' 'obsolete Text data set' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000117 obsolete CSV data set 'obsolete CSV data set' SubClassOf 'obsolete SWO class' 'obsolete CSV data set' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000125 obsolete 'DEDS' 'obsolete 'DEDS'' SubClassOf 'obsolete SWO class' 'obsolete 'DEDS'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/license/SWO_9000082 Artistic License 1.0 'Artistic License 1.0' SubClassOf 'has website homepage' value "https://opensource.org/licenses/Artistic-1.0" 'Artistic License 1.0' SubClassOf 'has clause' some 'Distribution with notices' http://www.ebi.ac.uk/efo/swo/SWO_0000126 obsolete 'DFP' 'obsolete 'DFP'' SubClassOf 'obsolete SWO class' 'obsolete 'DFP'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000123 obsolete Complex Estimation Algorithm 'obsolete Complex Estimation Algorithm' SubClassOf 'obsolete SWO class' 'obsolete Complex Estimation Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/license/SWO_9000080 GNU LGPL 'GNU LGPL' SubClassOf 'has clause' some 'Distribution unrestricted' 'GNU LGPL' SubClassOf 'software license' 'GNU LGPL' SubClassOf 'has clause' some 'Usage unrestricted' 'GNU LGPL' SubClassOf 'has clause' some 'No restrictions on derivatives' 'GNU LGPL' SubClassOf 'has clause' some 'Distribution with notices' 'GNU LGPL' SubClassOf 'has clause' some 'Source code available' 'GNU LGPL' SubClassOf 'has clause' some 'derivative code same license' http://www.ebi.ac.uk/efo/swo/SWO_0000124 obsolete Cyber-T 'obsolete Cyber-T' SubClassOf 'obsolete SWO class' 'obsolete Cyber-T' SubClassOf 'software' http://edamontology.org/format_1936 GenBank format 'GenBank format' SubClassOf 'data format specification' 'GenBank format' SubClassOf http://edamontology.org/format_2205 'GenBank format' SubClassOf http://edamontology.org/format_2206 http://www.ebi.ac.uk/efo/swo/SWO_0000121 obsolete CodeLink Expression Analysis Software 'obsolete CodeLink Expression Analysis Software' SubClassOf 'obsolete SWO class' 'obsolete CodeLink Expression Analysis Software' SubClassOf 'software' http://www.ebi.ac.uk/swo/license/SWO_9000086 LPPL 'LPPL' SubClassOf 'has clause' some 'Source code available' 'LPPL' SubClassOf 'software license' 'LPPL' SubClassOf 'has clause' some 'Restrictions on derivative software' 'LPPL' SubClassOf 'has clause' some 'Distribution with notices' 'LPPL' SubClassOf 'has clause' some 'Usage unrestricted' http://www.ebi.ac.uk/efo/swo/SWO_0000122 obsolete CodeLink Expression Scanning Software 'obsolete CodeLink Expression Scanning Software' SubClassOf 'obsolete SWO class' 'obsolete CodeLink Expression Scanning Software' SubClassOf 'software' http://www.ebi.ac.uk/swo/license/SWO_9000087 OPL v1.0 'OPL v1.0' SubClassOf 'is compatible license of' some (not ('GNU GPL v3' or 'GNU GPL v2')) 'OPL v1.0' SubClassOf 'software license' 'OPL v1.0' SubClassOf 'has clause' some 'Distribution restricted' 'OPL v1.0' SubClassOf 'has clause' some 'Derivatives allowed' 'OPL v1.0' SubClassOf 'has clause' some 'Source code available' http://www.ebi.ac.uk/swo/license/SWO_9000084 EPL v1 'EPL v1' SubClassOf 'is compatible license of' some (not ('GNU GPL v3' or 'GNU GPL v2')) 'EPL v1' SubClassOf 'has clause' some 'Source code available' 'EPL v1' SubClassOf 'software license' 'EPL v1' SubClassOf 'has clause' some ('Distribution unrestricted' or 'Distribution with notices') 'EPL v1' SubClassOf 'has clause' some 'Usage unrestricted' 'EPL v1' SubClassOf 'has website homepage' value "https://www.eclipse.org/legal/epl-v10.html" 'EPL v1' SubClassOf 'has clause' some 'derivative code same license' http://www.ebi.ac.uk/efo/swo/SWO_0000120 obsolete 'CoCiteStats' 'obsolete 'CoCiteStats'' SubClassOf 'obsolete SWO class' 'obsolete 'CoCiteStats'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/license/SWO_9000085 Modified BSD 'Modified BSD' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'Modified BSD' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'Modified BSD' SubClassOf 'has clause' some 'Source code available' 'Modified BSD' SubClassOf 'has website homepage' value "https://opensource.org/licenses/BSD-3-Clause" 'Modified BSD' SubClassOf 'has clause' some 'Distribution with notices' 'Modified BSD' SubClassOf 'software license' 'Modified BSD' SubClassOf 'has clause' some 'Derivatives allowed' 'Modified BSD' SubClassOf 'has clause' some 'Usage unrestricted' http://purl.obolibrary.org/obo/SWO_1100133 Stavrox 'Stavrox' SubClassOf 'has website homepage' value "http://www.stavrox.com" 'Stavrox' SubClassOf 'software' http://purl.obolibrary.org/obo/SWO_1100134 ProteomicsTools 'ProteomicsTools' SubClassOf 'has website homepage' value "https://github.com/shengqh/RCPA.Tools/wiki" 'ProteomicsTools' SubClassOf 'software' 'ProteomicsTools' SubClassOf 'has license' some 'GNU GPL v3' http://www.ebi.ac.uk/efo/swo/SWO_0000129 obsolete Digital gene expression (DGE) datasets 'obsolete Digital gene expression (DGE) datasets' SubClassOf 'obsolete SWO class' 'obsolete Digital gene expression (DGE) datasets' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000127 obsolete Discriminant Fuzzy Pattern Algorithm 'obsolete Discriminant Fuzzy Pattern Algorithm' SubClassOf 'obsolete SWO class' 'obsolete Discriminant Fuzzy Pattern Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000128 obsolete DFW 'obsolete DFW' SubClassOf 'obsolete SWO class' 'obsolete DFW' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000137 obsolete Empirical Bayes rule 'obsolete Empirical Bayes rule' SubClassOf 'obsolete SWO class' 'obsolete Empirical Bayes rule' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000134 obsolete 'EBarrays' 'obsolete 'EBarrays'' SubClassOf 'obsolete SWO class' 'obsolete 'EBarrays'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000135 obsolete Expectation-Maximization(EM) algorithm 'obsolete Expectation-Maximization(EM) algorithm' SubClassOf 'obsolete SWO class' 'obsolete Expectation-Maximization(EM) algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000132 obsolete 'DynDoc' 'obsolete 'DynDoc'' SubClassOf 'obsolete SWO class' 'obsolete 'DynDoc'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000133 obsolete 'EBImage' 'obsolete 'EBImage'' SubClassOf 'obsolete SWO class' 'obsolete 'EBImage'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000130 obsolete 'DNAcopy' 'obsolete 'DNAcopy'' SubClassOf 'obsolete SWO class' 'obsolete 'DNAcopy'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/license/SWO_1000118 LOINC RELMA Terms of Use 'LOINC RELMA Terms of Use' SubClassOf 'has clause' some 'Usage unrestricted' 'LOINC RELMA Terms of Use' SubClassOf 'has clause' some 'Distribution with notices' 'LOINC RELMA Terms of Use' SubClassOf 'has clause' some 'Attribution required' 'LOINC RELMA Terms of Use' SubClassOf 'has clause' some 'Number of installations unrestricted' 'LOINC RELMA Terms of Use' SubClassOf 'has clause' some 'Restrictions on derivative software' 'LOINC RELMA Terms of Use' SubClassOf 'has website homepage' value "https://loinc.org/terms-of-use/" http://www.ebi.ac.uk/swo/license/SWO_1000119 MIACA Full Copyright 'MIACA Full Copyright' SubClassOf 'has website homepage' value "http://miaca.sourceforge.net/copyrightNotice.txt" 'MIACA Full Copyright' SubClassOf 'has clause' some 'Usage unrestricted' 'MIACA Full Copyright' SubClassOf 'has clause' some 'Source code available' 'MIACA Full Copyright' SubClassOf 'has clause' some 'Derivatives not allowed' 'MIACA Full Copyright' SubClassOf 'has clause' some 'Distribution with notices' 'MIACA Full Copyright' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/swo/license/SWO_1000121 NIH Genomic Data Sharing Policy 'NIH Genomic Data Sharing Policy' SubClassOf 'has clause' some 'Distribution restricted' 'NIH Genomic Data Sharing Policy' SubClassOf 'has website homepage' value "https://gds.nih.gov/03policy2.html" 'NIH Genomic Data Sharing Policy' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/swo/license/SWO_1000122 Facebase Data Access Policy 'Facebase Data Access Policy' SubClassOf 'has website homepage' value "https://www.facebase.org/methods/policies/" 'Facebase Data Access Policy' SubClassOf 'has clause' some 'Distribution unrestricted' 'Facebase Data Access Policy' SubClassOf 'has clause' some 'Usage unrestricted' 'Facebase Data Access Policy' SubClassOf 'has clause' some 'Attribution not required' http://www.ebi.ac.uk/swo/license/SWO_1000123 ORCID Terms of Use 'ORCID Terms of Use' SubClassOf 'has clause' some 'Usage unrestricted' 'ORCID Terms of Use' SubClassOf 'has website homepage' value "http://orcid.org/content/orcid-terms-use" 'ORCID Terms of Use' SubClassOf 'has clause' some 'Distribution unrestricted' http://www.ebi.ac.uk/swo/license/SWO_1000124 PPDB Academic License 'PPDB Academic License' SubClassOf 'has website homepage' value "http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi" 'PPDB Academic License' SubClassOf 'has clause' some 'Attribution required' 'PPDB Academic License' SubClassOf 'has clause' some 'Non-commercial use only' 'PPDB Academic License' SubClassOf 'has clause' some 'Distribution restricted' http://www.ebi.ac.uk/swo/license/SWO_1000125 SciCrunch Terms and Conditions 'SciCrunch Terms and Conditions' SubClassOf 'has clause' some 'Distribution restricted' 'SciCrunch Terms and Conditions' SubClassOf 'has website homepage' value "https://neuinfo.org/page/terms" 'SciCrunch Terms and Conditions' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/swo/license/SWO_1000126 ProDom Commercial License 'ProDom Commercial License' SubClassOf 'has website homepage' value "http://prodom.prabi.fr/prodom/current/html/downcom.php" 'ProDom Commercial License' SubClassOf 'has clause' some 'Commercial use only' 'ProDom Commercial License' SubClassOf 'has clause' some 'Distribution restricted' 'ProDom Commercial License' SubClassOf 'has clause' some 'Not Free' http://www.ebi.ac.uk/swo/license/SWO_1000127 SBGN Open License with Attribution 'SBGN Open License with Attribution' SubClassOf 'has clause' some 'Usage unrestricted' 'SBGN Open License with Attribution' SubClassOf 'has clause' some 'Platform unrestricted' 'SBGN Open License with Attribution' SubClassOf 'has clause' some 'Number of installations unrestricted' 'SBGN Open License with Attribution' SubClassOf 'has clause' some 'Number of users unrestricted' 'SBGN Open License with Attribution' SubClassOf 'has website homepage' value "http://www.sbgn.org/About" 'SBGN Open License with Attribution' SubClassOf 'has clause' some 'Attribution required' 'SBGN Open License with Attribution' SubClassOf 'has clause' some 'Distribution unrestricted' 'SBGN Open License with Attribution' SubClassOf 'has clause' some 'Source code available' 'SBGN Open License with Attribution' SubClassOf 'has clause' some 'No restrictions on derivatives' 'SBGN Open License with Attribution' SubClassOf 'has clause' some 'Time for use unrestricted' http://www.ebi.ac.uk/swo/license/SWO_1000128 NLM Open License with Attribution 'NLM Open License with Attribution' SubClassOf 'has clause' some 'Number of users unrestricted' 'NLM Open License with Attribution' SubClassOf 'has clause' some 'Source code available' 'NLM Open License with Attribution' SubClassOf 'has clause' some 'Number of installations unrestricted' 'NLM Open License with Attribution' SubClassOf 'has clause' some 'Attribution required' 'NLM Open License with Attribution' SubClassOf 'has website homepage' value "https://www.nlm.nih.gov/copyright.html" 'NLM Open License with Attribution' SubClassOf 'has clause' some 'No restrictions on derivatives' 'NLM Open License with Attribution' SubClassOf 'has clause' some 'Time for use unrestricted' 'NLM Open License with Attribution' SubClassOf 'has clause' some 'Distribution unrestricted' 'NLM Open License with Attribution' SubClassOf 'has clause' some 'Usage unrestricted' 'NLM Open License with Attribution' SubClassOf 'has clause' some 'Platform unrestricted' http://www.ebi.ac.uk/efo/swo/SWO_0000138 obsolete Expert 2100 'obsolete Expert 2100' SubClassOf 'obsolete SWO class' 'obsolete Expert 2100' SubClassOf 'obsolete Agilent Technologies Software' http://www.ebi.ac.uk/swo/license/SWO_1000120 ORCID MIT-Style License (MIT) 'ORCID MIT-Style License (MIT)' SubClassOf 'has website homepage' value "https://github.com/ORCID/ORCID-Source/blob/master/LICENSE.md" 'ORCID MIT-Style License (MIT)' SubClassOf 'has clause' some 'Usage unrestricted' 'ORCID MIT-Style License (MIT)' SubClassOf 'is compatible license of' some ('GNU GPL v3' and 'GNU GPL v2') 'ORCID MIT-Style License (MIT)' SubClassOf 'has clause' some 'Number of installations unrestricted' 'ORCID MIT-Style License (MIT)' SubClassOf 'has clause' some 'Number of users unrestricted' 'ORCID MIT-Style License (MIT)' SubClassOf 'has clause' some 'Distribution with notices' 'ORCID MIT-Style License (MIT)' SubClassOf 'has clause' some 'Derivatives allowed' 'ORCID MIT-Style License (MIT)' SubClassOf 'has clause' some 'Time for use unrestricted' 'ORCID MIT-Style License (MIT)' SubClassOf 'has clause' some 'Source code available' http://www.ebi.ac.uk/efo/swo/SWO_0000147 obsolete Agilent Feature Extraction Software 'obsolete Agilent Feature Extraction Software' SubClassOf 'obsolete SWO class' 'obsolete Agilent Feature Extraction Software' SubClassOf 'obsolete Agilent Technologies Software' http://www.ebi.ac.uk/efo/swo/SWO_0000148 obsolete Firth's bias reduction procedure 'obsolete Firth's bias reduction procedure' SubClassOf 'obsolete SWO class' 'obsolete Firth's bias reduction procedure' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000145 obsolete 'FDR' 'obsolete 'FDR'' SubClassOf 'obsolete SWO class' 'obsolete 'FDR'' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000146 obsolete Fixed effect model 'obsolete Fixed effect model' SubClassOf 'obsolete SWO class' 'obsolete Fixed effect model' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000143 obsolete FC 'obsolete FC' SubClassOf 'obsolete SWO class' 'obsolete FC' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000141 obsolete FARMS 'obsolete FARMS' SubClassOf 'obsolete SWO class' 'obsolete FARMS' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/license/SWO_1000107 CellFinder Copyright 'CellFinder Copyright' SubClassOf 'has clause' some 'Non-commercial use only' 'CellFinder Copyright' SubClassOf 'has clause' some 'Distribution restricted' 'CellFinder Copyright' SubClassOf 'has clause' some 'Derivatives not allowed' 'CellFinder Copyright' SubClassOf 'has website homepage' value "http://cellfinder.de/contact/disclaimer/" http://www.ebi.ac.uk/efo/swo/SWO_0000140 obsolete FACS data 'obsolete FACS data' SubClassOf 'obsolete SWO class' 'obsolete FACS data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/license/SWO_1000108 LINCS Data Policy 'LINCS Data Policy' SubClassOf 'has clause' some 'Attribution required' 'LINCS Data Policy' SubClassOf 'has clause' some 'Distribution with notices' 'LINCS Data Policy' SubClassOf 'has clause' some 'Usage unrestricted' 'LINCS Data Policy' SubClassOf 'has website homepage' value "http://www.lincsproject.org/data/data-release-policy/" 'LINCS Data Policy' SubClassOf 'has clause' some 'Derivatives allowed' http://www.ebi.ac.uk/swo/license/SWO_1000109 GeneNetwork Conditions of Use 'GeneNetwork Conditions of Use' SubClassOf 'has clause' some 'Attribution required' 'GeneNetwork Conditions of Use' SubClassOf 'has website homepage' value "http://www.genenetwork.org/conditionsofUse.html" http://www.ebi.ac.uk/swo/license/SWO_1000110 GMD Academic License 'GMD Academic License' SubClassOf 'has clause' some 'Distribution restricted' 'GMD Academic License' SubClassOf 'has website homepage' value "http://gmd.mpimp-golm.mpg.de/termsconditions.aspx" 'GMD Academic License' SubClassOf 'has clause' some 'Attribution required' 'GMD Academic License' SubClassOf 'has clause' some 'Non-commercial use only' http://www.ebi.ac.uk/swo/license/SWO_1000111 GeneProf Academic License 'GeneProf Academic License' SubClassOf 'has clause' some 'Non-commercial use only' 'GeneProf Academic License' SubClassOf 'has website homepage' value "http://www.geneprof.org/GeneProf/terms_and_conditions.jsp" http://www.ebi.ac.uk/swo/license/SWO_1000112 European Medicines Agency Copyright 'European Medicines Agency Copyright' SubClassOf 'has website homepage' value "http://www.ema.europa.eu/ema/index.jsp?curl=pages/regulation/general/general_content_000178.jsp" 'European Medicines Agency Copyright' SubClassOf 'has clause' some 'Attribution required' 'European Medicines Agency Copyright' SubClassOf 'has clause' some 'Usage unrestricted' 'European Medicines Agency Copyright' SubClassOf 'has clause' some 'Distribution unrestricted' http://www.ebi.ac.uk/swo/license/SWO_1000113 miRTaBase Data License 'miRTaBase Data License' SubClassOf 'has clause' some 'Academic use only' 'miRTaBase Data License' SubClassOf 'has website homepage' value "http://mirtarbase.mbc.nctu.edu.tw/cache/download/LICENSE" 'miRTaBase Data License' SubClassOf 'has clause' some 'Distribution unrestricted' http://www.ebi.ac.uk/swo/license/SWO_1000114 GBIF Data Sharing Agreement 'GBIF Data Sharing Agreement' SubClassOf 'has website homepage' value "http://www.gbif.org/terms/licences/data-sharing" 'GBIF Data Sharing Agreement' SubClassOf 'has clause' some 'Distribution unrestricted' 'GBIF Data Sharing Agreement' SubClassOf 'has clause' some 'Usage unrestricted' 'GBIF Data Sharing Agreement' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/swo/license/SWO_1000115 IUPAC/InChI-Trust InChI Licence No. 1.0 'IUPAC/InChI-Trust InChI Licence No. 1.0' SubClassOf 'has clause' some 'Usage unrestricted' 'IUPAC/InChI-Trust InChI Licence No. 1.0' SubClassOf 'has website homepage' value "http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/LICENCE.pdf" 'IUPAC/InChI-Trust InChI Licence No. 1.0' SubClassOf 'has clause' some 'Source code available' 'IUPAC/InChI-Trust InChI Licence No. 1.0' SubClassOf 'has clause' some 'Distribution with notices' 'IUPAC/InChI-Trust InChI Licence No. 1.0' SubClassOf 'has clause' some 'Attribution required' 'IUPAC/InChI-Trust InChI Licence No. 1.0' SubClassOf 'has clause' some 'Copyleft' http://www.ebi.ac.uk/swo/license/SWO_1000116 Labome Copyright 'Labome Copyright' SubClassOf 'has clause' some 'Attribution required' 'Labome Copyright' SubClassOf 'has clause' some 'Usage unrestricted' 'Labome Copyright' SubClassOf 'has clause' some 'Derivatives not allowed' 'Labome Copyright' SubClassOf 'has clause' some 'Distribution restricted' 'Labome Copyright' SubClassOf 'has website homepage' value "http://www.labome.com/about/copyright.html" http://www.ebi.ac.uk/swo/license/SWO_1000117 CTD Legal Notice and Terms of Data Use 'CTD Legal Notice and Terms of Data Use' SubClassOf 'has clause' some 'Non-commercial use only' 'CTD Legal Notice and Terms of Data Use' SubClassOf 'has clause' some 'Attribution required' 'CTD Legal Notice and Terms of Data Use' SubClassOf 'has clause' some 'Distribution with notices' 'CTD Legal Notice and Terms of Data Use' SubClassOf 'has website homepage' value "http://ctdbase.org/about/legal.jsp" http://www.ebi.ac.uk/swo/SWO_0000305 Nested Effects Models 'Nested Effects Models' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000304 'Needleman-Wunsch' ''Needleman-Wunsch'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000307 OCplus 'OCplus' SubClassOf 'software' 'OCplus' SubClassOf 'has specified data input' some ('Gene expression data' and ('has format specification' some 'data format specification')) 'OCplus' SubClassOf 'R software' 'OCplus' SubClassOf 'is encoded in' some 'R language' 'OCplus' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'OCplus' SubClassOf 'implements' some ''FDR'' 'OCplus' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) http://www.ebi.ac.uk/swo/SWO_0000306 Nonlinear Estimation by Iterative Partial Least Squares 'Nonlinear Estimation by Iterative Partial Least Squares' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000309 OLINgui 'OLINgui' SubClassOf 'is executed in' some 'background correction' 'OLINgui' SubClassOf 'software' 'OLINgui' SubClassOf 'has specified data input' some ('Gene expression data' and ('has format specification' some 'data format specification')) 'OLINgui' SubClassOf 'is encoded in' some 'R language' 'OLINgui' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'OLINgui' SubClassOf 'is executed in' some 'data normalization' 'OLINgui' SubClassOf 'R software' 'OLINgui' SubClassOf 'is executed in' some 'data visualization' 'OLINgui' SubClassOf 'implements' some 'Iterative local regression and model selection' http://www.ebi.ac.uk/swo/SWO_0000308 OLIN 'OLIN' SubClassOf 'is executed in' some 'correction' 'OLIN' SubClassOf 'is executed in' some 'data normalization' 'OLIN' SubClassOf 'implements' some 'Iterative local regression and model selection' 'OLIN' SubClassOf 'R software' 'OLIN' SubClassOf 'is encoded in' some 'R language' 'OLIN' SubClassOf 'software' 'OLIN' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'OLIN' SubClassOf 'has specified data input' some ('Gene expression data' and ('has format specification' some 'data format specification')) http://www.ebi.ac.uk/efo/swo/SWO_0000149 obsolete Fischer's Exact Test 'obsolete Fischer's Exact Test' SubClassOf 'obsolete SWO class' 'obsolete Fischer's Exact Test' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/license/SWO_9000059 Distribution with notices 'Distribution with notices' SubClassOf 'has clause' some 'Time for use unrestricted' http://www.ebi.ac.uk/efo/swo/SWO_0000158 obsolete GEOmetadb 'obsolete GEOmetadb' SubClassOf 'obsolete SWO class' 'obsolete GEOmetadb' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000159 obsolete GEOquery 'obsolete GEOquery' SubClassOf 'obsolete SWO class' 'obsolete GEOquery' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000156 obsolete GEO data type 'obsolete GEO data type' SubClassOf 'obsolete SWO class' 'obsolete GEO data type' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000157 obsolete GEO Matrix Series format 'obsolete GEO Matrix Series format' SubClassOf 'obsolete SWO class' 'obsolete GEO Matrix Series format' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/efo/swo/SWO_0000154 obsolete GC-RMA Quantification 'obsolete GC-RMA Quantification' SubClassOf 'obsolete SWO class' 'obsolete GC-RMA Quantification' SubClassOf 'obsolete Agilent Technologies Software' http://www.ebi.ac.uk/efo/swo/SWO_0000155 obsolete GEMTools 2.4 'obsolete GEMTools 2.4' SubClassOf 'obsolete SWO class' 'obsolete GEMTools 2.4' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000152 obsolete GACK 'obsolete GACK' SubClassOf 'obsolete SWO class' 'obsolete GACK' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000710 sscore 'sscore' SubClassOf 'R software' 'sscore' SubClassOf 'is published by' value 'Bioconductor' 'sscore' SubClassOf 'software' 'sscore' SubClassOf 'has specified data input' some ('has format specification' only 'CEL binary format') 'sscore' SubClassOf 'implements' some 'S-Score algorithm' 'sscore' SubClassOf 'is encoded in' some 'R language' 'sscore' SubClassOf 'BioConductor Software' 'sscore' SubClassOf 'has specified data input' some 'Gene expression dataset' http://www.ebi.ac.uk/efo/swo/SWO_0000153 obsolete GASSCO method 'obsolete GASSCO method' SubClassOf 'obsolete SWO class' 'obsolete GASSCO method' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000150 obsolete FoxDimmicT 'obsolete FoxDimmicT' SubClassOf 'obsolete SWO class' 'obsolete FoxDimmicT' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000719 topGO 'topGO' SubClassOf 'R software' 'topGO' SubClassOf 'implements' some 'Kolmogorov Smirnov rank-sum based algorithm' 'topGO' SubClassOf 'BioConductor Software' 'topGO' SubClassOf 'has specified data input' some 'Gene list' 'topGO' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'topGO' SubClassOf 'is encoded in' some 'R language' 'topGO' SubClassOf 'software' 'topGO' SubClassOf 'is published by' value 'Bioconductor' 'topGO' SubClassOf 'is executed in' some 'differential expression analysis' http://www.ebi.ac.uk/swo/SWO_0000712 stam 'stam' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'stam' SubClassOf 'R software' 'stam' SubClassOf 'is encoded in' some 'R language' 'stam' SubClassOf 'is executed in' some ('data annotation' and 'cross validation') 'stam' SubClassOf 'software' 'stam' SubClassOf 'has specified data input' some 'Gene expression data' http://www.ebi.ac.uk/swo/SWO_0000711 ssize 'ssize' SubClassOf 'software' 'ssize' SubClassOf 'implements' some 'RMA' 'ssize' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'ssize' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'ssize' SubClassOf 'is executed in' some 'data visualization' 'ssize' SubClassOf 'is published by' value 'Bioconductor' 'ssize' SubClassOf 'R software' 'ssize' SubClassOf 'is encoded in' some 'R language' 'ssize' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000714 stepNorm 'stepNorm' SubClassOf 'has specified data input' some 'Gene expression data' 'stepNorm' SubClassOf 'is executed in' some 'data normalization' 'stepNorm' SubClassOf 'has specified data output' some 'Gene expression data' 'stepNorm' SubClassOf 'R software' 'stepNorm' SubClassOf 'is encoded in' some 'R language' 'stepNorm' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000713 Statistical tests 'Statistical tests' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000716 tilingArray 'tilingArray' SubClassOf 'BioConductor Software' 'tilingArray' SubClassOf 'is published by' value 'Bioconductor' 'tilingArray' SubClassOf 'R software' 'tilingArray' SubClassOf 'software' 'tilingArray' SubClassOf 'has specified data input' some ('has format specification' only 'CEL binary format') 'tilingArray' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'tilingArray' SubClassOf 'is executed in' some ('data visualization' and 'background correction' and 'data normalization') 'tilingArray' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000715 't-test' ''t-test'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000718 tkWidgets 'tkWidgets' SubClassOf 'software' 'tkWidgets' SubClassOf 'is encoded in' some 'R language' 'tkWidgets' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000717 timecourse 'timecourse' SubClassOf 'implements' some 'RMA' 'timecourse' SubClassOf 'is encoded in' some 'R language' 'timecourse' SubClassOf 'has specified data output' some ('has format specification' only 'CEL binary format') 'timecourse' SubClassOf 'R software' 'timecourse' SubClassOf 'has specified data input' some 'Gene expression dataset' 'timecourse' SubClassOf 'BioConductor Software' 'timecourse' SubClassOf 'is published by' value 'Bioconductor' 'timecourse' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000169 obsolete Gene Recommender algorithm 'obsolete Gene Recommender algorithm' SubClassOf 'obsolete SWO class' 'obsolete Gene Recommender algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000167 obsolete GMS 'obsolete GMS' SubClassOf 'obsolete SWO class' 'obsolete GMS' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000168 obsolete GOstats 'obsolete GOstats' SubClassOf 'obsolete SWO class' 'obsolete GOstats' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000165 obsolete Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA) 'obsolete Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)' SubClassOf 'obsolete SWO class' 'obsolete Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000166 obsolete GLEAMS software 'obsolete GLEAMS software' SubClassOf 'obsolete SWO class' 'obsolete GLEAMS software' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000163 obsolete GGtools 'obsolete GGtools' SubClassOf 'obsolete SWO class' 'obsolete GGtools' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000721 twilight 'twilight' SubClassOf 'software' 'twilight' SubClassOf 'BioConductor Software' 'twilight' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'twilight' SubClassOf 'has specified data input' some 'Gene expression dataset' 'twilight' SubClassOf 'implements' some ('Pearson correlation estimator' and ''t-test'') 'twilight' SubClassOf 'is encoded in' some 'R language' 'twilight' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'twilight' SubClassOf 'R software' 'twilight' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/efo/swo/SWO_0000164 obsolete GLAD 'obsolete GLAD' SubClassOf 'obsolete SWO class' 'obsolete GLAD' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000720 tspair 'tspair' SubClassOf 'is encoded in' some 'R language' 'tspair' SubClassOf 'is executed in' some ('cross validation' and 'descriptive statistical calculation') 'tspair' SubClassOf 'is published by' value 'Bioconductor' 'tspair' SubClassOf 'BioConductor Software' 'tspair' SubClassOf 'R software' 'tspair' SubClassOf 'has specified data input' some 'Gene expression dataset' 'tspair' SubClassOf 'software' 'tspair' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) http://www.ebi.ac.uk/efo/swo/SWO_0000161 obsolete GGBase 'obsolete GGBase' SubClassOf 'obsolete SWO class' 'obsolete GGBase' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_9000090 Dropbox 'Dropbox' SubClassOf 'has license' some 'Proprietary commercial software license' 'Dropbox' SubClassOf 'has website homepage' value "www.dropbox.com" 'Dropbox' SubClassOf 'output of' some ('software development' and ('has participant' value 'Dropbox')) 'Dropbox' SubClassOf 'has interface' some 'application programming interface' 'Dropbox' SubClassOf 'has interface' some 'command-line interface' 'Dropbox' SubClassOf 'software' 'Dropbox' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Dropbox')) http://www.ebi.ac.uk/efo/swo/SWO_0000162 obsolete Gamma Gamma Model 'obsolete Gamma Gamma Model' SubClassOf 'obsolete SWO class' 'obsolete Gamma Gamma Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_9000092 EMBOSS package 'EMBOSS package' SubClassOf 'has version' value '6.3.0' 'EMBOSS package' SubClassOf 'is executed in' some 'biological data processing' 'EMBOSS package' SubClassOf 'is executed in' some 'molecular sequence analysis' 'EMBOSS package' SubClassOf 'has license' some 'GNU LGPL' 'EMBOSS package' SubClassOf 'software' 'EMBOSS package' SubClassOf 'has interface' some 'command-line interface' 'EMBOSS package' SubClassOf 'has license' some 'GNU GPL' 'EMBOSS package' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'EMBL')) http://www.ebi.ac.uk/swo/SWO_9000091 Eclipse 'Eclipse' SubClassOf 'has interface' some 'graphical user interface' 'Eclipse' SubClassOf 'has website homepage' value "http://www.eclipse.org" 'Eclipse' SubClassOf 'has license' some 'EPL v1' 'Eclipse' SubClassOf 'has version' value 'Helios Service Release 2' 'Eclipse' SubClassOf 'output of' some ('software development' and ('has participant' value 'Eclipse Foundation')) 'Eclipse' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some http://edamontology.org/format_2330)) 'Eclipse' SubClassOf 'is executed in' some 'software development' http://www.ebi.ac.uk/swo/SWO_9000094 Grimoires 'Grimoires' SubClassOf 'has interface' some 'web service' 'Grimoires' SubClassOf 'has interface' some 'application programming interface' 'Grimoires' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'OMII-UK')) 'Grimoires' SubClassOf 'has license' some 'Modified BSD' 'Grimoires' SubClassOf 'has interface' some 'command-line interface' 'Grimoires' SubClassOf 'has website homepage' value "http://sf.net/projects/grimoires" 'Grimoires' SubClassOf 'has version' value '2.0.0' 'Grimoires' SubClassOf 'has declared status' some 'Latest release' 'Grimoires' SubClassOf 'software' 'Grimoires' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'XML')) http://www.ebi.ac.uk/swo/SWO_9000093 Endnote 'Endnote' SubClassOf 'is executed in' some 'citation management' 'Endnote' SubClassOf 'has interface' some 'graphical user interface' 'Endnote' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Thompson Reuters')) 'Endnote' SubClassOf 'has declared status' some 'Live' 'Endnote' SubClassOf 'has website homepage' value "http://www.endnote.com/" 'Endnote' SubClassOf 'has license' some 'Proprietary commercial software license' http://www.ebi.ac.uk/swo/SWO_0000723 vbmp 'vbmp' SubClassOf 'is encoded in' some 'R language' 'vbmp' SubClassOf 'BioConductor Software' 'vbmp' SubClassOf 'implements' some 'Multinomial probit regression with Gaussian Process priors' 'vbmp' SubClassOf 'software' 'vbmp' SubClassOf 'is executed in' some 'cross validation' 'vbmp' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'vbmp' SubClassOf 'is published by' value 'Bioconductor' 'vbmp' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'vbmp' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000722 Two-stage measurement error model 'Two-stage measurement error model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000725 vsn 'vsn' SubClassOf 'software' 'vsn' SubClassOf 'has specified data input' some 'Gene expression dataset' 'vsn' SubClassOf 'is executed in' some ('correction' and 'data normalization' and 'differential expression analysis') 'vsn' SubClassOf 'R software' 'vsn' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000727 webbioc 'webbioc' SubClassOf 'is encoded in' some 'R language' 'webbioc' SubClassOf 'implements' some 'Multiple testing' 'webbioc' SubClassOf 'software' 'webbioc' SubClassOf 'R software' 'webbioc' SubClassOf 'has specified data output' some 'HTML report' 'webbioc' SubClassOf 'has specified data input' some ('has format specification' only 'CEL binary format') 'webbioc' SubClassOf 'is published by' value 'Bioconductor' 'webbioc' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000726 weaver 'weaver' SubClassOf 'is published by' value 'Bioconductor' 'weaver' SubClassOf 'has specified data input' some ('has format specification' only 'Rnw') 'weaver' SubClassOf 'R software' 'weaver' SubClassOf 'has specified data output' some ('has format specification' only 'Rnw') 'weaver' SubClassOf 'is encoded in' some 'R language' 'weaver' SubClassOf 'software' 'weaver' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000729 xcms 'xcms' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'xcms' SubClassOf 'software' 'xcms' SubClassOf 'R software' 'xcms' SubClassOf 'is published by' value 'Bioconductor' 'xcms' SubClassOf 'is encoded in' some 'R language' 'xcms' SubClassOf 'has specified data input' some 'LC-MS data' 'xcms' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000728 widgetTools 'widgetTools' SubClassOf 'is encoded in' some 'R language' 'widgetTools' SubClassOf 'R software' 'widgetTools' SubClassOf 'software' 'widgetTools' SubClassOf 'has specified data input' some 'Text data set' http://edamontology.org/format_1929 FASTA format 'FASTA format' SubClassOf http://edamontology.org/format_2330 'FASTA format' SubClassOf http://edamontology.org/format_2200 'FASTA format' SubClassOf http://edamontology.org/format_2554 http://www.ebi.ac.uk/efo/swo/SWO_0000178 obsolete GenePix 4.1 'obsolete GenePix 4.1' SubClassOf 'obsolete SWO class' 'obsolete GenePix 4.1' SubClassOf 'obsolete Gene Pix' http://www.ebi.ac.uk/efo/swo/SWO_0000179 obsolete GenePix 4100A 'obsolete GenePix 4100A' SubClassOf 'obsolete SWO class' 'obsolete GenePix 4100A' SubClassOf 'obsolete GenePix' http://www.ebi.ac.uk/efo/swo/SWO_0000176 obsolete Gene Pix 'obsolete Gene Pix' SubClassOf 'obsolete SWO class' 'obsolete Gene Pix' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000730 xps 'xps' SubClassOf 'implements' some ('RMA' and ''MAS5'' and 'DFW' and 'FARMS') 'xps' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'xps' SubClassOf 'BioConductor Software' 'xps' SubClassOf 'is published by' value 'Bioconductor' 'xps' SubClassOf 'is encoded in' some 'R language' 'xps' SubClassOf 'has specified data input' some ('has format specification' only 'CEL binary format') 'xps' SubClassOf 'R software' 'xps' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000177 obsolete GenePix 3.0.6 'obsolete GenePix 3.0.6' SubClassOf 'obsolete SWO class' 'obsolete GenePix 3.0.6' SubClassOf 'obsolete Gene Pix' http://www.ebi.ac.uk/efo/swo/SWO_0000174 obsolete Gene-Set Enrichment Analysis 'obsolete Gene-Set Enrichment Analysis' SubClassOf 'obsolete SWO class' 'obsolete Gene-Set Enrichment Analysis' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000175 obsolete GeneData Expressionist Analyst v4.0.5 'obsolete GeneData Expressionist Analyst v4.0.5' SubClassOf 'obsolete SWO class' 'obsolete GeneData Expressionist Analyst v4.0.5' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000731 yaqcaffy 'yaqcaffy' SubClassOf 'has specified data output' some 'Graph plot' 'yaqcaffy' SubClassOf 'is encoded in' some 'R language' 'yaqcaffy' SubClassOf 'software' 'yaqcaffy' SubClassOf 'has specified data input' some 'Gene expression dataset' 'yaqcaffy' SubClassOf 'R software' http://purl.obolibrary.org/obo/SWO_1100144 FastQC 'FastQC' SubClassOf 'has website homepage' value "https://github.com/s-andrews/FastQC" 'FastQC' SubClassOf 'has license' some 'GNU GPL v2' 'FastQC' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000172 obsolete Gamma-Gamma hierarchical model 'obsolete Gamma-Gamma hierarchical model' SubClassOf 'obsolete SWO class' 'obsolete Gamma-Gamma hierarchical model' SubClassOf 'algorithm' http://purl.obolibrary.org/obo/SWO_1100145 CutAdapt 'CutAdapt' SubClassOf 'software' 'CutAdapt' SubClassOf 'has website homepage' value "https://cutadapt.readthedocs.io/en/stable/" 'CutAdapt' SubClassOf 'has license' some 'MIT License' http://www.ebi.ac.uk/efo/swo/SWO_0000173 obsolete Gaussian locally weighted regression 'obsolete Gaussian locally weighted regression' SubClassOf 'obsolete SWO class' 'obsolete Gaussian locally weighted regression' SubClassOf 'algorithm' http://purl.obolibrary.org/obo/SWO_1100142 RSeQC 'RSeQC' SubClassOf 'software' 'RSeQC' SubClassOf 'has license' some 'GNU GPL v3' 'RSeQC' SubClassOf 'has website homepage' value "http://rseqc.sourceforge.net/" http://www.ebi.ac.uk/efo/swo/SWO_0000170 obsolete GSEABase 'obsolete GSEABase' SubClassOf 'obsolete SWO class' 'obsolete GSEABase' SubClassOf 'obsolete R software' http://purl.obolibrary.org/obo/SWO_1100143 SAMtools 'SAMtools' SubClassOf 'has license' some 'MIT License' 'SAMtools' SubClassOf 'has website homepage' value "https://github.com/samtools/samtools" 'SAMtools' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000171 obsolete GSEAlm 'obsolete GSEAlm' SubClassOf 'obsolete SWO class' 'obsolete GSEAlm' SubClassOf 'obsolete R software' http://purl.obolibrary.org/obo/SWO_1100140 HTSeq 'HTSeq' SubClassOf 'has website homepage' value "https://htseq.readthedocs.io/en/release_0.11.1/" 'HTSeq' SubClassOf 'software' 'HTSeq' SubClassOf 'has license' some 'GNU GPL v3' http://purl.obolibrary.org/obo/SWO_1100141 RNA-SeQC 'RNA-SeQC' SubClassOf 'has license' some 'Modified BSD' 'RNA-SeQC' SubClassOf 'software' 'RNA-SeQC' SubClassOf 'has website homepage' value "https://github.com/broadinstitute/rnaseqc" http://purl.obolibrary.org/obo/SWO_1100139 PEAKS DB 'PEAKS DB' SubClassOf 'has license' some 'Proprietary commercial software license' 'PEAKS DB' SubClassOf 'has website homepage' value "http://www.bioinfor.com/peaksdb/" 'PEAKS DB' SubClassOf 'software' http://purl.obolibrary.org/obo/SWO_1100137 SWATH Software 'SWATH Software' SubClassOf 'software' 'SWATH Software' SubClassOf 'has website homepage' value "https://sciex.com/technology/swath-acquisition" 'SWATH Software' SubClassOf 'has license' some 'Proprietary commercial software license' http://purl.obolibrary.org/obo/SWO_1100138 Supernovo 'Supernovo' SubClassOf 'software' 'Supernovo' SubClassOf 'has website homepage' value "https://www.proteinmetrics.com/products/supernovo/" 'Supernovo' SubClassOf 'has license' some 'Proprietary commercial software license' http://purl.obolibrary.org/obo/SWO_1100135 Chromeleon 'Chromeleon' SubClassOf 'has license' some 'Proprietary commercial software license' 'Chromeleon' SubClassOf 'software' 'Chromeleon' SubClassOf 'has website homepage' value "https://www.thermofisher.com/order/catalog/product/CHROMELEON7#/CHROMELEON7" http://purl.obolibrary.org/obo/SWO_1100136 AnalyzerPro 'AnalyzerPro' SubClassOf 'software' 'AnalyzerPro' SubClassOf 'has license' some 'Proprietary commercial software license' 'AnalyzerPro' SubClassOf 'has website homepage' value "https://www.spectralworks.com/products/analyzerpro/" http://www.ebi.ac.uk/efo/swo/SWO_0000189 obsolete GeneRegionScan 'obsolete GeneRegionScan' SubClassOf 'obsolete SWO class' 'obsolete GeneRegionScan' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000187 obsolete GenePix Pro [Axon Instruments] 'obsolete GenePix Pro [Axon Instruments]' SubClassOf 'obsolete SWO class' 'obsolete GenePix Pro [Axon Instruments]' SubClassOf 'obsolete GenePix Pro' http://www.ebi.ac.uk/efo/swo/SWO_0000188 obsolete GeneR 'obsolete GeneR' SubClassOf 'obsolete SWO class' 'obsolete GeneR' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000185 obsolete GenePix Pro 6.0 'obsolete GenePix Pro 6.0' SubClassOf 'obsolete SWO class' 'obsolete GenePix Pro 6.0' SubClassOf 'obsolete GenePix Pro' http://www.ebi.ac.uk/efo/swo/SWO_0000186 obsolete GenePix Pro 6 [Axon Instruments] 'obsolete GenePix Pro 6 [Axon Instruments]' SubClassOf 'obsolete SWO class' 'obsolete GenePix Pro 6 [Axon Instruments]' SubClassOf 'obsolete GenePix Pro [Axon Instruments]' http://www.ebi.ac.uk/efo/swo/SWO_0000183 obsolete GenePix Pro 3 'obsolete GenePix Pro 3' SubClassOf 'obsolete SWO class' 'obsolete GenePix Pro 3' SubClassOf 'obsolete GenePix Pro' http://www.ebi.ac.uk/efo/swo/SWO_0000184 obsolete GenePix Pro 5.0 'obsolete GenePix Pro 5.0' SubClassOf 'obsolete SWO class' 'obsolete GenePix Pro 5.0' SubClassOf 'obsolete GenePix Pro' http://www.ebi.ac.uk/efo/swo/SWO_0000181 obsolete GenePix 'obsolete GenePix' SubClassOf 'obsolete SWO class' 'obsolete GenePix' SubClassOf 'obsolete Gene Pix' http://www.ebi.ac.uk/efo/swo/SWO_0000182 obsolete GenePix Pro 'obsolete GenePix Pro' SubClassOf 'obsolete SWO class' 'obsolete GenePix Pro' SubClassOf 'obsolete Gene Pix' http://www.ebi.ac.uk/efo/swo/SWO_0000180 obsolete GenePix 5.0.1 'obsolete GenePix 5.0.1' SubClassOf 'obsolete SWO class' 'obsolete GenePix 5.0.1' SubClassOf 'obsolete Gene Pix' http://edamontology.org/format_1910 newick 'newick' SubClassOf http://edamontology.org/format_2556 http://www.ebi.ac.uk/efo/swo/SWO_0000199 obsolete GenePix Pro 4.0 'obsolete GenePix Pro 4.0' SubClassOf 'obsolete SWO class' 'obsolete GenePix Pro 4.0' SubClassOf 'obsolete GenePix Pro' http://www.ebi.ac.uk/efo/swo/SWO_0000196 obsolete GeneTraffic 'obsolete GeneTraffic' SubClassOf 'obsolete SWO class' 'obsolete GeneTraffic' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000194 obsolete GeneSpringGX 'obsolete GeneSpringGX' SubClassOf 'obsolete SWO class' 'obsolete GeneSpringGX' SubClassOf 'obsolete GeneSpring' http://www.ebi.ac.uk/efo/swo/SWO_0000195 obsolete GeneTac Analyser 'obsolete GeneTac Analyser' SubClassOf 'obsolete SWO class' 'obsolete GeneTac Analyser' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000192 obsolete GeneSelector 'obsolete GeneSelector' SubClassOf 'obsolete SWO class' 'obsolete GeneSelector' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000193 obsolete GeneSpring 'obsolete GeneSpring' SubClassOf 'obsolete SWO class' 'obsolete GeneSpring' SubClassOf 'obsolete Agilent Technologies Software' 'obsolete GeneSpring' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000190 obsolete GeneRfold 'obsolete GeneRfold' SubClassOf 'obsolete SWO class' 'obsolete GeneRfold' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000191 obsolete GeneSelectMMD 'obsolete GeneSelectMMD' SubClassOf 'obsolete SWO class' 'obsolete GeneSelectMMD' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_9000081 BioPerl 'BioPerl' SubClassOf 'has website homepage' value "http://www.bioperl.org" 'BioPerl' SubClassOf 'has license' some 'Artistic License 1.0' 'BioPerl' SubClassOf 'is executed in' some 'biological data processing' 'BioPerl' SubClassOf 'has declared status' some 'Live' 'BioPerl' SubClassOf 'has interface' some 'application programming interface' 'BioPerl' SubClassOf 'has version' value '1.6.9' http://www.ebi.ac.uk/swo/SWO_9000083 DNDC 'DNDC' SubClassOf 'has interface' some 'graphical user interface' 'DNDC' SubClassOf 'has website homepage' value "http://www.dndc.sr.unh.edu/" 'DNDC' SubClassOf 'is executed in' some 'Modelling and simulation' 'DNDC' SubClassOf 'software' 'DNDC' SubClassOf 'output of' some ('software development' and ('has participant' value 'University of New Hampshire')) 'DNDC' SubClassOf 'has website homepage' value "http://ecobas.org/www-server/rem/mdb/dndc.html" 'DNDC' SubClassOf 'has interface' some 'command-line interface' 'DNDC' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'tab delimited file format')) http://www.ebi.ac.uk/swo/SWO_9000089 DROID 'DROID' SubClassOf 'software' 'DROID' SubClassOf 'has license' some 'FreeBSD' 'DROID' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'The National Archives')) 'DROID' SubClassOf 'has interface' some 'graphical user interface' 'DROID' SubClassOf 'has website homepage' value "http://sourceforge.net/projects/droid/" 'DROID' SubClassOf 'has version' value '6.02' 'DROID' SubClassOf 'has interface' some 'command-line interface' http://edamontology.org/data_2968 Image 'Image' SubClassOf http://edamontology.org/data_0006 http://www.ebi.ac.uk/swo/SWO_9000070 Microsoft Excel 'Microsoft Excel' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Microsoft')) 'Microsoft Excel' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'XLS spreadsheet')) 'Microsoft Excel' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'XLS spreadsheet')) 'Microsoft Excel' SubClassOf 'output of' some ('software development' and ('has participant' value 'Microsoft')) 'Microsoft Excel' SubClassOf 'is executed in' some 'spreadsheet editing' 'Microsoft Excel' SubClassOf 'has interface' some 'graphical user interface' 'Microsoft Excel' SubClassOf 'has license' some 'Proprietary commercial software license' 'Microsoft Excel' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_9000072 Microsoft Windows 'Microsoft Windows' SubClassOf 'output of' some ('software development' and ('has participant' value 'Microsoft')) 'Microsoft Windows' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Microsoft')) 'Microsoft Windows' SubClassOf 'software' 'Microsoft Windows' SubClassOf 'is executed in' some 'manage computer operations' 'Microsoft Windows' SubClassOf 'has interface' some 'graphical user interface' http://www.ebi.ac.uk/swo/SWO_9000071 Microsoft Excel for Windows 2010 'Microsoft Excel for Windows 2010' SubClassOf 'has declared status' some 'Latest release' 'Microsoft Excel for Windows 2010' SubClassOf 'has version' value 'Microsoft 2010 version' 'Microsoft Excel for Windows 2010' SubClassOf 'has release date' value "2010-06-15T0:00:00" 'Microsoft Excel for Windows 2010' SubClassOf 'has declared status' some 'Live' 'Microsoft Excel for Windows 2010' SubClassOf 'has version' value 'Excel 14' http://www.ebi.ac.uk/swo/SWO_9000074 Windows XP 'Windows XP' SubClassOf 'has version' value 'Microsoft XP' 'Windows XP' SubClassOf 'has release date' value "2001-10-25T0:00:00" 'Windows XP' SubClassOf 'has declared status' some 'Superseded' 'Windows XP' SubClassOf 'has version' value 'Windows 5.1' http://www.ebi.ac.uk/swo/SWO_9000073 Windows Vista 'Windows Vista' SubClassOf 'has version' value 'Windows 6.0' 'Windows Vista' SubClassOf 'directly preceded by' some 'Windows XP' 'Windows Vista' SubClassOf 'has release date' value "2006-11-08T0:00:00" http://www.ebi.ac.uk/swo/SWO_0000709 sqlite 'sqlite' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_9000076 software suite 'software suite' EquivalentTo 'software' and ('has_part' some 'software') http://www.ebi.ac.uk/swo/SWO_0000708 sproc 'sproc' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_9000075 Microsoft Office 2001 'Microsoft Office 2001' SubClassOf 'has_part' some 'Microsoft Word 2001' 'Microsoft Office 2001' SubClassOf 'software' 'Microsoft Office 2001' SubClassOf 'has_part' some 'Microsoft Excel 2002' http://www.ebi.ac.uk/swo/SWO_9000078 Annotare 'Annotare' SubClassOf 'is executed in' some 'annotation editing' 'Annotare' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'MAGE-TAB')) 'Annotare' SubClassOf 'has license' some 'MIT License' 'Annotare' SubClassOf 'has declared status' some 'Latest release' 'Annotare' SubClassOf 'has website homepage' value "http://code.google.com/p/annotare/" 'Annotare' SubClassOf 'MAGE-TAB inputting software' 'Annotare' SubClassOf 'has interface' some 'graphical user interface' 'Annotare' SubClassOf 'software' 'Annotare' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'MAGE-TAB')) 'Annotare' SubClassOf 'has version' value '1' 'Annotare' SubClassOf 'output of' some ('software development' and ('has participant' value 'Stanford University')) 'Annotare' SubClassOf 'obsolete MAGE-TAB inputting software' http://www.ebi.ac.uk/swo/SWO_9000077 Adobe Acrobat Reader 'Adobe Acrobat Reader' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Adobe Systems')) 'Adobe Acrobat Reader' SubClassOf 'is executed in' some 'file rendering' 'Adobe Acrobat Reader' SubClassOf 'has license' some 'Proprietary commercial software license' 'Adobe Acrobat Reader' SubClassOf 'has website homepage' value "http://get.adobe.com/reader/" 'Adobe Acrobat Reader' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'pdf')) 'Adobe Acrobat Reader' SubClassOf 'has interface' some 'graphical user interface' 'Adobe Acrobat Reader' SubClassOf 'has declared status' some 'Maintained' 'Adobe Acrobat Reader' SubClassOf 'has version' value 'Adobe Acrobat 10.1' http://www.ebi.ac.uk/swo/SWO_9000079 BioJava 'BioJava' SubClassOf 'has declared status' some 'Live' 'BioJava' SubClassOf 'has version' value '3.0.1' 'BioJava' SubClassOf 'has interface' some 'application programming interface' 'BioJava' SubClassOf 'has license' some 'GNU LGPL' 'BioJava' SubClassOf 'has website homepage' value "http://biojava.org" 'BioJava' SubClassOf 'output of' some ('software development' and ('has participant' value 'The Community')) 'BioJava' SubClassOf 'is executed in' some 'biological data processing' http://www.ebi.ac.uk/swo/SWO_0000701 snpMatrix 'snpMatrix' SubClassOf 'R software' 'snpMatrix' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'snpMatrix' SubClassOf 'software' 'snpMatrix' SubClassOf 'is published by' value 'Bioconductor' 'snpMatrix' SubClassOf 'BioConductor Software' 'snpMatrix' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'snpMatrix' SubClassOf 'is encoded in' some 'R language' 'snpMatrix' SubClassOf 'is executed in' some ('data visualization' and 'descriptive statistical calculation') 'snpMatrix' SubClassOf 'implements' some 'Chi-square' http://www.ebi.ac.uk/swo/SWO_0000700 snapCGH 'snapCGH' SubClassOf 'is executed in' some ('data visualization' and 'correction') 'snapCGH' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'snapCGH' SubClassOf 'BioConductor Software' 'snapCGH' SubClassOf 'R software' 'snapCGH' SubClassOf 'implements' some 'Hidden Markov Model' 'snapCGH' SubClassOf 'has specified data input' some 'Text data set' 'snapCGH' SubClassOf 'is published by' value 'Bioconductor' 'snapCGH' SubClassOf 'software' 'snapCGH' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000703 spikeLI 'spikeLI' SubClassOf 'has specified data input' some 'Gene expression dataset' 'spikeLI' SubClassOf 'software' 'spikeLI' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'spikeLI' SubClassOf 'is encoded in' some 'R language' 'spikeLI' SubClassOf 'implements' some 'Langmuir Isotherm' 'spikeLI' SubClassOf 'R software' 'spikeLI' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000705 splicegear 'splicegear' SubClassOf 'is encoded in' some 'R language' 'splicegear' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'splicegear' SubClassOf 'is published by' value 'Bioconductor' 'splicegear' SubClassOf 'software' 'splicegear' SubClassOf 'has specified data input' some ('has format specification' only 'XML') 'splicegear' SubClassOf 'R software' 'splicegear' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000704 spkTools 'spkTools' SubClassOf 'R software' 'spkTools' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'spkTools' SubClassOf 'software' 'spkTools' SubClassOf 'implements' some ('Average log expression across arrays (ALE)' and ''ANOVA'') 'spkTools' SubClassOf 'is encoded in' some 'R language' 'spkTools' SubClassOf 'has specified data input' some 'Gene expression dataset' http://www.ebi.ac.uk/swo/SWO_0000707 spotSegmentation 'spotSegmentation' SubClassOf 'is published by' value 'Bioconductor' 'spotSegmentation' SubClassOf 'implements' some 'clustering algorithm' 'spotSegmentation' SubClassOf 'software' 'spotSegmentation' SubClassOf 'is executed in' some 'background correction' 'spotSegmentation' SubClassOf 'is encoded in' some 'R language' 'spotSegmentation' SubClassOf 'BioConductor Software' 'spotSegmentation' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'spotSegmentation' SubClassOf 'R software' 'spotSegmentation' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000706 splots 'splots' SubClassOf 'is published by' value 'Bioconductor' 'splots' SubClassOf 'R software' 'splots' SubClassOf 'is encoded in' some 'R language' 'splots' SubClassOf 'has specified data output' some 'Graph plot' 'splots' SubClassOf 'software' 'splots' SubClassOf 'is executed in' some 'data visualization' 'splots' SubClassOf 'BioConductor Software' 'splots' SubClassOf 'has specified data input' some ('has format specification' only 'chamber slide format') http://www.ebi.ac.uk/swo/SWO_9000021 Source code unavailable 'Source code available' DisjointWith 'Source code unavailable' http://www.ebi.ac.uk/swo/SWO_9000020 Source code available 'Source code available' DisjointWith 'Source code unavailable' http://www.ebi.ac.uk/swo/SWO_9000023 Platform unrestricted 'Platform restricted' DisjointWith 'Platform unrestricted' http://www.ebi.ac.uk/swo/SWO_9000022 Platform restricted 'Platform restricted' DisjointWith 'Platform unrestricted' http://www.ebi.ac.uk/swo/SWO_9000025 Number of installations unrestricted 'Number of installations restricted' DisjointWith 'Number of installations unrestricted' http://www.ebi.ac.uk/swo/SWO_9000024 Number of installations restricted 'Number of installations restricted' DisjointWith 'Number of installations unrestricted' http://www.ebi.ac.uk/swo/SWO_9000027 Number of users unrestricted 'Number of users restricted' DisjointWith 'Number of users unrestricted' http://www.ebi.ac.uk/swo/SWO_9000026 Number of users restricted 'Number of users restricted' DisjointWith 'Number of users unrestricted' http://www.ebi.ac.uk/swo/SWO_9000029 Time for use unrestricted 'Time for use restricted' DisjointWith 'Time for use unrestricted' http://www.ebi.ac.uk/swo/SWO_9000028 Time for use restricted 'Time for use restricted' DisjointWith 'Time for use unrestricted' http://www.ebi.ac.uk/swo/SWO_9000016 No restrictions on derivatives 'No restrictions on derivatives' DisjointWith 'Restrictions on derivative software' http://www.ebi.ac.uk/swo/SWO_9000018 Derivatives not allowed 'Derivatives not allowed' DisjointWith 'Derivatives allowed' http://www.ebi.ac.uk/swo/SWO_9000017 Restrictions on derivative software 'No restrictions on derivatives' DisjointWith 'Restrictions on derivative software' http://www.ebi.ac.uk/swo/license/SWO_9000088 MPL 'MPL' SubClassOf 'software license' 'MPL' SubClassOf 'has clause' some 'Derivatives allowed' 'MPL' SubClassOf 'has clause' some 'Distribution with notices' 'MPL' SubClassOf 'has clause' some 'Source code available' http://www.ebi.ac.uk/swo/SWO_9000030 Usage unrestricted 'Usage unrestricted' DisjointWith 'Usage restricted' http://www.ebi.ac.uk/swo/SWO_9000031 Usage restricted 'Usage unrestricted' DisjointWith 'Usage restricted' http://www.ontodm.com/OntoDM-core/OntoDM_419460 single generalization specification 'single generalization specification' SubClassOf 'generalization specification' http://edamontology.org/operation_0224 Query and retrieval 'Query and retrieval' SubClassOf 'data transformation' 'Query and retrieval' SubClassOf http://edamontology.org/operation_0004 http://www.ebi.ac.uk/swo/SWO_0000077 Sequence Alignment and Modeling System 'Sequence Alignment and Modeling System' SubClassOf 'is executed in' some 'multiple sequence alignment' http://www.ebi.ac.uk/swo/SWO_0000076 SPSS 20.0 'SPSS 20.0' SubClassOf 'has download location' value "http://www-01.ibm.com/software/uk/analytics/spss/downloads.html" 'SPSS 20.0' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'IBM')) http://www.ebi.ac.uk/swo/SWO_0000079 Cytoscape 'Cytoscape' SubClassOf 'is executed in' some 'data visualization' 'Cytoscape' SubClassOf 'has specified data input' only 'Interaction data' 'Cytoscape' SubClassOf 'has documentation' value "http://dx.doi.org/10.1101/gr.1239303" http://www.ebi.ac.uk/swo/SWO_0000078 SAM 3.5 'SAM 3.5' SubClassOf 'implements' some 'Hidden Markov Model' 'SAM 3.5' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'UC Santa Cruz Computational Biology Group ')) http://www.ebi.ac.uk/swo/SWO_0000071 CRG PSICoffee Web Tool 'CRG PSICoffee Web Tool' SubClassOf 'has interface' some 'web user interface' 'CRG PSICoffee Web Tool' SubClassOf 'uses software' some 'CRG TCoffee 9.02.r1228' 'CRG PSICoffee Web Tool' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Centre for Genomic Regulation (CRG) of Barcelona')) 'CRG PSICoffee Web Tool' SubClassOf 'has documentation' value "http://dx.doi.org/10.1093/nar/gkr245" http://www.ebi.ac.uk/swo/SWO_0000070 CRG Expresso Web Tool 'CRG Expresso Web Tool' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Centre for Genomic Regulation (CRG) of Barcelona')) 'CRG Expresso Web Tool' SubClassOf 'has interface' some 'web user interface' 'CRG Expresso Web Tool' SubClassOf 'uses software' some 'CRG TCoffee 9.02.r1228' 'CRG Expresso Web Tool' SubClassOf 'has documentation' value "http://dx.doi.org/10.1093/nar/gkl092" http://www.ebi.ac.uk/swo/SWO_0000073 Q 'Q' SubClassOf 'is executed in' some 'data visualization' 'Q' SubClassOf 'is executed in' some 'data processing task' 'Q' SubClassOf 'has website homepage' value "http://xray.bmc.uu.se/~aqwww/q/"@en http://www.ebi.ac.uk/swo/SWO_0000072 CRG TCoffee 9.02.r1228 'CRG TCoffee 9.02.r1228' SubClassOf 'has version' value 'CRG TCoffee version 9.02.r1228' 'CRG TCoffee 9.02.r1228' SubClassOf 'has interface' some 'graphical user interface' 'CRG TCoffee 9.02.r1228' SubClassOf 'has interface' some 'command-line interface' 'CRG TCoffee 9.02.r1228' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Centre for Genomic Regulation (CRG) of Barcelona')) http://www.ebi.ac.uk/swo/SWO_0000075 SPSS 'SPSS' SubClassOf 'is executed in' some 'data visualization' 'SPSS' SubClassOf 'has interface' some 'graphical user interface' 'SPSS' SubClassOf 'is executed in' some 'data processing task' http://www.ebi.ac.uk/swo/SWO_0000074 Q 4.2 'Q 4.2' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Uppsala Molekylmekaniska HB')) http://www.ebi.ac.uk/swo/SWO_0000080 Cytoscape 2.8 'Cytoscape 2.8' SubClassOf 'has download location' value "http://www.cytoscape.org/download.html" 'Cytoscape 2.8' SubClassOf 'has specified data input' some ('Interaction data' and ('has format specification' some ('SBML' or http://edamontology.org/format_3158 or 'SIF' or 'GML' or 'XGMML' or 'BioPAX RDF/XML format'))) http://www.ebi.ac.uk/swo/SWO_0000084 CEL binary format 'CEL binary format' SubClassOf 'binary format' 'CEL binary format' SubClassOf 'is published by' value 'Affymetrix' http://www.ebi.ac.uk/swo/SWO_0000083 Plugin 'Plugin' SubClassOf 'role' 'Plugin' SubClassOf http://www.ifomis.org/bfo/1.1/snap#Role http://www.ebi.ac.uk/swo/SWO_1100113 GGBase 'GGBase' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'GGBase' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GGBase' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'rda')) 'GGBase' SubClassOf 'software' 'GGBase' SubClassOf 'is encoded in' some 'R language' 'GGBase' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GGBase' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000090 Gene Expression Atlas at EBI R statistics package 'Gene Expression Atlas at EBI R statistics package' SubClassOf 'has support URL' value "https://github.com/gxa/gxa/blob/develop/atlas-analytics/src/main/resources/R/analytics.R" http://www.ebi.ac.uk/swo/SWO_1100114 Gamma Gamma Model 'Gamma Gamma Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100115 matlab software 'matlab software' SubClassOf 'software' 'matlab software' EquivalentTo 'is encoded in' some 'MATLAB language' http://www.ontodm.com/OntoDM-core/OntoDM_000285 probability distribution specification 'probability distribution specification' SubClassOf 'single generalization specification' http://www.ebi.ac.uk/swo/SWO_1100116 AtlasImage 'AtlasImage' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Clontech Laboratories, Inc')) 'AtlasImage' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100110 GEO data type 'GEO data type' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_1100111 GEOmetadb 'GEOmetadb' SubClassOf 'R software' 'GEOmetadb' SubClassOf 'software' 'GEOmetadb' SubClassOf 'is encoded in' some 'R language' 'GEOmetadb' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) http://www.ebi.ac.uk/swo/SWO_1100112 GEOquery 'GEOquery' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GEOquery' SubClassOf 'software' 'GEOquery' SubClassOf 'R software' 'GEOquery' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_1100117 CBS 'CBS' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100118 CBS algorithm 'CBS algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100119 'CGHbase' ''CGHbase'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''CGHbase'' SubClassOf 'is executed in' some 'data normalization' ''CGHbase'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) ''CGHbase'' SubClassOf 'software' ''CGHbase'' SubClassOf 'is executed in' some 'averaging' ''CGHbase'' SubClassOf 'is encoded in' some 'R language' ''CGHbase'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100102 'FDR' ''FDR'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100103 Fixed effect model 'Fixed effect model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100104 Agilent Feature Extraction Software 'Agilent Feature Extraction Software' SubClassOf 'software' 'Agilent Feature Extraction Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) 'Agilent Feature Extraction Software' SubClassOf 'Agilent Technologies Software' 'Agilent Feature Extraction Software' SubClassOf 'is executed in' some 'feature extraction' http://www.ebi.ac.uk/swo/SWO_1100105 Fischer's Exact Test 'Fischer's Exact Test' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100100 FARMS 'FARMS' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100101 FC 'FC' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100106 GACK 'GACK' SubClassOf 'software' 'GACK' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Stanford University')) http://www.ebi.ac.uk/swo/SWO_1100107 GASSCO method 'GASSCO method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100108 GC-RMA Quantification 'GC-RMA Quantification' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) 'GC-RMA Quantification' SubClassOf 'Agilent Technologies Software' 'GC-RMA Quantification' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100109 GEMTools 2.4 'GEMTools 2.4' SubClassOf 'software' 'GEMTools 2.4' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Incyte Genomics')) http://www.ebi.ac.uk/swo/SWO_0000032 Agilent Scan Control 'Agilent Scan Control' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) 'Agilent Scan Control' SubClassOf 'software' 'Agilent Scan Control' SubClassOf 'Agilent Technologies Software' http://www.ebi.ac.uk/swo/SWO_0000035 'AnnotationDbi' ''AnnotationDbi'' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'sqlite')) ''AnnotationDbi'' SubClassOf 'software' ''AnnotationDbi'' SubClassOf 'is encoded in' some 'R language' ''AnnotationDbi'' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''AnnotationDbi'' SubClassOf 'has specified data output' some ('Bitmap object' and ('has format specification' some 'data format specification')) ''AnnotationDbi'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000034 Agilent Technologies Software 'Agilent Technologies Software' SubClassOf 'software' 'Agilent Technologies Software' EquivalentTo 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) http://www.ebi.ac.uk/swo/SWO_1100130 Seurat 'Seurat' SubClassOf 'has license' some 'GNU GPL v3' 'Seurat' SubClassOf 'has website homepage' value "https://satijalab.org/seurat/" 'Seurat' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000037 Applied Biosystems 1700 Expression Array System Software 'Applied Biosystems 1700 Expression Array System Software' SubClassOf 'software' 'Applied Biosystems 1700 Expression Array System Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Applied Biosystems')) http://www.ebi.ac.uk/swo/SWO_0000039 ArrayGauge 'ArrayGauge' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Fujifilm')) 'ArrayGauge' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100131 Graphpad Prism 'Graphpad Prism' SubClassOf 'has website homepage' value "https://www.graphpad.com/scientific-software/prism/" 'Graphpad Prism' SubClassOf 'has license' some 'Proprietary commercial software license' 'Graphpad Prism' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100132 Salmon 'Salmon' SubClassOf 'has website homepage' value "https://combine-lab.github.io/salmon/" 'Salmon' SubClassOf 'software' 'Salmon' SubClassOf 'has license' some 'GNU GPL v3' http://www.ebi.ac.uk/swo/SWO_0000031 Smultron 'Smultron' SubClassOf 'has declared status' some 'Latest release' 'Smultron' SubClassOf 'has website homepage' value "http://www.peterborgapps.com/smultron/" 'Smultron' SubClassOf 'has specified data input' some ('Ontology' and ('has format specification' some http://edamontology.org/format_2330)) 'Smultron' SubClassOf 'has version' value '3.5.1' 'Smultron' SubClassOf 'is executed in' some 'text editing' http://www.ebi.ac.uk/swo/SWO_0000030 software with command line interface 'software with command line interface' EquivalentTo 'has interface' some 'command-line interface' http://www.ebi.ac.uk/swo/SWO_0000044 BLAST+ 2.2.26 'BLAST+ 2.2.26' SubClassOf 'has specified data input' some ('DNA nucleotide sequence' and ('has format specification' some 'GenBank format')) 'BLAST+ 2.2.26' SubClassOf 'has download location' value "ftp://ftp.ncbi.nih.gov/blast/executables/" 'BLAST+ 2.2.26' SubClassOf 'has specified data input' some ('DNA nucleotide sequence' and ('has format specification' some 'FASTA format')) 'BLAST+ 2.2.26' SubClassOf 'BLAST' 'BLAST+ 2.2.26' SubClassOf 'has interface' some 'command-line interface' 'BLAST+ 2.2.26' SubClassOf 'has interface' some 'web user interface' 'BLAST+ 2.2.26' SubClassOf 'has version' value 'BLAST+ version 2.2.26' 'BLAST+ 2.2.26' SubClassOf 'obsolete BLAST' http://www.ebi.ac.uk/swo/SWO_0000045 Array_vision_(Interfocus) 'Array_vision_(Interfocus)' SubClassOf 'ArrayVision' http://www.ebi.ac.uk/swo/SWO_0000048 BAC 'BAC' SubClassOf 'has specified data output' some ('has format specification' some 'BED format') 'BAC' SubClassOf 'implements' some 'Bayesian Model' 'BAC' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'BAC' SubClassOf 'software' 'BAC' SubClassOf 'BioConductor Software' 'BAC' SubClassOf 'is encoded in' some 'R language' 'BAC' SubClassOf 'R software' 'BAC' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000047 Axon GenePix Pro 3 'Axon GenePix Pro 3' SubClassOf 'GenePix Pro [Axon Instruments]' http://www.ebi.ac.uk/swo/SWO_0000049 Binning clustering method 'Binning clustering method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/license/SWO_1000090 CC BY-NC-SA 4.0 'CC BY-NC-SA 4.0' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY-NC-SA 4.0' SubClassOf 'has clause' some 'Non-commercial use only' 'CC BY-NC-SA 4.0' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-nc-sa/4.0/" 'CC BY-NC-SA 4.0' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY-NC-SA 4.0' SubClassOf 'has clause' some 'Free' 'CC BY-NC-SA 4.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY-NC-SA 4.0' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-NC-SA 4.0' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY-NC-SA 4.0' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-NC-SA 4.0' SubClassOf 'has clause' some 'Derivatives allowed' 'CC BY-NC-SA 4.0' SubClassOf 'has clause' some 'Platform unrestricted' http://www.ebi.ac.uk/swo/SWO_1100124 'DynDoc' ''DynDoc'' SubClassOf 'is encoded in' some 'R language' ''DynDoc'' SubClassOf 'R software' ''DynDoc'' SubClassOf 'software' ''DynDoc'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'Rnw')) http://www.ebi.ac.uk/swo/SWO_1100125 FoxDimmicT 'FoxDimmicT' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100126 GEO Matrix Series format 'GEO Matrix Series format' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_1100127 software before Microsoft 2007 'software before Microsoft 2007' EquivalentTo 'software' and ('has version' some ('version name' and ('followed by' value 'Microsoft 2007 version'))) 'software before Microsoft 2007' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000040 ArrayNorm 'ArrayNorm' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Institute for Genomics and Bioinformatics Graz University of Technology')) 'ArrayNorm' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100120 'CGHcall' ''CGHcall'' SubClassOf 'implements' some 'CBS algorithm' ''CGHcall'' SubClassOf 'software' ''CGHcall'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) ''CGHcall'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''CGHcall'' SubClassOf 'R software' ''CGHcall'' SubClassOf 'is executed in' some 'data normalization' ''CGHcall'' SubClassOf 'is executed in' some 'averaging' ''CGHcall'' SubClassOf 'is encoded in' some 'R language' ''CGHcall'' SubClassOf 'is executed in' some 'descriptive statistical calculation' http://www.ebi.ac.uk/swo/SWO_1100121 'CGHregions' ''CGHregions'' SubClassOf 'implements' some 'CBS algorithm' ''CGHregions'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) ''CGHregions'' SubClassOf 'R software' ''CGHregions'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''CGHregions'' SubClassOf 'software' ''CGHregions'' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000042 ArrayVision 'ArrayVision' SubClassOf 'software' 'ArrayVision' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'GE Healthcare Life Sciences')) http://www.ebi.ac.uk/swo/SWO_1100122 CHP binary format 'CHP binary format' SubClassOf 'binary format' 'CHP binary format' SubClassOf 'is published by' value 'Affymetrix' http://www.ebi.ac.uk/swo/SWO_0000041 'ArrayTools' ''ArrayTools'' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) ''ArrayTools'' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'R data frame')) ''ArrayTools'' SubClassOf 'R software' ''ArrayTools'' SubClassOf 'implements' some 'RMA' ''ArrayTools'' SubClassOf 'is encoded in' some 'R language' ''ArrayTools'' SubClassOf 'software' ''ArrayTools'' SubClassOf 'is executed in' some 'differential expression analysis' http://www.ebi.ac.uk/swo/SWO_1100123 CLR algorithm 'CLR algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/license/SWO_1000099 FlowRepository Open Access Terms of Use 'FlowRepository Open Access Terms of Use' SubClassOf 'has clause' some 'Distribution unrestricted' 'FlowRepository Open Access Terms of Use' SubClassOf 'has clause' some 'No restrictions on derivatives' 'FlowRepository Open Access Terms of Use' SubClassOf 'has clause' some 'Number of users unrestricted' 'FlowRepository Open Access Terms of Use' SubClassOf 'has clause' some 'Number of installations unrestricted' 'FlowRepository Open Access Terms of Use' SubClassOf 'has clause' some 'Usage unrestricted' 'FlowRepository Open Access Terms of Use' SubClassOf 'has clause' some 'Attribution not required' 'FlowRepository Open Access Terms of Use' SubClassOf 'has clause' some 'Time for use unrestricted' 'FlowRepository Open Access Terms of Use' SubClassOf 'has clause' some 'Source code available' 'FlowRepository Open Access Terms of Use' SubClassOf 'has clause' some 'Platform unrestricted' 'FlowRepository Open Access Terms of Use' SubClassOf 'has website homepage' value "http://flowrepository.org/terms_of_service" http://www.ebi.ac.uk/swo/SWO_1100128 bcbio 'bcbio' SubClassOf 'has website homepage' value "https://github.com/bcbio/bcbio-nextgen" 'bcbio' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100129 shinyNGS 'shinyNGS' SubClassOf 'has license' some 'GNU AGPL v3' 'shinyNGS' SubClassOf 'software' 'shinyNGS' SubClassOf 'has website homepage' value "https://github.com/pinin4fjords/shinyngs" http://www.ebi.ac.uk/swo/license/SWO_1000091 CC BY-SA 2.1 JP 'CC BY-SA 2.1 JP' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-SA 2.1 JP' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-SA 2.1 JP' SubClassOf 'has clause' some 'Attribution required' 'CC BY-SA 2.1 JP' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-sa/2.1/jp/deed.en" 'CC BY-SA 2.1 JP' SubClassOf 'has clause' some 'Source code available' 'CC BY-SA 2.1 JP' SubClassOf 'has clause' some 'Copyleft' 'CC BY-SA 2.1 JP' SubClassOf 'has clause' some 'Usage unrestricted' http://edamontology.org/format_2305 GFF 'GFF' SubClassOf http://edamontology.org/format_2206 http://www.ebi.ac.uk/swo/license/SWO_1000092 CC BY-SA 3.0 'CC BY-SA 3.0' SubClassOf 'has clause' some 'Source code available' 'CC BY-SA 3.0' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-SA 3.0' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-SA 3.0' SubClassOf 'has website homepage' value "http://creativecommons.org/licenses/by-sa/3.0/" 'CC BY-SA 3.0' SubClassOf 'has clause' some 'Copyleft' 'CC BY-SA 3.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY-SA 3.0' SubClassOf 'has clause' some 'Usage unrestricted' http://www.ebi.ac.uk/swo/license/SWO_1000093 CC BY-SA 3.0 US 'CC BY-SA 3.0 US' SubClassOf 'has clause' some 'Attribution required' 'CC BY-SA 3.0 US' SubClassOf 'has clause' some 'Usage unrestricted' 'CC BY-SA 3.0 US' SubClassOf 'has clause' some 'Copyleft' 'CC BY-SA 3.0 US' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-SA 3.0 US' SubClassOf 'has website homepage' value "http://creativecommons.org/licenses/by-sa/3.0/us/" 'CC BY-SA 3.0 US' SubClassOf 'has clause' some 'Source code available' 'CC BY-SA 3.0 US' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) http://www.ebi.ac.uk/swo/license/SWO_1000094 CC BY-SA 4.0 'CC BY-SA 4.0' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-SA 4.0' SubClassOf 'has clause' some 'Copyleft' 'CC BY-SA 4.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY-SA 4.0' SubClassOf 'has website homepage' value "http://creativecommons.org/licenses/by-sa/4.0/" 'CC BY-SA 4.0' SubClassOf 'has clause' some 'Usage unrestricted' 'CC BY-SA 4.0' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-SA 4.0' SubClassOf 'has clause' some 'Source code available' http://www.ebi.ac.uk/swo/license/SWO_1000096 ODbL v1.0 'ODbL v1.0' SubClassOf 'has clause' some 'Attribution required' 'ODbL v1.0' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'ODbL v1.0' SubClassOf 'has website homepage' value "http://www.opendatacommons.org/licenses/odbl/1.0/" 'ODbL v1.0' SubClassOf 'has clause' some 'Source code available' 'ODbL v1.0' SubClassOf 'has clause' some 'Copyleft' 'ODbL v1.0' SubClassOf 'has clause' some 'Distribution with notices' 'ODbL v1.0' SubClassOf 'has clause' some 'Usage unrestricted' http://www.ebi.ac.uk/swo/license/SWO_1000097 DbCL v1.0 'DbCL v1.0' SubClassOf 'has clause' some 'Usage unrestricted' 'DbCL v1.0' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'DbCL v1.0' SubClassOf 'has clause' some 'Distribution with notices' 'DbCL v1.0' SubClassOf 'has website homepage' value "http://opendatacommons.org/licenses/dbcl/1.0/" 'DbCL v1.0' SubClassOf 'has clause' some 'Copyleft' 'DbCL v1.0' SubClassOf 'has clause' some 'Source code available' 'DbCL v1.0' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/swo/license/SWO_1000098 EMBLEM ELM Academic License 'EMBLEM ELM Academic License' SubClassOf 'has clause' some 'Source code unavailable' 'EMBLEM ELM Academic License' SubClassOf 'has website homepage' value "http://elm.eu.org/media/Elm_academic_license.pdf" 'EMBLEM ELM Academic License' SubClassOf 'has clause' some 'Derivatives not allowed' 'EMBLEM ELM Academic License' SubClassOf 'has clause' some 'Distribution restricted' 'EMBLEM ELM Academic License' SubClassOf 'has clause' some 'Non-commercial use only' http://www.ebi.ac.uk/swo/SWO_0000055 Clustal Omega 1.1 'Clustal Omega 1.1' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Conway Institute UCD Dublin')) 'Clustal Omega 1.1' SubClassOf 'has interface' only 'command-line interface' 'Clustal Omega 1.1' SubClassOf 'has documentation' value "http://dx.doi.org/10.1038/msb.2011.75" 'Clustal Omega 1.1' SubClassOf 'has version' value 'Clustal Omega version 1.1' http://www.ebi.ac.uk/swo/SWO_0000057 ClustalX 2.1 'ClustalX 2.1' SubClassOf 'has version' value 'ClustalX version 2.1' 'ClustalX 2.1' SubClassOf 'has documentation' value "http://dx.doi.org/10.1093/bioinformatics/btm404" 'ClustalX 2.1' SubClassOf 'has interface' only 'graphical user interface' 'ClustalX 2.1' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Conway Institute UCD Dublin')) http://www.ebi.ac.uk/swo/SWO_0000056 ClustalW 2.1 'ClustalW 2.1' SubClassOf 'has documentation' value "http://dx.doi.org/10.1093/bioinformatics/btm404" 'ClustalW 2.1' SubClassOf 'has version' value 'ClustalW version 2.1' 'ClustalW 2.1' SubClassOf 'has interface' only 'command-line interface' 'ClustalW 2.1' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Conway Institute UCD Dublin')) http://www.ebi.ac.uk/swo/SWO_0000059 EBI Clustal Omega Web Tool 'EBI Clustal Omega Web Tool' SubClassOf 'uses software' some 'Clustal Omega 1.1' 'EBI Clustal Omega Web Tool' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'European Bioinformatics Institute')) 'EBI Clustal Omega Web Tool' SubClassOf 'has interface' some 'web user interface' http://www.ebi.ac.uk/swo/SWO_0000058 EBI Clustal W2 Web Tool 'EBI Clustal W2 Web Tool' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'European Bioinformatics Institute')) 'EBI Clustal W2 Web Tool' SubClassOf 'has interface' some 'web user interface' 'EBI Clustal W2 Web Tool' SubClassOf 'uses software' some 'ClustalW 2.1' http://edamontology.org/operation_2426 Modelling and simulation 'Modelling and simulation' SubClassOf 'data transformation' 'Modelling and simulation' SubClassOf http://edamontology.org/operation_0004 http://www.ebi.ac.uk/swo/SWO_0000051 Clustal 'Clustal' SubClassOf 'is executed in' some 'multiple sequence alignment' http://edamontology.org/format_2331 HTML 'HTML' SubClassOf http://edamontology.org/format_1915 http://edamontology.org/format_2330 http://edamontology.org/format_2330 SubClassOf http://edamontology.org/format_1915 http://edamontology.org/format_2333 binary format 'binary format' SubClassOf http://edamontology.org/format_1915 http://edamontology.org/format_2332 XML 'XML' SubClassOf http://edamontology.org/format_1915 http://www.ebi.ac.uk/swo/SWO_0000066 EBI TCoffee Web Tool 'EBI TCoffee Web Tool' SubClassOf 'has interface' some 'web service' 'EBI TCoffee Web Tool' SubClassOf 'has interface' some 'web user interface' 'EBI TCoffee Web Tool' SubClassOf 'uses software' some 'CRG TCoffee 9.02.r1228' 'EBI TCoffee Web Tool' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'European Bioinformatics Institute')) http://www.ebi.ac.uk/swo/SWO_0000065 CRG TCoffee 'CRG TCoffee' SubClassOf 'has documentation' value "http://dx.doi.org/10.1006/jmbi.2000.4042" http://www.ebi.ac.uk/swo/SWO_0000068 CRG TCoffee Web Tool 'CRG TCoffee Web Tool' SubClassOf 'has documentation' value "http://dx.doi.org/10.1093/nar/gkr245" 'CRG TCoffee Web Tool' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Centre for Genomic Regulation (CRG) of Barcelona')) 'CRG TCoffee Web Tool' SubClassOf 'has interface' some 'web user interface' 'CRG TCoffee Web Tool' SubClassOf 'uses software' some 'CRG TCoffee 9.02.r1228' http://www.ebi.ac.uk/swo/SWO_0000067 CRG RCoffee Web Tool 'CRG RCoffee Web Tool' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Centre for Genomic Regulation (CRG) of Barcelona')) 'CRG RCoffee Web Tool' SubClassOf 'has interface' some 'web user interface' 'CRG RCoffee Web Tool' SubClassOf 'has documentation' value "http://dx.doi.org/10.1093/nar/gkn278" 'CRG RCoffee Web Tool' SubClassOf 'uses software' some 'CRG TCoffee 9.02.r1228' http://www.ebi.ac.uk/swo/SWO_0000069 CRG MCoffee Web Tool 'CRG MCoffee Web Tool' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Centre for Genomic Regulation (CRG) of Barcelona')) 'CRG MCoffee Web Tool' SubClassOf 'uses software' some 'CRG TCoffee 9.02.r1228' 'CRG MCoffee Web Tool' SubClassOf 'has interface' some 'web user interface' 'CRG MCoffee Web Tool' SubClassOf 'has documentation' value "http://dx.doi.org/10.1093/nar/gkm333" http://www.ebi.ac.uk/swo/SWO_0000060 MUSCLE 'MUSCLE' SubClassOf 'is executed in' some 'multiple sequence alignment' http://www.ebi.ac.uk/swo/SWO_0000062 MUSCLE 3.8.31 'MUSCLE 3.8.31' SubClassOf 'has download location' value "http://www.drive5.com/muscle/downloads.htm" 'MUSCLE 3.8.31' SubClassOf 'has interface' some 'command-line interface' 'MUSCLE 3.8.31' SubClassOf 'has documentation' value "http://www.drive5.com/muscle/muscle_userguide3.8.html" 'MUSCLE 3.8.31' SubClassOf 'has version' value 'MUSCLE version 3.8.31' 'MUSCLE 3.8.31' SubClassOf 'has documentation' value "http://dx.doi.org/10.1093/nar/gkh340" http://www.ebi.ac.uk/swo/SWO_0000061 EBI Muscle Web Tool 'EBI Muscle Web Tool' SubClassOf 'uses software' some 'MUSCLE 3.8.31' 'EBI Muscle Web Tool' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'European Bioinformatics Institute')) 'EBI Muscle Web Tool' SubClassOf 'has interface' some 'web user interface' http://www.ebi.ac.uk/swo/SWO_0000064 TCoffee 'TCoffee' SubClassOf 'is executed in' some 'multiple sequence alignment' http://www.ebi.ac.uk/swo/SWO_0000063 Drive5 MUSCLE 'Drive5 MUSCLE' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Drive5')) http://www.ebi.ac.uk/efo/swo/SWO_0000509 obsolete database creation 'obsolete database creation' SubClassOf 'obsolete SWO class' 'obsolete database creation' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000507 obsolete cosmoGUI 'obsolete cosmoGUI' SubClassOf 'obsolete SWO class' 'obsolete cosmoGUI' SubClassOf 'obsolete R software' 'obsolete cosmoGUI' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000508 obsolete covdesc file 'obsolete covdesc file' SubClassOf 'obsolete SWO class' 'obsolete covdesc file' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000505 obsolete copa 'obsolete copa' SubClassOf 'obsolete SWO class' 'obsolete copa' SubClassOf 'obsolete R software' 'obsolete copa' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000506 obsolete cosmo 'obsolete cosmo' SubClassOf 'obsolete SWO class' 'obsolete cosmo' SubClassOf 'obsolete R software' 'obsolete cosmo' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000503 obsolete Concordance 'obsolete Concordance' SubClassOf 'obsolete SWO class' 'obsolete Concordance' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000504 obsolete convert 'obsolete convert' SubClassOf 'obsolete SWO class' 'obsolete convert' SubClassOf 'obsolete BioConductor Software' 'obsolete convert' SubClassOf 'obsolete R software' http://edamontology.org/format_1478 PDBML 'PDBML' SubClassOf http://edamontology.org/format_1475 http://www.ebi.ac.uk/efo/swo/SWO_0000501 obsolete 'codelink' 'obsolete 'codelink'' SubClassOf 'obsolete SWO class' 'obsolete 'codelink'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000502 obsolete dataset comparison 'obsolete dataset comparison' SubClassOf 'obsolete SWO class' 'obsolete dataset comparison' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000510 obsolete crlmm 'obsolete crlmm' SubClassOf 'obsolete SWO class' 'obsolete crlmm' SubClassOf 'obsolete R software' 'obsolete crlmm' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000473 arrayQuality 'arrayQuality' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'arrayQuality' SubClassOf 'is encoded in' some 'R language' 'arrayQuality' SubClassOf 'has specified data input' some ('Gene list' and 'Graph plot') 'arrayQuality' SubClassOf 'software' 'arrayQuality' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000472 arrayMvout 'arrayMvout' SubClassOf 'has specified data input' some 'MAQC data' 'arrayMvout' SubClassOf 'is encoded in' some 'R language' 'arrayMvout' SubClassOf 'BioConductor Software' 'arrayMvout' SubClassOf 'software' 'arrayMvout' SubClassOf 'R software' 'arrayMvout' SubClassOf 'is published by' value 'Bioconductor' 'arrayMvout' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only ('R data frame' and 'PNG'))) http://www.ebi.ac.uk/swo/SWO_0000475 arrayWoRx 2.0 'arrayWoRx 2.0' SubClassOf 'arrayWoRx' http://www.ebi.ac.uk/swo/SWO_0000474 arrayQualityMetrics 'arrayQualityMetrics' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'arrayQualityMetrics' SubClassOf 'R software' 'arrayQualityMetrics' SubClassOf 'is encoded in' some 'R language' 'arrayQualityMetrics' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'arrayQualityMetrics' SubClassOf 'BioConductor Software' 'arrayQualityMetrics' SubClassOf 'is published by' value 'Bioconductor' 'arrayQualityMetrics' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000477 Associative T method 'Associative T method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000476 arrayWoRx 'arrayWoRx' SubClassOf 'is published by' value 'Applied Precision Life Science' 'arrayWoRx' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000479 'beadarray' ''beadarray'' SubClassOf 'R software' ''beadarray'' SubClassOf 'has specified data input' some 'Text data set' ''beadarray'' SubClassOf 'is encoded in' some 'R language' ''beadarray'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000478 AvgNRRs 'AvgNRRs' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000471 aroma.light 'aroma.light' SubClassOf 'has specified data output' some 'Graph plot' 'aroma.light' SubClassOf 'is encoded in' some 'R language' 'aroma.light' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'aroma.light' SubClassOf 'is published by' value 'Bioconductor' 'aroma.light' SubClassOf 'software' 'aroma.light' SubClassOf 'BioConductor Software' 'aroma.light' SubClassOf 'R software' 'aroma.light' SubClassOf 'is executed in' some ('averaging' and 'correction' and 'data normalization') http://www.ebi.ac.uk/swo/SWO_0000470 'apComplex' ''apComplex'' SubClassOf 'R software' ''apComplex'' SubClassOf 'software' ''apComplex'' SubClassOf 'is encoded in' some 'R language' ''apComplex'' SubClassOf 'has specified data output' some 'Graph plot' ''apComplex'' SubClassOf 'implements' some 'PCMG' ''apComplex'' SubClassOf 'has specified data input' some 'AP-MS data' http://www.ebi.ac.uk/swo/license/SWO_1000067 CC BY 2.0 UK 'CC BY 2.0 UK' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'CC BY 2.0 UK' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'CC BY 2.0 UK' SubClassOf 'has clause' some 'Source code available' 'CC BY 2.0 UK' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY 2.0 UK' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY 2.0 UK' SubClassOf 'has clause' some 'Usage unrestricted' 'CC BY 2.0 UK' SubClassOf 'has clause' some 'Attribution required' 'CC BY 2.0 UK' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY 2.0 UK' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY 2.0 UK' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY 2.0 UK' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by/2.0/uk/" 'CC BY 2.0 UK' SubClassOf 'has clause' some 'Derivatives allowed' http://www.ebi.ac.uk/swo/license/SWO_1000068 GNU LGPL v3 'GNU LGPL v3' SubClassOf 'has clause' some ('Free' or 'Not Free') 'GNU LGPL v3' SubClassOf 'is compatible license of' some 'GNU GPL v3' http://www.ebi.ac.uk/efo/swo/SWO_0000518 obsolete dcf 'obsolete dcf' SubClassOf 'obsolete SWO class' 'obsolete dcf' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/efo/swo/SWO_0000519 obsolete design file 'obsolete design file' SubClassOf 'obsolete SWO class' 'obsolete design file' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000516 obsolete .data 'obsolete .data' SubClassOf 'obsolete SWO class' 'obsolete .data' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/license/SWO_1000061 free to use license 'free to use license' SubClassOf 'has clause' some 'Usage unrestricted' http://www.ebi.ac.uk/efo/swo/SWO_0000514 obsolete daMA 'obsolete daMA' SubClassOf 'obsolete SWO class' 'obsolete daMA' SubClassOf 'obsolete R software' 'obsolete daMA' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000512 obsolete ctc 'obsolete ctc' SubClassOf 'obsolete SWO class' 'obsolete ctc' SubClassOf 'obsolete R software' 'obsolete ctc' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000513 obsolete dChip 'obsolete dChip' SubClassOf 'obsolete SWO class' 'obsolete dChip' SubClassOf 'software' http://www.ebi.ac.uk/swo/license/SWO_1000065 CC BY 4.0 'CC BY 4.0' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY 4.0' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY 4.0' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'CC BY 4.0' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'CC BY 4.0' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY 4.0' SubClassOf 'has clause' some 'Source code available' 'CC BY 4.0' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY 4.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY 4.0' SubClassOf 'has clause' some 'Restrictions on derivative software' 'CC BY 4.0' SubClassOf 'has website homepage' value "http://creativecommons.org/licenses/by/4.0/" 'CC BY 4.0' SubClassOf 'has clause' some 'Usage unrestricted' 'CC BY 4.0' SubClassOf 'has clause' some 'Distribution unrestricted' http://www.ebi.ac.uk/efo/swo/SWO_0000521 obsolete 'domainsignatures' 'obsolete 'domainsignatures'' SubClassOf 'obsolete SWO class' 'obsolete 'domainsignatures'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000484 Bitmap object 'Bitmap object' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000522 obsolete 'dualKS' 'obsolete 'dualKS'' SubClassOf 'obsolete SWO class' 'obsolete 'dualKS'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000483 bgx 'bgx' SubClassOf 'is encoded in' some 'R language' 'bgx' SubClassOf 'BioConductor Software' 'bgx' SubClassOf 'R software' 'bgx' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'bgx' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'bgx' SubClassOf 'is published by' value 'Bioconductor' 'bgx' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000002 licence software license 'software license' EquivalentTo inverse ('has license') some 'software' http://www.ebi.ac.uk/swo/SWO_0000486 'biocDatasets' ''biocDatasets'' SubClassOf 'is encoded in' some 'R language' ''biocDatasets'' SubClassOf 'software' ''biocDatasets'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000001 software 'software' SubClassOf 'is executed in' some 'data transformation' http://www.ebi.ac.uk/efo/swo/SWO_0000520 obsolete 'diffGeneAnalysis' 'obsolete 'diffGeneAnalysis'' SubClassOf 'obsolete SWO class' 'obsolete 'diffGeneAnalysis'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000485 bioDist 'bioDist' SubClassOf 'implements' some (''KLD'' and ''MI'') 'bioDist' SubClassOf 'is published by' value 'Bioconductor' 'bioDist' SubClassOf 'BioConductor Software' 'bioDist' SubClassOf 'R software' 'bioDist' SubClassOf 'software' 'bioDist' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'bioDist' SubClassOf 'is encoded in' some 'R language' 'bioDist' SubClassOf 'is executed in' some 'distance calculation' http://www.ebi.ac.uk/swo/SWO_0000004 Microsoft Excel 2007 'Microsoft Excel 2007' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'XLS spreadsheet')) 'Microsoft Excel 2007' SubClassOf 'directly followed by' some 'Microsoft Excel for Windows 2010' 'Microsoft Excel 2007' SubClassOf 'has version' value 'Microsoft 2007 version' 'Microsoft Excel 2007' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'tab delimited file format')) 'Microsoft Excel 2007' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'tab delimited file format')) 'Microsoft Excel 2007' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'XLS spreadsheet')) 'Microsoft Excel 2007' SubClassOf 'has release date' value "2007-01-30T0:00:00" 'Microsoft Excel 2007' SubClassOf 'has website homepage' value "http://office.microsoft.com/" 'Microsoft Excel 2007' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'XML spreadsheet')) http://www.ebi.ac.uk/swo/SWO_0000488 'biocViews' ''biocViews'' SubClassOf 'has specified data output' some 'HTML report' ''biocViews'' SubClassOf 'software' ''biocViews'' SubClassOf 'is encoded in' some 'R language' ''biocViews'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000003 obsolete information processing 'obsolete information processing' SubClassOf 'obsolete SWO class' 'obsolete information processing' SubClassOf http://purl.obolibrary.org/obo/BFO_0000007 http://www.ebi.ac.uk/swo/SWO_0000487 'biocGraph' ''biocGraph'' SubClassOf 'software' ''biocGraph'' SubClassOf 'is encoded in' some 'R language' ''biocGraph'' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') ''biocGraph'' SubClassOf 'has specified data input' some 'Graph plot' ''biocGraph'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000006 Protege 4 'Protege 4' SubClassOf 'has specified data input' some ('Ontology' and ('has format specification' some 'RDF-XML')) 'Protege 4' SubClassOf 'has specified data output' some ('Ontology' and ('has format specification' some 'RDF-XML')) 'Protege 4' SubClassOf 'output of' some ('software development' and ('has participant' value 'Stanford University')) 'Protege 4' SubClassOf 'has specified data input' some ('Ontology' and ('has format specification' some 'OWL2-XML')) 'Protege 4' SubClassOf 'has website homepage' value "http://protege.stanford.edu/" 'Protege 4' SubClassOf 'has specified data input' some ('Ontology' and ('has format specification' some 'OWL-XML')) 'Protege 4' SubClassOf 'software' 'Protege 4' SubClassOf 'has license' some 'MPL v1.1' 'Protege 4' SubClassOf 'is executed in' some 'ontology engineering' 'Protege 4' SubClassOf 'has interface' some 'graphical user interface' 'Protege 4' SubClassOf 'has specified data output' some ('Ontology' and ('has format specification' some 'OWL-XML')) 'Protege 4' SubClassOf 'has specified data output' some ('Ontology' and ('has format specification' some 'OWL2-XML')) 'Protege 4' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Stanford University')) http://www.ebi.ac.uk/swo/SWO_0000005 MATLAB 'MATLAB' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'MathWorks')) 'MATLAB' SubClassOf 'has website homepage' value "http://www.mathworks.com/products/matlab/" 'MATLAB' SubClassOf 'is executed in' some 'matrix manipulation' 'MATLAB' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'Matlab .m file')) 'MATLAB' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'Matlab .m file')) 'MATLAB' SubClassOf 'output of' some ('software development' and ('has participant' value 'MathWorks')) 'MATLAB' SubClassOf 'has license' some 'Proprietary commercial software license' http://www.ebi.ac.uk/swo/SWO_0000489 biomaRT 'biomaRT' SubClassOf 'has specified data input' some ('has format specification' only 'FASTA format') 'biomaRT' SubClassOf 'BioConductor Software' 'biomaRT' SubClassOf 'software' 'biomaRT' SubClassOf 'is published by' value 'Bioconductor' 'biomaRT' SubClassOf 'R software' 'biomaRT' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000480 'beadarraySNP' ''beadarraySNP'' SubClassOf 'is encoded in' some 'R language' ''beadarraySNP'' SubClassOf 'software' ''beadarraySNP'' SubClassOf 'has specified data input' some 'Text data set' ''beadarraySNP'' SubClassOf 'has specified data output' some 'Graph plot' ''beadarraySNP'' SubClassOf 'is executed in' some 'data normalization' ''beadarraySNP'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000482 bgafun 'bgafun' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'bgafun' SubClassOf 'is published by' value 'Bioconductor' 'bgafun' SubClassOf 'BioConductor Software' 'bgafun' SubClassOf 'has specified data input' some ('has format specification' only 'FASTA format') 'bgafun' SubClassOf 'R software' 'bgafun' SubClassOf 'software' 'bgafun' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000481 'betr' ''betr'' SubClassOf 'has specified data input' some 'Gene list' ''betr'' SubClassOf 'R software' ''betr'' SubClassOf 'BioConductor Software' ''betr'' SubClassOf 'is published by' value 'Bioconductor' ''betr'' SubClassOf 'implements' some 'Bayesian Model' ''betr'' SubClassOf 'is encoded in' some 'R language' ''betr'' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') ''betr'' SubClassOf 'software' ''betr'' SubClassOf 'is executed in' some 'differential expression analysis' http://www.ebi.ac.uk/swo/license/SWO_1000055 MPL v2.0 Mozilla Public License Version 2.0 'Mozilla Public License Version 2.0' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'Mozilla Public License Version 2.0' SubClassOf 'is compatible license of' some 'GNU LGPL v2.1' 'Mozilla Public License Version 2.0' SubClassOf 'has clause' some 'Usage unrestricted' 'Mozilla Public License Version 2.0' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'Mozilla Public License Version 2.0' SubClassOf 'is compatible license of' some 'GNU LGPL v3' 'Mozilla Public License Version 2.0' SubClassOf 'is compatible license of' some 'GNU AGPL v3' http://www.ebi.ac.uk/swo/license/SWO_1000057 Artistic License 2.0 'Artistic License 2.0' SubClassOf 'has clause' some 'Distribution with notices' 'Artistic License 2.0' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'Artistic License 2.0' SubClassOf 'has clause' some 'Derivatives allowed' 'Artistic License 2.0' SubClassOf 'has clause' some 'Free' 'Artistic License 2.0' SubClassOf 'has clause' some 'Usage unrestricted' 'Artistic License 2.0' SubClassOf 'has clause' some 'Source code available' 'Artistic License 2.0' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'Artistic License 2.0' SubClassOf 'has website homepage' value "https://opensource.org/licenses/Artistic-2.0" http://www.ebi.ac.uk/efo/swo/SWO_0000529 obsolete 'explorase' 'obsolete 'explorase'' SubClassOf 'obsolete SWO class' 'obsolete 'explorase'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000008 Racket 'Racket' SubClassOf 'has license' some 'GNU GPL' 'Racket' SubClassOf 'output of' some ('software development' and ('has participant' value 'PLT Scheme Inc')) http://www.ebi.ac.uk/swo/SWO_0000007 OmniOutliner 'OmniOutliner' SubClassOf 'has license' some 'Proprietary commercial software license' 'OmniOutliner' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'OmniOutline format')) 'OmniOutliner' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Omni')) 'OmniOutliner' SubClassOf 'has website homepage' value "http://www.omnigroup.com/products/omnioutliner/" 'OmniOutliner' SubClassOf 'output of' some ('software development' and ('has participant' value 'Omni')) 'OmniOutliner' SubClassOf 'is executed in' some 'document outlining' http://www.ebi.ac.uk/efo/swo/SWO_0000527 obsolete 'edgeR' 'obsolete 'edgeR'' SubClassOf 'obsolete SWO class' 'obsolete 'edgeR'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000528 obsolete exonmap 'obsolete exonmap' SubClassOf 'obsolete SWO class' 'obsolete exonmap' SubClassOf 'obsolete BioConductor Software' 'obsolete exonmap' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000009 Kakadu 'Kakadu' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'JPEG 2000')) 'Kakadu' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'image format')) 'Kakadu' SubClassOf 'software' 'Kakadu' SubClassOf 'has website homepage' value "http://www.kakadusoftware.com" 'Kakadu' SubClassOf 'is executed in' some 'image compression' 'Kakadu' SubClassOf 'has interface' some 'graphical user interface' http://www.ebi.ac.uk/swo/license/SWO_1000050 CC BY 2.0 'CC BY 2.0' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'CC BY 2.0' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'CC BY 2.0' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY 2.0' SubClassOf 'has clause' some 'Usage unrestricted' 'CC BY 2.0' SubClassOf 'has clause' some 'Source code available' 'CC BY 2.0' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY 2.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY 2.0' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY 2.0' SubClassOf 'has website homepage' value "http://creativecommons.org/licenses/by/2.0/" 'CC BY 2.0' SubClassOf 'has clause' some 'Derivatives allowed' http://www.ebi.ac.uk/efo/swo/SWO_0000525 obsolete ecolitk 'obsolete ecolitk' SubClassOf 'obsolete SWO class' 'obsolete ecolitk' SubClassOf 'obsolete BioConductor Software' 'obsolete ecolitk' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000526 obsolete edd 'obsolete edd' SubClassOf 'obsolete SWO class' 'obsolete edd' SubClassOf 'obsolete R software' 'obsolete edd' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/license/SWO_1000052 CC BY-SA 2.0 'CC BY-SA 2.0' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-sa/2.0/" 'CC BY-SA 2.0' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-SA 2.0' SubClassOf 'has clause' some 'Source code available' 'CC BY-SA 2.0' SubClassOf 'has clause' some 'Usage unrestricted' 'CC BY-SA 2.0' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-SA 2.0' SubClassOf 'has clause' some 'Copyleft' 'CC BY-SA 2.0' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/efo/swo/SWO_0000523 obsolete dyebias 'obsolete dyebias' SubClassOf 'obsolete SWO class' 'obsolete dyebias' SubClassOf 'obsolete R software' 'obsolete dyebias' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/license/SWO_1000053 LPPL v1.3c 'LPPL v1.3c' SubClassOf 'has website homepage' value "https://latex-project.org/lppl/lppl-1-3c.html" 'LPPL v1.3c' SubClassOf 'is compatible license of' some ('GNU GPL v2' or (not ('GNU GPL v3'))) http://www.ebi.ac.uk/efo/swo/SWO_0000524 obsolete Dynamic programming algorithm 'obsolete Dynamic programming algorithm' SubClassOf 'obsolete SWO class' 'obsolete Dynamic programming algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/license/SWO_1000054 LPPL v1.2 'LPPL v1.2' SubClassOf 'is compatible license of' some ('GNU GPL v2' or (not ('GNU GPL v3'))) 'LPPL v1.2' SubClassOf 'has website homepage' value "https://latex-project.org/lppl/lppl-1-2.html" http://www.ebi.ac.uk/efo/swo/SWO_0000532 obsolete factDesign 'obsolete factDesign' SubClassOf 'obsolete SWO class' 'obsolete factDesign' SubClassOf 'obsolete BioConductor Software' 'obsolete factDesign' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000011 IntelliJ IDEA 'IntelliJ IDEA' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some '.java file')) 'IntelliJ IDEA' SubClassOf 'is executed in' some 'software development' 'IntelliJ IDEA' SubClassOf 'has website homepage' value "http://www.jetbrains.com/idea/" 'IntelliJ IDEA' SubClassOf 'has license' some ('Proprietary commercial software license' or 'Apache License Version 2.0') 'IntelliJ IDEA' SubClassOf 'has interface' some 'graphical user interface' 'IntelliJ IDEA' SubClassOf 'output of' some ('software development' and ('has participant' value 'JetBrains')) 'IntelliJ IDEA' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some '.java file')) http://www.ebi.ac.uk/swo/SWO_0000495 'cellHTS2' ''cellHTS2'' SubClassOf 'has specified data input' some 'Text data set' ''cellHTS2'' SubClassOf 'is executed in' some ('data annotation' and 'data normalization' and 'descriptive statistical calculation') ''cellHTS2'' SubClassOf 'R software' ''cellHTS2'' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') ''cellHTS2'' SubClassOf 'is encoded in' some 'R language' ''cellHTS2'' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000533 obsolete fbat 'obsolete fbat' SubClassOf 'obsolete SWO class' 'obsolete fbat' SubClassOf 'obsolete BioConductor Software' 'obsolete fbat' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000010 WordStar 'WordStar' SubClassOf 'has interface' some 'graphical user interface' 'WordStar' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'MicroPro International')) 'WordStar' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'WordStar format')) 'WordStar' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'WordStar format')) 'WordStar' SubClassOf 'is executed in' some 'word processing' http://www.ebi.ac.uk/swo/SWO_0000494 'cellHTS' ''cellHTS'' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') ''cellHTS'' SubClassOf 'is encoded in' some 'R language' ''cellHTS'' SubClassOf 'R software' ''cellHTS'' SubClassOf 'has specified data input' some 'Text data set' ''cellHTS'' SubClassOf 'software' ''cellHTS'' SubClassOf 'is executed in' some ('data normalization' and 'descriptive statistical calculation') http://www.ebi.ac.uk/efo/swo/SWO_0000530 obsolete 'externalVector' 'obsolete 'externalVector'' SubClassOf 'obsolete SWO class' 'obsolete 'externalVector'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000013 COPASI 'COPASI' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'SBML')) 'COPASI' SubClassOf 'has license' only 'Artistic License 2.0' 'COPASI' SubClassOf 'has website homepage' value "http://www.copasi.org" 'COPASI' SubClassOf 'uses platform' some 'Microsoft Windows' 'COPASI' SubClassOf 'uses platform' some 'OS X' 'COPASI' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'SBML')) 'COPASI' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'CopasiML')) 'COPASI' SubClassOf 'implements' some 'ODE Algorithm' 'COPASI' SubClassOf 'uses platform' some 'Linux' 'COPASI' SubClassOf 'has license' some 'Artistic License 2.0' 'COPASI' SubClassOf 'implements' some 'Gillespie's Stochastic Simulation Algorithm' 'COPASI' SubClassOf 'is executed in' some 'simulation and analysis of biochemical networks' http://www.ebi.ac.uk/swo/SWO_0000497 chamber slide format 'chamber slide format' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000531 obsolete f-test 'obsolete f-test' SubClassOf 'obsolete SWO class' 'obsolete f-test' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000012 Java 'Java' SubClassOf 'has website homepage' value "http://www.java.com" http://www.ebi.ac.uk/swo/SWO_0000496 cghMCR 'cghMCR' SubClassOf 'is published by' value 'Bioconductor' 'cghMCR' SubClassOf 'R software' 'cghMCR' SubClassOf 'implements' some 'MCR algorithm' 'cghMCR' SubClassOf 'software' 'cghMCR' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'cghMCR' SubClassOf 'BioConductor Software' 'cghMCR' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'cghMCR' SubClassOf 'is executed in' some 'data normalization' 'cghMCR' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000015 Microsoft Excel 2002 'Microsoft Excel 2002' SubClassOf 'has version' value 'Microsoft 2002 version' 'Microsoft Excel 2002' SubClassOf 'software before Microsoft 2007' 'Microsoft Excel 2002' SubClassOf 'obsolete software before Microsoft 2007' http://www.ebi.ac.uk/swo/SWO_0000499 'clusterStab' ''clusterStab'' SubClassOf 'software' ''clusterStab'' SubClassOf 'is encoded in' some 'R language' ''clusterStab'' SubClassOf 'has specified data output' some ('Heat map' and 'Graph plot') ''clusterStab'' SubClassOf 'R software' ''clusterStab'' SubClassOf 'implements' some 'Hierarchical clustering' ''clusterStab'' SubClassOf 'has specified data input' some 'Gene list' ''clusterStab'' SubClassOf 'is executed in' some ('decision tree induction' and 'differential expression analysis') http://www.ebi.ac.uk/swo/SWO_0000014 Microsoft Excel 2003 'Microsoft Excel 2003' SubClassOf 'software before Microsoft 2007' 'Microsoft Excel 2003' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'XML spreadsheet')) 'Microsoft Excel 2003' SubClassOf 'has version' value 'Microsoft 2003 version' 'Microsoft Excel 2003' SubClassOf 'obsolete software before Microsoft 2007' http://www.ebi.ac.uk/swo/SWO_0000498 cls 'cls' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_0000017 MATLAB 6 'MATLAB 6' SubClassOf 'has version' value 'Matlab R12' http://www.ebi.ac.uk/swo/SWO_0000016 MATLAB 7 'MATLAB 7' SubClassOf 'has version' value 'Matlab R14' http://www.ebi.ac.uk/swo/SWO_0000491 'bridge' ''bridge'' SubClassOf 'software' ''bridge'' SubClassOf 'implements' some ('Markov Chain Monte Carlo' and 'Bayesian Model') ''bridge'' SubClassOf 'R software' ''bridge'' SubClassOf 'is executed in' some 'differential expression analysis' ''bridge'' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000490 Bootstrap 'Bootstrap' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000493 cdt 'cdt' SubClassOf 'tab delimited file format' http://www.ebi.ac.uk/swo/license/SWO_1000088 CC BY-NC-SA 3.0 US 'CC BY-NC-SA 3.0 US' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-nc-sa/3.0/us/" 'CC BY-NC-SA 3.0 US' SubClassOf 'has clause' some 'Free' 'CC BY-NC-SA 3.0 US' SubClassOf 'has clause' some 'Non-commercial use only' 'CC BY-NC-SA 3.0 US' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY-NC-SA 3.0 US' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY-NC-SA 3.0 US' SubClassOf 'has clause' some 'Derivatives allowed' 'CC BY-NC-SA 3.0 US' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-NC-SA 3.0 US' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY-NC-SA 3.0 US' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY-NC-SA 3.0 US' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-NC-SA 3.0 US' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/swo/license/SWO_1000089 CC BY-NC-SA 2.5 IN 'CC BY-NC-SA 2.5 IN' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-NC-SA 2.5 IN' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY-NC-SA 2.5 IN' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-nc-sa/2.5/in/" 'CC BY-NC-SA 2.5 IN' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-NC-SA 2.5 IN' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY-NC-SA 2.5 IN' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY-NC-SA 2.5 IN' SubClassOf 'has clause' some 'Free' 'CC BY-NC-SA 2.5 IN' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY-NC-SA 2.5 IN' SubClassOf 'has clause' some 'Non-commercial use only' 'CC BY-NC-SA 2.5 IN' SubClassOf 'has clause' some 'Derivatives allowed' 'CC BY-NC-SA 2.5 IN' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/swo/SWO_0000019 STARLIMS 'STARLIMS' SubClassOf 'is executed in' some 'laboratory information management' http://www.ebi.ac.uk/swo/license/SWO_1000080 CC BY-NC 4.0 'CC BY-NC 4.0' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY-NC 4.0' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY-NC 4.0' SubClassOf 'has clause' some 'Derivatives allowed' 'CC BY-NC 4.0' SubClassOf 'has clause' some 'Non-commercial use only' 'CC BY-NC 4.0' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-nc/4.0/" 'CC BY-NC 4.0' SubClassOf 'has clause' some 'Free' 'CC BY-NC 4.0' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-NC 4.0' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-NC 4.0' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY-NC 4.0' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY-NC 4.0' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/swo/SWO_0000018 MATLAB 7.12 'MATLAB 7.12' SubClassOf 'has version' value 'R2011a' http://www.ebi.ac.uk/swo/license/SWO_1000081 CC BY-NC-ND 3.0 'CC BY-NC-ND 3.0' SubClassOf 'has clause' some 'Non-commercial use only' 'CC BY-NC-ND 3.0' SubClassOf 'has clause' some 'Free' 'CC BY-NC-ND 3.0' SubClassOf 'has clause' some 'Derivatives not allowed' 'CC BY-NC-ND 3.0' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY-NC-ND 3.0' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-nc-nd/3.0/" 'CC BY-NC-ND 3.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY-NC-ND 3.0' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-NC-ND 3.0' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY-NC-ND 3.0' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY-NC-ND 3.0' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-NC-ND 3.0' SubClassOf 'has clause' some 'Number of installations unrestricted' http://www.ebi.ac.uk/efo/swo/SWO_0000538 obsolete flowCore 'obsolete flowCore' SubClassOf 'obsolete SWO class' 'obsolete flowCore' SubClassOf 'obsolete R software' 'obsolete flowCore' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000539 obsolete flowFlowJo 'obsolete flowFlowJo' SubClassOf 'obsolete SWO class' 'obsolete flowFlowJo' SubClassOf 'obsolete R software' 'obsolete flowFlowJo' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/license/SWO_1000083 CC BY-NC-ND 2.5 'CC BY-NC-ND 2.5' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY-NC-ND 2.5' SubClassOf 'has clause' some 'Free' 'CC BY-NC-ND 2.5' SubClassOf 'has clause' some 'Attribution required' 'CC BY-NC-ND 2.5' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-nc-nd/2.5/" 'CC BY-NC-ND 2.5' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY-NC-ND 2.5' SubClassOf 'has clause' some 'Non-commercial use only' 'CC BY-NC-ND 2.5' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-NC-ND 2.5' SubClassOf 'has clause' some 'Derivatives not allowed' 'CC BY-NC-ND 2.5' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY-NC-ND 2.5' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-NC-ND 2.5' SubClassOf 'has clause' some 'Number of users unrestricted' http://www.ebi.ac.uk/efo/swo/SWO_0000536 obsolete flagme 'obsolete flagme' SubClassOf 'obsolete SWO class' 'obsolete flagme' SubClassOf 'obsolete BioConductor Software' 'obsolete flagme' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/license/SWO_1000084 CC BY-NC-ND 2.5 CH 'CC BY-NC-ND 2.5 CH' SubClassOf 'has website homepage' value "http://creativecommons.org/licenses/by-nc-nd/2.5/ch/deed.en" 'CC BY-NC-ND 2.5 CH' SubClassOf 'has clause' some 'Non-commercial use only' 'CC BY-NC-ND 2.5 CH' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY-NC-ND 2.5 CH' SubClassOf 'has clause' some 'Free' 'CC BY-NC-ND 2.5 CH' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-NC-ND 2.5 CH' SubClassOf 'has clause' some 'Derivatives not allowed' 'CC BY-NC-ND 2.5 CH' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY-NC-ND 2.5 CH' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY-NC-ND 2.5 CH' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-NC-ND 2.5 CH' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY-NC-ND 2.5 CH' SubClassOf 'has clause' some 'Attribution required' http://www.ebi.ac.uk/efo/swo/SWO_0000537 obsolete flowClust 'obsolete flowClust' SubClassOf 'obsolete SWO class' 'obsolete flowClust' SubClassOf 'obsolete R software' 'obsolete flowClust' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/license/SWO_1000085 CC BY-NC-ND 4.0 'CC BY-NC-ND 4.0' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY-NC-ND 4.0' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY-NC-ND 4.0' SubClassOf 'has clause' some 'Non-commercial use only' 'CC BY-NC-ND 4.0' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY-NC-ND 4.0' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-NC-ND 4.0' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY-NC-ND 4.0' SubClassOf 'has clause' some 'Free' 'CC BY-NC-ND 4.0' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-nc-nd/4.0/" 'CC BY-NC-ND 4.0' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-NC-ND 4.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY-NC-ND 4.0' SubClassOf 'has clause' some 'Derivatives not allowed' http://www.ebi.ac.uk/efo/swo/SWO_0000534 obsolete fdrame 'obsolete fdrame' SubClassOf 'obsolete SWO class' 'obsolete fdrame' SubClassOf 'obsolete R software' 'obsolete fdrame' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/license/SWO_1000086 CC BY-NC-SA 2.5 'CC BY-NC-SA 2.5' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY-NC-SA 2.5' SubClassOf 'has clause' some 'Free' 'CC BY-NC-SA 2.5' SubClassOf 'has clause' some 'Non-commercial use only' 'CC BY-NC-SA 2.5' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-NC-SA 2.5' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-NC-SA 2.5' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-nc-sa/2.5/" 'CC BY-NC-SA 2.5' SubClassOf 'has clause' some 'Attribution required' 'CC BY-NC-SA 2.5' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY-NC-SA 2.5' SubClassOf 'has clause' some 'Derivatives allowed' 'CC BY-NC-SA 2.5' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY-NC-SA 2.5' SubClassOf 'has clause' some 'Number of users unrestricted' http://www.ebi.ac.uk/swo/license/SWO_1000087 CC BY-NC-SA 3.0 'CC BY-NC-SA 3.0' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY-NC-SA 3.0' SubClassOf 'has clause' some 'Non-commercial use only' 'CC BY-NC-SA 3.0' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-NC-SA 3.0' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY-NC-SA 3.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY-NC-SA 3.0' SubClassOf 'has clause' some 'Free' 'CC BY-NC-SA 3.0' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-NC-SA 3.0' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY-NC-SA 3.0' SubClassOf 'has clause' some 'Derivatives allowed' 'CC BY-NC-SA 3.0' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY-NC-SA 3.0' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-nc-sa/3.0/" http://www.ebi.ac.uk/efo/swo/SWO_0000543 obsolete flowViz 'obsolete flowViz' SubClassOf 'obsolete SWO class' 'obsolete flowViz' SubClassOf 'obsolete BioConductor Software' 'obsolete flowViz' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000022 Linux 'Linux' SubClassOf 'has interface' some 'command-line interface' 'Linux' SubClassOf 'is executed in' some 'manage computer operations' 'Linux' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000544 obsolete gaga 'obsolete gaga' SubClassOf 'obsolete SWO class' 'obsolete gaga' SubClassOf 'obsolete BioConductor Software' 'obsolete gaga' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000021 operating system 'operating system' EquivalentTo 'is executed in' some 'manage computer operations' http://www.ebi.ac.uk/efo/swo/SWO_0000541 obsolete flowStats 'obsolete flowStats' SubClassOf 'obsolete SWO class' 'obsolete flowStats' SubClassOf 'obsolete R software' 'obsolete flowStats' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000024 Adobe Illustrator 10 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'BMP')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'pdf')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'pdf')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'SVG')) 'Adobe Illustrator 10' SubClassOf 'output of' some ('software development' and ('has participant' value 'Adobe Systems')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'SVG')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'DXF')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'DWG')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'Microsoft Word doc')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'AI')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'CGM')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'DXF')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'JPEG')) 'Adobe Illustrator 10' SubClassOf 'software' 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'BMP')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'AI')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'DWG')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'TIFF')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'GIF')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'JPEG')) 'Adobe Illustrator 10' SubClassOf 'has interface' some 'graphical user interface' 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'PNG')) http://www.ebi.ac.uk/efo/swo/SWO_0000542 obsolete flowUtils 'obsolete flowUtils' SubClassOf 'obsolete SWO class' 'obsolete flowUtils' SubClassOf 'obsolete BioConductor Software' 'obsolete flowUtils' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000026 software with image input 'software with image input' EquivalentTo 'has specified data input' some ('data item' and ('has format specification' some 'image format')) http://www.ebi.ac.uk/swo/objective/SWO_40000002 matrix manipulation 'matrix manipulation' SubClassOf 'data transformation' 'matrix manipulation' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000540 obsolete flowQ 'obsolete flowQ' SubClassOf 'obsolete SWO class' 'obsolete flowQ' SubClassOf 'obsolete BioConductor Software' 'obsolete flowQ' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000025 Microsoft Word 'Microsoft Word' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'Microsoft Word doc')) 'Microsoft Word' SubClassOf 'is executed in' some 'word processing' 'Microsoft Word' SubClassOf 'output of' some ('software development' and ('has participant' value 'Microsoft')) 'Microsoft Word' SubClassOf 'has interface' some 'graphical user interface' 'Microsoft Word' SubClassOf 'software' 'Microsoft Word' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'Microsoft Word doc')) 'Microsoft Word' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Microsoft')) http://www.ebi.ac.uk/swo/SWO_0000028 ontology engineering software 'ontology engineering software' EquivalentTo 'is executed in' some 'ontology engineering' http://www.ebi.ac.uk/swo/SWO_0000027 OBO-Edit 'OBO-Edit' SubClassOf 'is executed in' some 'ontology engineering' 'OBO-Edit' SubClassOf 'software' 'OBO-Edit' SubClassOf 'has specified data output' some ('Ontology' and ('has format specification' some 'OBO Flat File Format')) 'OBO-Edit' SubClassOf 'has interface' some 'graphical user interface' 'OBO-Edit' SubClassOf 'has website homepage' value "http://oboedit.org/" 'OBO-Edit' SubClassOf 'has specified data input' some ('Ontology' and ('has format specification' some 'OBO Flat File Format')) http://www.ebi.ac.uk/swo/SWO_0000020 Unix 'Unix' SubClassOf 'software' 'Unix' SubClassOf 'is executed in' some 'manage computer operations' 'Unix' SubClassOf 'has interface' some 'command-line interface' http://www.ebi.ac.uk/swo/license/SWO_1000077 CC BY-ND 3.0 'CC BY-ND 3.0' SubClassOf 'has clause' some 'Usage unrestricted' 'CC BY-ND 3.0' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY-ND 3.0' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-ND 3.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY-ND 3.0' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-ND 3.0' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY-ND 3.0' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY-ND 3.0' SubClassOf 'has clause' some 'Derivatives not allowed' 'CC BY-ND 3.0' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-nd/3.0/" 'CC BY-ND 3.0' SubClassOf 'has clause' some 'Platform unrestricted' http://www.ebi.ac.uk/swo/license/SWO_1000078 CC BY-ND 4.0 'CC BY-ND 4.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY-ND 4.0' SubClassOf 'has clause' some 'Derivatives not allowed' 'CC BY-ND 4.0' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY-ND 4.0' SubClassOf 'has clause' some 'Usage unrestricted' 'CC BY-ND 4.0' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-ND 4.0' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-ND 4.0' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY-ND 4.0' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY-ND 4.0' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY-ND 4.0' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-nd/4.0/" http://www.ebi.ac.uk/swo/license/SWO_1000079 CC BY-NC 3.0 'CC BY-NC 3.0' SubClassOf 'has clause' some 'Free' 'CC BY-NC 3.0' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY-NC 3.0' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by-nc/3.0/" 'CC BY-NC 3.0' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY-NC 3.0' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY-NC 3.0' SubClassOf 'has clause' some 'Non-commercial use only' 'CC BY-NC 3.0' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY-NC 3.0' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY-NC 3.0' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2')) 'CC BY-NC 3.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY-NC 3.0' SubClassOf 'has clause' some 'Derivatives allowed' http://www.ebi.ac.uk/swo/SWO_0000029 Microsoft developed software 'Microsoft developed software' EquivalentTo 'output of' some ('software development' and ('has participant' value 'Microsoft')) http://www.ebi.ac.uk/swo/license/SWO_1000070 GNU AGPL v3 'GNU AGPL v3' SubClassOf 'has clause' some 'Usage unrestricted' 'GNU AGPL v3' SubClassOf 'has clause' some 'Distribution with notices' 'GNU AGPL v3' SubClassOf 'has clause' some 'Source code available' 'GNU AGPL v3' SubClassOf 'is compatible license of' only (not ('GNU GPL v2')) 'GNU AGPL v3' SubClassOf 'has clause' some 'Copyleft' 'GNU AGPL v3' SubClassOf 'is compatible license of' some 'GNU GPL v3' http://www.ebi.ac.uk/efo/swo/SWO_0000549 obsolete 'genArise' 'obsolete 'genArise'' SubClassOf 'obsolete SWO class' 'obsolete 'genArise'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/license/SWO_1000071 GNU LGPL v2.1 'GNU LGPL v2.1' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'GNU LGPL v2.1' SubClassOf 'is compatible license of' some 'GNU GPL v2' http://www.ebi.ac.uk/swo/license/SWO_1000072 CC BY 2.1 JP 'CC BY 2.1 JP' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY 2.1 JP' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY 2.1 JP' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY 2.1 JP' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY 2.1 JP' SubClassOf 'has clause' some 'Usage unrestricted' 'CC BY 2.1 JP' SubClassOf 'has clause' some 'Source code available' 'CC BY 2.1 JP' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'CC BY 2.1 JP' SubClassOf 'has website homepage' value "http://creativecommons.org/licenses/by/2.1/jp/deed.en" 'CC BY 2.1 JP' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'CC BY 2.1 JP' SubClassOf 'has clause' some 'Attribution required' 'CC BY 2.1 JP' SubClassOf 'has clause' some 'Derivatives allowed' 'CC BY 2.1 JP' SubClassOf 'has clause' some 'Platform unrestricted' http://www.ebi.ac.uk/efo/swo/SWO_0000547 obsolete gcrma 'obsolete gcrma' SubClassOf 'obsolete SWO class' 'obsolete gcrma' SubClassOf 'obsolete R software' 'obsolete gcrma' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/license/SWO_1000073 CC BY 2.5 'CC BY 2.5' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY 2.5' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY 2.5' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY 2.5' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by/2.5/" 'CC BY 2.5' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY 2.5' SubClassOf 'has clause' some 'Derivatives allowed' 'CC BY 2.5' SubClassOf 'has clause' some 'Source code available' 'CC BY 2.5' SubClassOf 'has clause' some 'Attribution required' 'CC BY 2.5' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY 2.5' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'CC BY 2.5' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'CC BY 2.5' SubClassOf 'has clause' some 'Usage unrestricted' http://www.ebi.ac.uk/efo/swo/SWO_0000548 obsolete gct 'obsolete gct' SubClassOf 'obsolete SWO class' 'obsolete gct' SubClassOf 'tab delimited file format' http://www.ebi.ac.uk/swo/license/SWO_1000074 CC BY 3.0 AU 'CC BY 3.0 AU' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY 3.0 AU' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by/3.0/au/" 'CC BY 3.0 AU' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY 3.0 AU' SubClassOf 'has clause' some 'Source code available' 'CC BY 3.0 AU' SubClassOf 'has clause' some 'Usage unrestricted' 'CC BY 3.0 AU' SubClassOf 'has clause' some 'Attribution required' 'CC BY 3.0 AU' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'CC BY 3.0 AU' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'CC BY 3.0 AU' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY 3.0 AU' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY 3.0 AU' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY 3.0 AU' SubClassOf 'has clause' some 'Derivatives allowed' http://www.ebi.ac.uk/efo/swo/SWO_0000545 obsolete 'gaggle' 'obsolete 'gaggle'' SubClassOf 'obsolete SWO class' 'obsolete 'gaggle'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/license/SWO_1000075 CC BY 3.0 'CC BY 3.0' SubClassOf 'has clause' some 'Source code available' 'CC BY 3.0' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY 3.0' SubClassOf 'has clause' some 'Derivatives allowed' 'CC BY 3.0' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'CC BY 3.0' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY 3.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY 3.0' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'CC BY 3.0' SubClassOf 'has clause' some 'Usage unrestricted' 'CC BY 3.0' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by/3.0/" 'CC BY 3.0' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY 3.0' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY 3.0' SubClassOf 'has clause' some 'Number of installations unrestricted' http://www.ebi.ac.uk/efo/swo/SWO_0000546 obsolete gcRMA quantification 'obsolete gcRMA quantification' SubClassOf 'obsolete SWO class' 'obsolete gcRMA quantification' SubClassOf 'software' http://www.ebi.ac.uk/swo/license/SWO_1000076 CC BY 3.0 US 'CC BY 3.0 US' SubClassOf 'has clause' some 'Attribution required' 'CC BY 3.0 US' SubClassOf 'has website homepage' value "https://creativecommons.org/licenses/by/3.0/us/" 'CC BY 3.0 US' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC BY 3.0 US' SubClassOf 'has clause' some 'Derivatives allowed' 'CC BY 3.0 US' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'CC BY 3.0 US' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC BY 3.0 US' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'CC BY 3.0 US' SubClassOf 'has clause' some 'Distribution with notices' 'CC BY 3.0 US' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC BY 3.0 US' SubClassOf 'has clause' some 'Platform unrestricted' 'CC BY 3.0 US' SubClassOf 'has clause' some 'Source code available' 'CC BY 3.0 US' SubClassOf 'has clause' some 'Usage unrestricted' http://www.ebi.ac.uk/efo/swo/SWO_0000554 obsolete Gene expression dataset 'obsolete Gene expression dataset' SubClassOf 'obsolete SWO class' 'obsolete Gene expression dataset' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000555 obsolete genefilter 'obsolete genefilter' SubClassOf 'obsolete SWO class' 'obsolete genefilter' SubClassOf 'obsolete R software' 'obsolete genefilter' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000552 obsolete Gene array analysis algorithm 'obsolete Gene array analysis algorithm' SubClassOf 'obsolete SWO class' 'obsolete Gene array analysis algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000553 obsolete gene expression analysis 'obsolete gene expression analysis' SubClassOf 'obsolete SWO class' 'obsolete gene expression analysis' SubClassOf 'obsolete information processing' http://www.ebi.ac.uk/swo/SWO_0000430 Spotfire 'Spotfire' SubClassOf 'is developed by' value 'TIBCO Software Inc' 'Spotfire' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000550 obsolete gene2pathway 'obsolete gene2pathway' SubClassOf 'obsolete SWO class' 'obsolete gene2pathway' SubClassOf 'obsolete BioConductor Software' 'obsolete gene2pathway' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000551 obsolete geneRecommender 'obsolete geneRecommender' SubClassOf 'obsolete SWO class' 'obsolete geneRecommender' SubClassOf 'obsolete R software' 'obsolete geneRecommender' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000432 TAS Software 'TAS Software' SubClassOf 'software' 'TAS Software' SubClassOf 'Affymetrix Software' 'TAS Software' SubClassOf 'is published by' value 'Affymetrix' http://www.ebi.ac.uk/swo/SWO_0000435 TargetSearch 'TargetSearch' SubClassOf 'is encoded in' some 'R language' 'TargetSearch' SubClassOf 'has specified data input' some 'Text data set' 'TargetSearch' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set' and ('has format specification' only 'pdf')) 'TargetSearch' SubClassOf 'software' 'TargetSearch' SubClassOf 'R software' 'TargetSearch' SubClassOf 'implements' some ('Library Search Algorithm' and 'PPC algorithm') 'TargetSearch' SubClassOf 'is published by' value 'Bioconductor' 'TargetSearch' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000437 Theodore Ts’o’s 'Theodore Ts’o’s' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000438 TypeInfo 'TypeInfo' SubClassOf 'software' 'TypeInfo' SubClassOf 'has specified data input' some ('Gene expression dataset' or ('has format specification' only 'R data frame')) 'TypeInfo' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' only 'R data frame')) 'TypeInfo' SubClassOf 'is published by' value 'Bioconductor' 'TypeInfo' SubClassOf 'BioConductor Software' 'TypeInfo' SubClassOf 'is encoded in' some 'R language' 'TypeInfo' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000558 obsolete genomeIntervals 'obsolete genomeIntervals' SubClassOf 'obsolete SWO class' 'obsolete genomeIntervals' SubClassOf 'obsolete BioConductor Software' 'obsolete genomeIntervals' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000556 obsolete genemeta 'obsolete genemeta' SubClassOf 'obsolete SWO class' 'obsolete genemeta' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000557 obsolete geneplotter 'obsolete geneplotter' SubClassOf 'obsolete SWO class' 'obsolete geneplotter' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000565 obsolete gpls 'obsolete gpls' SubClassOf 'obsolete SWO class' 'obsolete gpls' SubClassOf 'obsolete BioConductor Software' 'obsolete gpls' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000566 obsolete gpr format 'obsolete gpr format' SubClassOf 'obsolete SWO class' 'obsolete gpr format' SubClassOf 'tab delimited file format' http://www.ebi.ac.uk/efo/swo/SWO_0000563 obsolete goProfiles 'obsolete goProfiles' SubClassOf 'obsolete SWO class' 'obsolete goProfiles' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000442 VanillaICE 'VanillaICE' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'VanillaICE' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'VanillaICE' SubClassOf 'BioConductor Software' 'VanillaICE' SubClassOf 'implements' some 'Hidden Markov Model' 'VanillaICE' SubClassOf 'is published by' value 'Bioconductor' 'VanillaICE' SubClassOf 'R software' 'VanillaICE' SubClassOf 'is encoded in' some 'R language' 'VanillaICE' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000564 obsolete goTools 'obsolete goTools' SubClassOf 'obsolete SWO class' 'obsolete goTools' SubClassOf 'obsolete R software' 'obsolete goTools' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000441 Variance-stabilizing transformation (VST) algorithm 'Variance-stabilizing transformation (VST) algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000561 obsolete globaltest 'obsolete globaltest' SubClassOf 'obsolete SWO class' 'obsolete globaltest' SubClassOf 'obsolete BioConductor Software' 'obsolete globaltest' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000444 WilcEbam 'WilcEbam' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000562 obsolete gmt format 'obsolete gmt format' SubClassOf 'obsolete SWO class' 'obsolete gmt format' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000446 XDE 'XDE' SubClassOf 'is encoded in' some 'R language' 'XDE' SubClassOf 'R software' 'XDE' SubClassOf 'is published by' value 'Bioconductor' 'XDE' SubClassOf 'BioConductor Software' 'XDE' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'XDE' SubClassOf 'implements' some ('Markov Chain Monte Carlo' and 'Bayesian Model') 'XDE' SubClassOf 'is executed in' some ('cross validation' and 'differential expression analysis') 'XDE' SubClassOf 'has specified data input' some 'Gene expression dataset' 'XDE' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000560 obsolete Global test 'obsolete Global test' SubClassOf 'obsolete SWO class' 'obsolete Global test' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000445 Wilcoxon 'Wilcoxon' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/license/SWO_1000008 Open source software license 'Open source software license' EquivalentTo 'has clause' some 'Source code available' http://www.ebi.ac.uk/swo/license/SWO_1000009 License without restrictions on derivatives 'License without restrictions on derivatives' EquivalentTo 'has clause' some 'No restrictions on derivatives' http://www.ebi.ac.uk/swo/SWO_0000447 XDotsReader 'XDotsReader' SubClassOf 'software' 'XDotsReader' SubClassOf 'is developed by' value 'COSE, France' http://www.ebi.ac.uk/swo/SWO_0000449 Xba.CQV and Xba.regions 'Xba.CQV and Xba.regions' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000569 obsolete gtr 'obsolete gtr' SubClassOf 'obsolete SWO class' 'obsolete gtr' SubClassOf 'tab delimited file format' http://edamontology.org/format_3239 CopasiML 'CopasiML' SubClassOf http://edamontology.org/format_2013 'CopasiML' SubClassOf http://edamontology.org/format_3166 http://www.ebi.ac.uk/efo/swo/SWO_0000567 obsolete graph 'obsolete graph' SubClassOf 'obsolete SWO class' 'obsolete graph' SubClassOf 'obsolete R software' 'obsolete graph' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000576 obsolete Hypergeometric enrichment 'obsolete Hypergeometric enrichment' SubClassOf 'obsolete SWO class' 'obsolete Hypergeometric enrichment' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000451 Acuity 'Acuity' SubClassOf 'software' 'Acuity' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Molecular Devices')) http://www.ebi.ac.uk/efo/swo/SWO_0000577 obsolete hypergraph 'obsolete hypergraph' SubClassOf 'obsolete SWO class' 'obsolete hypergraph' SubClassOf 'obsolete BioConductor Software' 'obsolete hypergraph' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000450 Array Comparative Genomic Hybridization 'Array Comparative Genomic Hybridization' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'Array Comparative Genomic Hybridization' SubClassOf 'R software' 'Array Comparative Genomic Hybridization' SubClassOf 'is encoded in' some 'R language' 'Array Comparative Genomic Hybridization' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some http://edamontology.org/format_2330)) 'Array Comparative Genomic Hybridization' SubClassOf 'implements' some ''FDR'' 'Array Comparative Genomic Hybridization' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'sproc')) 'Array Comparative Genomic Hybridization' SubClassOf 'implements' some 'Hidden Markov Model' 'Array Comparative Genomic Hybridization' SubClassOf 'implements' some ''t-test'' 'Array Comparative Genomic Hybridization' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000574 obsolete hopach 'obsolete hopach' SubClassOf 'obsolete SWO class' 'obsolete hopach' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000453 affyContam 'affyContam' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'affyContam' SubClassOf 'R software' 'affyContam' SubClassOf 'BioConductor Software' 'affyContam' SubClassOf 'software' 'affyContam' SubClassOf 'is encoded in' some 'R language' 'affyContam' SubClassOf 'is published by' value 'Bioconductor' 'affyContam' SubClassOf 'has specified data output' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) http://www.ebi.ac.uk/efo/swo/SWO_0000575 obsolete HTML report 'obsolete HTML report' SubClassOf 'obsolete SWO class' 'obsolete HTML report' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000452 affxparser 'affxparser' SubClassOf 'is encoded in' some 'R language' 'affxparser' SubClassOf 'R software' 'affxparser' SubClassOf 'has specified data input' only 'Affymetrix-compliant data' 'affxparser' SubClassOf 'has specified data input' some 'Affymetrix-compliant data' 'affxparser' SubClassOf 'BioConductor Software' 'affxparser' SubClassOf 'software' 'affxparser' SubClassOf 'has specified data output' some 'Text data set' 'affxparser' SubClassOf 'is executed in' some 'parse' 'affxparser' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/efo/swo/SWO_0000572 obsolete hexbin 'obsolete hexbin' SubClassOf 'obsolete SWO class' 'obsolete hexbin' SubClassOf 'obsolete R software' 'obsolete hexbin' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000455 'affyPLM' ''affyPLM'' SubClassOf 'is executed in' some ('correction' and 'data normalization') ''affyPLM'' SubClassOf 'implements' some (''PLM'' and 'RMA' and 'M-estimation regression') ''affyPLM'' SubClassOf 'affypdnn' ''affyPLM'' SubClassOf 'is encoded in' some 'R language' ''affyPLM'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) ''affyPLM'' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') http://www.ebi.ac.uk/efo/swo/SWO_0000573 obsolete Hierarchical clustering 'obsolete Hierarchical clustering' SubClassOf 'obsolete SWO class' 'obsolete Hierarchical clustering' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000454 affyImGUI 'affyImGUI' SubClassOf 'software' 'affyImGUI' SubClassOf 'implements' some (''PLM'' or 'RMA') 'affyImGUI' SubClassOf 'BioConductor Software' 'affyImGUI' SubClassOf 'is encoded in' some 'R language' 'affyImGUI' SubClassOf 'is published by' value 'Bioconductor' 'affyImGUI' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000570 obsolete gxl format 'obsolete gxl format' SubClassOf 'obsolete SWO class' 'obsolete gxl format' SubClassOf 'XML' http://www.ebi.ac.uk/swo/SWO_0000457 affyQCReport 'affyQCReport' SubClassOf 'R software' 'affyQCReport' SubClassOf 'BioConductor Software' 'affyQCReport' SubClassOf 'is published by' value 'Bioconductor' 'affyQCReport' SubClassOf 'is executed in' some 'differential expression analysis' 'affyQCReport' SubClassOf 'is encoded in' some 'R language' 'affyQCReport' SubClassOf 'has specified data input' some ('has format specification' some ('CEL binary format' or 'CEL ASCII format')) 'affyQCReport' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'pdf')) 'affyQCReport' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000456 affyPara 'affyPara' SubClassOf 'BioConductor Software' 'affyPara' SubClassOf 'is encoded in' some 'R language' 'affyPara' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'affyPara' SubClassOf 'is published by' value 'Bioconductor' 'affyPara' SubClassOf 'software' 'affyPara' SubClassOf 'R software' 'affyPara' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) 'affyPara' SubClassOf 'is executed in' some ('averaging' and 'correction' and 'data normalization') http://www.ebi.ac.uk/swo/license/SWO_1000044 GNU GPL Compatible License Type 'GNU GPL Compatible License Type' EquivalentTo 'GNU Project Free License Type' and ('is compatible license of' some ('GNU GPL v3' or 'GNU GPL v2')) http://www.ebi.ac.uk/swo/license/SWO_1000049 CC0 1.0 'CC0 1.0' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC0 1.0' SubClassOf 'has clause' some 'No restrictions on derivatives' 'CC0 1.0' SubClassOf 'has clause' some 'Usage unrestricted' 'CC0 1.0' SubClassOf 'has clause' some 'Attribution not required' 'CC0 1.0' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC0 1.0' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC0 1.0' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'CC0 1.0' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'CC0 1.0' SubClassOf 'has clause' some 'Source code available' 'CC0 1.0' SubClassOf 'has website homepage' value "https://creativecommons.org/publicdomain/zero/1.0/" 'CC0 1.0' SubClassOf 'has clause' some 'Distribution unrestricted' http://www.ebi.ac.uk/swo/SWO_0000459 'affycoretools' ''affycoretools'' SubClassOf 'has specified data input' some ('Rnw' or 'Text data set') ''affycoretools'' SubClassOf 'is encoded in' some 'R language' ''affycoretools'' SubClassOf 'R software' ''affycoretools'' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot' and 'Text data set') ''affycoretools'' SubClassOf 'implements' some ('RMA' and ''FDR'') ''affycoretools'' SubClassOf 'is executed in' some 'differential expression analysis' ''affycoretools'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000458 affyTiling 'affyTiling' SubClassOf 'R software' 'affyTiling' SubClassOf 'has specified data output' some 'CSV data set' 'affyTiling' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' and 'BPMAP')) 'affyTiling' SubClassOf 'BioConductor Software' 'affyTiling' SubClassOf 'is published by' value 'Bioconductor' 'affyTiling' SubClassOf 'is executed in' some ('correction' and 'data normalization') 'affyTiling' SubClassOf 'implements' some 'RMA' 'affyTiling' SubClassOf 'software' 'affyTiling' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/efo/swo/SWO_0000578 obsolete Icens 'obsolete Icens' SubClassOf 'obsolete SWO class' 'obsolete Icens' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000579 obsolete idiogram 'obsolete idiogram' SubClassOf 'obsolete SWO class' 'obsolete idiogram' SubClassOf 'obsolete BioConductor Software' 'obsolete idiogram' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/license/SWO_1000043 GNU Project Free License Type 'GNU Project Free License Type' EquivalentTo 'software license' and ('has clause' some 'Source code available') and ('has clause' some 'Usage unrestricted') and ('has clause' some 'Derivatives allowed') and ('has clause' some ('Distribution unrestricted' or 'Distribution with notices')) 'GNU Project Free License Type' SubClassOf 'software license' http://www.ebi.ac.uk/efo/swo/SWO_0000103 obsolete multiscan 'obsolete multiscan' SubClassOf 'obsolete SWO class' 'obsolete multiscan' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000587 obsolete k-cores 'obsolete k-cores' SubClassOf 'obsolete SWO class' 'obsolete k-cores' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000104 obsolete affy 'obsolete affy' SubClassOf 'obsolete SWO class' 'obsolete affy' SubClassOf 'obsolete BioConductor Software' 'obsolete affy' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000588 obsolete k-means 'obsolete k-means' SubClassOf 'obsolete SWO class' 'obsolete k-means' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000461 affypdnn 'affypdnn' SubClassOf 'R software' 'affypdnn' SubClassOf 'has specified data output' some 'Graph plot' 'affypdnn' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some 'R data frame')) 'affypdnn' SubClassOf 'software' 'affypdnn' SubClassOf 'BioConductor Software' 'affypdnn' SubClassOf 'is published by' value 'Bioconductor' 'affypdnn' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/efo/swo/SWO_0000101 obsolete ChipSkipper 'obsolete ChipSkipper' SubClassOf 'obsolete SWO class' 'obsolete ChipSkipper' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000102 obsolete ChipSkipper V0.99 'obsolete ChipSkipper V0.99' SubClassOf 'obsolete SWO class' 'obsolete ChipSkipper V0.99' SubClassOf 'obsolete ChipSkipper' http://www.ebi.ac.uk/swo/SWO_0000463 altcdfenvs 'altcdfenvs' SubClassOf 'is encoded in' some 'R language' 'altcdfenvs' SubClassOf 'is published by' value 'Bioconductor' 'altcdfenvs' SubClassOf 'has specified data input' some ('has format specification' only 'FASTA format') 'altcdfenvs' SubClassOf 'BioConductor Software' 'altcdfenvs' SubClassOf 'R software' 'altcdfenvs' SubClassOf 'software' 'altcdfenvs' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/efo/swo/SWO_0000583 obsolete iterativeBMAsurv 'obsolete iterativeBMAsurv' SubClassOf 'obsolete SWO class' 'obsolete iterativeBMAsurv' SubClassOf 'obsolete R software' 'obsolete iterativeBMAsurv' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000466 'annotate' ''annotate'' SubClassOf 'has specified data output' some 'HTML report' ''annotate'' SubClassOf 'software' ''annotate'' SubClassOf 'has specified data input' some 'CSV data set' ''annotate'' SubClassOf 'is encoded in' some 'R language' ''annotate'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000100 obsolete ChipReader 3.1 'obsolete ChipReader 3.1' SubClassOf 'obsolete SWO class' 'obsolete ChipReader 3.1' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000584 obsolete Iterative local regression and model selection 'obsolete Iterative local regression and model selection' SubClassOf 'obsolete SWO class' 'obsolete Iterative local regression and model selection' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000465 annaffy 'annaffy' SubClassOf 'is published by' value 'Bioconductor' 'annaffy' SubClassOf 'R software' 'annaffy' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'annaffy' SubClassOf 'is encoded in' some 'R language' 'annaffy' SubClassOf 'software' 'annaffy' SubClassOf 'BioConductor Software' 'annaffy' SubClassOf 'has specified data output' some 'HTML report' http://www.ebi.ac.uk/efo/swo/SWO_0000581 obsolete impute 'obsolete impute' SubClassOf 'obsolete SWO class' 'obsolete impute' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000468 annotationTools 'annotationTools' SubClassOf 'is encoded in' some 'R language' 'annotationTools' SubClassOf 'is published by' value 'Bioconductor' 'annotationTools' SubClassOf 'R software' 'annotationTools' SubClassOf 'BioConductor Software' 'annotationTools' SubClassOf 'is executed in' some ('data annotation' and 'gene expression analysis') 'annotationTools' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'annotationTools' SubClassOf 'has specified data input' some 'CSV data set' 'annotationTools' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000582 obsolete iterativeBMA 'obsolete iterativeBMA' SubClassOf 'obsolete SWO class' 'obsolete iterativeBMA' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000467 data annotation 'data annotation' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_0000460 affyio 'affyio' SubClassOf 'R software' 'affyio' SubClassOf 'BioConductor Software' 'affyio' SubClassOf 'is encoded in' some 'R language' 'affyio' SubClassOf 'is published by' value 'Bioconductor' 'affyio' SubClassOf 'is executed in' some 'parse' 'affyio' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CDF binary format' or 'CDF ASCII format' or 'CEL ASCII format')) 'affyio' SubClassOf 'software' 'affyio' SubClassOf 'has specified data output' some ('has format specification' only ('CEL binary format' or 'CDF binary format' or 'CDF ASCII format' or 'CEL ASCII format')) http://www.ebi.ac.uk/swo/SWO_0000469 Annotation data packages 'Annotation data packages' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000109 obsolete Annotation-Driven Clustering 'obsolete Annotation-Driven Clustering' SubClassOf 'obsolete SWO class' 'obsolete Annotation-Driven Clustering' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000107 obsolete Feature Extraction Software 'obsolete Feature Extraction Software' SubClassOf 'obsolete SWO class' 'obsolete Feature Extraction Software' SubClassOf 'obsolete Affymetrix GeneChip Operating Software' http://www.ebi.ac.uk/efo/swo/SWO_0000108 obsolete Chi-square 'obsolete Chi-square' SubClassOf 'obsolete SWO class' 'obsolete Chi-square' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000105 obsolete affycomp 'obsolete affycomp' SubClassOf 'obsolete SWO class' 'obsolete affycomp' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000589 obsolete k-nearest neighbour classification 'obsolete k-nearest neighbour classification' SubClassOf 'obsolete SWO class' 'obsolete k-nearest neighbour classification' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000106 obsolete PCMG 'obsolete PCMG' SubClassOf 'obsolete SWO class' 'obsolete PCMG' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000477 obsolete Associative T method 'obsolete Associative T method' SubClassOf 'obsolete SWO class' 'obsolete Associative T method' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000478 obsolete AvgNRRs 'obsolete AvgNRRs' SubClassOf 'obsolete SWO class' 'obsolete AvgNRRs' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000475 obsolete arrayWoRx 2.0 'obsolete arrayWoRx 2.0' SubClassOf 'obsolete SWO class' 'obsolete arrayWoRx 2.0' SubClassOf 'obsolete arrayWoRx' http://www.ebi.ac.uk/efo/swo/SWO_0000476 obsolete arrayWoRx 'obsolete arrayWoRx' SubClassOf 'obsolete SWO class' 'obsolete arrayWoRx' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000473 obsolete arrayQuality 'obsolete arrayQuality' SubClassOf 'obsolete SWO class' 'obsolete arrayQuality' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000474 obsolete arrayQualityMetrics 'obsolete arrayQualityMetrics' SubClassOf 'obsolete SWO class' 'obsolete arrayQualityMetrics' SubClassOf 'obsolete BioConductor Software' 'obsolete arrayQualityMetrics' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000471 obsolete aroma.light 'obsolete aroma.light' SubClassOf 'obsolete SWO class' 'obsolete aroma.light' SubClassOf 'obsolete BioConductor Software' 'obsolete aroma.light' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000472 obsolete arrayMvout 'obsolete arrayMvout' SubClassOf 'obsolete SWO class' 'obsolete arrayMvout' SubClassOf 'obsolete R software' 'obsolete arrayMvout' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000470 obsolete 'apComplex' 'obsolete 'apComplex'' SubClassOf 'obsolete SWO class' 'obsolete 'apComplex'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000479 obsolete 'beadarray' 'obsolete 'beadarray'' SubClassOf 'obsolete SWO class' 'obsolete 'beadarray'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000004 obsolete 50-50 MANOVA 'obsolete 50-50 MANOVA' SubClassOf 'obsolete SWO class' 'obsolete 50-50 MANOVA' SubClassOf 'obsolete R software' 'obsolete 50-50 MANOVA' SubClassOf 'obsolete matlab software' http://www.ebi.ac.uk/efo/swo/SWO_0000488 obsolete 'biocViews' 'obsolete 'biocViews'' SubClassOf 'obsolete SWO class' 'obsolete 'biocViews'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000005 obsolete ABarray 'obsolete ABarray' SubClassOf 'obsolete SWO class' 'obsolete ABarray' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000489 obsolete biomaRT 'obsolete biomaRT' SubClassOf 'obsolete SWO class' 'obsolete biomaRT' SubClassOf 'obsolete BioConductor Software' 'obsolete biomaRT' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000486 obsolete 'biocDatasets' 'obsolete 'biocDatasets'' SubClassOf 'obsolete SWO class' 'obsolete 'biocDatasets'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000003 obsolete 2-sample pooled t-test 'obsolete 2-sample pooled t-test' SubClassOf 'obsolete SWO class' 'obsolete 2-sample pooled t-test' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000487 obsolete 'biocGraph' 'obsolete 'biocGraph'' SubClassOf 'obsolete SWO class' 'obsolete 'biocGraph'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000484 obsolete Bitmap object 'obsolete Bitmap object' SubClassOf 'obsolete SWO class' 'obsolete Bitmap object' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000485 obsolete bioDist 'obsolete bioDist' SubClassOf 'obsolete SWO class' 'obsolete bioDist' SubClassOf 'obsolete R software' 'obsolete bioDist' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000482 obsolete bgafun 'obsolete bgafun' SubClassOf 'obsolete SWO class' 'obsolete bgafun' SubClassOf 'obsolete BioConductor Software' 'obsolete bgafun' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000483 obsolete bgx 'obsolete bgx' SubClassOf 'obsolete SWO class' 'obsolete bgx' SubClassOf 'obsolete BioConductor Software' 'obsolete bgx' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000480 obsolete 'beadarraySNP' 'obsolete 'beadarraySNP'' SubClassOf 'obsolete SWO class' 'obsolete 'beadarraySNP'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000481 obsolete 'betr' 'obsolete 'betr'' SubClassOf 'obsolete SWO class' 'obsolete 'betr'' SubClassOf 'obsolete R software' 'obsolete 'betr'' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000406 Gene list 'Gene list' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000405 ArrayExpress Bioconductor 'ArrayExpress Bioconductor' SubClassOf 'is encoded in' some 'R language' 'ArrayExpress Bioconductor' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'MAGE-TAB')) 'ArrayExpress Bioconductor' SubClassOf 'R software' 'ArrayExpress Bioconductor' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Bioconductor')) 'ArrayExpress Bioconductor' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'R data frame')) 'ArrayExpress Bioconductor' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'European Bioinformatics Institute')) 'ArrayExpress Bioconductor' SubClassOf 'software' 'ArrayExpress Bioconductor' SubClassOf 'MAGE-TAB inputting software' 'ArrayExpress Bioconductor' SubClassOf 'output of' some ('software development' and ('has participant' value 'European Bioinformatics Institute')) http://www.ebi.ac.uk/efo/swo/SWO_0000008 obsolete Affymetrix Expression Console 'obsolete Affymetrix Expression Console' SubClassOf 'obsolete SWO class' 'obsolete Affymetrix Expression Console' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000408 Clustered data set 'Clustered data set' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000009 obsolete AIDA 'obsolete AIDA' SubClassOf 'obsolete SWO class' 'obsolete AIDA' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000006 obsolete 'ACME' 'obsolete 'ACME'' SubClassOf 'obsolete SWO class' 'obsolete 'ACME'' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000007 obsolete Algorithms for Calculating Microarray Enrichment 'obsolete Algorithms for Calculating Microarray Enrichment' SubClassOf 'obsolete SWO class' 'obsolete Algorithms for Calculating Microarray Enrichment' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000409 R data frame 'R data frame' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/efo/swo/SWO_0000015 obsolete AP-MS data 'obsolete AP-MS data' SubClassOf 'obsolete SWO class' 'obsolete AP-MS data' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000499 obsolete 'clusterStab' 'obsolete 'clusterStab'' SubClassOf 'obsolete SWO class' 'obsolete 'clusterStab'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000016 obsolete ARACNE algorithm 'obsolete ARACNE algorithm' SubClassOf 'obsolete SWO class' 'obsolete ARACNE algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000013 obsolete ANCOVA 'obsolete ANCOVA' SubClassOf 'obsolete SWO class' 'obsolete ANCOVA' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000497 obsolete chamber slide format 'obsolete chamber slide format' SubClassOf 'obsolete SWO class' 'obsolete chamber slide format' SubClassOf 'data format specification' http://www.ebi.ac.uk/efo/swo/SWO_0000014 obsolete 'ANOVA' 'obsolete 'ANOVA'' SubClassOf 'obsolete SWO class' 'obsolete 'ANOVA'' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000498 obsolete cls 'obsolete cls' SubClassOf 'obsolete SWO class' 'obsolete cls' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/efo/swo/SWO_0000011 obsolete ALL/AML data set 'obsolete ALL/AML data set' SubClassOf 'obsolete SWO class' 'obsolete ALL/AML data set' SubClassOf 'data item' http://www.ebi.ac.uk/efo/swo/SWO_0000495 obsolete 'cellHTS2' 'obsolete 'cellHTS2'' SubClassOf 'obsolete SWO class' 'obsolete 'cellHTS2'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000012 obsolete AMDIS 'obsolete AMDIS' SubClassOf 'obsolete SWO class' 'obsolete AMDIS' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000496 obsolete cghMCR 'obsolete cghMCR' SubClassOf 'obsolete SWO class' 'obsolete cghMCR' SubClassOf 'obsolete BioConductor Software' 'obsolete cghMCR' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000493 obsolete cdt 'obsolete cdt' SubClassOf 'obsolete SWO class' 'obsolete cdt' SubClassOf 'tab delimited file format' http://www.ebi.ac.uk/efo/swo/SWO_0000010 obsolete Average log expression across arrays (ALE) 'obsolete Average log expression across arrays (ALE)' SubClassOf 'obsolete SWO class' 'obsolete Average log expression across arrays (ALE)' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000494 obsolete 'cellHTS' 'obsolete 'cellHTS'' SubClassOf 'obsolete SWO class' 'obsolete 'cellHTS'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000491 obsolete 'bridge' 'obsolete 'bridge'' SubClassOf 'obsolete SWO class' 'obsolete 'bridge'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000490 obsolete Bootstrap 'obsolete Bootstrap' SubClassOf 'obsolete SWO class' 'obsolete Bootstrap' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/license/SWO_1000003 MPL v1.1 'MPL v1.1' SubClassOf 'is compatible license of' only (not ('GNU GPL v3' or 'GNU GPL v2' or 'GNU AGPL v3')) http://www.ebi.ac.uk/swo/license/SWO_1000004 GNU GPL 'GNU GPL' SubClassOf 'has clause' some 'Source code available' 'GNU GPL' SubClassOf 'has clause' some 'Copyleft' 'GNU GPL' SubClassOf 'has clause' some 'Free' 'GNU GPL' SubClassOf 'software license' 'GNU GPL' SubClassOf 'has clause' some 'Number of users unrestricted' 'GNU GPL' SubClassOf 'has clause' some 'Distribution with notices' 'GNU GPL' SubClassOf 'has clause' some 'Usage unrestricted' 'GNU GPL' SubClassOf 'has clause' some 'Time for use unrestricted' 'GNU GPL' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Free Software Foundation')) 'GNU GPL' SubClassOf 'has clause' some 'Number of installations unrestricted' http://www.ebi.ac.uk/swo/license/SWO_1000005 Apache License Version 2.0 'Apache License Version 2.0' SubClassOf 'has clause' some 'No restrictions on derivatives' 'Apache License Version 2.0' SubClassOf 'has clause' some 'Distribution with notices' 'Apache License Version 2.0' SubClassOf 'has clause' some 'Attribution required' 'Apache License Version 2.0' SubClassOf 'has clause' some 'Source code available' 'Apache License Version 2.0' SubClassOf 'has website homepage' value "http://www.apache.org/licenses/LICENSE-2.0" 'Apache License Version 2.0' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'Apache License Version 2.0' SubClassOf 'software license' 'Apache License Version 2.0' SubClassOf 'has clause' some 'Usage unrestricted' http://www.ebi.ac.uk/swo/license/SWO_1000006 Academic Free License version 3 'Academic Free License version 3' SubClassOf 'has clause' some 'Usage unrestricted' 'Academic Free License version 3' SubClassOf 'has clause' some 'Derivatives allowed' 'Academic Free License version 3' SubClassOf 'has clause' some 'Distribution with notices' 'Academic Free License version 3' SubClassOf 'has clause' some 'Source code available' 'Academic Free License version 3' SubClassOf 'has website homepage' value "https://opensource.org/licenses/AFL-3.0" 'Academic Free License version 3' SubClassOf 'has clause' some 'Attribution required' 'Academic Free License version 3' SubClassOf 'has website homepage' value "http://www.opensource.org/licenses/afl-3.0.php" 'Academic Free License version 3' SubClassOf 'software license' http://www.ebi.ac.uk/swo/license/SWO_1000007 FreeBSD 'FreeBSD' SubClassOf 'has website homepage' value "http://www.freebsd.org/copyright/freebsd-license.html" 'FreeBSD' SubClassOf 'has clause' some 'Usage unrestricted' 'FreeBSD' SubClassOf 'has clause' some 'Source code available' 'FreeBSD' SubClassOf 'has clause' some 'Distribution with notices' 'FreeBSD' SubClassOf 'software license' 'FreeBSD' SubClassOf 'has clause' some 'Derivatives allowed' 'FreeBSD' SubClassOf 'is compatible license of' some ('GNU GPL v3' and 'GNU GPL v2') http://www.ebi.ac.uk/swo/SWO_0000415 R language 'R language' SubClassOf 'programming language' http://www.ebi.ac.uk/swo/SWO_0000417 ScanAlyze 'ScanAlyze' SubClassOf 'software' 'ScanAlyze' SubClassOf 'is developed by' value 'obsolete_Stanford University' http://www.ebi.ac.uk/swo/SWO_0000416 ScISI 'ScISI' SubClassOf 'is encoded in' some 'R language' 'ScISI' SubClassOf 'R software' 'ScISI' SubClassOf 'is published by' value 'Bioconductor' 'ScISI' SubClassOf 'BioConductor Software' 'ScISI' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'ScISI' SubClassOf 'software' 'ScISI' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'ScISI' SubClassOf 'is executed in' some ('data annotation' and 'descriptive statistical calculation') http://www.ebi.ac.uk/efo/swo/SWO_0000019 obsolete Absolute Expression Analysis 'obsolete Absolute Expression Analysis' SubClassOf 'obsolete SWO class' 'obsolete Absolute Expression Analysis' SubClassOf 'obsolete MicroArraySuite 4.0' http://www.ebi.ac.uk/swo/SWO_0000419 ScanArray v3.1 software 'ScanArray v3.1 software' SubClassOf 'ScanArray' http://www.ebi.ac.uk/swo/SWO_0000418 ScanArray 'ScanArray' SubClassOf 'software' 'ScanArray' SubClassOf 'is developed by' value 'PerkinElmer' http://www.ebi.ac.uk/efo/swo/SWO_0000017 obsolete ARR 'obsolete ARR' SubClassOf 'obsolete SWO class' 'obsolete ARR' SubClassOf 'XML' http://www.ebi.ac.uk/efo/swo/SWO_0000018 obsolete AWS algorithm 'obsolete AWS algorithm' SubClassOf 'obsolete SWO class' 'obsolete AWS algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000026 obsolete Affymetrix Software 'obsolete Affymetrix Software' SubClassOf 'obsolete SWO class' 'obsolete Affymetrix Software' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000027 obsolete Agi4x44PreProcess 'obsolete Agi4x44PreProcess' SubClassOf 'obsolete SWO class' 'obsolete Agi4x44PreProcess' SubClassOf 'software with image input' 'obsolete Agi4x44PreProcess' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000024 obsolete Affymetrix GCOS v1.2 'obsolete Affymetrix GCOS v1.2' SubClassOf 'obsolete SWO class' 'obsolete Affymetrix GCOS v1.2' SubClassOf 'obsolete Affymetrix GeneChip Operating Software' http://www.ebi.ac.uk/swo/SWO_0000420 scanning software 'scanning software' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000025 obsolete Affymetrix GeneChip Operating Software 'obsolete Affymetrix GeneChip Operating Software' SubClassOf 'obsolete SWO class' 'obsolete Affymetrix GeneChip Operating Software' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000022 obsolete 'AffyExpress' 'obsolete 'AffyExpress'' SubClassOf 'obsolete SWO class' 'obsolete 'AffyExpress'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000422 ShortRead 'ShortRead' SubClassOf 'R software' 'ShortRead' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'ShortRead' SubClassOf 'has specified data input' some 'Text data set' 'ShortRead' SubClassOf 'is published by' value 'Bioconductor' 'ShortRead' SubClassOf 'software' 'ShortRead' SubClassOf 'BioConductor Software' 'ShortRead' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000421 Scanning software G2565AA version A6.3.1 'Scanning software G2565AA version A6.3.1' SubClassOf 'scanning software' 'Scanning software G2565AA version A6.3.1' SubClassOf 'is developed by' value 'Agilent Technologies' http://www.ebi.ac.uk/efo/swo/SWO_0000020 obsolete Absolute Expression Analysis 'obsolete Absolute Expression Analysis' SubClassOf 'obsolete SWO class' 'obsolete Absolute Expression Analysis' SubClassOf 'obsolete MicroArraySuite 5.0' http://www.ebi.ac.uk/swo/SWO_0000424 Silicon Genetics Genespring 'Silicon Genetics Genespring' SubClassOf 'is developed by' value 'Agilent Technologies' 'Silicon Genetics Genespring' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000021 obsolete 'AffyCompatible' 'obsolete 'AffyCompatible'' SubClassOf 'obsolete SWO class' 'obsolete 'AffyCompatible'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/swo/SWO_0000423 Signaling Pathway Impact Analysis (SPIA) algorithm 'Signaling Pathway Impact Analysis (SPIA) algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000426 'Smith-Waterman' ''Smith-Waterman'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000425 Similarity score 'Similarity score' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000428 Spot quantification 'Spot quantification' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000429 Spotfinder [TIGR] 'Spotfinder [TIGR]' SubClassOf 'software' 'Spotfinder [TIGR]' SubClassOf 'is developed by' value 'Dana-Farber Cancer Institute and Harvard School of Public Health' 'Spotfinder [TIGR]' SubClassOf 'is developed by' value 'J. Craig Venter Institute' http://www.ebi.ac.uk/efo/swo/SWO_0000028 obsolete Agilent Feature Extraction 5.1.1 'obsolete Agilent Feature Extraction 5.1.1' SubClassOf 'obsolete SWO class' 'obsolete Agilent Feature Extraction 5.1.1' SubClassOf 'obsolete Agilent Feature Extraction Software' http://www.ebi.ac.uk/efo/swo/SWO_0000029 obsolete Agilent Feature Extraction software version 7.1 'obsolete Agilent Feature Extraction software version 7.1' SubClassOf 'obsolete SWO class' 'obsolete Agilent Feature Extraction software version 7.1' SubClassOf 'obsolete Agilent Feature Extraction Software' http://www.ebi.ac.uk/efo/swo/SWO_0000037 obsolete Applied Biosystems 1700 Expression Array System Software 'obsolete Applied Biosystems 1700 Expression Array System Software' SubClassOf 'obsolete SWO class' 'obsolete Applied Biosystems 1700 Expression Array System Software' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000035 obsolete 'AnnotationDbi' 'obsolete 'AnnotationDbi'' SubClassOf 'obsolete SWO class' 'obsolete 'AnnotationDbi'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000034 obsolete Agilent Technologies Software 'obsolete Agilent Technologies Software' SubClassOf 'obsolete SWO class' 'obsolete Agilent Technologies Software' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000031 obsolete Agilent Feature Extraction software version A.5.1.1 'obsolete Agilent Feature Extraction software version A.5.1.1' SubClassOf 'obsolete SWO class' 'obsolete Agilent Feature Extraction software version A.5.1.1' SubClassOf 'obsolete Agilent Feature Extraction Software' http://www.ebi.ac.uk/efo/swo/SWO_0000032 obsolete Agilent Scan Control 'obsolete Agilent Scan Control' SubClassOf 'obsolete SWO class' 'obsolete Agilent Scan Control' SubClassOf 'obsolete Agilent Technologies Software' http://www.ebi.ac.uk/efo/swo/SWO_0000030 obsolete Agilent Feature Extraction software version 7.5 'obsolete Agilent Feature Extraction software version 7.5' SubClassOf 'obsolete SWO class' 'obsolete Agilent Feature Extraction software version 7.5' SubClassOf 'obsolete Agilent Feature Extraction Software' http://www.ebi.ac.uk/efo/swo/SWO_0000039 obsolete ArrayGauge 'obsolete ArrayGauge' SubClassOf 'obsolete SWO class' 'obsolete ArrayGauge' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000048 obsolete BAC 'obsolete BAC' SubClassOf 'obsolete SWO class' 'obsolete BAC' SubClassOf 'obsolete BioConductor Software' 'obsolete BAC' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000049 obsolete Binning clustering method 'obsolete Binning clustering method' SubClassOf 'obsolete SWO class' 'obsolete Binning clustering method' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000046 obsolete AtlasImage 'obsolete AtlasImage' SubClassOf 'obsolete SWO class' 'obsolete AtlasImage' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000047 obsolete Axon GenePix Pro 3 'obsolete Axon GenePix Pro 3' SubClassOf 'obsolete SWO class' 'obsolete Axon GenePix Pro 3' SubClassOf 'obsolete GenePix Pro [Axon Instruments]' http://www.ebi.ac.uk/efo/swo/SWO_0000044 obsolete ArrayVision 6.0 (Imaging Research Inc.) 'obsolete ArrayVision 6.0 (Imaging Research Inc.)' SubClassOf 'obsolete SWO class' 'obsolete ArrayVision 6.0 (Imaging Research Inc.)' SubClassOf 'obsolete ArrayVision' http://www.ebi.ac.uk/efo/swo/SWO_0000045 obsolete Array_vision_(Interfocus) 'obsolete Array_vision_(Interfocus)' SubClassOf 'obsolete SWO class' 'obsolete Array_vision_(Interfocus)' SubClassOf 'obsolete ArrayVision' http://www.ebi.ac.uk/efo/swo/SWO_0000042 obsolete ArrayVision 'obsolete ArrayVision' SubClassOf 'obsolete SWO class' 'obsolete ArrayVision' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000040 obsolete ArrayNorm 'obsolete ArrayNorm' SubClassOf 'obsolete SWO class' 'obsolete ArrayNorm' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000041 obsolete 'ArrayTools' 'obsolete 'ArrayTools'' SubClassOf 'obsolete SWO class' 'obsolete 'ArrayTools'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000059 obsolete 'BSgenome' 'obsolete 'BSgenome'' SubClassOf 'obsolete SWO class' 'obsolete 'BSgenome'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000057 obsolete BPMAP 'obsolete BPMAP' SubClassOf 'obsolete SWO class' 'obsolete BPMAP' SubClassOf 'binary format' http://www.ebi.ac.uk/efo/swo/SWO_0000058 obsolete BRB-ArrayTools 'obsolete BRB-ArrayTools' SubClassOf 'obsolete SWO class' 'obsolete BRB-ArrayTools' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000055 obsolete Iterative Bayesian Model Averaging (BMA) 'obsolete Iterative Bayesian Model Averaging (BMA)' SubClassOf 'obsolete SWO class' 'obsolete Iterative Bayesian Model Averaging (BMA)' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000056 obsolete Base-Pair-Distance Kernel 'obsolete Base-Pair-Distance Kernel' SubClassOf 'obsolete SWO class' 'obsolete Base-Pair-Distance Kernel' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000053 obsolete 'BGmix' 'obsolete 'BGmix'' SubClassOf 'obsolete SWO class' 'obsolete 'BGmix'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000054 obsolete BLAST 'obsolete BLAST' SubClassOf 'obsolete SWO class' 'obsolete BLAST' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000052 obsolete BGL 'obsolete BGL' SubClassOf 'obsolete SWO class' 'obsolete BGL' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000050 obsolete 'BCRANK' 'obsolete 'BCRANK'' SubClassOf 'obsolete SWO class' 'obsolete 'BCRANK'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000068 obsolete 'BioMVCClass' 'obsolete 'BioMVCClass'' SubClassOf 'obsolete SWO class' 'obsolete 'BioMVCClass'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000066 obsolete 'BicARE' 'obsolete 'BicARE'' SubClassOf 'obsolete SWO class' 'obsolete 'BicARE'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000064 obsolete Bayesian Model 'obsolete Bayesian Model' SubClassOf 'obsolete SWO class' 'obsolete Bayesian Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000065 obsolete Beadstudio 'obsolete Beadstudio' SubClassOf 'obsolete SWO class' 'obsolete Beadstudio' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000062 obsolete BaldiLongT 'obsolete BaldiLongT' SubClassOf 'obsolete SWO class' 'obsolete BaldiLongT' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000063 obsolete BasReader 3.01 'obsolete BasReader 3.01' SubClassOf 'obsolete SWO class' 'obsolete BasReader 3.01' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000060 obsolete BZScan 'obsolete BZScan' SubClassOf 'obsolete SWO class' 'obsolete BZScan' SubClassOf 'software' http://www.ontodm.com/OntoDM-core/OntoDM_731692 single generalization algorithm 'ensemble algorithm' DisjointWith 'single generalization algorithm' 'single generalization algorithm' SubClassOf 'data mining algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000079 obsolete 'CALIB' 'obsolete 'CALIB'' SubClassOf 'obsolete SWO class' 'obsolete 'CALIB'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000077 obsolete 'BufferedMatrix' 'obsolete 'BufferedMatrix'' SubClassOf 'obsolete SWO class' 'obsolete 'BufferedMatrix'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000078 obsolete 'BufferedMatrixMethods' 'obsolete 'BufferedMatrixMethods'' SubClassOf 'obsolete SWO class' 'obsolete 'BufferedMatrixMethods'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000075 obsolete 'Biostrings' 'obsolete 'Biostrings'' SubClassOf 'obsolete SWO class' 'obsolete 'Biostrings'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000076 obsolete BlueFuse 'obsolete BlueFuse' SubClassOf 'obsolete SWO class' 'obsolete BlueFuse' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000071 obsolete 'BiocCaseStudies' 'obsolete 'BiocCaseStudies'' SubClassOf 'obsolete SWO class' 'obsolete 'BiocCaseStudies'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000072 obsolete BioConductor Software 'obsolete BioConductor Software' SubClassOf 'obsolete SWO class' 'obsolete BioConductor Software' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000070 obsolete 'Biobase' 'obsolete 'Biobase'' SubClassOf 'obsolete SWO class' 'obsolete 'Biobase'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000088 obsolete CHP binary format 'obsolete CHP binary format' SubClassOf 'obsolete SWO class' 'obsolete CHP binary format' SubClassOf 'binary format' http://www.ebi.ac.uk/efo/swo/SWO_0000089 obsolete CLR algorithm 'obsolete CLR algorithm' SubClassOf 'obsolete SWO class' 'obsolete CLR algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000086 obsolete 'CGHcall' 'obsolete 'CGHcall'' SubClassOf 'obsolete SWO class' 'obsolete 'CGHcall'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000087 obsolete 'CGHregions' 'obsolete 'CGHregions'' SubClassOf 'obsolete SWO class' 'obsolete 'CGHregions'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000084 obsolete CEL binary format 'obsolete CEL binary format' SubClassOf 'obsolete SWO class' 'obsolete CEL binary format' SubClassOf 'binary format' http://www.ebi.ac.uk/efo/swo/SWO_0000085 obsolete 'CGHbase' 'obsolete 'CGHbase'' SubClassOf 'obsolete SWO class' 'obsolete 'CGHbase'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000082 obsolete CBS algorithm 'obsolete CBS algorithm' SubClassOf 'obsolete SWO class' 'obsolete CBS algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000083 obsolete CDF binary format 'obsolete CDF binary format' SubClassOf 'obsolete SWO class' 'obsolete CDF binary format' SubClassOf 'binary format' http://www.ebi.ac.uk/efo/swo/SWO_0000080 obsolete 'CAMERA' 'obsolete 'CAMERA'' SubClassOf 'obsolete SWO class' 'obsolete 'CAMERA'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000081 obsolete CBS 'obsolete CBS' SubClassOf 'obsolete SWO class' 'obsolete CBS' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000099 obsolete 'ChemmineR' 'obsolete 'ChemmineR'' SubClassOf 'obsolete SWO class' 'obsolete 'ChemmineR'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000097 obsolete Category analysis 'obsolete Category analysis' SubClassOf 'obsolete SWO class' 'obsolete Category analysis' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000098 obsolete Category 'obsolete Category' SubClassOf 'obsolete SWO class' 'obsolete Category' SubClassOf 'obsolete R software' 'obsolete Category' SubClassOf 'obsolete BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000095 obsolete Continuous Wavelet Transform (CWT)-based peak detection algorithm 'obsolete Continuous Wavelet Transform (CWT)-based peak detection algorithm' SubClassOf 'obsolete SWO class' 'obsolete Continuous Wavelet Transform (CWT)-based peak detection algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000096 obsolete CARMAweb 'obsolete CARMAweb' SubClassOf 'obsolete SWO class' 'obsolete CARMAweb' SubClassOf 'software' http://www.ebi.ac.uk/efo/swo/SWO_0000094 obsolete CRLMM algorithm 'obsolete CRLMM algorithm' SubClassOf 'obsolete SWO class' 'obsolete CRLMM algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000091 obsolete CMA 'obsolete CMA' SubClassOf 'obsolete SWO class' 'obsolete CMA' SubClassOf 'algorithm' http://www.ebi.ac.uk/efo/swo/SWO_0000092 obsolete 'CORREP' 'obsolete 'CORREP'' SubClassOf 'obsolete SWO class' 'obsolete 'CORREP'' SubClassOf 'obsolete R software' http://www.ebi.ac.uk/efo/swo/SWO_0000090 obsolete 'CMA' 'obsolete 'CMA'' SubClassOf 'obsolete SWO class' 'obsolete 'CMA'' SubClassOf 'obsolete R software' http://edamontology.org/data_2603 Microarray data Gene expression data 'Gene expression data' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/operation_0345 Sequence retrieval (by keyword) 'Sequence retrieval (by keyword)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0346 Sequence similarity search 'Sequence similarity search' SubClassOf 'Structure database search' 'Sequence similarity search' SubClassOf 'Sequence comparison' 'Sequence similarity search' SubClassOf 'Sequence database search' http://edamontology.org/operation_0343 Transmembrane protein database search 'Transmembrane protein database search' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0344 Sequence retrieval (by code) 'Sequence retrieval (by code)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0349 Sequence database search (by property) 'Sequence database search (by property)' SubClassOf 'Sequence database search' http://edamontology.org/operation_0347 Sequence database search (by motif or pattern) 'Sequence database search (by motif or pattern)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0348 Sequence database search (by amino acid composition) 'Sequence database search (by amino acid composition)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0341 Motif database search 'Motif database search' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0342 Sequence profile database search 'Sequence profile database search' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0340 Protein secondary database search 'Protein secondary database search' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2308 Virus annotation (taxonomy) 'Virus annotation (taxonomy)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0356 Sequence database search (by isoelectric point) 'Sequence database search (by isoelectric point)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2309 Reaction ID (SABIO-RK) 'Reaction ID (SABIO-RK)' SubClassOf 'Reaction ID' http://edamontology.org/operation_0357 Structure retrieval (by code) 'Structure retrieval (by code)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0354 Sequence database search (by sequence for primer sequences) 'Sequence database search (by sequence for primer sequences)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0355 Sequence database search (by molecular weight) 'Sequence database search (by molecular weight)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0358 Structure retrieval (by keyword) 'Structure retrieval (by keyword)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2307 Virus annotation 'Virus annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0359 Structure database search (by sequence) 'Structure database search (by sequence)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2300 Gene name (NCBI) 'Gene name (NCBI)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2301 SMILES string 'SMILES string' SubClassOf 'Chemical formula' http://edamontology.org/data_2302 STRING ID 'STRING ID' SubClassOf 'Protein interaction ID' http://edamontology.org/operation_0352 Sequence database search (by sequence using local alignment-based methods) 'Sequence database search (by sequence using local alignment-based methods)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0353 Sequence database search (by sequence using global alignment-based methods) 'Sequence database search (by sequence using global alignment-based methods)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0350 Sequence database search (by sequence using word-based methods) 'Sequence database search (by sequence using word-based methods)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0351 Sequence database search (by sequence using profile-based methods) 'Sequence database search (by sequence using profile-based methods)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1370 HMMER format 'HMMER format' SubClassOf 'Textual format' 'HMMER format' SubClassOf 'Hidden Markov model format' http://edamontology.org/data_2319 Cell line name (no punctuation) 'Cell line name (no punctuation)' SubClassOf 'Cell line name' http://edamontology.org/operation_0323 Phylogenetic tree generation 'Phylogenetic tree generation' SubClassOf 'Phylogenetic tree analysis' 'Phylogenetic tree generation' SubClassOf 'Generation' http://edamontology.org/operation_0324 Phylogenetic tree analysis 'Phylogenetic tree analysis' SubClassOf 'Analysis' http://edamontology.org/operation_0321 Protein model validation 'Protein model validation' SubClassOf 'Protein structure analysis' 'Protein model validation' SubClassOf 'Validation' http://edamontology.org/operation_0322 Molecular model refinement 'Molecular model refinement' SubClassOf 'Optimisation and refinement' 'Molecular model refinement' SubClassOf 'Structure analysis' http://edamontology.org/data_2315 NCBI version 'NCBI version' SubClassOf 'Sequence accession (hybrid)' http://edamontology.org/operation_0327 Phylogenetic footprinting / shadowing 'Phylogenetic footprinting / shadowing' SubClassOf 'Phylogenetic tree generation (from molecular sequences)' http://edamontology.org/data_2316 Cell line name 'Cell line name' SubClassOf 'Strain name' http://edamontology.org/operation_0328 Protein folding simulation 'Protein folding simulation' SubClassOf 'Protein folding analysis' http://edamontology.org/data_2317 Cell line name (exact) 'Cell line name (exact)' SubClassOf 'Cell line name' http://edamontology.org/operation_0325 Phylogenetic tree comparison 'Phylogenetic tree comparison' SubClassOf 'Comparison' 'Phylogenetic tree comparison' SubClassOf 'Phylogenetic tree analysis' http://edamontology.org/data_2318 Cell line name (truncated) 'Cell line name (truncated)' SubClassOf 'Cell line name' http://edamontology.org/operation_0326 Phylogenetic tree editing 'Phylogenetic tree editing' SubClassOf 'Phylogenetic tree analysis' 'Phylogenetic tree editing' SubClassOf 'Editing' http://edamontology.org/data_2313 Carbohydrate report 'Carbohydrate report' SubClassOf 'Structure report' http://edamontology.org/data_2314 GI number 'GI number' SubClassOf 'Sequence accession (hybrid)' http://edamontology.org/operation_0320 Protein structure assignment 'Protein structure assignment' SubClassOf 'Protein structure analysis' http://edamontology.org/format_3100 CATH domain report format 'CATH domain report format' SubClassOf 'Protein domain classification format' http://edamontology.org/operation_0318 Structural genomics target selection 'Structural genomics target selection' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0319 Protein secondary structure assignment 'Protein secondary structure assignment' SubClassOf 'Prediction and recognition (protein)' http://edamontology.org/operation_2997 Protein comparison 'Protein comparison' SubClassOf 'Comparison' http://edamontology.org/operation_0334 Enzyme kinetics calculation 'Enzyme kinetics calculation' SubClassOf 'Protein property calculation (from sequence)' http://edamontology.org/operation_0335 Formatting 'Formatting' SubClassOf 'Data handling' http://edamontology.org/operation_2996 Structure classification 'Structure classification' SubClassOf 'Classification' 'Structure classification' SubClassOf 'Structure analysis' http://edamontology.org/operation_0332 Immunogen design 'Immunogen design' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2995 Sequence classification 'Sequence classification' SubClassOf 'Sequence analysis' 'Sequence classification' SubClassOf 'Classification' http://edamontology.org/operation_0333 Zinc finger prediction 'Zinc finger prediction' SubClassOf 'Protein-nucleic acid binding prediction' http://edamontology.org/data_2326 DrugBank ID 'DrugBank ID' SubClassOf 'Drug accession' http://edamontology.org/operation_0338 Sequence database search 'Sequence database search' SubClassOf 'Sequence analysis' 'Sequence database search' SubClassOf 'Database search' http://edamontology.org/data_2327 GI number (protein) 'GI number (protein)' SubClassOf 'GI number' http://edamontology.org/operation_0339 Structure database search 'Structure database search' SubClassOf 'Database search' http://edamontology.org/operation_0336 Format validation 'Format validation' SubClassOf 'Validation' http://edamontology.org/operation_2998 Nucleic acid comparison 'Nucleic acid comparison' SubClassOf 'Comparison' http://edamontology.org/operation_0337 Visualisation 'Visualisation' SubClassOf 'Operation' http://edamontology.org/data_2325 REBASE enzyme number 'REBASE enzyme number' SubClassOf 'Enzyme ID' http://edamontology.org/operation_0330 Protein SNP mapping 'Protein SNP mapping' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2993 Molecular interaction data processing 'Molecular interaction data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0331 Protein modelling (mutation) 'Protein modelling (mutation)' SubClassOf 'Protein modelling' http://edamontology.org/data_2320 Cell line name (assonant) 'Cell line name (assonant)' SubClassOf 'Cell line name' http://edamontology.org/data_2321 Enzyme ID 'Enzyme ID' SubClassOf 'Protein accession' 'Enzyme ID' SubClassOf 'Enzyme identifier' http://edamontology.org/operation_2990 Classification 'Classification' SubClassOf 'Operation' http://edamontology.org/format_1391 HMMER-aln 'HMMER-aln' SubClassOf 'Alignment format (text)' 'HMMER-aln' SubClassOf 'FASTA-like (text)' http://edamontology.org/format_1392 DIALIGN format 'DIALIGN format' SubClassOf 'Alignment format (text)' 'DIALIGN format' SubClassOf 'Textual format' http://edamontology.org/format_1393 daf 'daf' SubClassOf 'Textual format' 'daf' SubClassOf 'Alignment format (text)' http://edamontology.org/operation_0329 Protein folding pathway prediction 'Protein folding pathway prediction' SubClassOf 'Protein folding analysis' 'Protein folding pathway prediction' SubClassOf 'Prediction and recognition (protein)' http://edamontology.org/data_1009 Protein name 'Protein name' SubClassOf 'Molecule name' 'Protein name' SubClassOf 'Protein identifier' http://edamontology.org/operation_0389 Protein-nucleic acid binding site analysis 'Protein-nucleic acid binding site analysis' SubClassOf 'Protein interaction analysis' http://edamontology.org/data_1008 Polypeptide chain ID 'Polypeptide chain ID' SubClassOf 'Peptide identifier' http://edamontology.org/data_1007 Nucleotide code 'Nucleotide code' SubClassOf 'Nucleotide identifier' 'Nucleotide code' SubClassOf 'Compound name' http://edamontology.org/operation_0387 Molecular surface calculation 'Molecular surface calculation' SubClassOf 'Molecular surface analysis' http://edamontology.org/data_1006 Amino acid name 'Amino acid name' SubClassOf 'Amino acid identifier' http://edamontology.org/operation_0388 Protein binding site prediction (from structure) 'Protein binding site prediction (from structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2337 Resource metadata 'Resource metadata' SubClassOf 'Report' http://edamontology.org/data_3668 Disease name 'Disease name' SubClassOf 'Name' 'Disease name' SubClassOf 'Disease identifier' http://edamontology.org/data_2338 Ontology identifier 'Ontology identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_3669 Training material 'Training material' SubClassOf 'Data' http://edamontology.org/data_2339 Ontology concept name 'Ontology concept name' SubClassOf 'Ontology concept identifier' 'Ontology concept name' SubClassOf 'Name' http://edamontology.org/data_1001 Chemical name (synonymous) 'Chemical name (synonymous)' SubClassOf 'Compound name' http://edamontology.org/data_1000 Chemical name (brand) 'Chemical name (brand)' SubClassOf 'Compound name' http://edamontology.org/data_2335 Bit score 'Bit score' SubClassOf 'Sequence similarity' http://edamontology.org/data_3667 Disease identifier 'Disease identifier' SubClassOf 'Identifier (typed)' 'Disease identifier' SubClassOf 'Accession' http://edamontology.org/data_2336 Translation phase specification 'Translation phase specification' SubClassOf 'Sequence attribute' http://edamontology.org/operation_0380 Repeat sequence organisation analysis 'Repeat sequence organisation analysis' SubClassOf 'Repeat sequence analysis' 'Repeat sequence organisation analysis' SubClassOf 'Sequence composition calculation' http://edamontology.org/data_1005 HET group name 'HET group name' SubClassOf 'Compound name' http://edamontology.org/operation_0385 Protein hydropathy cluster calculation 'Protein hydropathy cluster calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1004 Chemical registry number (Gmelin) 'Chemical registry number (Gmelin)' SubClassOf 'Chemical registry number' http://edamontology.org/operation_0386 Protein dipole moment calculation 'Protein dipole moment calculation' SubClassOf 'Protein property calculation (from sequence)' http://edamontology.org/data_1003 Chemical registry number (Beilstein) 'Chemical registry number (Beilstein)' SubClassOf 'Chemical registry number' http://edamontology.org/operation_0383 Protein hydropathy calculation (from structure) 'Protein hydropathy calculation (from structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1002 Chemical registry number (CAS) 'Chemical registry number (CAS)' SubClassOf 'Chemical registry number' http://edamontology.org/operation_0384 Accessible surface calculation 'Accessible surface calculation' SubClassOf 'Molecular surface analysis' http://edamontology.org/format_1341 InterPro hits format 'InterPro hits format' SubClassOf 'Textual format' 'InterPro hits format' SubClassOf 'Database hits (sequence) format' http://edamontology.org/format_1342 InterPro protein view report format 'InterPro protein view report format' SubClassOf 'InterPro hits format' http://edamontology.org/format_1343 InterPro match table format 'InterPro match table format' SubClassOf 'InterPro hits format' http://edamontology.org/format_1349 HMMER Dirichlet prior 'HMMER Dirichlet prior' SubClassOf 'Dirichlet distribution format' 'HMMER Dirichlet prior' SubClassOf 'Textual format' http://edamontology.org/data_1019 Protein feature identifier 'Protein feature identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1018 Nucleic acid feature identifier 'Nucleic acid feature identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0398 Protein molecular weight calculation 'Protein molecular weight calculation' SubClassOf 'Protein property calculation (from sequence)' http://edamontology.org/data_1017 Sequence range 'Sequence range' SubClassOf 'Sequence attribute' http://edamontology.org/operation_0399 Protein extinction coefficient calculation 'Protein extinction coefficient calculation' SubClassOf 'Protein property calculation (from sequence)' http://edamontology.org/data_2348 Sequence cluster ID (UniRef90) 'Sequence cluster ID (UniRef90)' SubClassOf 'Sequence cluster ID (UniRef)' http://edamontology.org/data_2349 Sequence cluster ID (UniRef50) 'Sequence cluster ID (UniRef50)' SubClassOf 'Sequence cluster ID (UniRef)' http://edamontology.org/operation_3429 Generation 'Generation' SubClassOf 'Operation' http://edamontology.org/data_1012 Enzyme name 'Enzyme name' SubClassOf 'Protein name' 'Enzyme name' SubClassOf 'Enzyme identifier' http://edamontology.org/data_2344 Pathway ID (NCI-Nature) 'Pathway ID (NCI-Nature)' SubClassOf 'Pathway or network accession' http://edamontology.org/operation_0392 Protein contact map calculation 'Protein contact map calculation' SubClassOf 'Protein distance matrix calculation' http://edamontology.org/data_1011 EC number 'EC number' SubClassOf 'Enzyme ID' http://edamontology.org/data_2345 Pathway ID (ConsensusPathDB) 'Pathway ID (ConsensusPathDB)' SubClassOf 'Pathway or network accession' 'Pathway ID (ConsensusPathDB)' SubClassOf 'ConsensusPathDB identifier' http://edamontology.org/operation_0393 Residue cluster calculation 'Residue cluster calculation' SubClassOf 'Residue distance calculation' http://edamontology.org/data_1010 Enzyme identifier 'Enzyme identifier' SubClassOf 'Protein identifier' http://edamontology.org/data_2346 Sequence cluster ID (UniRef) 'Sequence cluster ID (UniRef)' SubClassOf 'Sequence cluster ID' http://edamontology.org/operation_0390 Protein peeling 'Protein peeling' SubClassOf 'Protein domain recognition' http://edamontology.org/data_2347 Sequence cluster ID (UniRef100) 'Sequence cluster ID (UniRef100)' SubClassOf 'Sequence cluster ID (UniRef)' http://edamontology.org/operation_0391 Protein distance matrix calculation 'Protein distance matrix calculation' SubClassOf 'Residue distance calculation' http://edamontology.org/data_3671 Text 'Text' SubClassOf 'Text data' http://edamontology.org/data_1016 Sequence position 'Sequence position' SubClassOf 'Sequence attribute' http://edamontology.org/data_2340 Genome build identifier 'Genome build identifier' SubClassOf 'Genome identifier' http://edamontology.org/operation_0396 Ramachandran plot calculation 'Ramachandran plot calculation' SubClassOf 'Protein geometry calculation' http://edamontology.org/data_1015 Sequence feature ID 'Sequence feature ID' SubClassOf 'Accession' 'Sequence feature ID' SubClassOf 'Sequence feature identifier' http://edamontology.org/operation_0397 Ramachandran plot validation 'Ramachandran plot validation' SubClassOf 'Protein geometry validation' http://edamontology.org/data_1014 Sequence position specification 'Sequence position specification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2342 Pathway or network name 'Pathway or network name' SubClassOf 'Pathway or network identifier' http://edamontology.org/operation_0394 Hydrogen bond calculation 'Hydrogen bond calculation' SubClassOf 'Residue interaction calculation' http://edamontology.org/data_1013 Restriction enzyme name 'Restriction enzyme name' SubClassOf 'Enzyme name' http://edamontology.org/data_2343 Pathway ID (KEGG) 'Pathway ID (KEGG)' SubClassOf 'Pathway or network accession' 'Pathway ID (KEGG)' SubClassOf 'KEGG object identifier' http://edamontology.org/operation_0395 Residue non-canonical interaction detection 'Residue non-canonical interaction detection' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3670 Online course 'Online course' SubClassOf 'Training material' http://edamontology.org/format_1332 FASTA search results format 'FASTA search results format' SubClassOf 'Textual format' 'FASTA search results format' SubClassOf 'Database hits (sequence) format' http://edamontology.org/format_1337 lhf 'lhf' SubClassOf 'Textual format' 'lhf' SubClassOf 'Database hits (sequence) format' http://edamontology.org/format_1333 BLAST results 'BLAST results' SubClassOf 'Textual format' 'BLAST results' SubClassOf 'Database hits (sequence) format' http://edamontology.org/format_1334 mspcrunch 'mspcrunch' SubClassOf 'Database hits (sequence) format' 'mspcrunch' SubClassOf 'Textual format' http://edamontology.org/format_1335 Smith-Waterman format 'Smith-Waterman format' SubClassOf 'Textual format' 'Smith-Waterman format' SubClassOf 'Database hits (sequence) format' http://edamontology.org/format_1336 dhf 'dhf' SubClassOf 'Database hits (sequence) format' 'dhf' SubClassOf 'Textual format' http://edamontology.org/operation_0367 Sequence mutation and randomisation 'Sequence mutation and randomisation' SubClassOf 'Sequence editing' http://edamontology.org/operation_0368 Sequence masking 'Sequence masking' SubClassOf 'Sequence editing' http://edamontology.org/data_1029 Gene identifier (NCBI UniGene) 'Gene identifier (NCBI UniGene)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0365 Nucleic acid restriction digest 'Nucleic acid restriction digest' SubClassOf 'Sequence generation (nucleic acid)' 'Nucleic acid restriction digest' SubClassOf 'Nucleic acid property calculation' http://edamontology.org/data_1028 Gene identifier (NCBI RefSeq) 'Gene identifier (NCBI RefSeq)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0366 Protein sequence cleavage 'Protein sequence cleavage' SubClassOf 'Protein property calculation (from sequence)' 'Protein sequence cleavage' SubClassOf 'Sequence generation (protein)' http://edamontology.org/data_2359 Domain-domain interactions 'Domain-domain interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0369 Sequence cutting 'Sequence cutting' SubClassOf 'Sequence editing' http://edamontology.org/data_1023 EMBOSS Uniform Feature Object 'EMBOSS Uniform Feature Object' SubClassOf 'Sequence feature identifier' 'EMBOSS Uniform Feature Object' SubClassOf 'Name' http://edamontology.org/data_2355 RNA family identifier 'RNA family identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_1022 Sequence feature label 'Sequence feature label' SubClassOf 'Sequence features metadata' 'Sequence feature label' SubClassOf 'Sequence feature identifier' 'Sequence feature label' SubClassOf 'Name' http://edamontology.org/data_2356 RFAM accession 'RFAM accession' SubClassOf 'RNA family identifier' 'RFAM accession' SubClassOf 'Accession' http://edamontology.org/operation_0360 Structural similarity search 'Structural similarity search' SubClassOf 'Structure comparison' 'Structural similarity search' SubClassOf 'Structure database search' http://edamontology.org/data_1021 Sequence feature qualifier 'Sequence feature qualifier' SubClassOf 'Sequence features metadata' http://edamontology.org/data_2357 Protein signature type 'Protein signature type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1020 Sequence feature key 'Sequence feature key' SubClassOf 'Sequence features metadata' http://edamontology.org/data_2358 Domain-nucleic acid interaction report 'Domain-nucleic acid interaction report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1027 Gene ID (NCBI) 'Gene ID (NCBI)' SubClassOf 'RefSeq accession' 'Gene ID (NCBI)' SubClassOf 'Gene ID' http://edamontology.org/operation_0363 Nucleic acid sequence reverse and complement 'Nucleic acid sequence reverse and complement' SubClassOf 'Sequence generation (nucleic acid)' http://edamontology.org/data_1026 Gene symbol 'Gene symbol' SubClassOf 'Gene name' http://edamontology.org/operation_0364 Random sequence generation 'Random sequence generation' SubClassOf 'Sequence generation' http://edamontology.org/data_2353 Ontology data 'Ontology data' SubClassOf 'Data' http://edamontology.org/data_1025 Gene identifier 'Gene identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/operation_0361 Sequence annotation 'Sequence annotation' SubClassOf 'Annotation' http://edamontology.org/data_1024 Codon name 'Codon name' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2354 RNA family report 'RNA family report' SubClassOf 'Gene family report' http://edamontology.org/format_1360 meme-motif 'meme-motif' SubClassOf 'Sequence motif format' 'meme-motif' SubClassOf 'Textual format' http://edamontology.org/format_1366 prosite-profile 'prosite-profile' SubClassOf 'Textual format' 'prosite-profile' SubClassOf 'Sequence profile format' http://edamontology.org/format_1367 JASPAR format 'JASPAR format' SubClassOf 'Textual format' 'JASPAR format' SubClassOf 'Sequence profile format' http://edamontology.org/format_1369 MEME background Markov model 'MEME background Markov model' SubClassOf 'Hidden Markov model format' 'MEME background Markov model' SubClassOf 'Textual format' http://edamontology.org/operation_0378 Sequence composition calculation (protein) 'Sequence composition calculation (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0379 Repeat sequence detection 'Repeat sequence detection' SubClassOf 'Repeat sequence analysis' 'Repeat sequence detection' SubClassOf 'Nucleic acid feature detection' http://edamontology.org/data_1039 SCOP domain identifier 'SCOP domain identifier' SubClassOf 'Protein domain ID' http://edamontology.org/operation_0377 Sequence composition calculation (nucleic acid) 'Sequence composition calculation (nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2366 Secondary structure alignment 'Secondary structure alignment' SubClassOf 'Alignment' http://edamontology.org/data_1034 Gene ID (SGD) 'Gene ID (SGD)' SubClassOf 'SGD ID' 'Gene ID (SGD)' SubClassOf 'Gene ID' http://edamontology.org/operation_0370 Restriction site creation 'Restriction site creation' SubClassOf 'Sequence editing' http://edamontology.org/data_1033 Ensembl gene ID 'Ensembl gene ID' SubClassOf 'Ensembl ID' 'Ensembl gene ID' SubClassOf 'Gene ID' http://edamontology.org/data_2367 ASTD ID 'ASTD ID' SubClassOf 'Sequence accession (nucleic acid)' 'ASTD ID' SubClassOf 'Identifier (hybrid)' http://edamontology.org/operation_0371 DNA translation 'DNA translation' SubClassOf 'Sequence conversion' http://edamontology.org/data_1032 Gene ID (DictyBase) 'Gene ID (DictyBase)' SubClassOf 'Gene ID' http://edamontology.org/data_2368 ASTD ID (exon) 'ASTD ID (exon)' SubClassOf 'ASTD ID' http://edamontology.org/data_1031 Gene ID (CGD) 'Gene ID (CGD)' SubClassOf 'Gene ID' http://edamontology.org/data_2369 ASTD ID (intron) 'ASTD ID (intron)' SubClassOf 'ASTD ID' http://edamontology.org/data_1038 Protein domain ID 'Protein domain ID' SubClassOf 'Accession' 'Protein domain ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2362 Sequence accession (hybrid) 'Sequence accession (hybrid)' SubClassOf 'Sequence accession' http://edamontology.org/data_1037 TAIR accession (gene) 'TAIR accession (gene)' SubClassOf 'TAIR accession' 'TAIR accession (gene)' SubClassOf 'Gene ID' http://edamontology.org/data_2363 2D PAGE data '2D PAGE data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1036 TIGR identifier 'TIGR identifier' SubClassOf 'Gene ID' 'TIGR identifier' SubClassOf 'Identifier (hybrid)' http://edamontology.org/data_2364 2D PAGE report '2D PAGE report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0372 DNA transcription 'DNA transcription' SubClassOf 'Sequence conversion' http://edamontology.org/data_1035 Gene ID (GeneDB) 'Gene ID (GeneDB)' SubClassOf 'Gene ID' http://edamontology.org/data_2365 Pathway or network accession 'Pathway or network accession' SubClassOf 'Pathway or network identifier' 'Pathway or network accession' SubClassOf 'Accession' http://edamontology.org/format_1351 HMMER emission and transition 'HMMER emission and transition' SubClassOf 'Textual format' 'HMMER emission and transition' SubClassOf 'HMM emission and transition counts format' http://edamontology.org/data_2360 Domain-domain interaction (indirect) 'Domain-domain interaction (indirect)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1030 Gene identifier (Entrez) 'Gene identifier (Entrez)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1350 MEME Dirichlet prior 'MEME Dirichlet prior' SubClassOf 'Textual format' 'MEME Dirichlet prior' SubClassOf 'Dirichlet distribution format' http://edamontology.org/topic_2953 Nucleic acid design 'Nucleic acid design' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1356 prosite-pattern 'prosite-pattern' SubClassOf 'Sequence motif format' 'prosite-pattern' SubClassOf 'Textual format' http://edamontology.org/format_1357 EMBOSS sequence pattern 'EMBOSS sequence pattern' SubClassOf 'Textual format' 'EMBOSS sequence pattern' SubClassOf 'Sequence motif format' http://edamontology.org/operation_3459 Functional clustering 'Functional clustering' SubClassOf 'Sequence clustering' http://edamontology.org/operation_3458 Single particle alignment and classification 'Single particle alignment and classification' SubClassOf 'Single particle analysis' 'Single particle alignment and classification' SubClassOf 'Classification' http://edamontology.org/operation_3457 Single particle analysis 'Single particle analysis' SubClassOf 'Structure analysis' 'Single particle analysis' SubClassOf 'Image analysis' http://edamontology.org/operation_3456 Rigid body refinement 'Rigid body refinement' SubClassOf 'Molecular model refinement' http://edamontology.org/data_1045 Species name 'Species name' SubClassOf 'Taxon' http://edamontology.org/operation_2120 Listfile processing 'Listfile processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1044 Kingdom name 'Kingdom name' SubClassOf 'Taxon' http://edamontology.org/data_2378 Protein-motif interaction 'Protein-motif interaction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3450 Neurite measurement 'Neurite measurement' SubClassOf 'Image analysis' http://edamontology.org/data_1043 CATH node ID 'CATH node ID' SubClassOf 'CATH identifier' http://edamontology.org/data_2379 Strain identifier 'Strain identifier' SubClassOf 'Organism identifier' http://edamontology.org/data_1042 SCOP sunid 'SCOP sunid' SubClassOf 'SCOP domain identifier' http://edamontology.org/data_1049 Directory name 'Directory name' SubClassOf 'Name' http://edamontology.org/data_2373 Spot ID 'Spot ID' SubClassOf 'Accession' 'Spot ID' SubClassOf 'Identifier (typed)' http://edamontology.org/operation_3455 Molecular replacement 'Molecular replacement' SubClassOf 'Molecular model refinement' http://edamontology.org/data_1048 Database ID 'Database ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2374 Spot serial number 'Spot serial number' SubClassOf 'Spot ID' http://edamontology.org/operation_2123 Small molecule data processing 'Small molecule data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3454 Phasing 'Phasing' SubClassOf 'Diffraction data analysis' http://edamontology.org/data_1047 URI 'URI' SubClassOf 'Identifier' http://edamontology.org/data_2375 Spot ID (HSC-2DPAGE) 'Spot ID (HSC-2DPAGE)' SubClassOf 'Spot ID' http://edamontology.org/operation_2122 Sequence alignment file processing 'Sequence alignment file processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3453 Diffraction data integration 'Diffraction data integration' SubClassOf 'Diffraction data analysis' http://edamontology.org/data_1046 Strain name 'Strain name' SubClassOf 'Organism name' 'Strain name' SubClassOf 'Strain identifier' http://edamontology.org/operation_2121 Sequence file editing 'Sequence file editing' SubClassOf 'Sequence editing' http://edamontology.org/format_3167 Experiment annotation format 'Experiment annotation format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_2370 ASTD ID (polya) 'ASTD ID (polya)' SubClassOf 'ASTD ID' http://edamontology.org/format_3166 Biological pathway or network report format 'Biological pathway or network report format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_2371 ASTD ID (tss) 'ASTD ID (tss)' SubClassOf 'ASTD ID' http://edamontology.org/data_2372 2D PAGE spot report '2D PAGE spot report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1041 SCOP concise classification string (sccs) 'SCOP concise classification string (sccs)' SubClassOf 'SCOP domain identifier' http://edamontology.org/format_3163 GCDML 'GCDML' SubClassOf 'Experiment annotation format' 'GCDML' SubClassOf 'XML' http://edamontology.org/data_1040 CATH domain ID 'CATH domain ID' SubClassOf 'CATH identifier' http://edamontology.org/format_3164 GTrack 'GTrack' SubClassOf 'Sequence annotation track format' 'GTrack' SubClassOf 'Sequence feature table format (text)' 'GTrack' SubClassOf 'Textual format' http://edamontology.org/operation_3469 RNA structure covariance model generation 'RNA structure covariance model generation' SubClassOf 'Generation' 'RNA structure covariance model generation' SubClassOf 'RNA secondary structure analysis' http://edamontology.org/data_1056 Database name 'Database name' SubClassOf 'Name' 'Database name' SubClassOf 'Database ID' http://edamontology.org/data_2388 TAIR accession (At gene) 'TAIR accession (At gene)' SubClassOf 'TAIR accession (gene)' http://edamontology.org/data_1055 LSID 'LSID' SubClassOf 'URN' http://edamontology.org/data_2389 UniSTS accession 'UniSTS accession' SubClassOf 'Sequence accession (nucleic acid)' http://edamontology.org/operation_3461 Virulence prediction 'Virulence prediction' SubClassOf 'Prediction and recognition' 'Virulence prediction' SubClassOf 'Sequence analysis' http://edamontology.org/operation_3460 Taxonomic classification 'Taxonomic classification' SubClassOf 'Sequence classification' http://edamontology.org/data_1053 URN 'URN' SubClassOf 'URI' http://edamontology.org/format_3160 NeXML 'NeXML' SubClassOf 'Phylogenetic tree format (XML)' 'NeXML' SubClassOf 'XML' http://edamontology.org/data_2384 IPI protein ID 'IPI protein ID' SubClassOf 'Sequence accession (protein)' http://edamontology.org/data_1059 File name extension 'File name extension' SubClassOf 'File name' http://edamontology.org/data_2385 RefSeq accession (protein) 'RefSeq accession (protein)' SubClassOf 'RefSeq accession' http://edamontology.org/operation_3465 Correlation 'Correlation' SubClassOf 'Operation' http://edamontology.org/data_1058 Enumerated file name 'Enumerated file name' SubClassOf 'File name' http://edamontology.org/data_2386 EPD ID 'EPD ID' SubClassOf 'Promoter ID' http://edamontology.org/data_2387 TAIR accession 'TAIR accession' SubClassOf 'Identifier (hybrid)' 'TAIR accession' SubClassOf 'Accession' http://edamontology.org/data_1057 Sequence database name 'Sequence database name' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3463 Gene expression correlation analysis 'Gene expression correlation analysis' SubClassOf 'Correlation' 'Gene expression correlation analysis' SubClassOf 'Gene expression profile comparison' http://edamontology.org/data_2380 CABRI accession 'CABRI accession' SubClassOf 'Accession' 'CABRI accession' SubClassOf 'Identifier (hybrid)' http://edamontology.org/format_3156 BioPAX 'BioPAX' SubClassOf 'Biological pathway or network format' http://edamontology.org/data_2381 Experiment report (genotyping) 'Experiment report (genotyping)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3155 SBRML 'SBRML' SubClassOf 'Biological pathway or network report format' 'SBRML' SubClassOf 'XML' http://edamontology.org/data_2382 Genotype experiment ID 'Genotype experiment ID' SubClassOf 'Accession' 'Genotype experiment ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2383 EGA accession 'EGA accession' SubClassOf 'Genotype experiment ID' http://edamontology.org/format_3157 EBI Application Result XML 'EBI Application Result XML' SubClassOf 'Alignment format (pair only)' 'EBI Application Result XML' SubClassOf 'Database hits (sequence) format' 'EBI Application Result XML' SubClassOf 'XML' http://edamontology.org/data_1052 URL 'URL' SubClassOf 'URI' http://edamontology.org/data_1051 Ontology name 'Ontology name' SubClassOf 'Ontology identifier' 'Ontology name' SubClassOf 'Name' http://edamontology.org/data_1050 File name 'File name' SubClassOf 'Name' http://edamontology.org/format_3159 phyloXML 'phyloXML' SubClassOf 'XML' 'phyloXML' SubClassOf 'Phylogenetic tree format (XML)' http://edamontology.org/operation_3437 Article comparison 'Article comparison' SubClassOf 'Comparison' http://edamontology.org/operation_3436 Aggregation 'Aggregation' SubClassOf 'Data handling' http://edamontology.org/operation_3435 Standardisation and normalisation 'Standardisation and normalisation' SubClassOf 'Statistical calculation' http://edamontology.org/operation_3434 Conversion 'Conversion' SubClassOf 'Operation' http://edamontology.org/operation_3439 Pathway or network prediction 'Pathway or network prediction' SubClassOf 'Prediction and recognition' 'Pathway or network prediction' SubClassOf 'Pathway or network analysis' http://edamontology.org/operation_3438 Calculation 'Calculation' SubClassOf 'Operation' http://edamontology.org/data_1067 Phylogenetic distance matrix identifier 'Phylogenetic distance matrix identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2399 Gene transcriptional features report 'Gene transcriptional features report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1066 Sequence alignment ID 'Sequence alignment ID' SubClassOf 'Accession' 'Sequence alignment ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_1065 Sequence signature identifier 'Sequence signature identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1064 Sequence set ID 'Sequence set ID' SubClassOf 'Accession' 'Sequence set ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2395 Fungi annotation 'Fungi annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3433 Assembly 'Assembly' SubClassOf 'Operation' http://edamontology.org/data_2396 Fungi annotation (anamorph) 'Fungi annotation (anamorph)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3432 Clustering 'Clustering' SubClassOf 'Operation' http://edamontology.org/data_1069 Comparison matrix identifier 'Comparison matrix identifier' SubClassOf 'Matrix identifier' http://edamontology.org/data_2397 Gene features report (exon) 'Gene features report (exon)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3431 Deposition 'Deposition' SubClassOf 'Operation' http://edamontology.org/data_1068 Phylogenetic tree ID 'Phylogenetic tree ID' SubClassOf 'Accession' 'Phylogenetic tree ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2398 Ensembl protein ID 'Ensembl protein ID' SubClassOf 'Ensembl ID' 'Ensembl protein ID' SubClassOf 'Protein accession' http://edamontology.org/operation_3430 Nucleic acid sequence feature detection 'Nucleic acid sequence feature detection' SubClassOf 'Nucleic acid feature detection' 'Nucleic acid sequence feature detection' SubClassOf 'Sequence feature detection' http://edamontology.org/data_2391 UTR accession 'UTR accession' SubClassOf 'Sequence accession (nucleic acid)' http://edamontology.org/data_2392 UniParc accession 'UniParc accession' SubClassOf 'Sequence accession (protein)' http://edamontology.org/data_2393 mFLJ/mKIAA number 'mFLJ/mKIAA number' SubClassOf 'Gene ID' http://edamontology.org/data_1063 Sequence identifier 'Sequence identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_1062 Database entry identifier 'Database entry identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1061 QSAR descriptor name 'QSAR descriptor name' SubClassOf 'Molecular property identifier' 'QSAR descriptor name' SubClassOf 'Name' http://edamontology.org/data_1060 File base name 'File base name' SubClassOf 'File name' http://edamontology.org/data_2390 UNITE accession 'UNITE accession' SubClassOf 'Sequence accession (nucleic acid)' http://edamontology.org/operation_3447 Diffraction data reduction 'Diffraction data reduction' SubClassOf 'Diffraction data analysis' http://edamontology.org/operation_3446 Cell migration analysis 'Cell migration analysis' SubClassOf 'Image analysis' http://edamontology.org/operation_3445 Diffraction data analysis 'Diffraction data analysis' SubClassOf 'Structure analysis' http://edamontology.org/data_1078 Experiment annotation ID 'Experiment annotation ID' SubClassOf 'Identifier (typed)' http://edamontology.org/operation_3440 Genome assembly 'Genome assembly' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1077 Transcription factor identifier 'Transcription factor identifier' SubClassOf 'Protein identifier' http://edamontology.org/data_1076 Codon usage table name 'Codon usage table name' SubClassOf 'Name' 'Codon usage table name' SubClassOf 'Codon usage table ID' http://edamontology.org/data_1075 Protein family identifier 'Protein family identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/operation_3443 Image analysis 'Image analysis' SubClassOf 'Analysis' http://edamontology.org/data_1079 Electron microscopy model ID 'Electron microscopy model ID' SubClassOf 'Accession' 'Electron microscopy model ID' SubClassOf 'Identifier (typed)' http://edamontology.org/operation_3441 Plotting 'Plotting' SubClassOf 'Operation' http://edamontology.org/data_1070 Structure ID 'Structure ID' SubClassOf 'Accession' 'Structure ID' SubClassOf 'Structure identifier' http://edamontology.org/data_1074 Protein interaction ID 'Protein interaction ID' SubClassOf 'Identifier (typed)' 'Protein interaction ID' SubClassOf 'Accession' http://edamontology.org/data_1073 Amino acid index ID 'Amino acid index ID' SubClassOf 'Accession' 'Amino acid index ID' SubClassOf 'Matrix identifier' http://edamontology.org/data_1072 Structure alignment ID 'Structure alignment ID' SubClassOf 'Identifier (typed)' 'Structure alignment ID' SubClassOf 'Accession' http://edamontology.org/data_1071 Structural (3D) profile ID 'Structural (3D) profile ID' SubClassOf 'Identifier (typed)' 'Structural (3D) profile ID' SubClassOf 'Accession' http://edamontology.org/data_1089 FlyBase ID 'FlyBase ID' SubClassOf 'Accession' 'FlyBase ID' SubClassOf 'Identifier (hybrid)' http://edamontology.org/data_1088 Article ID 'Article ID' SubClassOf 'Accession' 'Article ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_1087 Ontology concept ID 'Ontology concept ID' SubClassOf 'Accession' 'Ontology concept ID' SubClassOf 'Ontology concept identifier' http://edamontology.org/data_1086 Compound identifier 'Compound identifier' SubClassOf 'Molecule identifier' http://edamontology.org/data_1081 Genotype and phenotype annotation ID 'Genotype and phenotype annotation ID' SubClassOf 'Identifier (typed)' 'Genotype and phenotype annotation ID' SubClassOf 'Accession' http://edamontology.org/data_1080 Gene expression report ID 'Gene expression report ID' SubClassOf 'Identifier (typed)' 'Gene expression report ID' SubClassOf 'Accession' http://edamontology.org/data_1085 Biological model ID 'Biological model ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_1084 Data resource definition ID 'Data resource definition ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_1083 Workflow ID 'Workflow ID' SubClassOf 'Identifier (typed)' 'Workflow ID' SubClassOf 'Accession' http://edamontology.org/data_1082 Pathway or network identifier 'Pathway or network identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_1099 UniProt accession (extended) 'UniProt accession (extended)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1098 RefSeq accession 'RefSeq accession' SubClassOf 'Sequence accession (hybrid)' http://edamontology.org/data_1097 Sequence accession (nucleic acid) 'Sequence accession (nucleic acid)' SubClassOf 'Sequence accession' http://edamontology.org/data_1092 WormBase class 'WormBase class' SubClassOf 'WormBase identifier' http://edamontology.org/data_1091 WormBase name 'WormBase name' SubClassOf 'Name' 'WormBase name' SubClassOf 'WormBase identifier' http://edamontology.org/data_1096 Sequence accession (protein) 'Sequence accession (protein)' SubClassOf 'Sequence accession' http://edamontology.org/data_1095 EMBOSS Uniform Sequence Address 'EMBOSS Uniform Sequence Address' SubClassOf 'Name' 'EMBOSS Uniform Sequence Address' SubClassOf 'Sequence identifier' http://edamontology.org/data_1094 Sequence type 'Sequence type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1093 Sequence accession 'Sequence accession' SubClassOf 'Sequence identifier' 'Sequence accession' SubClassOf 'Accession' http://edamontology.org/operation_3478 Phylogenetic tree reconstruction 'Phylogenetic tree reconstruction' SubClassOf 'Phylogenetic tree generation' http://edamontology.org/operation_3472 k-mer counting 'k-mer counting' SubClassOf 'Sequence composition calculation' http://edamontology.org/operation_3471 Nucleic acid folding prediction (alignment-based) 'Nucleic acid folding prediction (alignment-based)' SubClassOf 'Nucleic acid folding analysis' http://edamontology.org/operation_3470 RNA secondary structure prediction (shape-based) 'RNA secondary structure prediction (shape-based)' SubClassOf 'RNA secondary structure prediction' http://edamontology.org/topic_3400 Allergy, clinical immunology and immunotherapeutics. 'Allergy, clinical immunology and immunotherapeutics.' SubClassOf 'Medicine' http://edamontology.org/operation_3482 Antimicrobial resistance prediction 'Antimicrobial resistance prediction' SubClassOf 'Sequence analysis' 'Antimicrobial resistance prediction' SubClassOf 'Prediction and recognition' http://edamontology.org/operation_3481 Probabilistic sequence generation 'Probabilistic sequence generation' SubClassOf 'Probabilistic data generation' 'Probabilistic sequence generation' SubClassOf 'Sequence generation' http://edamontology.org/topic_3409 Gastroenterology 'Gastroenterology' SubClassOf 'Medicine' http://edamontology.org/operation_3480 Probabilistic data generation 'Probabilistic data generation' SubClassOf 'Generation' http://edamontology.org/topic_3404 Dermatology 'Dermatology' SubClassOf 'Medicine' http://edamontology.org/topic_3403 Critical care medicine 'Critical care medicine' SubClassOf 'Medicine' http://edamontology.org/topic_3402 Anaesthesiology 'Anaesthesiology' SubClassOf 'Medicine' http://edamontology.org/topic_3401 Pain medicine 'Pain medicine' SubClassOf 'Medicine' http://edamontology.org/topic_3408 Haematology 'Haematology' SubClassOf 'Medicine' http://edamontology.org/topic_3407 Endocrinology and metabolism 'Endocrinology and metabolism' SubClassOf 'Medicine' http://edamontology.org/topic_3406 Ear, nose and throat medicine 'Ear, nose and throat medicine' SubClassOf 'Medicine' http://edamontology.org/topic_3405 Dentistry 'Dentistry' SubClassOf 'Medicine' http://edamontology.org/operation_2089 Sequence alignment refinement 'Sequence alignment refinement' SubClassOf 'Sequence alignment analysis' 'Sequence alignment refinement' SubClassOf 'Optimisation and refinement' http://edamontology.org/topic_3301 Microbiology 'Microbiology' SubClassOf 'Biology' http://edamontology.org/topic_3300 Physiology 'Physiology' SubClassOf 'Medicine' http://edamontology.org/topic_3305 Public health and epidemiology 'Public health and epidemiology' SubClassOf 'Medicine' http://edamontology.org/topic_3304 Neurobiology 'Neurobiology' SubClassOf 'Biomedical science' http://edamontology.org/topic_3303 Medicine 'Medicine' SubClassOf 'Topic' http://edamontology.org/topic_3302 Parasitology 'Parasitology' SubClassOf 'Biomedical science' http://edamontology.org/topic_3308 Transcriptomics 'Transcriptomics' SubClassOf 'Genomics' 'Transcriptomics' SubClassOf 'Gene expression' http://edamontology.org/topic_3307 Computational biology 'Computational biology' SubClassOf 'Topic' http://edamontology.org/topic_3306 Biophysics 'Biophysics' SubClassOf 'Biology' 'Biophysics' SubClassOf 'Physics' http://edamontology.org/topic_3316 Computer science 'Computer science' SubClassOf 'Topic' http://edamontology.org/topic_3315 Mathematics 'Mathematics' SubClassOf 'Topic' http://edamontology.org/topic_3314 Chemistry 'Chemistry' SubClassOf 'Topic' http://edamontology.org/topic_3318 Physics 'Physics' SubClassOf 'Topic' http://edamontology.org/topic_3323 Metabolic disease 'Metabolic disease' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3322 Respiratory medicine 'Respiratory medicine' SubClassOf 'Medicine' http://edamontology.org/topic_3321 Molecular genetics 'Molecular genetics' SubClassOf 'Genetics' 'Molecular genetics' SubClassOf 'Computational biology' http://edamontology.org/topic_3320 RNA splicing 'RNA splicing' SubClassOf 'RNA' 'RNA splicing' SubClassOf 'Gene expression' http://edamontology.org/topic_3325 Rare diseases 'Rare diseases' SubClassOf 'Pathology' http://edamontology.org/topic_3324 Infectious disease 'Infectious disease' SubClassOf 'Pathology' http://edamontology.org/data_1801 Gene ID (GeneDB Trypanosoma brucei) 'Gene ID (GeneDB Trypanosoma brucei)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1800 Gene ID (GeneDB Schizosaccharomyces pombe) 'Gene ID (GeneDB Schizosaccharomyces pombe)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1805 Gene ID (WormBase) 'Gene ID (WormBase)' SubClassOf 'Gene ID' 'Gene ID (WormBase)' SubClassOf 'WormBase identifier' http://edamontology.org/topic_3334 Neurology 'Neurology' SubClassOf 'Medicine' http://edamontology.org/data_1804 Gene ID (SGN) 'Gene ID (SGN)' SubClassOf 'Gene ID' http://edamontology.org/data_1803 Gene ID (Virginia microbial) 'Gene ID (Virginia microbial)' SubClassOf 'Gene ID' http://edamontology.org/topic_3332 Computational chemistry 'Computational chemistry' SubClassOf 'Chemistry' 'Computational chemistry' SubClassOf 'Computer science' http://edamontology.org/data_1802 Gene ID (Gramene) 'Gene ID (Gramene)' SubClassOf 'Gene ID' http://edamontology.org/topic_3338 Mouse clinic 'Mouse clinic' SubClassOf 'Sample collections' http://edamontology.org/topic_3337 Biobank 'Biobank' SubClassOf 'Sample collections' http://edamontology.org/topic_3336 Drug discovery 'Drug discovery' SubClassOf 'Chemistry' 'Drug discovery' SubClassOf 'Medicine research and development' http://edamontology.org/topic_3335 Cardiology 'Cardiology' SubClassOf 'Medicine' http://edamontology.org/topic_3339 Microbial collection 'Microbial collection' SubClassOf 'Sample collections' http://edamontology.org/topic_3341 Clone library 'Clone library' SubClassOf 'Sample collections' http://edamontology.org/topic_3340 Cell culture collection 'Cell culture collection' SubClassOf 'Sample collections' http://edamontology.org/topic_3345 Data identity and mapping 'Data identity and mapping' SubClassOf 'Data management' http://edamontology.org/topic_3344 Biomedical science 'Biomedical science' SubClassOf 'Topic' http://edamontology.org/topic_3343 Compound libraries and screening 'Compound libraries and screening' SubClassOf 'Drug discovery' http://edamontology.org/topic_3342 Translational medicine 'Translational medicine' SubClassOf 'Medicine' http://edamontology.org/data_1807 ORF name 'ORF name' SubClassOf 'ORF identifier' 'ORF name' SubClassOf 'Name' http://edamontology.org/data_1806 Gene synonym 'Gene synonym' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3346 Sequence search 'Sequence search' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3361 Laboratory techniques 'Laboratory techniques' SubClassOf 'Topic' http://edamontology.org/topic_3360 Biomarkers 'Biomarkers' SubClassOf 'Biology' http://edamontology.org/topic_3366 Data integration and warehousing 'Data integration and warehousing' SubClassOf 'Data management' http://edamontology.org/topic_3365 Data architecture, analysis and design 'Data architecture, analysis and design' SubClassOf 'Data management' http://edamontology.org/format_3097 Protein domain classification format 'Protein domain classification format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_3099 Raw CATH domain classification format 'Raw CATH domain classification format' SubClassOf 'Protein domain classification format' http://edamontology.org/format_3098 Raw SCOP domain classification format 'Raw SCOP domain classification format' SubClassOf 'Protein domain classification format' http://edamontology.org/topic_3369 Chemical biology 'Chemical biology' SubClassOf 'Synthetic chemistry' 'Chemical biology' SubClassOf 'Biology' http://edamontology.org/topic_3368 Biomaterials 'Biomaterials' SubClassOf 'Biotechnology' http://edamontology.org/topic_3374 Drug formulation and delivery 'Drug formulation and delivery' SubClassOf 'Medicine research and development' http://edamontology.org/topic_3373 Drug development 'Drug development' SubClassOf 'Medicine research and development' http://edamontology.org/topic_3372 Software engineering 'Software engineering' SubClassOf 'Computer science' http://edamontology.org/topic_3371 Synthetic chemistry 'Synthetic chemistry' SubClassOf 'Chemistry' http://edamontology.org/topic_3378 Pharmacovigilence 'Pharmacovigilence' SubClassOf 'Safety sciences' http://edamontology.org/topic_3377 Safety sciences 'Safety sciences' SubClassOf 'Medicine research and development' http://edamontology.org/topic_3376 Medicines research and development Medicine research and development 'Medicine research and development' SubClassOf 'Biomedical science' http://edamontology.org/topic_3375 Pharmacokinetics and pharmacodynamics 'Pharmacokinetics and pharmacodynamics' SubClassOf 'Medicine research and development' http://edamontology.org/topic_3370 Analytical chemistry 'Analytical chemistry' SubClassOf 'Chemistry' http://edamontology.org/topic_3379 Preclinical and clinical studies 'Preclinical and clinical studies' SubClassOf 'Experimental design and studies' 'Preclinical and clinical studies' SubClassOf 'Medicine research and development' http://kt.ijs.si/panovp/OntoDM#OntoDM_000078 pattern specification 'pattern specification' SubClassOf 'single generalization specification' http://edamontology.org/data_1856 PDB insertion code 'PDB insertion code' SubClassOf 'Sequence position' http://edamontology.org/operation_2931 Secondary structure comparison 'Secondary structure comparison' SubClassOf 'Comparison' http://edamontology.org/topic_3385 Light microscopy 'Light microscopy' SubClassOf 'Imaging' http://edamontology.org/data_1855 Clone ID 'Clone ID' SubClassOf 'Transcript ID' http://edamontology.org/operation_2930 Protein property comparison 'Protein property comparison' SubClassOf 'Protein comparison' http://edamontology.org/topic_3384 Medical imaging 'Medical imaging' SubClassOf 'Imaging' http://edamontology.org/topic_3383 Biological imaging 'Biological imaging' SubClassOf 'Imaging' http://edamontology.org/data_1853 Chromosome annotation (aberration) 'Chromosome annotation (aberration)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3382 Imaging 'Imaging' SubClassOf 'Laboratory techniques' http://edamontology.org/operation_2935 Microarray wave graph plotting 'Microarray wave graph plotting' SubClassOf 'Microarray data rendering' http://edamontology.org/data_1859 Deletion map 'Deletion map' SubClassOf 'Cytogenetic map' http://edamontology.org/operation_2934 Microarray cluster textual view generation 'Microarray cluster textual view generation' SubClassOf 'Microarray data rendering' http://edamontology.org/topic_3388 Molecular medicine 'Molecular medicine' SubClassOf 'Translational medicine' http://edamontology.org/data_1858 Isotropic B factor 'Isotropic B factor' SubClassOf 'Atomic property' http://edamontology.org/topic_3387 Marine biology 'Marine biology' SubClassOf 'Biology' http://edamontology.org/data_1857 Atomic occupancy 'Atomic occupancy' SubClassOf 'Atomic property' http://edamontology.org/operation_2932 Hopp and Woods plotting 'Hopp and Woods plotting' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3386 Laboratory animal science 'Laboratory animal science' SubClassOf 'Biomedical science' http://edamontology.org/data_1852 Sequence assembly component 'Sequence assembly component' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2928 Alignment 'Alignment' SubClassOf 'Generation' http://kt.ijs.si/panovp/OntoDM#OntoDM_000087 probability distribution estimation task 'probability distribution estimation task' SubClassOf 'data mining task' http://edamontology.org/operation_2929 Protein fragment weight comparison 'Protein fragment weight comparison' SubClassOf 'Protein molecular weight calculation' 'Protein fragment weight comparison' SubClassOf 'Protein property comparison' http://edamontology.org/data_1867 Protein fold name 'Protein fold name' SubClassOf 'Name' http://edamontology.org/topic_3396 Systems medicine 'Systems medicine' SubClassOf 'Medicine' http://edamontology.org/data_1866 Map type 'Map type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3395 Regnerative medicine 'Regnerative medicine' SubClassOf 'Biomedical science' http://edamontology.org/data_1865 Map feature 'Map feature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3394 Regulatory affairs 'Regulatory affairs' SubClassOf 'Medicine research and development' http://edamontology.org/data_1864 Map set data 'Map set data' SubClassOf 'Map data' http://edamontology.org/topic_3393 Quality affairs 'Quality affairs' SubClassOf 'Medicine research and development' http://kt.ijs.si/panovp/OntoDM#OntoDM_000092 pattern discovery task 'pattern discovery task' SubClassOf 'data mining task' http://edamontology.org/topic_3399 Geriatric medicine 'Geriatric medicine' SubClassOf 'Medicine' http://edamontology.org/data_1869 Organism identifier 'Organism identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/topic_3398 Bioengineering 'Bioengineering' SubClassOf 'Biotechnology' http://edamontology.org/data_1868 Taxon 'Taxon' SubClassOf 'Organism name' http://edamontology.org/topic_3397 Veterinary medicine 'Veterinary medicine' SubClassOf 'Medicine' http://edamontology.org/data_1863 Haplotype map 'Haplotype map' SubClassOf 'Genetic map' http://edamontology.org/topic_3391 Omics 'Omics' SubClassOf 'Topic' http://edamontology.org/topic_3390 Nutritional science 'Nutritional science' SubClassOf 'Biomedical science' http://edamontology.org/data_1860 QTL map 'QTL map' SubClassOf 'Genetic map' http://edamontology.org/format_1320 REBASE restriction sites 'REBASE restriction sites' SubClassOf 'Nucleic acid features (restriction sites) format' 'REBASE restriction sites' SubClassOf 'Textual format' http://kt.ijs.si/panovp/OntoDM#OntoDM_000098 data mining task 'data mining task' SubClassOf 'information processing' http://edamontology.org/data_1878 Misspelling 'Misspelling' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1877 Synonym 'Synonym' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1875 NCBI taxon 'NCBI taxon' SubClassOf 'Taxon' http://edamontology.org/format_1319 restover format 'restover format' SubClassOf 'Textual format' 'restover format' SubClassOf 'Nucleic acid features (restriction sites) format' http://edamontology.org/data_1879 Acronym 'Acronym' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1870 Genus name 'Genus name' SubClassOf 'Taxon' http://edamontology.org/data_1874 Genbank common name 'Genbank common name' SubClassOf 'Organism name' http://edamontology.org/data_1873 iHOP organism ID 'iHOP organism ID' SubClassOf 'Organism accession' http://edamontology.org/data_1872 Taxonomic classification 'Taxonomic classification' SubClassOf 'Organism name' http://edamontology.org/format_1316 est2genome format 'est2genome format' SubClassOf 'Gene annotation format' 'est2genome format' SubClassOf 'Textual format' http://edamontology.org/format_1318 restrict format 'restrict format' SubClassOf 'Nucleic acid features (restriction sites) format' 'restrict format' SubClassOf 'Textual format' http://edamontology.org/data_1889 Gene name (DragonDB) 'Gene name (DragonDB)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0301 Sequence-to-3D-profile alignment 'Sequence-to-3D-profile alignment' SubClassOf 'Protein fold recognition' 'Sequence-to-3D-profile alignment' SubClassOf 'Alignment' http://edamontology.org/operation_2964 Codon usage fraction calculation 'Codon usage fraction calculation' SubClassOf 'Codon usage analysis' http://edamontology.org/data_1888 Gene ID (MIPS Medicago) 'Gene ID (MIPS Medicago)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0302 Protein threading 'Protein threading' SubClassOf 'Alignment' 'Protein threading' SubClassOf 'Protein fold recognition' http://edamontology.org/operation_2963 Codon usage bias plotting 'Codon usage bias plotting' SubClassOf 'Plotting' 'Codon usage bias plotting' SubClassOf 'Codon usage bias calculation' http://edamontology.org/data_1887 Gene ID (MIPS Maize) 'Gene ID (MIPS Maize)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2962 Codon usage bias calculation 'Codon usage bias calculation' SubClassOf 'Codon usage analysis' http://edamontology.org/data_1886 Blattner number 'Blattner number' SubClassOf 'Gene ID' http://edamontology.org/operation_0300 Sequence-to-profile alignment 'Sequence-to-profile alignment' SubClassOf 'Sequence alignment' http://edamontology.org/operation_0305 Literature search 'Literature search' SubClassOf 'Database search' http://edamontology.org/operation_0306 Text mining 'Text mining' SubClassOf 'Analysis' 'Text mining' SubClassOf 'Prediction and recognition' http://edamontology.org/operation_0303 Protein fold recognition 'Protein fold recognition' SubClassOf 'Protein feature detection' 'Protein fold recognition' SubClassOf 'Protein sequence analysis' 'Protein fold recognition' SubClassOf 'Protein structure analysis' 'Protein fold recognition' SubClassOf 'Protein comparison' http://edamontology.org/operation_0304 Metadata retrieval 'Metadata retrieval' SubClassOf 'Data retrieval' http://edamontology.org/data_1881 Author ID 'Author ID' SubClassOf 'Person identifier' http://edamontology.org/data_1880 Misnomer 'Misnomer' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1885 Gene ID (GeneFarm) 'Gene ID (GeneFarm)' SubClassOf 'Gene ID' http://edamontology.org/data_1884 UniProt keywords 'UniProt keywords' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1883 Annotated URI 'Annotated URI' SubClassOf 'Data reference' http://edamontology.org/data_1882 DragonDB author identifier 'DragonDB author identifier' SubClassOf 'Author ID' http://kt.ijs.si/panovp/OntoDM#OntoDM_000038 data mining algorithm 'data mining algorithm' SubClassOf 'algorithm' http://kt.ijs.si/panovp/OntoDM#OntoDM_000037 ensemble specification 'ensemble specification' SubClassOf 'generalization specification' http://edamontology.org/operation_0312 Sequencing-based expression profile data processing 'Sequencing-based expression profile data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1899 Locus ID (CMR) 'Locus ID (CMR)' SubClassOf 'Locus ID' http://edamontology.org/operation_0313 Gene expression profile clustering 'Gene expression profile clustering' SubClassOf 'Clustering' 'Gene expression profile clustering' SubClassOf 'Gene expression profile comparison' http://edamontology.org/data_1898 Locus ID (CGD) 'Locus ID (CGD)' SubClassOf 'Locus ID' http://edamontology.org/operation_0310 Sequence assembly 'Sequence assembly' SubClassOf 'Assembly' 'Sequence assembly' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/data_1897 Locus ID (MGG) 'Locus ID (MGG)' SubClassOf 'Locus ID' http://edamontology.org/operation_0311 Microarray data standardisation and normalisation 'Microarray data standardisation and normalisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0316 Functional profiling 'Functional profiling' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0317 EST and cDNA sequence analysis 'EST and cDNA sequence analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0314 Gene expression profiling 'Gene expression profiling' SubClassOf 'Gene expression analysis' 'Gene expression profiling' SubClassOf 'Generation' http://edamontology.org/operation_0315 Gene expression profile comparison 'Gene expression profile comparison' SubClassOf 'Nucleic acid comparison' 'Gene expression profile comparison' SubClassOf 'Gene expression analysis' http://edamontology.org/data_1892 Gene name (GeneFarm) 'Gene name (GeneFarm)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1891 iHOP symbol 'iHOP symbol' SubClassOf 'Identifier (hybrid)' 'iHOP symbol' SubClassOf 'Protein accession' 'iHOP symbol' SubClassOf 'Gene ID' http://edamontology.org/data_1890 Gene name (Arabidopsis) 'Gene name (Arabidopsis)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1896 Locus ID (ASPGD) 'Locus ID (ASPGD)' SubClassOf 'Locus ID' http://edamontology.org/data_1895 Locus ID (AGI) 'Locus ID (AGI)' SubClassOf 'Locus ID' http://edamontology.org/data_1893 Locus ID 'Locus ID' SubClassOf 'Identifier (typed)' 'Locus ID' SubClassOf 'Accession' http://edamontology.org/operation_0309 Microarray probe design 'Microarray probe design' SubClassOf 'Primer and probe design' http://edamontology.org/operation_0307 Virtual PCR 'Virtual PCR' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/operation_0308 PCR primer design 'PCR primer design' SubClassOf 'Primer and probe design' http://edamontology.org/operation_2942 Microarray tree-map rendering 'Microarray tree-map rendering' SubClassOf 'Microarray data rendering' http://edamontology.org/operation_2941 Whole microarray graph plotting 'Whole microarray graph plotting' SubClassOf 'Microarray data rendering' http://edamontology.org/operation_2940 Microarray scatter plot plotting 'Microarray scatter plot plotting' SubClassOf 'Microarray data rendering' http://edamontology.org/operation_2946 Alignment analysis 'Alignment analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2945 Analysis 'Analysis' SubClassOf 'Operation' http://edamontology.org/operation_2944 Physical mapping 'Physical mapping' SubClassOf 'DNA mapping' http://edamontology.org/operation_2943 Microarray Box-Whisker plot plotting 'Microarray Box-Whisker plot plotting' SubClassOf 'Microarray data rendering' http://edamontology.org/operation_2939 Microarray principal component plotting 'Microarray principal component plotting' SubClassOf 'Microarray data rendering' http://edamontology.org/operation_2938 Microarray tree or dendrogram rendering 'Microarray tree or dendrogram rendering' SubClassOf 'Microarray data rendering' http://edamontology.org/operation_2937 Microarray proximity map plotting 'Microarray proximity map plotting' SubClassOf 'Microarray data rendering' http://edamontology.org/operation_2936 Microarray dendrograph plotting 'Microarray dendrograph plotting' SubClassOf 'Microarray data rendering' http://edamontology.org/operation_2952 Structure alignment processing 'Structure alignment processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2951 Alignment processing 'Alignment processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2950 Residue distance calculation 'Residue distance calculation' SubClassOf 'Residue interaction calculation' http://edamontology.org/format_2607 completely unambiguous pure protein 'completely unambiguous pure protein' SubClassOf 'protein' 'completely unambiguous pure protein' SubClassOf 'completely unambiguous pure' http://edamontology.org/data_0583 Directory metadata 'Directory metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0581 Database 'Database' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2949 Protein interaction analysis 'Protein interaction analysis' SubClassOf 'Protein analysis' http://edamontology.org/operation_2948 Molecular interaction analysis 'Molecular interaction analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2947 Article analysis 'Article analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0467 Protein secondary structure prediction (integrated) 'Protein secondary structure prediction (integrated)' SubClassOf 'Protein secondary structure prediction' http://edamontology.org/operation_0464 tRNA gene prediction 'tRNA gene prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_0465 siRNA binding specificity prediction 'siRNA binding specificity prediction' SubClassOf 'Transcription regulatory element prediction (trans)' http://edamontology.org/operation_0468 Protein secondary structure prediction (helices) 'Protein secondary structure prediction (helices)' SubClassOf 'Protein secondary structure prediction' http://edamontology.org/operation_0469 Protein secondary structure prediction (turns) 'Protein secondary structure prediction (turns)' SubClassOf 'Protein secondary structure prediction' http://edamontology.org/data_3743 Ordination plot 'Ordination plot' SubClassOf 'Protein property' 'Ordination plot' SubClassOf 'Plot' http://edamontology.org/operation_0463 microRNA detection 'microRNA detection' SubClassOf 'Transcription regulatory element prediction (trans)' http://edamontology.org/operation_0460 Nucleic acid temperature profile plotting 'Nucleic acid temperature profile plotting' SubClassOf 'Nucleic acid melting profile plotting' http://edamontology.org/operation_0461 Nucleic acid curvature calculation 'Nucleic acid curvature calculation' SubClassOf 'Nucleic acid property calculation' http://edamontology.org/operation_0477 Protein modelling 'Protein modelling' SubClassOf 'Modelling and simulation' 'Protein modelling' SubClassOf 'Protein structure analysis' 'Protein modelling' SubClassOf 'Protein structure prediction' http://edamontology.org/operation_3503 Incident curve plotting 'Incident curve plotting' SubClassOf 'Plotting' http://edamontology.org/operation_0478 Molecular docking 'Molecular docking' SubClassOf 'Protein interaction prediction' 'Molecular docking' SubClassOf 'Structure analysis' http://edamontology.org/operation_3502 Chemical class enrichment 'Chemical class enrichment' SubClassOf 'Over-representation analysis' http://edamontology.org/operation_0475 Nucleic acid structure prediction 'Nucleic acid structure prediction' SubClassOf 'Structure prediction' 'Nucleic acid structure prediction' SubClassOf 'Prediction and recognition (nucleic acid)' 'Nucleic acid structure prediction' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/operation_3501 Over-representation analysis 'Over-representation analysis' SubClassOf 'Analysis' http://edamontology.org/operation_0476 Ab initio structure prediction 'Ab initio structure prediction' SubClassOf 'Protein structure prediction' http://edamontology.org/data_3756 Localisation score 'Localisation score' SubClassOf 'Score' http://edamontology.org/data_3757 Unimod ID 'Unimod ID' SubClassOf 'Protein modification ID' http://edamontology.org/operation_0479 Protein modelling (backbone) 'Protein modelling (backbone)' SubClassOf 'Protein modelling' http://edamontology.org/data_3759 ProteomeXchange ID 'ProteomeXchange ID' SubClassOf 'Experiment annotation ID' http://edamontology.org/operation_3504 Variant pattern analysis 'Variant pattern analysis' SubClassOf 'Genetic variation analysis' http://edamontology.org/data_3753 Over-representation report 'Over-representation report' SubClassOf 'Report' http://edamontology.org/operation_0470 Protein secondary structure prediction (coils) 'Protein secondary structure prediction (coils)' SubClassOf 'Protein secondary structure prediction' http://edamontology.org/data_3754 GO-term enrichment report 'GO-term enrichment report' SubClassOf 'Over-representation report' http://edamontology.org/operation_0473 GPCR analysis 'GPCR analysis' SubClassOf 'Transmembrane protein analysis' http://edamontology.org/operation_0474 Protein structure prediction 'Protein structure prediction' SubClassOf 'Structure prediction' 'Protein structure prediction' SubClassOf 'Protein sequence analysis' 'Protein structure prediction' SubClassOf 'Prediction and recognition (protein)' http://edamontology.org/operation_0471 Protein secondary structure prediction (disulfide bonds) 'Protein secondary structure prediction (disulfide bonds)' SubClassOf 'Protein secondary structure prediction' http://edamontology.org/operation_0472 GPCR prediction 'GPCR prediction' SubClassOf 'GPCR analysis' 'GPCR prediction' SubClassOf 'Transmembrane protein prediction' http://edamontology.org/operation_0444 Matrix/scaffold attachment site prediction 'Matrix/scaffold attachment site prediction' SubClassOf 'Regulatory element prediction' http://edamontology.org/operation_0445 Transcription factor binding site prediction 'Transcription factor binding site prediction' SubClassOf 'Promoter prediction' http://edamontology.org/data_1106 dbSNP ID 'dbSNP ID' SubClassOf 'Sequence variation ID' http://edamontology.org/operation_0442 Transcription regulatory element prediction (RNA-cis) 'Transcription regulatory element prediction (RNA-cis)' SubClassOf 'Regulatory element prediction' http://edamontology.org/operation_1774 Annotation retrieval 'Annotation retrieval' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1105 dbEST accession 'dbEST accession' SubClassOf 'EST accession' 'dbEST accession' SubClassOf 'GenBank accession' http://edamontology.org/operation_0443 Transcription regulatory element prediction (trans) 'Transcription regulatory element prediction (trans)' SubClassOf 'Regulatory element prediction' http://edamontology.org/operation_0448 Sequence alignment analysis (conservation) 'Sequence alignment analysis (conservation)' SubClassOf 'Sequence alignment analysis' http://edamontology.org/operation_0449 Sequence alignment analysis (site correlation) 'Sequence alignment analysis (site correlation)' SubClassOf 'Correlation' 'Sequence alignment analysis (site correlation)' SubClassOf 'Sequence alignment analysis' http://edamontology.org/data_3769 BRENDA ontology concept ID 'BRENDA ontology concept ID' SubClassOf 'Ontology concept ID' http://edamontology.org/operation_1778 Protein function comparison 'Protein function comparison' SubClassOf 'Protein comparison' 'Protein function comparison' SubClassOf 'Protein function analysis' http://edamontology.org/operation_0446 Exonic splicing enhancer prediction 'Exonic splicing enhancer prediction' SubClassOf 'Promoter prediction' http://edamontology.org/operation_0447 Sequence alignment validation 'Sequence alignment validation' SubClassOf 'Sequence alignment analysis' 'Sequence alignment validation' SubClassOf 'Validation' http://edamontology.org/operation_1777 Protein function prediction 'Protein function prediction' SubClassOf 'Protein function analysis' 'Protein function prediction' SubClassOf 'Prediction and recognition (protein)' http://edamontology.org/data_1100 PIR identifier 'PIR identifier' SubClassOf 'Sequence accession (protein)' http://edamontology.org/data_1104 Sequence cluster ID (UniGene) 'Sequence cluster ID (UniGene)' SubClassOf 'Sequence cluster ID' http://edamontology.org/operation_0440 Promoter prediction 'Promoter prediction' SubClassOf 'Regulatory element prediction' http://edamontology.org/data_1103 EMBL/GenBank/DDBJ ID 'EMBL/GenBank/DDBJ ID' SubClassOf 'Sequence accession (nucleic acid)' http://edamontology.org/operation_0441 Transcription regulatory element prediction (DNA-cis) 'Transcription regulatory element prediction (DNA-cis)' SubClassOf 'Regulatory element prediction' http://edamontology.org/data_1102 Gramene primary identifier 'Gramene primary identifier' SubClassOf 'Gramene identifier' http://edamontology.org/data_1101 TREMBL accession 'TREMBL accession' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/algorithm/OntoDM_170075 clustering algorithm 'clustering algorithm' SubClassOf 'single generalization algorithm' http://edamontology.org/operation_0439 Translation initiation site prediction 'Translation initiation site prediction' SubClassOf 'Coding region prediction' http://edamontology.org/data_1119 JASPAR profile ID 'JASPAR profile ID' SubClassOf 'Sequence profile ID' http://edamontology.org/operation_0455 Nucleic acid thermodynamic property calculation 'Nucleic acid thermodynamic property calculation' SubClassOf 'Nucleic acid property calculation' http://edamontology.org/data_1118 HMMER hidden Markov model ID 'HMMER hidden Markov model ID' SubClassOf 'Sequence profile ID' http://edamontology.org/operation_0456 Nucleic acid melting profile plotting 'Nucleic acid melting profile plotting' SubClassOf 'Nucleic acid property calculation' 'Nucleic acid melting profile plotting' SubClassOf 'Plotting' http://edamontology.org/data_1117 Prosite accession number 'Prosite accession number' SubClassOf 'Sequence motif identifier' http://edamontology.org/operation_0453 Nucleosome formation potential prediction 'Nucleosome formation potential prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1116 ELM ID 'ELM ID' SubClassOf 'Sequence motif identifier' http://edamontology.org/operation_0459 Nucleic acid probability profile plotting 'Nucleic acid probability profile plotting' SubClassOf 'Nucleic acid melting profile plotting' http://edamontology.org/data_3779 Annotated text 'Annotated text' SubClassOf 'Text' http://edamontology.org/operation_0457 Nucleic acid stitch profile plotting 'Nucleic acid stitch profile plotting' SubClassOf 'Nucleic acid melting profile plotting' http://edamontology.org/operation_0458 Nucleic acid melting curve plotting 'Nucleic acid melting curve plotting' SubClassOf 'Nucleic acid melting profile plotting' http://edamontology.org/data_1111 EMBOSS listfile 'EMBOSS listfile' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1110 EMBOSS sequence type 'EMBOSS sequence type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1115 Sequence profile ID 'Sequence profile ID' SubClassOf 'Accession' 'Sequence profile ID' SubClassOf 'Identifier (typed)' http://edamontology.org/operation_0451 Recombination detection 'Recombination detection' SubClassOf 'Nucleic acid sequence alignment analysis' http://edamontology.org/data_1114 Sequence motif identifier 'Sequence motif identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/operation_0452 Indel detection 'Indel detection' SubClassOf 'Nucleic acid sequence alignment analysis' 'Indel detection' SubClassOf 'Polymorphism detection' http://edamontology.org/data_1113 Sequence cluster ID (COG) 'Sequence cluster ID (COG)' SubClassOf 'Sequence cluster ID' http://edamontology.org/operation_1781 Gene regulatory network analysis 'Gene regulatory network analysis' SubClassOf 'Pathway or network analysis' http://edamontology.org/data_1112 Sequence cluster ID 'Sequence cluster ID' SubClassOf 'Sequence set ID' http://edamontology.org/operation_0450 Chimeric sequence detection 'Chimeric sequence detection' SubClassOf 'Nucleic acid sequence alignment analysis' http://edamontology.org/operation_1780 Sequence submission 'Sequence submission' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1129 BIND accession number 'BIND accession number' SubClassOf 'Protein interaction ID' http://edamontology.org/data_1128 AAindex ID 'AAindex ID' SubClassOf 'Amino acid index ID' http://edamontology.org/data_1127 PDB ID 'PDB ID' SubClassOf 'Structure ID' http://edamontology.org/data_1122 Phylogenetic tree type 'Phylogenetic tree type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1121 BLAST sequence alignment type 'BLAST sequence alignment type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3786 Query script 'Query script' SubClassOf 'Data' http://edamontology.org/data_1120 Sequence alignment type 'Sequence alignment type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1126 Comparison matrix name 'Comparison matrix name' SubClassOf 'Comparison matrix identifier' 'Comparison matrix name' SubClassOf 'Name' http://edamontology.org/data_1125 Comparison matrix type 'Comparison matrix type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1124 TreeFam accession number 'TreeFam accession number' SubClassOf 'Phylogenetic tree ID' http://edamontology.org/data_1123 TreeBASE study accession number 'TreeBASE study accession number' SubClassOf 'Phylogenetic tree ID' http://edamontology.org/format_2551 Sequence record format (text) 'Sequence record format (text)' SubClassOf 'Sequence record format' http://edamontology.org/topic_2807 Tool topic 'Tool topic' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2550 OBO-XML 'OBO-XML' SubClassOf 'OBO format' 'OBO-XML' SubClassOf 'XML' http://edamontology.org/format_2553 Sequence feature table format (XML) 'Sequence feature table format (XML)' SubClassOf 'Sequence feature table format' http://edamontology.org/format_2552 Sequence record format (XML) 'Sequence record format (XML)' SubClassOf 'Sequence record format' http://edamontology.org/topic_2809 Study topic 'Study topic' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2559 GenBank-like format 'GenBank-like format' SubClassOf 'Sequence record format' http://edamontology.org/format_1228 UniGene entry format 'UniGene entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2558 EMBL-like (XML) 'EMBL-like (XML)' SubClassOf 'EMBL-like format' 'EMBL-like (XML)' SubClassOf 'XML' http://edamontology.org/format_2555 Alignment format (XML) 'Alignment format (XML)' SubClassOf 'Alignment format' http://edamontology.org/format_2554 Alignment format (text) 'Alignment format (text)' SubClassOf 'Alignment format' http://edamontology.org/format_2557 Phylogenetic tree format (XML) 'Phylogenetic tree format (XML)' SubClassOf 'Phylogenetic tree format' http://edamontology.org/format_2556 Phylogenetic tree format (text) 'Phylogenetic tree format (text)' SubClassOf 'Phylogenetic tree format' http://edamontology.org/data_1139 SMART accession number 'SMART accession number' SubClassOf 'Protein family accession' http://edamontology.org/operation_3545 Mathematical modelling 'Mathematical modelling' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1138 Pfam accession number 'Pfam accession number' SubClassOf 'Protein family accession' http://edamontology.org/data_1133 InterPro accession 'InterPro accession' SubClassOf 'Protein family accession' http://edamontology.org/data_1132 InterPro entry name 'InterPro entry name' SubClassOf 'Protein family name' http://edamontology.org/data_1131 Protein family name 'Protein family name' SubClassOf 'Protein family identifier' 'Protein family name' SubClassOf 'Name' http://edamontology.org/data_1130 IntAct accession number 'IntAct accession number' SubClassOf 'Protein interaction ID' http://edamontology.org/data_1137 PRINTS code 'PRINTS code' SubClassOf 'Protein family accession' http://edamontology.org/data_1136 PIRSF ID 'PIRSF ID' SubClassOf 'Protein family accession' http://edamontology.org/data_1135 Gene3D ID 'Gene3D ID' SubClassOf 'Protein family accession' http://edamontology.org/data_1134 InterPro secondary accession 'InterPro secondary accession' SubClassOf 'InterPro accession' http://edamontology.org/topic_2818 Eukaryotes 'Eukaryotes' SubClassOf 'Model organisms' http://edamontology.org/topic_2817 Yeast 'Yeast' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1210 pure nucleotide 'pure nucleotide' SubClassOf 'pure' 'pure nucleotide' SubClassOf 'nucleotide' http://edamontology.org/format_2542 Protein features (domains) format 'Protein features (domains) format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2816 Gene resources 'Gene resources' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1211 unambiguous pure nucleotide 'unambiguous pure nucleotide' SubClassOf 'unambiguous pure' 'unambiguous pure nucleotide' SubClassOf 'nucleotide' http://edamontology.org/topic_2815 Humans 'Humans' SubClassOf 'Vertebrates' http://edamontology.org/topic_2819 Invertebrates 'Invertebrates' SubClassOf 'Animals' http://edamontology.org/format_1216 unambiguous pure rna sequence 'unambiguous pure rna sequence' SubClassOf 'unambiguous pure' 'unambiguous pure rna sequence' SubClassOf 'rna' http://edamontology.org/format_2548 Sequence feature table format 'Sequence feature table format' SubClassOf 'Sequence feature annotation format' http://edamontology.org/format_1217 pure rna 'pure rna' SubClassOf 'pure nucleotide' 'pure rna' SubClassOf 'rna' http://edamontology.org/format_2547 uniprotkb-like format 'uniprotkb-like format' SubClassOf 'Sequence feature table format' 'uniprotkb-like format' SubClassOf 'Sequence record format' http://edamontology.org/format_1218 unambiguous pure protein 'unambiguous pure protein' SubClassOf 'protein' 'unambiguous pure protein' SubClassOf 'unambiguous pure' http://edamontology.org/format_1219 pure protein 'pure protein' SubClassOf 'protein' 'pure protein' SubClassOf 'pure' http://edamontology.org/format_1212 dna 'dna' SubClassOf 'nucleotide' http://edamontology.org/topic_2814 Protein structure analysis 'Protein structure analysis' SubClassOf 'Structure analysis' 'Protein structure analysis' SubClassOf 'Proteins' http://edamontology.org/format_1213 rna 'rna' SubClassOf 'nucleotide' http://edamontology.org/format_2543 EMBL-like format 'EMBL-like format' SubClassOf 'Sequence record format' http://edamontology.org/topic_2813 Disease genes and proteins 'Disease genes and proteins' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1214 unambiguous pure dna 'unambiguous pure dna' SubClassOf 'dna' 'unambiguous pure dna' SubClassOf 'unambiguous pure' http://edamontology.org/format_2546 FASTA-like 'FASTA-like' SubClassOf 'Sequence record format' http://edamontology.org/format_1215 pure dna 'pure dna' SubClassOf 'pure nucleotide' 'pure dna' SubClassOf 'dna' http://edamontology.org/format_2545 FASTQ-like format 'FASTQ-like format' SubClassOf 'Sequence trace format' http://edamontology.org/topic_2811 Nomenclature 'Nomenclature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0488 Linkage disequilibrium calculation 'Linkage disequilibrium calculation' SubClassOf 'Linkage analysis' http://edamontology.org/operation_0489 Genetic code prediction 'Genetic code prediction' SubClassOf 'Prediction and recognition (nucleic acid)' 'Genetic code prediction' SubClassOf 'Codon usage analysis' http://edamontology.org/operation_0486 Functional mapping 'Functional mapping' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1149 EMAGE ID 'EMAGE ID' SubClassOf 'Gene expression report ID' http://edamontology.org/operation_0487 Haplotype mapping 'Haplotype mapping' SubClassOf 'Linkage analysis' 'Haplotype mapping' SubClassOf 'Genetic mapping' http://edamontology.org/data_1144 ArrayExpress accession number 'ArrayExpress accession number' SubClassOf 'Experiment annotation ID' http://edamontology.org/operation_0480 Protein modelling (side chains) 'Protein modelling (side chains)' SubClassOf 'Protein modelling' http://edamontology.org/data_1143 TRANSFAC accession number 'TRANSFAC accession number' SubClassOf 'Transcription factor accession' http://edamontology.org/operation_0481 Protein modelling (loops) 'Protein modelling (loops)' SubClassOf 'Protein modelling' http://edamontology.org/data_1142 ProDom accession number 'ProDom accession number' SubClassOf 'Protein family accession' http://edamontology.org/data_1141 TIGRFam ID 'TIGRFam ID' SubClassOf 'Protein family accession' http://edamontology.org/data_1148 GermOnline ID 'GermOnline ID' SubClassOf 'Gene expression report ID' http://edamontology.org/operation_0484 SNP detection 'SNP detection' SubClassOf 'Polymorphism detection' 'SNP detection' SubClassOf 'Nucleic acid sequence alignment analysis' http://edamontology.org/data_1147 GEO accession number 'GEO accession number' SubClassOf 'Gene expression report ID' http://edamontology.org/operation_0485 Radiation Hybrid Mapping 'Radiation Hybrid Mapping' SubClassOf 'Physical mapping' http://edamontology.org/data_1146 EMDB ID 'EMDB ID' SubClassOf 'Electron microscopy model ID' http://edamontology.org/operation_0482 Protein-ligand docking 'Protein-ligand docking' SubClassOf 'Molecular docking' http://edamontology.org/data_1145 PRIDE experiment accession number 'PRIDE experiment accession number' SubClassOf 'Experiment annotation ID' http://edamontology.org/operation_0483 Structured RNA prediction and optimisation 'Structured RNA prediction and optimisation' SubClassOf 'Nucleic acid design' http://edamontology.org/format_2573 SAM 'SAM' SubClassOf 'Textual format' 'SAM' SubClassOf 'Alignment format (pair only)' 'SAM' SubClassOf 'Sequence trace format' http://edamontology.org/topic_2829 Ontologies, nomenclature and classification 'Ontologies, nomenclature and classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2572 BAM 'BAM' SubClassOf 'binary format' 'BAM' SubClassOf 'Sequence trace format' 'BAM' SubClassOf 'Alignment format (pair only)' http://edamontology.org/topic_2828 X-ray diffraction 'X-ray diffraction' SubClassOf 'Structural biology' 'X-ray diffraction' SubClassOf 'Imaging' http://edamontology.org/topic_2826 Protein structure alignment 'Protein structure alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1140 Superfamily hidden Markov model number 'Superfamily hidden Markov model number' SubClassOf 'Protein family accession' http://edamontology.org/format_2571 Raw sequence format 'Raw sequence format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2570 completely unambiguous pure rna sequence 'completely unambiguous pure rna sequence' SubClassOf 'completely unambiguous pure' 'completely unambiguous pure rna sequence' SubClassOf 'rna' http://edamontology.org/topic_2821 Unicellular eukaryotes 'Unicellular eukaryotes' SubClassOf 'Eukaryotes' http://edamontology.org/topic_2820 Vertebrates 'Vertebrates' SubClassOf 'Animals' http://edamontology.org/format_1247 COG sequence cluster format 'COG sequence cluster format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1248 EMBL feature location 'EMBL feature location' SubClassOf 'Sequence range format' 'EMBL feature location' SubClassOf 'Textual format' http://edamontology.org/operation_0499 Tree-based sequence alignment 'Tree-based sequence alignment' SubClassOf 'Sequence alignment' http://edamontology.org/operation_0497 Constrained sequence alignment 'Constrained sequence alignment' SubClassOf 'Sequence alignment' http://edamontology.org/operation_0498 Consensus-based sequence alignment 'Consensus-based sequence alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1155 Pathway ID (reactome) 'Pathway ID (reactome)' SubClassOf 'Pathway or network accession' http://edamontology.org/operation_0491 Pairwise sequence alignment 'Pairwise sequence alignment' SubClassOf 'Sequence alignment' http://edamontology.org/data_1154 KEGG object identifier 'KEGG object identifier' SubClassOf 'Identifier (hybrid)' 'KEGG object identifier' SubClassOf 'Accession' http://edamontology.org/operation_0492 Multiple sequence alignment 'Multiple sequence alignment' SubClassOf 'Sequence alignment' http://edamontology.org/data_1153 OMIM ID 'OMIM ID' SubClassOf 'Genotype and phenotype annotation ID' http://edamontology.org/data_1152 HIVDB identifier 'HIVDB identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0490 Dotplot plotting 'Dotplot plotting' SubClassOf 'Sequence visualisation' 'Dotplot plotting' SubClassOf 'Plotting' 'Dotplot plotting' SubClassOf 'Sequence word comparison' http://edamontology.org/data_1159 Pathway ID (PATIKA) 'Pathway ID (PATIKA)' SubClassOf 'Pathway or network accession' http://edamontology.org/operation_0495 Local alignment 'Local alignment' SubClassOf 'Sequence alignment' http://edamontology.org/data_1158 Pathway ID (INOH) 'Pathway ID (INOH)' SubClassOf 'Pathway or network accession' http://edamontology.org/operation_0496 Global alignment 'Global alignment' SubClassOf 'Sequence alignment' http://edamontology.org/data_1157 Pathway ID (BioCyc) 'Pathway ID (BioCyc)' SubClassOf 'BioCyc ID' 'Pathway ID (BioCyc)' SubClassOf 'Pathway or network accession' http://edamontology.org/operation_0493 Pairwise sequence alignment generation (local) 'Pairwise sequence alignment generation (local)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1156 Pathway ID (aMAZE) 'Pathway ID (aMAZE)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0494 Pairwise sequence alignment generation (global) 'Pairwise sequence alignment generation (global)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2562 Amino acid identifier format 'Amino acid identifier format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2561 Sequence assembly format (text) 'Sequence assembly format (text)' SubClassOf 'Sequence assembly format' http://edamontology.org/topic_2839 Molecules 'Molecules' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1151 HGVbase ID 'HGVbase ID' SubClassOf 'Genotype and phenotype annotation ID' http://edamontology.org/data_1150 Disease ID 'Disease ID' SubClassOf 'Disease identifier' http://edamontology.org/format_2560 STRING entry format 'STRING entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2569 completely unambiguous pure dna 'completely unambiguous pure dna' SubClassOf 'dna' 'completely unambiguous pure dna' SubClassOf 'completely unambiguous pure' http://edamontology.org/topic_2830 Immunoproteins, genes and antigens 'Immunoproteins, genes and antigens' SubClassOf 'Gene and protein families' 'Immunoproteins, genes and antigens' SubClassOf 'Immunology' http://edamontology.org/format_2566 completely unambiguous 'completely unambiguous' SubClassOf 'Textual format' 'completely unambiguous' SubClassOf 'Raw sequence format' http://edamontology.org/format_2568 completely unambiguous pure nucleotide 'completely unambiguous pure nucleotide' SubClassOf 'nucleotide' 'completely unambiguous pure nucleotide' SubClassOf 'completely unambiguous pure' http://edamontology.org/format_2567 completely unambiguous pure 'completely unambiguous pure' SubClassOf 'completely unambiguous' 'completely unambiguous pure' SubClassOf 'pure' http://edamontology.org/operation_2246 Demonstration 'Demonstration' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1166 MIRIAM data type synonymous name 'MIRIAM data type synonymous name' SubClassOf 'MIRIAM data type name' http://edamontology.org/operation_2241 Transmembrane protein visualisation 'Transmembrane protein visualisation' SubClassOf 'Transmembrane protein analysis' 'Transmembrane protein visualisation' SubClassOf 'Structure visualisation' http://edamontology.org/data_1165 MIRIAM data type primary name 'MIRIAM data type primary name' SubClassOf 'MIRIAM data type name' http://edamontology.org/data_1164 MIRIAM URI 'MIRIAM URI' SubClassOf 'URI' 'MIRIAM URI' SubClassOf 'Data resource definition accession' http://edamontology.org/data_1163 MIRIAM data type name 'MIRIAM data type name' SubClassOf 'Data resource definition name' http://edamontology.org/data_1167 Taverna workflow ID 'Taverna workflow ID' SubClassOf 'Workflow ID' http://edamontology.org/data_1162 MIRIAM identifier 'MIRIAM identifier' SubClassOf 'Data resource definition accession' http://edamontology.org/data_1161 Pathway ID (Panther) 'Pathway ID (Panther)' SubClassOf 'Pathway or network accession' http://edamontology.org/data_1160 Pathway ID (CPDB) 'Pathway ID (CPDB)' SubClassOf 'Pathway or network accession' http://edamontology.org/topic_2842 High-throughput sequencing 'High-throughput sequencing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2840 Toxicology 'Toxicology' SubClassOf 'Safety sciences' 'Toxicology' SubClassOf 'Medicine' http://edamontology.org/topic_2847 Disease (specific) 'Disease (specific)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2846 Gene regulatory networks 'Gene regulatory networks' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2844 Structural clustering 'Structural clustering' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1177 MeSH concept ID 'MeSH concept ID' SubClassOf 'Ontology concept ID' http://edamontology.org/data_1176 GO concept ID 'GO concept ID' SubClassOf 'Ontology concept ID' http://edamontology.org/data_1175 BioPax concept ID 'BioPax concept ID' SubClassOf 'Ontology concept ID' http://edamontology.org/data_1174 ChEBI ID 'ChEBI ID' SubClassOf 'Compound accession' http://edamontology.org/data_1179 NCBI taxonomy ID 'NCBI taxonomy ID' SubClassOf 'Organism accession' 'NCBI taxonomy ID' SubClassOf 'Ontology concept ID' http://edamontology.org/data_1178 HGNC concept ID 'HGNC concept ID' SubClassOf 'Ontology concept ID' http://edamontology.org/data_1173 ChemSpider ID 'ChemSpider ID' SubClassOf 'Compound accession' http://edamontology.org/data_1172 PubChem CID 'PubChem CID' SubClassOf 'Compound accession' 'PubChem CID' SubClassOf 'PubChem ID' http://edamontology.org/data_1171 BioModel ID 'BioModel ID' SubClassOf 'Biological model accession' http://edamontology.org/format_3033 Matrix format 'Matrix format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_1170 Biological model name 'Biological model name' SubClassOf 'Biological model ID' 'Biological model name' SubClassOf 'Name' http://edamontology.org/operation_3557 Imputation 'Imputation' SubClassOf 'Statistical calculation' http://edamontology.org/operation_2224 Data retrieval (ontology concept) 'Data retrieval (ontology concept)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3559 Ontology visualisation 'Ontology visualisation' SubClassOf 'Visualisation' http://edamontology.org/data_1188 DOI 'DOI' SubClassOf 'Article ID' http://edamontology.org/data_1187 PubMed ID 'PubMed ID' SubClassOf 'Article ID' http://edamontology.org/data_1186 myGrid concept ID 'myGrid concept ID' SubClassOf 'Ontology concept ID' http://edamontology.org/data_1185 MGED concept ID 'MGED concept ID' SubClassOf 'Ontology concept ID' http://edamontology.org/operation_2222 Data retrieval (ontology annotation) 'Data retrieval (ontology annotation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3553 Image annotation 'Image annotation' SubClassOf 'Annotation' http://edamontology.org/operation_3552 Microscope image visualisation 'Microscope image visualisation' SubClassOf 'Visualisation' http://edamontology.org/data_1189 Medline UI 'Medline UI' SubClassOf 'Article ID' http://edamontology.org/data_1180 Plant Ontology concept ID 'Plant Ontology concept ID' SubClassOf 'Ontology concept ID' http://edamontology.org/topic_0208 Pharmacogenomics 'Pharmacogenomics' SubClassOf 'Genomics' 'Pharmacogenomics' SubClassOf 'Pharmacology' http://edamontology.org/topic_0209 Medicinal chemistry 'Medicinal chemistry' SubClassOf 'Synthetic chemistry' 'Medicinal chemistry' SubClassOf 'Drug discovery' http://edamontology.org/data_1184 ChEBI concept ID 'ChEBI concept ID' SubClassOf 'Ontology concept ID' http://edamontology.org/data_1183 EMAP concept ID 'EMAP concept ID' SubClassOf 'Ontology concept ID' http://edamontology.org/data_1182 FMA concept ID 'FMA concept ID' SubClassOf 'Ontology concept ID' http://edamontology.org/data_1181 UMLS concept ID 'UMLS concept ID' SubClassOf 'Ontology concept ID' http://edamontology.org/topic_0202 Pharmacology 'Pharmacology' SubClassOf 'Biomedical science' http://edamontology.org/topic_0203 Gene expression 'Gene expression' SubClassOf 'Molecular genetics' http://edamontology.org/topic_0200 Microarrays 'Microarrays' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2869 RFLP 'RFLP' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2868 Microsatellites 'Microsatellites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0204 Gene regulation 'Gene regulation' SubClassOf 'Gene expression' http://edamontology.org/topic_2867 VNTR 'VNTR' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2238 Statistical calculation 'Statistical calculation' SubClassOf 'Calculation' http://edamontology.org/operation_2237 Data retrieval (sequence profile) 'Data retrieval (sequence profile)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3566 Simulated gene expression data generation 'Simulated gene expression data generation' SubClassOf 'Modelling and simulation' http://edamontology.org/topic_0210 Fish 'Fish' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2239 3D-1D scoring matrix generation '3D-1D scoring matrix generation' SubClassOf 'Protein property calculation (from sequence)' '3D-1D scoring matrix generation' SubClassOf 'Generation' '3D-1D scoring matrix generation' SubClassOf 'Protein property calculation (from structure)' http://edamontology.org/operation_3561 Database comparison 'Database comparison' SubClassOf 'Mapping' 'Database comparison' SubClassOf 'Comparison' http://edamontology.org/operation_3560 Maximum occurence analysis 'Maximum occurence analysis' SubClassOf 'Protein model validation' http://edamontology.org/operation_2234 Structure file processing 'Structure file processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3565 RNA-seq time series data analysis 'RNA-seq time series data analysis' SubClassOf 'RNA-Seq analysis' http://edamontology.org/operation_2233 Representative sequence identification 'Representative sequence identification' SubClassOf 'Sequence comparison' http://edamontology.org/operation_3564 Chemical redundancy removal 'Chemical redundancy removal' SubClassOf 'Structure comparison' http://edamontology.org/operation_3563 RNA-seq read count analysis 'RNA-seq read count analysis' SubClassOf 'RNA-Seq analysis' http://edamontology.org/operation_3562 Network simulation 'Network simulation' SubClassOf 'Modelling and simulation' http://edamontology.org/data_1191 Tool name (signature) 'Tool name (signature)' SubClassOf 'Tool name' http://edamontology.org/data_1190 Tool name 'Tool name' SubClassOf 'Tool identifier' http://edamontology.org/topic_0219 Data submission, annotation and curation 'Data submission, annotation and curation' SubClassOf 'Data management' http://edamontology.org/data_1195 Tool name (EMBASSY package) 'Tool name (EMBASSY package)' SubClassOf 'Tool name' http://edamontology.org/data_1194 Tool name (EMBOSS) 'Tool name (EMBOSS)' SubClassOf 'Tool name' http://edamontology.org/data_1193 Tool name (FASTA) 'Tool name (FASTA)' SubClassOf 'Tool name' http://edamontology.org/data_1192 Tool name (BLAST) 'Tool name (BLAST)' SubClassOf 'Tool name' http://edamontology.org/topic_0213 Mice or rats 'Mice or rats' SubClassOf 'Vertebrates' http://edamontology.org/topic_0211 Flies 'Flies' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0217 Literature analysis 'Literature analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0218 Natural language processing 'Natural language processing' SubClassOf 'Literature and language' 'Natural language processing' SubClassOf 'Computer science' http://edamontology.org/topic_0215 Worms 'Worms' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0220 Document, record and content management 'Document, record and content management' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0221 Sequence annotation 'Sequence annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2284 Nucleic acid density plotting 'Nucleic acid density plotting' SubClassOf 'Sequence composition calculation' 'Nucleic acid density plotting' SubClassOf 'Plotting' http://edamontology.org/format_3001 ACE 'ACE' SubClassOf 'Textual format' 'ACE' SubClassOf 'Sequence assembly format' http://edamontology.org/format_3004 bigBed 'bigBed' SubClassOf 'Sequence annotation track format' 'bigBed' SubClassOf 'binary format' http://edamontology.org/format_3000 AB1 'AB1' SubClassOf 'Sequence trace format' 'AB1' SubClassOf 'binary format' http://edamontology.org/format_3009 2bit '2bit' SubClassOf 'Raw sequence format' '2bit' SubClassOf 'binary format' http://edamontology.org/topic_0222 Genome annotation 'Genome annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2885 DNA polymorphism 'DNA polymorphism' SubClassOf 'DNA' 'DNA polymorphism' SubClassOf 'Genetic variation' http://edamontology.org/format_3006 bigWig 'bigWig' SubClassOf 'Sequence annotation track format' 'bigWig' SubClassOf 'binary format' http://edamontology.org/format_3005 WIG 'WIG' SubClassOf 'Textual format' 'WIG' SubClassOf 'Sequence annotation track format' http://edamontology.org/format_3008 MAF 'MAF' SubClassOf 'Alignment format (text)' 'MAF' SubClassOf 'Textual format' 'MAF' SubClassOf 'Sequence annotation track format' http://edamontology.org/format_3007 PSL 'PSL' SubClassOf 'Alignment format (pair only)' 'PSL' SubClassOf 'Sequence annotation track format' 'PSL' SubClassOf 'Textual format' http://edamontology.org/format_1296 Sanger inverted repeats 'Sanger inverted repeats' SubClassOf 'Sequence features (repeats) format' 'Sanger inverted repeats' SubClassOf 'Textual format' http://edamontology.org/format_1297 EMBOSS repeat 'EMBOSS repeat' SubClassOf 'Textual format' 'EMBOSS repeat' SubClassOf 'Sequence features (repeats) format' http://edamontology.org/format_1295 quicktandem 'quicktandem' SubClassOf 'Textual format' 'quicktandem' SubClassOf 'Sequence features (repeats) format' http://edamontology.org/operation_2265 Data retrieval (identifier) 'Data retrieval (identifier)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2264 Data retrieval (pathway or network) 'Data retrieval (pathway or network)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3020 BCF 'BCF' SubClassOf 'Sequence variation annotation format' 'BCF' SubClassOf 'binary format' http://edamontology.org/format_3013 axt 'axt' SubClassOf 'Alignment format (pair only)' 'axt' SubClassOf 'Textual format' http://edamontology.org/format_3012 pgSnp 'pgSnp' SubClassOf 'Textual format' 'pgSnp' SubClassOf 'Sequence annotation track format' http://edamontology.org/format_3015 Pileup 'Pileup' SubClassOf 'Alignment format (pair only)' 'Pileup' SubClassOf 'Textual format' http://edamontology.org/format_3014 LAV 'LAV' SubClassOf 'Textual format' 'LAV' SubClassOf 'Alignment format (pair only)' http://edamontology.org/format_3011 genePred 'genePred' SubClassOf 'Textual format' 'genePred' SubClassOf 'Sequence annotation track format' http://edamontology.org/format_3010 .nib '.nib' SubClassOf 'Raw sequence format' '.nib' SubClassOf 'binary format' http://edamontology.org/format_3017 SRF 'SRF' SubClassOf 'binary format' 'SRF' SubClassOf 'Sequence trace format' http://edamontology.org/format_3016 VCF 'VCF' SubClassOf 'Textual format' 'VCF' SubClassOf 'Sequence variation annotation format' http://edamontology.org/format_3019 GVF 'GVF' SubClassOf 'GFF3' 'GVF' SubClassOf 'Sequence variation annotation format' http://edamontology.org/format_3018 ZTR 'ZTR' SubClassOf 'binary format' 'ZTR' SubClassOf 'Sequence trace format' http://edamontology.org/topic_0140 Protein targeting and localisation 'Protein targeting and localisation' SubClassOf 'Protein expression' http://edamontology.org/topic_0143 Protein structure comparison 'Protein structure comparison' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0144 Protein residue interactions 'Protein residue interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0141 Protein cleavage sites and proteolysis 'Protein cleavage sites and proteolysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0147 Protein-protein interactions 'Protein-protein interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0148 Protein-ligand interactions 'Protein-ligand interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0149 Protein-nucleic acid interactions 'Protein-nucleic acid interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0150 Protein design 'Protein design' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0151 G protein-coupled receptors (GPCR) 'G protein-coupled receptors (GPCR)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0154 Small molecules 'Small molecules' SubClassOf 'Structure analysis' http://edamontology.org/topic_0152 Carbohydrates 'Carbohydrates' SubClassOf 'Structure analysis' http://edamontology.org/topic_0153 Lipids 'Lipids' SubClassOf 'Structure analysis' http://edamontology.org/topic_0158 Sequence motifs 'Sequence motifs' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0159 Sequence comparison 'Sequence comparison' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0156 Sequence editing 'Sequence editing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0157 Sequence composition, complexity and repeats 'Sequence composition, complexity and repeats' SubClassOf 'Sequence analysis' http://edamontology.org/data_1900 NCBI locus tag 'NCBI locus tag' SubClassOf 'Locus ID' http://edamontology.org/topic_0160 Sequence sites, features and motifs 'Sequence sites, features and motifs' SubClassOf 'Computational biology' http://edamontology.org/data_1904 Locus ID (EntrezGene) 'Locus ID (EntrezGene)' SubClassOf 'Locus ID' http://edamontology.org/data_1903 Locus ID (DictyBase) 'Locus ID (DictyBase)' SubClassOf 'Locus ID' http://edamontology.org/topic_0166 Protein structural motifs and surfaces 'Protein structural motifs and surfaces' SubClassOf 'Protein structure analysis' http://edamontology.org/data_1902 Locus ID (MMP) 'Locus ID (MMP)' SubClassOf 'Locus ID' http://edamontology.org/topic_0163 Sequence database search 'Sequence database search' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1901 Locus ID (SGD) 'Locus ID (SGD)' SubClassOf 'Locus ID' 'Locus ID (SGD)' SubClassOf 'SGD ID' http://edamontology.org/topic_0164 Sequence clustering 'Sequence clustering' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0167 Structural (3D) profiles 'Structural (3D) profiles' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0172 Protein structure prediction 'Protein structure prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0173 Nucleic acid structure prediction 'Nucleic acid structure prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0176 Molecular dynamics 'Molecular dynamics' SubClassOf 'Structure prediction' http://edamontology.org/topic_0177 Molecular docking 'Molecular docking' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0174 Ab initio structure prediction 'Ab initio structure prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0175 Homology modelling 'Homology modelling' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1908 Locus ID (Tropgene) 'Locus ID (Tropgene)' SubClassOf 'Locus ID' http://edamontology.org/data_1907 Gene ID (KOME) 'Gene ID (KOME)' SubClassOf 'Gene ID' http://edamontology.org/data_1906 Quantitative trait locus 'Quantitative trait locus' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0178 Protein secondary structure prediction 'Protein secondary structure prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1905 Locus ID (MaizeGDB) 'Locus ID (MaizeGDB)' SubClassOf 'Locus ID' http://edamontology.org/topic_0179 Protein tertiary structure prediction 'Protein tertiary structure prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0183 Structure alignment 'Structure alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0184 Threading 'Threading' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0182 Sequence alignment 'Sequence alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0188 Sequence profiles and HMMs 'Sequence profiles and HMMs' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0180 Protein fold recognition 'Protein fold recognition' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1917 Atomic property 'Atomic property' SubClassOf 'Molecular property' http://edamontology.org/data_1916 Alignment 'Alignment' SubClassOf 'Data' http://edamontology.org/topic_0194 Phylogenomics 'Phylogenomics' SubClassOf 'Sequence analysis' 'Phylogenomics' SubClassOf 'Genomics' http://edamontology.org/topic_0195 Virtual PCR 'Virtual PCR' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0199 Genetic variation 'Genetic variation' SubClassOf 'Molecular genetics' http://edamontology.org/topic_0196 Sequence assembly 'Sequence assembly' SubClassOf 'Sequence analysis' http://edamontology.org/topic_0191 Phylogeny reconstruction 'Phylogeny reconstruction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://purl.obolibrary.org/obo/BFO_0000007 process http://edamontology.org/topic_3263 Data security 'Data security' SubClassOf 'Data management' http://edamontology.org/format_1209 consensus 'consensus' SubClassOf 'unpure' 'consensus' SubClassOf 'ambiguous' http://edamontology.org/topic_3277 Sample collections 'Sample collections' SubClassOf 'Biomedical science' http://edamontology.org/format_1200 smarts 'smarts' SubClassOf 'SMILES' http://edamontology.org/format_1206 unambiguous pure 'unambiguous pure' SubClassOf 'unambiguous sequence' 'unambiguous pure' SubClassOf 'pure' http://edamontology.org/format_1207 nucleotide 'nucleotide' SubClassOf 'Textual format' 'nucleotide' SubClassOf 'Raw sequence format' http://edamontology.org/format_1208 protein 'protein' SubClassOf 'Textual format' 'protein' SubClassOf 'Raw sequence format' http://edamontology.org/format_2532 GenBank-HTML 'GenBank-HTML' SubClassOf 'GenBank-like format' 'GenBank-HTML' SubClassOf 'HTML' http://edamontology.org/operation_0422 Protein cleavage site prediction 'Protein cleavage site prediction' SubClassOf 'Protein sequence feature detection' http://edamontology.org/topic_3297 Biotechnology 'Biotechnology' SubClassOf 'Biology' http://edamontology.org/operation_0423 Epitope mapping (MHC Class I) 'Epitope mapping (MHC Class I)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3707 Biodiversity report 'Biodiversity report' SubClassOf 'Ecological data' 'Biodiversity report' SubClassOf 'Report' http://edamontology.org/operation_0420 Protein-nucleic acid binding prediction 'Protein-nucleic acid binding prediction' SubClassOf 'Protein binding site prediction' http://edamontology.org/topic_3295 Epigenetics 'Epigenetics' SubClassOf 'Genetics' http://edamontology.org/operation_0421 Protein folding site prediction 'Protein folding site prediction' SubClassOf 'Protein folding analysis' 'Protein folding site prediction' SubClassOf 'Protein sequence feature detection' http://edamontology.org/operation_0426 Gene component prediction 'Gene component prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0427 Transposon prediction 'Transposon prediction' SubClassOf 'Nucleic acid sequence feature detection' http://edamontology.org/operation_0424 Epitope mapping (MHC Class II) 'Epitope mapping (MHC Class II)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3299 Evolutionary biology 'Evolutionary biology' SubClassOf 'Biology' http://edamontology.org/operation_0425 Whole gene prediction 'Whole gene prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3298 Phenomics 'Phenomics' SubClassOf 'Evolutionary biology' 'Phenomics' SubClassOf 'Genotype and phenotype' 'Phenomics' SubClassOf 'Omics' http://edamontology.org/topic_3293 Phylogenetics 'Phylogenetics' SubClassOf 'Sequence analysis' 'Phylogenetics' SubClassOf 'Phylogeny' http://edamontology.org/topic_3292 Biochemistry 'Biochemistry' SubClassOf 'Biology' 'Biochemistry' SubClassOf 'Chemistry' http://edamontology.org/operation_0419 Protein binding site prediction (from sequence) 'Protein binding site prediction (from sequence)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0417 Protein post-translation modification site prediction 'Protein post-translation modification site prediction' SubClassOf 'Protein sequence feature detection' http://edamontology.org/operation_0418 Protein signal peptide detection 'Protein signal peptide detection' SubClassOf 'Protein subcellular localisation prediction' 'Protein signal peptide detection' SubClassOf 'Protein sequence feature detection' http://edamontology.org/data_3716 Biosafety report 'Biosafety report' SubClassOf 'Report' http://edamontology.org/operation_0433 Splice site prediction 'Splice site prediction' SubClassOf 'Nucleic acid sequence feature detection' http://edamontology.org/data_3717 Isolation report 'Isolation report' SubClassOf 'Report' http://edamontology.org/operation_0434 Integrated gene prediction 'Integrated gene prediction' SubClassOf 'Gene prediction' http://edamontology.org/data_3718 Pathogenicity report 'Pathogenicity report' SubClassOf 'Biosafety report' http://edamontology.org/operation_0431 Restriction site recognition 'Restriction site recognition' SubClassOf 'Nucleic acid sequence feature detection' http://edamontology.org/data_3719 Biosafety classification 'Biosafety classification' SubClassOf 'Biosafety report' http://edamontology.org/operation_0432 Nucleosome formation or exclusion sequence prediction 'Nucleosome formation or exclusion sequence prediction' SubClassOf 'Nucleic acid sequence feature detection' http://edamontology.org/operation_0437 Selenocysteine insertion sequence (SECIS) prediction 'Selenocysteine insertion sequence (SECIS) prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_1769 Nucleic acid folding energy calculation 'Nucleic acid folding energy calculation' SubClassOf 'Nucleic acid folding analysis' http://edamontology.org/operation_0438 Regulatory element prediction 'Regulatory element prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_1768 Nucleic acid folding family identification 'Nucleic acid folding family identification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0435 Operon prediction 'Operon prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_0436 Coding region prediction 'Coding region prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_0430 CpG island and isochore detection 'CpG island and isochore detection' SubClassOf 'Nucleic acid sequence feature detection' http://edamontology.org/operation_0428 PolyA signal detection 'PolyA signal detection' SubClassOf 'Nucleic acid sequence feature detection' http://edamontology.org/operation_0429 Quadruplex formation site detection 'Quadruplex formation site detection' SubClassOf 'Nucleic acid sequence feature detection' http://edamontology.org/operation_0400 Protein pH-dependent property calculation 'Protein pH-dependent property calculation' SubClassOf 'Protein property calculation (from sequence)' http://edamontology.org/operation_0401 Protein hydropathy calculation (from sequence) 'Protein hydropathy calculation (from sequence)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3723 Morphology parameter 'Morphology parameter' SubClassOf 'Experimental measurement' http://edamontology.org/operation_0404 Protein hydrogen exchange rate calculation 'Protein hydrogen exchange rate calculation' SubClassOf 'Protein pH-dependent property calculation' http://edamontology.org/data_3724 Cultivation parameter 'Cultivation parameter' SubClassOf 'Experimental measurement' http://edamontology.org/operation_0405 Protein hydrophobic region calculation 'Protein hydrophobic region calculation' SubClassOf 'Protein hydropathy calculation' http://edamontology.org/operation_0402 Protein titration curve plotting 'Protein titration curve plotting' SubClassOf 'Plotting' 'Protein titration curve plotting' SubClassOf 'Protein pH-dependent property calculation' http://edamontology.org/operation_0403 Protein isoelectric point calculation 'Protein isoelectric point calculation' SubClassOf 'Protein pH-dependent property calculation' http://edamontology.org/data_3720 Geographic location 'Geographic location' SubClassOf 'Isolation report' http://edamontology.org/data_3721 Isolation source 'Isolation source' SubClassOf 'Isolation report' http://edamontology.org/data_3722 Physiology parameter 'Physiology parameter' SubClassOf 'Experimental measurement' http://edamontology.org/data_3738 Beta diversity data 'Beta diversity data' SubClassOf 'Biodiversity report' http://edamontology.org/operation_0411 Protein signal peptide detection (eukaryotes) 'Protein signal peptide detection (eukaryotes)' SubClassOf 'Protein signal peptide detection' http://edamontology.org/data_3739 Gamma diversity data 'Gamma diversity data' SubClassOf 'Biodiversity report' http://edamontology.org/operation_0412 Protein signal peptide detection (bacteria) 'Protein signal peptide detection (bacteria)' SubClassOf 'Protein signal peptide detection' http://edamontology.org/operation_0410 Protein crystallizability prediction 'Protein crystallizability prediction' SubClassOf 'Protein hydropathy calculation' http://edamontology.org/data_3734 Lane identifier 'Lane identifier' SubClassOf 'Sequencing metadata name' http://edamontology.org/operation_0415 Nucleic acid feature detection 'Nucleic acid feature detection' SubClassOf 'Prediction and recognition (nucleic acid)' 'Nucleic acid feature detection' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/data_3735 Run number 'Run number' SubClassOf 'Sequencing metadata name' http://edamontology.org/operation_0416 Epitope mapping 'Epitope mapping' SubClassOf 'Protein sequence feature detection' 'Epitope mapping' SubClassOf 'Mapping' http://edamontology.org/data_3736 Ecological data 'Ecological data' SubClassOf 'Data' http://edamontology.org/operation_0413 MHC peptide immunogenicity prediction 'MHC peptide immunogenicity prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3737 Alpha diversity data 'Alpha diversity data' SubClassOf 'Biodiversity report' http://edamontology.org/operation_0414 Protein feature prediction (from sequence) 'Protein feature prediction (from sequence)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2400 Toxin annotation 'Toxin annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2401 Protein report (membrane protein) 'Protein report (membrane protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3732 Sequencing metadata name 'Sequencing metadata name' SubClassOf 'Name' http://edamontology.org/data_2402 Protein-drug interaction report 'Protein-drug interaction report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3733 Flow cell identifier 'Flow cell identifier' SubClassOf 'Sequencing metadata name' http://edamontology.org/operation_0408 Protein globularity prediction 'Protein globularity prediction' SubClassOf 'Protein hydropathy calculation' http://edamontology.org/operation_0409 Protein solubility prediction 'Protein solubility prediction' SubClassOf 'Protein hydropathy calculation' http://edamontology.org/operation_0406 Protein aliphatic index calculation 'Protein aliphatic index calculation' SubClassOf 'Protein hydropathy calculation' http://edamontology.org/operation_0407 Protein hydrophobic moment plotting 'Protein hydrophobic moment plotting' SubClassOf 'Protein hydropathy calculation' 'Protein hydrophobic moment plotting' SubClassOf 'Plotting' http://edamontology.org/data_1689 Username 'Username' SubClassOf 'User ID' http://edamontology.org/data_1688 EMBOSS vectorstrip log file 'EMBOSS vectorstrip log file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1683 EMBOSS domainatrix log file 'EMBOSS domainatrix log file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1682 EMBOSS wordfinder log file 'EMBOSS wordfinder log file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1681 NACCESS log file 'NACCESS log file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1680 STRIDE log file 'STRIDE log file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1687 EMBOSS whichdb log file 'EMBOSS whichdb log file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1686 EMBOSS megamerger log file 'EMBOSS megamerger log file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1685 EMBOSS supermatcher error file 'EMBOSS supermatcher error file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1684 EMBOSS sites log file 'EMBOSS sites log file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3329 HMMER3 'HMMER3' SubClassOf 'HMMER format' http://edamontology.org/format_3328 HMMER2 'HMMER2' SubClassOf 'HMMER format' http://edamontology.org/format_3327 BAI 'BAI' SubClassOf 'Data index format' http://edamontology.org/format_3326 Data index format 'Data index format' SubClassOf 'Format (by type of data)' 'Data index format' SubClassOf 'binary format' http://edamontology.org/data_1694 Number of output entities 'Number of output entities' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1693 Number of iterations 'Number of iterations' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1692 Person name 'Person name' SubClassOf 'Person identifier' http://edamontology.org/data_1691 Email address 'Email address' SubClassOf 'User ID' http://edamontology.org/data_1696 Drug report 'Drug report' SubClassOf 'Small molecule report' http://edamontology.org/data_1695 Hit sort order 'Hit sort order' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3310 SS 'SS' SubClassOf 'Textual format' 'SS' SubClassOf 'RNA secondary structure format' http://edamontology.org/format_3312 GDE 'GDE' SubClassOf 'Sequence record format (text)' 'GDE' SubClassOf 'Textual format' http://edamontology.org/format_3311 RNAML 'RNAML' SubClassOf 'Alignment format' 'RNAML' SubClassOf 'XML' 'RNAML' SubClassOf 'RNA secondary structure format' http://edamontology.org/data_1690 Password 'Password' SubClassOf 'User ID' http://edamontology.org/format_3313 BLC 'BLC' SubClassOf 'Alignment format (text)' http://edamontology.org/format_2014 Sequence-profile alignment format 'Sequence-profile alignment format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2013 Biological pathway or network format 'Biological pathway or network format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2015 Sequence-profile alignment (HMM) format 'Sequence-profile alignment (HMM) format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2017 Amino acid index format 'Amino acid index format' SubClassOf 'Matrix format' http://edamontology.org/format_2001 EMBOSS simple format 'EMBOSS simple format' SubClassOf 'Textual format' 'EMBOSS simple format' SubClassOf 'Alignment format (text)' http://edamontology.org/format_2000 selex 'selex' SubClassOf 'Alignment format (text)' 'selex' SubClassOf 'Textual format' 'selex' SubClassOf 'Sequence record format (text)' http://edamontology.org/format_3331 BLAST XML results format 'BLAST XML results format' SubClassOf 'XML' 'BLAST XML results format' SubClassOf 'BLAST results' http://edamontology.org/format_2003 srspair 'srspair' SubClassOf 'Textual format' 'srspair' SubClassOf 'Alignment format (pair only)' http://edamontology.org/format_2002 srs format 'srs format' SubClassOf 'Alignment format (text)' 'srs format' SubClassOf 'Textual format' http://edamontology.org/format_3330 PO 'PO' SubClassOf 'Alignment format (text)' http://edamontology.org/format_2005 TreeCon-seq 'TreeCon-seq' SubClassOf 'Sequence record format (text)' 'TreeCon-seq' SubClassOf 'Alignment format (text)' 'TreeCon-seq' SubClassOf 'Textual format' http://edamontology.org/format_2004 T-Coffee format 'T-Coffee format' SubClassOf 'Alignment format (text)' 'T-Coffee format' SubClassOf 'Textual format' http://edamontology.org/format_2006 Phylogenetic tree format 'Phylogenetic tree format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_3426 Proteomics experiment report 'Proteomics experiment report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3427 RNAi report 'RNAi report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3428 Simulation experiment report 'Simulation experiment report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3424 Raw image 'Raw image' SubClassOf 'Image' http://edamontology.org/data_3425 Carbohydrate property 'Carbohydrate property' SubClassOf 'Molecular property' http://edamontology.org/format_1582 findkm 'findkm' SubClassOf 'Textual format' 'findkm' SubClassOf 'Enzyme kinetics report format' http://edamontology.org/format_1580 ProDom entry format 'ProDom entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1581 FSSP entry format 'FSSP entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2106 Reaction ID (BioCyc) 'Reaction ID (BioCyc)' SubClassOf 'Reaction ID' 'Reaction ID (BioCyc)' SubClassOf 'BioCyc ID' http://edamontology.org/data_2107 Enzyme ID (BioCyc) 'Enzyme ID (BioCyc)' SubClassOf 'Enzyme ID' 'Enzyme ID (BioCyc)' SubClassOf 'BioCyc ID' http://edamontology.org/data_2108 Reaction ID 'Reaction ID' SubClassOf 'Identifier (typed)' 'Reaction ID' SubClassOf 'Accession' http://edamontology.org/data_2109 Identifier (hybrid) 'Identifier (hybrid)' SubClassOf 'Identifier' http://edamontology.org/data_2102 KEGG organism code 'KEGG organism code' SubClassOf 'KEGG object identifier' 'KEGG organism code' SubClassOf 'Organism name' http://edamontology.org/data_2103 Gene name (KEGG GENES) 'Gene name (KEGG GENES)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://kt.ijs.si/panovp/OntoDM#OntoDM_419460 single generalization specification 'single generalization specification' SubClassOf 'generalization specification' http://edamontology.org/data_2104 BioCyc ID 'BioCyc ID' SubClassOf 'Accession' 'BioCyc ID' SubClassOf 'Identifier (hybrid)' http://edamontology.org/data_2105 Compound ID (BioCyc) 'Compound ID (BioCyc)' SubClassOf 'Compound accession' 'Compound ID (BioCyc)' SubClassOf 'BioCyc ID' http://edamontology.org/data_2100 Type 'Type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2101 User ID 'User ID' SubClassOf 'Person identifier' http://edamontology.org/format_1571 InterPro entry abstract format 'InterPro entry abstract format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1572 Gene3D entry format 'Gene3D entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1573 PIRSF entry format 'PIRSF entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1574 PRINTS entry format 'PRINTS entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1570 InterPro entry format 'InterPro entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1579 TIGRFam entry format 'TIGRFam entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1575 Panther Families and HMMs entry format 'Panther Families and HMMs entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1576 Pfam entry format 'Pfam entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1577 SMART entry format 'SMART entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1578 Superfamily entry format 'Superfamily entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2117 Map identifier 'Map identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2118 Person identifier 'Person identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_3449 Cell migration track image 'Cell migration track image' SubClassOf 'Image' http://edamontology.org/data_2119 Nucleic acid identifier 'Nucleic acid identifier' SubClassOf 'Molecule identifier' http://edamontology.org/data_2113 WormBase identifier 'WormBase identifier' SubClassOf 'Identifier (hybrid)' http://edamontology.org/data_2114 WormBase wormpep ID 'WormBase wormpep ID' SubClassOf 'Protein accession' 'WormBase wormpep ID' SubClassOf 'WormBase identifier' http://edamontology.org/data_2116 Nucleic acid features (codon) 'Nucleic acid features (codon)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2110 Molecular property identifier 'Molecular property identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2111 Codon usage table ID 'Codon usage table ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_3442 MRI image 'MRI image' SubClassOf 'Raw image' http://edamontology.org/data_2112 FlyBase primary identifier 'FlyBase primary identifier' SubClassOf 'FlyBase ID' http://edamontology.org/format_3309 CT 'CT' SubClassOf 'Textual format' 'CT' SubClassOf 'RNA secondary structure format' http://edamontology.org/data_2128 Genetic code name 'Genetic code name' SubClassOf 'Name' 'Genetic code name' SubClassOf 'Genetic code identifier' http://edamontology.org/data_2129 File format name 'File format name' SubClassOf 'Name' 'File format name' SubClassOf 'Format identifier' http://edamontology.org/data_2126 Translation frame specification 'Translation frame specification' SubClassOf 'Sequence attribute' http://edamontology.org/data_2127 Genetic code identifier 'Genetic code identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_3451 Rate of association 'Rate of association' SubClassOf 'Protein property' http://edamontology.org/operation_3217 Scaffold gap completion 'Scaffold gap completion' SubClassOf 'Scaffolding' http://edamontology.org/operation_3216 Scaffolding 'Scaffolding' SubClassOf 'Generation' 'Scaffolding' SubClassOf 'Sequence assembly' http://edamontology.org/operation_3215 Peak detection 'Peak detection' SubClassOf 'Spectral analysis' http://edamontology.org/operation_3214 Spectral analysis 'Spectral analysis' SubClassOf 'Analysis' http://edamontology.org/data_2139 Nucleic acid melting temperature 'Nucleic acid melting temperature' SubClassOf 'Nucleic acid thermodynamic data' http://edamontology.org/operation_3219 Read pre-processing 'Read pre-processing' SubClassOf 'Sequencing quality control' http://edamontology.org/operation_3218 Sequencing quality control 'Sequencing quality control' SubClassOf 'Nucleic acid sequence analysis' 'Sequencing quality control' SubClassOf 'Validation' http://edamontology.org/data_2135 Toggle 'Toggle' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2136 Sequence width 'Sequence width' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2137 Gap penalty 'Gap penalty' SubClassOf 'Alignment score or penalty' http://edamontology.org/data_2131 Operating system name 'Operating system name' SubClassOf 'Name' http://edamontology.org/operation_3213 Genome indexing (suffix arrays) 'Genome indexing (suffix arrays)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2132 Mutation type 'Mutation type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3212 Genome indexing (Burrows-Wheeler) 'Genome indexing (Burrows-Wheeler)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2133 Logical operator 'Logical operator' SubClassOf 'Name' http://edamontology.org/operation_3211 Genome indexing 'Genome indexing' SubClassOf 'Indexing' http://edamontology.org/data_2134 Results sort order 'Results sort order' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2078 Sequence range format 'Sequence range format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2077 Protein secondary structure format 'Protein secondary structure format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_2130 Sequence profile type 'Sequence profile type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2074 Dirichlet distribution format 'Dirichlet distribution format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2076 RNA secondary structure format 'RNA secondary structure format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2075 HMM emission and transition counts format 'HMM emission and transition counts format' SubClassOf 'Format (by type of data)' http://edamontology.org/operation_3228 Structural variation discovery 'Structural variation discovery' SubClassOf 'Genetic variation analysis' http://edamontology.org/operation_3227 Variant calling 'Variant calling' SubClassOf 'Genetic variation analysis' http://edamontology.org/operation_3226 Variant prioritisation 'Variant prioritisation' SubClassOf 'Genetic variation analysis' http://edamontology.org/operation_3225 Variant classification 'Variant classification' SubClassOf 'Genetic variation analysis' 'Variant classification' SubClassOf 'Sequence classification' http://edamontology.org/operation_3229 Exome analysis Exome assembly 'Exome assembly' SubClassOf 'Sequence assembly' http://edamontology.org/data_2146 Threshold 'Threshold' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2147 Protein report (transcription factor) 'Protein report (transcription factor)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3479 Gene order 'Gene order' SubClassOf 'Matrix' http://edamontology.org/format_2072 Hidden Markov model format 'Hidden Markov model format' SubClassOf 'Sequence profile format' http://edamontology.org/data_2149 Database category name 'Database category name' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2142 EMBOSS graph 'EMBOSS graph' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3224 Gene set testing 'Gene set testing' SubClassOf 'Gene expression analysis' http://edamontology.org/data_2143 EMBOSS report 'EMBOSS report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3223 Differential gene expression analysis 'Differential gene expression analysis' SubClassOf 'Differential gene expression analysis' 'Differential gene expression analysis' SubClassOf 'Nucleic acid comparison' http://edamontology.org/operation_3222 Peak calling 'Peak calling' SubClassOf 'Nucleic acid sequence feature detection' http://edamontology.org/data_2145 Sequence offset 'Sequence offset' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3221 Species frequency estimation 'Species frequency estimation' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/format_2067 Sequence distance matrix format 'Sequence distance matrix format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2066 Database hits (sequence) format 'Database hits (sequence) format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_2140 Concentration 'Concentration' SubClassOf 'Molecular property (general)' http://edamontology.org/format_2069 Sequence profile format 'Sequence profile format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_2141 Window step size 'Window step size' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2068 Sequence motif format 'Sequence motif format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2063 Protein report (enzyme) format 'Protein report (enzyme) format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2062 Protein report format 'Protein report format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2065 Protein structure report (quality evaluation) format 'Protein structure report (quality evaluation) format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2064 3D-1D scoring matrix format '3D-1D scoring matrix format' SubClassOf 'Matrix format' http://edamontology.org/data_2157 Word composition 'Word composition' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3488 NMR spectrum 'NMR spectrum' SubClassOf 'Spectrum' http://edamontology.org/data_2154 Sequence name 'Sequence name' SubClassOf 'Sequence identifier' 'Sequence name' SubClassOf 'Name' http://edamontology.org/data_2156 Date 'Date' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2150 Sequence profile name 'Sequence profile name' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2151 Color 'Color' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2152 Rendering parameter 'Rendering parameter' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3483 Spectrum 'Spectrum' SubClassOf 'Data' http://edamontology.org/format_2096 unambiguous sequence 'unambiguous sequence' SubClassOf 'Textual format' 'unambiguous sequence' SubClassOf 'Raw sequence format' http://edamontology.org/format_2095 unpure 'unpure' SubClassOf 'Textual format' 'unpure' SubClassOf 'Raw sequence format' http://edamontology.org/format_2097 ambiguous 'ambiguous' SubClassOf 'Raw sequence format' 'ambiguous' SubClassOf 'Textual format' http://edamontology.org/operation_3206 Methylation level analysis (global) 'Methylation level analysis (global)' SubClassOf 'Methylation calling' http://edamontology.org/operation_3205 Methylation calling 'Methylation calling' SubClassOf 'Physical mapping' 'Methylation calling' SubClassOf 'Methylation analysis' http://edamontology.org/operation_3204 Methylation analysis 'Methylation analysis' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/operation_3203 Chromatogram visualisation 'Chromatogram visualisation' SubClassOf 'Visualisation' http://edamontology.org/operation_3209 Genome comparison 'Genome comparison' SubClassOf 'Nucleic acid sequence comparison' http://edamontology.org/operation_3208 Genome visualisation 'Genome visualisation' SubClassOf 'Sequence visualisation' http://edamontology.org/operation_3207 Methylation level analysis (gene-specific) 'Methylation level analysis (gene-specific)' SubClassOf 'Methylation calling' http://edamontology.org/data_2168 Sequence trace image 'Sequence trace image' SubClassOf 'Sequence image' http://edamontology.org/data_2169 Nucleic acid features (siRNA) 'Nucleic acid features (siRNA)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2094 pure 'pure' SubClassOf 'Raw sequence format' 'pure' SubClassOf 'Textual format' http://edamontology.org/data_2164 Protein sequence properties plot 'Protein sequence properties plot' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3495 RNA sequence 'RNA sequence' SubClassOf 'Nucleic acid sequence' http://edamontology.org/operation_3202 Polymorphism detection 'Polymorphism detection' SubClassOf 'Genetic variation analysis' http://edamontology.org/data_2165 Protein ionisation curve 'Protein ionisation curve' SubClassOf 'Protein property' 'Protein ionisation curve' SubClassOf 'Plot' http://edamontology.org/data_3496 RNA sequence (raw) 'RNA sequence (raw)' SubClassOf 'Nucleic acid sequence (raw)' 'RNA sequence (raw)' SubClassOf 'RNA sequence' http://edamontology.org/operation_3201 SNP calling 'SNP calling' SubClassOf 'SNP detection' http://edamontology.org/data_2166 Sequence composition plot 'Sequence composition plot' SubClassOf 'Plot' 'Sequence composition plot' SubClassOf 'Sequence composition report' http://edamontology.org/data_3497 DNA sequence (raw) 'DNA sequence (raw)' SubClassOf 'DNA sequence' 'DNA sequence (raw)' SubClassOf 'Nucleic acid sequence (raw)' http://edamontology.org/operation_3200 Community profiling 'Community profiling' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/data_2167 Nucleic acid density plot 'Nucleic acid density plot' SubClassOf 'Sequence composition report' 'Nucleic acid density plot' SubClassOf 'Plot' http://edamontology.org/data_3498 Sequence variations 'Sequence variations' SubClassOf 'Data' http://edamontology.org/data_2160 Fickett testcode plot 'Fickett testcode plot' SubClassOf 'Plot' http://edamontology.org/data_2161 Sequence similarity plot 'Sequence similarity plot' SubClassOf 'Plot' 'Sequence similarity plot' SubClassOf 'Sequence alignment report' http://edamontology.org/data_3492 Nucleic acid signature 'Nucleic acid signature' SubClassOf 'Sequence signature report' http://edamontology.org/data_2162 Helical wheel 'Helical wheel' SubClassOf 'Protein secondary structure image' http://edamontology.org/data_2163 Helical net 'Helical net' SubClassOf 'Protein secondary structure image' http://edamontology.org/data_3494 DNA sequence 'DNA sequence' SubClassOf 'Nucleic acid sequence' http://edamontology.org/data_3490 Chemical structure sketch 'Chemical structure sketch' SubClassOf 'Chemical structure image' http://edamontology.org/topic_2754 Introns 'Introns' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3259 Transcriptome assembly (de novo) 'Transcriptome assembly (de novo)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3258 Transcriptome assembly 'Transcriptome assembly' SubClassOf 'Sequence assembly' http://edamontology.org/topic_0100 Nucleic acid restriction 'Nucleic acid restriction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2179 Exactly 2 'Exactly 2' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2176 Cardinality 'Cardinality' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2177 Exactly 1 'Exactly 1' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2178 1 or more '1 or more' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2034 Biological model format 'Biological model format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2033 Tertiary structure format 'Tertiary structure format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_2173 Sequence set (stream) 'Sequence set (stream)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2036 Phylogenetic character data format 'Phylogenetic character data format' SubClassOf 'Format (by type of data)' http://edamontology.org/topic_0109 Gene finding 'Gene finding' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2174 FlyBase secondary identifier 'FlyBase secondary identifier' SubClassOf 'FlyBase ID' http://edamontology.org/format_2035 Chemical formula format 'Chemical formula format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2030 Small molecule report format 'Small molecule report format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2032 Workflow format 'Workflow format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2031 Gene annotation format 'Gene annotation format' SubClassOf 'Format (by type of data)' http://edamontology.org/topic_0102 Mapping 'Mapping' SubClassOf 'Sequence analysis' http://edamontology.org/format_2038 Phylogenetic discrete states format 'Phylogenetic discrete states format' SubClassOf 'Phylogenetic character data format' http://edamontology.org/topic_0107 Genetic codes and codon usage 'Genetic codes and codon usage' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2037 Phylogenetic continuous quantitative character format 'Phylogenetic continuous quantitative character format' SubClassOf 'Phylogenetic character data format' http://edamontology.org/topic_0108 Protein expression 'Protein expression' SubClassOf 'Proteins' http://edamontology.org/format_2039 Phylogenetic tree report (cliques) format 'Phylogenetic tree report (cliques) format' SubClassOf 'Phylogenetic character data format' http://edamontology.org/topic_0110 Transcription 'Transcription' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0111 Promoters 'Promoters' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3267 Sequence coordinate conversion 'Sequence coordinate conversion' SubClassOf 'Conversion' http://edamontology.org/operation_3260 Transcriptome assembly (mapping) 'Transcriptome assembly (mapping)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2180 2 or more '2 or more' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2021 Text mining report format 'Text mining report format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2020 Article format 'Article format' SubClassOf 'Format (by type of data)' http://edamontology.org/topic_0114 Gene structure 'Gene structure' SubClassOf 'Molecular genetics' http://edamontology.org/topic_0112 Nucleic acid folding 'Nucleic acid folding' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2027 Enzyme kinetics report format 'Enzyme kinetics report format' SubClassOf 'Format (by type of data)' http://edamontology.org/operation_3237 Primer removal 'Primer removal' SubClassOf 'Sequence cutting' http://edamontology.org/topic_0121 Proteomics 'Proteomics' SubClassOf 'Omics' http://edamontology.org/topic_0122 Structural genomics 'Structural genomics' SubClassOf 'Structural biology' 'Structural genomics' SubClassOf 'Genomics' http://edamontology.org/operation_3230 Read depth analysis 'Read depth analysis' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/format_2061 Nucleic acid features (primers) format 'Nucleic acid features (primers) format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2060 Map format 'Map format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_2198 Gene cluster 'Gene cluster' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3233 Copy number estimation 'Copy number estimation' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/operation_3232 Gene expression QTL analysis 'Gene expression QTL analysis' SubClassOf 'Gene expression analysis' http://edamontology.org/data_2193 Database entry metadata 'Database entry metadata' SubClassOf 'Resource metadata' http://edamontology.org/format_2056 Microarray experiment data format 'Microarray experiment data format' SubClassOf 'Experiment annotation format' http://edamontology.org/format_2055 Sequence assembly format 'Sequence assembly format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2058 Gene expression report format 'Gene expression report format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2057 Sequence trace format 'Sequence trace format' SubClassOf 'Sequence record format' http://edamontology.org/format_2052 Protein family report format 'Protein family report format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_2190 Sequence checksum 'Sequence checksum' SubClassOf 'Sequence attribute' http://edamontology.org/format_2051 Polymorphism report format 'Polymorphism report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2191 Protein features report (chemical modifications) 'Protein features report (chemical modifications)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2054 Protein interaction format 'Protein interaction format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_2192 Error 'Error' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_1456 Protein membrane regions 'Protein membrane regions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0123 Protein properties 'Protein properties' SubClassOf 'Proteins' http://edamontology.org/format_2059 Genotype and phenotype annotation format 'Genotype and phenotype annotation format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0128 Protein interactions 'Protein interactions' SubClassOf 'Proteins' 'Protein interactions' SubClassOf 'Molecular interactions, pathways and networks' http://edamontology.org/topic_0133 Two-dimensional gel electrophoresis 'Two-dimensional gel electrophoresis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0130 Protein folding, stability and design 'Protein folding, stability and design' SubClassOf 'Protein structure analysis' http://edamontology.org/format_2045 Electron microscopy model format 'Electron microscopy model format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2040 Phylogenetic tree report (invariants) format 'Phylogenetic tree report (invariants) format' SubClassOf 'Phylogenetic character data format' http://edamontology.org/topic_0137 Protein hydropathy 'Protein hydropathy' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0134 Mass spectrometry 'Mass spectrometry' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0135 Protein microarrays 'Protein microarrays' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2049 Phylogenetic tree report (tree distances) format 'Phylogenetic tree report (tree distances) format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_2098 Job identifier 'Job identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2099 Name 'Name' SubClassOf 'Identifier' http://kt.ijs.si/panovp/OntoDM#OntoDM_000235 predictive modeling task 'predictive modeling task' SubClassOf 'data mining task' http://edamontology.org/data_2090 Database entry version information 'Database entry version information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2091 Accession 'Accession' SubClassOf 'Identifier' http://edamontology.org/data_2092 SNP 'SNP' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2093 Data reference 'Data reference' SubClassOf 'Data' http://edamontology.org/operation_3187 Sequence contamination filtering 'Sequence contamination filtering' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/operation_3186 Bisulfite mapping 'Bisulfite mapping' SubClassOf 'Physical mapping' http://edamontology.org/operation_3185 Base-calling 'Base-calling' SubClassOf 'Sequence generation (nucleic acid)' http://edamontology.org/operation_3184 Sequence assembly visualisation 'Sequence assembly visualisation' SubClassOf 'Sequence visualisation' http://edamontology.org/operation_3189 Trim ends 'Trim ends' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3183 Localised reassembly 'Localised reassembly' SubClassOf 'Sequence assembly' http://edamontology.org/operation_3182 Genome alignment 'Genome alignment' SubClassOf 'Sequence alignment' http://edamontology.org/operation_3180 Sequence assembly validation 'Sequence assembly validation' SubClassOf 'Validation' 'Sequence assembly validation' SubClassOf 'Nucleic acid sequence analysis' http://www.ebi.ac.uk/swo/algorithm/OntoDM_584946 clustering specification 'clustering specification' SubClassOf 'single generalization specification' http://kt.ijs.si/panovp/OntoDM#OntoDM_000253 probability distribution estimation algorithm 'probability distribution estimation algorithm' SubClassOf 'single generalization algorithm' http://kt.ijs.si/panovp/OntoDM#OntoDM_000264 clustering task 'clustering task' SubClassOf 'data mining task' http://edamontology.org/data_2902 Data resource definition accession 'Data resource definition accession' SubClassOf 'Data resource definition ID' 'Data resource definition accession' SubClassOf 'Accession' http://edamontology.org/data_2903 Genome accession 'Genome accession' SubClassOf 'Accession' 'Genome accession' SubClassOf 'Genome identifier' http://edamontology.org/data_2904 Map accession 'Map accession' SubClassOf 'Accession' 'Map accession' SubClassOf 'Map identifier' http://edamontology.org/data_2905 Lipid accession 'Lipid accession' SubClassOf 'Lipid identifier' 'Lipid accession' SubClassOf 'Molecule accession' http://edamontology.org/topic_0077 Nucleic acids 'Nucleic acids' SubClassOf 'Computational biology' http://edamontology.org/topic_0078 Proteins 'Proteins' SubClassOf 'Computational biology' http://edamontology.org/data_2900 Carbohydrate accession 'Carbohydrate accession' SubClassOf 'Molecule accession' 'Carbohydrate accession' SubClassOf 'Carbohydrate identifier' http://edamontology.org/data_2901 Molecule accession 'Molecule accession' SubClassOf 'Molecule identifier' 'Molecule accession' SubClassOf 'Accession' http://edamontology.org/topic_0079 Metabolites 'Metabolites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2913 Virus identifier 'Virus identifier' SubClassOf 'Organism identifier' http://edamontology.org/topic_0084 Phylogeny 'Phylogeny' SubClassOf 'Computational biology' 'Phylogeny' SubClassOf 'Evolutionary biology' http://edamontology.org/data_2914 Sequence features metadata 'Sequence features metadata' SubClassOf 'Data' http://edamontology.org/topic_0085 Functional genomics 'Functional genomics' SubClassOf 'Genomics' 'Functional genomics' SubClassOf 'Function analysis' http://edamontology.org/data_2915 Gramene identifier 'Gramene identifier' SubClassOf 'Sequence accession (protein)' http://edamontology.org/topic_0082 Structure prediction 'Structure prediction' SubClassOf 'Structure analysis' http://edamontology.org/data_2916 DDBJ accession 'DDBJ accession' SubClassOf 'EMBL/GenBank/DDBJ ID' http://edamontology.org/topic_0083 Alignment 'Alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2910 Protein family accession 'Protein family accession' SubClassOf 'Accession' 'Protein family accession' SubClassOf 'Protein family identifier' http://edamontology.org/topic_0089 Ontology and terminology 'Ontology and terminology' SubClassOf 'Informatics' http://edamontology.org/data_2911 Transcription factor accession 'Transcription factor accession' SubClassOf 'Protein accession' 'Transcription factor accession' SubClassOf 'Transcription factor identifier' http://edamontology.org/data_2912 Strain accession 'Strain accession' SubClassOf 'Organism accession' 'Strain accession' SubClassOf 'Strain identifier' http://edamontology.org/operation_3198 Read mapping 'Read mapping' SubClassOf 'Physical mapping' 'Read mapping' SubClassOf 'Sequence alignment' http://edamontology.org/operation_3197 Genetic variation analysis 'Genetic variation analysis' SubClassOf 'Nucleic acid sequence feature detection' 'Genetic variation analysis' SubClassOf 'Nucleic acid sequence comparison' http://edamontology.org/operation_3196 Genotyping 'Genotyping' SubClassOf 'Genetic variation analysis' http://edamontology.org/operation_3195 Sequencing error detection 'Sequencing error detection' SubClassOf 'Nucleic acid sequence comparison' http://edamontology.org/topic_0080 Sequence analysis 'Sequence analysis' SubClassOf 'Computational biology' http://edamontology.org/topic_0081 Structure analysis 'Structure analysis' SubClassOf 'Computational biology' http://edamontology.org/operation_3199 Split read mapping 'Split read mapping' SubClassOf 'Read mapping' http://edamontology.org/operation_3190 Trim vector 'Trim vector' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3194 Genome feature comparison 'Genome feature comparison' SubClassOf 'Sequence feature comparison' http://edamontology.org/operation_3192 Sequence trimming 'Sequence trimming' SubClassOf 'Sequence cutting' http://edamontology.org/operation_3191 Trim to reference 'Trim to reference' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3118 Protein topological domains 'Protein topological domains' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2906 Peptide ID 'Peptide ID' SubClassOf 'Peptide identifier' 'Peptide ID' SubClassOf 'Molecule accession' http://edamontology.org/data_2907 Protein accession 'Protein accession' SubClassOf 'Molecule accession' 'Protein accession' SubClassOf 'Protein identifier' http://edamontology.org/data_2908 Organism accession 'Organism accession' SubClassOf 'Accession' 'Organism accession' SubClassOf 'Organism identifier' http://edamontology.org/data_2909 Organism name 'Organism name' SubClassOf 'Name' 'Organism name' SubClassOf 'Organism identifier' http://edamontology.org/data_2925 Sequence data 'Sequence data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3120 Protein variants 'Protein variants' SubClassOf 'Protein expression' http://edamontology.org/data_2927 Codon usage 'Codon usage' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0094 Nucleic acid thermodynamics 'Nucleic acid thermodynamics' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0099 RNA 'RNA' SubClassOf 'Nucleic acids' http://edamontology.org/topic_3125 DNA binding sites 'DNA binding sites' SubClassOf 'Nucleic acid sites, features and motifs' 'DNA binding sites' SubClassOf 'DNA' http://edamontology.org/topic_0097 Nucleic acid structure analysis 'Nucleic acid structure analysis' SubClassOf 'Structure analysis' 'Nucleic acid structure analysis' SubClassOf 'Nucleic acids' http://edamontology.org/topic_3123 Expression signals 'Expression signals' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0091 Bioinformatics 'Bioinformatics' SubClassOf 'Informatics' http://edamontology.org/topic_0092 Data visualisation 'Data visualisation' SubClassOf 'Computer science' http://edamontology.org/topic_0090 Information retrieval 'Information retrieval' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://kt.ijs.si/panovp/OntoDM#OntoDM_000228 predictive model specification 'predictive model specification' SubClassOf 'single generalization specification' http://edamontology.org/topic_3127 DNA replication and recombination 'DNA replication and recombination' SubClassOf 'DNA' http://edamontology.org/topic_3126 Nucleic acid repeats 'Nucleic acid repeats' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2917 ConsensusPathDB identifier 'ConsensusPathDB identifier' SubClassOf 'Identifier (hybrid)' http://edamontology.org/data_1602 Codon usage fraction difference 'Codon usage fraction difference' SubClassOf 'Codon usage data' http://edamontology.org/data_1601 Nc statistic 'Nc statistic' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1600 Codon usage bias plot 'Codon usage bias plot' SubClassOf 'Codon usage data' http://edamontology.org/topic_3135 Signal or transit peptide 'Signal or transit peptide' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3139 Sequence tagged sites 'Sequence tagged sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2957 Hopp and Woods plot 'Hopp and Woods plot' SubClassOf 'Plot' 'Hopp and Woods plot' SubClassOf 'Peptide immunogenicity data' http://edamontology.org/data_2958 Nucleic acid melting curve 'Nucleic acid melting curve' SubClassOf 'Nucleic acid melting profile' 'Nucleic acid melting curve' SubClassOf 'Plot' http://edamontology.org/data_2959 Nucleic acid probability profile 'Nucleic acid probability profile' SubClassOf 'Nucleic acid melting profile' http://edamontology.org/data_1622 Disease report 'Disease report' SubClassOf 'Genotype/phenotype report' http://edamontology.org/data_2954 Article report 'Article report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2955 Sequence report 'Sequence report' SubClassOf 'Report' http://edamontology.org/data_2956 Protein secondary structure report 'Protein secondary structure report' SubClassOf 'Protein structure report' http://edamontology.org/data_1621 Pharmacogenomic test report 'Pharmacogenomic test report' SubClassOf 'Genotype/phenotype report' http://edamontology.org/format_1563 SMART domain assignment report format 'SMART domain assignment report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1568 BIND entry format 'BIND entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1569 IntAct entry format 'IntAct entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2969 Sequence image 'Sequence image' SubClassOf 'Sequence report' 'Sequence image' SubClassOf 'Image' http://edamontology.org/data_1634 Linkage disequilibrium (report) 'Linkage disequilibrium (report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3169 ChIP-seq 'ChIP-seq' SubClassOf 'Sequencing' 'ChIP-seq' SubClassOf 'Immunoprecipitation experiment' http://edamontology.org/data_2965 2D PAGE gel report '2D PAGE gel report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3168 Sequencing 'Sequencing' SubClassOf 'Laboratory techniques' http://edamontology.org/data_2966 Oligonucleotide probe sets annotation 'Oligonucleotide probe sets annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2967 Microarray image 'Microarray image' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2960 Nucleic acid temperature profile 'Nucleic acid temperature profile' SubClassOf 'Nucleic acid melting profile' http://edamontology.org/data_2961 Gene regulatory network report 'Gene regulatory network report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1551 Pcons report format 'Pcons report format' SubClassOf 'Textual format' 'Pcons report format' SubClassOf 'Protein structure report (quality evaluation) format' http://edamontology.org/format_1552 ProQ report format 'ProQ report format' SubClassOf 'Textual format' 'ProQ report format' SubClassOf 'Protein structure report (quality evaluation) format' http://edamontology.org/data_2979 Peptide property 'Peptide property' SubClassOf 'Molecular property' http://edamontology.org/topic_3176 DNA packaging 'DNA packaging' SubClassOf 'DNA' http://edamontology.org/data_1646 Molecular weights standard fingerprint 'Molecular weights standard fingerprint' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3175 DNA structural variation 'DNA structural variation' SubClassOf 'DNA' 'DNA structural variation' SubClassOf 'Genetic variation' http://edamontology.org/topic_3174 Metagenomics 'Metagenomics' SubClassOf 'Ecology' 'Metagenomics' SubClassOf 'Genomics' http://edamontology.org/topic_3173 Epigenomics 'Epigenomics' SubClassOf 'Genomics' 'Epigenomics' SubClassOf 'Epigenetics' http://edamontology.org/data_2975 Nucleic acid sequence (raw) 'Nucleic acid sequence (raw)' SubClassOf 'Nucleic acid sequence' 'Nucleic acid sequence (raw)' SubClassOf 'Raw sequence' http://edamontology.org/data_2976 Protein sequence 'Protein sequence' SubClassOf 'Sequence' http://edamontology.org/topic_3179 ChIP-on-chip 'ChIP-on-chip' SubClassOf 'Immunoprecipitation experiment' http://edamontology.org/data_2977 Nucleic acid sequence 'Nucleic acid sequence' SubClassOf 'Sequence' http://edamontology.org/topic_3178 RNA-Seq alignment 'RNA-Seq alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2978 Reaction data 'Reaction data' SubClassOf 'Data' http://edamontology.org/topic_3177 DNA-Seq 'DNA-Seq' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2971 Workflow data 'Workflow data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2972 Workflow 'Workflow' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2973 Secondary structure data 'Secondary structure data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2974 Protein sequence (raw) 'Protein sequence (raw)' SubClassOf 'Protein sequence' 'Protein sequence (raw)' SubClassOf 'Raw sequence' http://edamontology.org/data_1643 Affymetrix probe sets information library file 'Affymetrix probe sets information library file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3172 Metabolomics 'Metabolomics' SubClassOf 'Omics' http://edamontology.org/data_1642 Affymetrix probe sets library file 'Affymetrix probe sets library file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3171 DNA methylation 'DNA methylation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3170 RNA-Seq 'RNA-Seq' SubClassOf 'Sequencing' http://edamontology.org/data_2970 Protein hydropathy data 'Protein hydropathy data' SubClassOf 'Protein property' http://edamontology.org/format_1504 aaindex 'aaindex' SubClassOf 'Textual format' 'aaindex' SubClassOf 'Amino acid index format' http://edamontology.org/format_1500 Domainatrix 3D-1D scoring matrix format 'Domainatrix 3D-1D scoring matrix format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1658 Environmental information processing pathway report 'Environmental information processing pathway report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1657 Genetic information processing pathway report 'Genetic information processing pathway report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1656 Metabolic pathway report 'Metabolic pathway report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2986 Nucleic acid classification 'Nucleic acid classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2987 Classification report 'Classification report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1659 Signal transduction pathway report 'Signal transduction pathway report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2989 Protein features report (key folding sites) 'Protein features report (key folding sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2982 Sequence profile data 'Sequence profile data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2983 Pathway or network data 'Pathway or network data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2984 Pathway or network report 'Pathway or network report' SubClassOf 'Over-representation report' http://edamontology.org/data_2985 Nucleic acid thermodynamic data 'Nucleic acid thermodynamic data' SubClassOf 'Nucleic acid property' http://edamontology.org/data_2980 Protein classification 'Protein classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2981 Sequence motif data 'Sequence motif data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://kt.ijs.si/panovp/OntoDM#OntoDM_000285 probability distribution specification 'probability distribution specification' SubClassOf 'single generalization specification' http://kt.ijs.si/panovp/OntoDM#OntoDM_530819 ensemble algorithm 'ensemble algorithm' SubClassOf 'data mining algorithm' http://edamontology.org/data_1669 P-value 'P-value' SubClassOf 'Statistical estimate score' http://edamontology.org/data_1668 Z-value 'Z-value' SubClassOf 'Statistical estimate score' http://edamontology.org/data_1667 E-value 'E-value' SubClassOf 'Statistical estimate score' http://edamontology.org/data_1661 Disease pathway or network report 'Disease pathway or network report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1660 Cellular process pathways report 'Cellular process pathways report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2994 Phylogenetic character weights 'Phylogenetic character weights' SubClassOf 'Phylogenetic data' http://edamontology.org/data_1664 MIRIAM datatype 'MIRIAM datatype' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2991 Protein geometry report 'Protein geometry report' SubClassOf 'Protein structure report' http://edamontology.org/data_1663 Protein interaction networks 'Protein interaction networks' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1662 Drug structure relationship map 'Drug structure relationship map' SubClassOf 'Drug report' http://edamontology.org/data_2992 Protein structure image 'Protein structure image' SubClassOf 'Structure image' 'Protein structure image' SubClassOf 'Protein image' http://edamontology.org/topic_0922 Primers 'Primers' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1679 DaliLite log file 'DaliLite log file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1678 Tool log 'Tool log' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1677 Job type 'Job type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2848 Bibliographic reference format 'Bibliographic reference format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_1672 CATH version information 'CATH version information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1671 Tool version information 'Tool version information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1670 Database version information 'Database version information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1676 Job ID 'Job ID' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1675 Job status 'Job status' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1674 Sequence database cross-references 'Sequence database cross-references' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1673 Swiss-Prot to PDB mapping 'Swiss-Prot to PDB mapping' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1513 KEGG REACTION enzyme report format 'KEGG REACTION enzyme report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1514 KEGG ENZYME enzyme report format 'KEGG ENZYME enzyme report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1515 REBASE proto enzyme report format 'REBASE proto enzyme report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1516 REBASE withrefm enzyme report format 'REBASE withrefm enzyme report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1511 IntEnz enzyme report format 'IntEnz enzyme report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1512 BRENDA enzyme report format 'BRENDA enzyme report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0225 Data retrieval (database cross-reference) 'Data retrieval (database cross-reference)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3509 Ontology mapping 'Ontology mapping' SubClassOf 'Data reference' http://edamontology.org/operation_0228 Data index analysis 'Data index analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0229 Annotation retrieval (sequence) 'Annotation retrieval (sequence)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3505 Bibliography 'Bibliography' SubClassOf 'Text data' http://edamontology.org/operation_0226 Annotation 'Annotation' SubClassOf 'Operation' http://edamontology.org/operation_0227 Indexing 'Indexing' SubClassOf 'Operation' http://edamontology.org/topic_0820 Membrane and lipoproteins 'Membrane and lipoproteins' SubClassOf 'Proteins' http://edamontology.org/topic_0821 Enzymes 'Enzymes' SubClassOf 'Proteins' http://edamontology.org/operation_0235 Sequence ambiguity calculation 'Sequence ambiguity calculation' SubClassOf 'Sequence composition calculation' http://edamontology.org/operation_0236 Sequence composition calculation 'Sequence composition calculation' SubClassOf 'Calculation' 'Sequence composition calculation' SubClassOf 'Sequence analysis' http://edamontology.org/operation_0233 Sequence conversion 'Sequence conversion' SubClassOf 'Conversion' 'Sequence conversion' SubClassOf 'Sequence editing' http://edamontology.org/operation_0234 Sequence complexity calculation 'Sequence complexity calculation' SubClassOf 'Sequence composition calculation' http://edamontology.org/operation_0239 Sequence motif recognition 'Sequence motif recognition' SubClassOf 'Sequence feature detection' 'Sequence motif recognition' SubClassOf 'Sequence motif analysis' http://edamontology.org/operation_0237 Repeat sequence analysis 'Repeat sequence analysis' SubClassOf 'Sequence analysis' http://edamontology.org/operation_0238 Sequence motif discovery 'Sequence motif discovery' SubClassOf 'Sequence motif analysis' 'Sequence motif discovery' SubClassOf 'Sequence feature detection' http://edamontology.org/operation_0231 Sequence editing 'Sequence editing' SubClassOf 'Editing' 'Sequence editing' SubClassOf 'Sequence analysis' http://edamontology.org/operation_0232 Sequence merging 'Sequence merging' SubClassOf 'Sequence editing' http://edamontology.org/operation_0230 Sequence generation 'Sequence generation' SubClassOf 'Generation' 'Sequence generation' SubClassOf 'Sequence analysis' http://edamontology.org/data_2209 Mutation ID 'Mutation ID' SubClassOf 'Accession' 'Mutation ID' SubClassOf 'Mutation identifier' http://edamontology.org/data_2208 Plasmid identifier 'Plasmid identifier' SubClassOf 'Nucleic acid identifier' http://edamontology.org/data_2201 Sequence record full 'Sequence record full' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2871 Sequence tagged site (STS) mapping 'Sequence tagged site (STS) mapping' SubClassOf 'Physical mapping' http://edamontology.org/operation_0268 Protein super-secondary structure prediction 'Protein super-secondary structure prediction' SubClassOf 'Protein secondary structure prediction' http://edamontology.org/operation_0269 Transmembrane protein prediction 'Transmembrane protein prediction' SubClassOf 'Transmembrane protein analysis' 'Transmembrane protein prediction' SubClassOf 'Protein secondary structure prediction' http://edamontology.org/operation_0266 Vector sequence detection 'Vector sequence detection' SubClassOf 'Nucleic acid feature detection' 'Vector sequence detection' SubClassOf 'Nucleic acid sequence comparison' http://edamontology.org/operation_0267 Protein secondary structure prediction 'Protein secondary structure prediction' SubClassOf 'Protein sequence analysis' 'Protein secondary structure prediction' SubClassOf 'Protein feature detection' http://edamontology.org/data_2216 Codon number 'Codon number' SubClassOf 'Sequence position' http://edamontology.org/data_2217 Tumor annotation 'Tumor annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2218 Server metadata 'Server metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2219 Database field name 'Database field name' SubClassOf 'Name' http://edamontology.org/data_2212 Mutation annotation (basic) 'Mutation annotation (basic)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0260 Sequence alignment conversion 'Sequence alignment conversion' SubClassOf 'Conversion' 'Sequence alignment conversion' SubClassOf 'Sequence alignment editing' http://edamontology.org/data_2213 Mutation annotation (prevalence) 'Mutation annotation (prevalence)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0261 Nucleic acid property processing 'Nucleic acid property processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2214 Mutation annotation (prognostic) 'Mutation annotation (prognostic)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2215 Mutation annotation (functional) 'Mutation annotation (functional)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3546 Image metadata 'Image metadata' SubClassOf 'Report' http://edamontology.org/operation_0264 Splice transcript prediction 'Splice transcript prediction' SubClassOf 'Splicing model analysis' http://edamontology.org/operation_0265 Frameshift detection 'Frameshift detection' SubClassOf 'Polymorphism detection' 'Frameshift detection' SubClassOf 'Sequencing error detection' http://edamontology.org/operation_0262 Nucleic acid property calculation 'Nucleic acid property calculation' SubClassOf 'Nucleic acid sequence analysis' 'Nucleic acid property calculation' SubClassOf 'Calculation' http://edamontology.org/operation_0279 Nucleic acid folding analysis 'Nucleic acid folding analysis' SubClassOf 'Nucleic acid structure analysis' 'Nucleic acid folding analysis' SubClassOf 'Prediction and recognition (nucleic acid)' 'Nucleic acid folding analysis' SubClassOf 'Modelling and simulation' http://edamontology.org/operation_0277 Protein interaction network comparison 'Protein interaction network comparison' SubClassOf 'Protein interaction network analysis' 'Protein interaction network comparison' SubClassOf 'Protein function comparison' http://edamontology.org/operation_0278 RNA secondary structure prediction 'RNA secondary structure prediction' SubClassOf 'Nucleic acid folding analysis' 'RNA secondary structure prediction' SubClassOf 'Nucleic acid feature detection' 'RNA secondary structure prediction' SubClassOf 'RNA secondary structure analysis' http://edamontology.org/data_3558 Clinical trial report 'Clinical trial report' SubClassOf 'Report' http://edamontology.org/data_2223 Ontology metadata 'Ontology metadata' SubClassOf 'Resource metadata' http://edamontology.org/operation_0271 Structure prediction 'Structure prediction' SubClassOf 'Prediction and recognition' 'Structure prediction' SubClassOf 'Structure analysis' http://edamontology.org/operation_0272 Residue interaction prediction 'Residue interaction prediction' SubClassOf 'Protein sequence alignment analysis' 'Residue interaction prediction' SubClassOf 'Protein property calculation (from structure)' http://edamontology.org/operation_0270 Transmembrane protein analysis 'Transmembrane protein analysis' SubClassOf 'Protein analysis' http://edamontology.org/operation_0275 Protein-protein interaction prediction (from protein structure) 'Protein-protein interaction prediction (from protein structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2220 Sequence cluster ID (SYSTERS) 'Sequence cluster ID (SYSTERS)' SubClassOf 'Sequence cluster ID' http://edamontology.org/operation_0276 Protein interaction network analysis 'Protein interaction network analysis' SubClassOf 'Protein interaction analysis' 'Protein interaction network analysis' SubClassOf 'Pathway or network analysis' http://edamontology.org/operation_0273 Protein interaction raw data analysis 'Protein interaction raw data analysis' SubClassOf 'Protein interaction analysis' http://edamontology.org/operation_0274 Protein-protein interaction prediction (from protein sequence) 'Protein-protein interaction prediction (from protein sequence)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1458 Vienna local RNA secondary structure format 'Vienna local RNA secondary structure format' SubClassOf 'Dot-bracket format' http://edamontology.org/format_1454 dssp 'dssp' SubClassOf 'Textual format' 'dssp' SubClassOf 'Protein secondary structure format' http://edamontology.org/format_1455 hssp 'hssp' SubClassOf 'Textual format' 'hssp' SubClassOf 'Protein secondary structure format' http://edamontology.org/format_1457 Dot-bracket format 'Dot-bracket format' SubClassOf 'RNA secondary structure format' 'Dot-bracket format' SubClassOf 'Textual format' http://edamontology.org/operation_0246 Protein domain recognition 'Protein domain recognition' SubClassOf 'Protein structure analysis' 'Protein domain recognition' SubClassOf 'Protein feature detection' http://edamontology.org/operation_0247 Protein architecture analysis 'Protein architecture analysis' SubClassOf 'Protein structure analysis' http://edamontology.org/operation_0244 Protein flexibility and motion analysis 'Protein flexibility and motion analysis' SubClassOf 'Molecular dynamics simulation' 'Protein flexibility and motion analysis' SubClassOf 'Protein property calculation (from structure)' http://edamontology.org/operation_0245 Protein structural motif recognition 'Protein structural motif recognition' SubClassOf 'Protein structure analysis' 'Protein structural motif recognition' SubClassOf 'Protein feature detection' http://edamontology.org/operation_0248 Residue interaction calculation 'Residue interaction calculation' SubClassOf 'Protein property calculation (from structure)' http://edamontology.org/operation_0249 Protein geometry calculation 'Protein geometry calculation' SubClassOf 'Protein property calculation (from structure)' http://edamontology.org/data_2235 Raw SCOP domain classification 'Raw SCOP domain classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2236 Raw CATH domain classification 'Raw CATH domain classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3567 Reference sample report 'Reference sample report' SubClassOf 'Report' http://edamontology.org/data_3568 Gene Expression Atlas Experiment ID 'Gene Expression Atlas Experiment ID' SubClassOf 'Experiment annotation ID' http://edamontology.org/operation_0242 Conserved transcription regulatory sequence identification 'Conserved transcription regulatory sequence identification' SubClassOf 'Regulatory element prediction' http://edamontology.org/operation_0243 Protein property calculation (from structure) 'Protein property calculation (from structure)' SubClassOf 'Protein structure analysis' 'Protein property calculation (from structure)' SubClassOf 'Protein property calculation' http://edamontology.org/operation_0240 Sequence motif comparison 'Sequence motif comparison' SubClassOf 'Sequence motif analysis' 'Sequence motif comparison' SubClassOf 'Sequence comparison' http://edamontology.org/operation_0241 Transcription regulatory sequence analysis 'Transcription regulatory sequence analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0257 Data retrieval (sequence alignment) 'Data retrieval (sequence alignment)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0258 Sequence alignment analysis 'Sequence alignment analysis' SubClassOf 'Sequence analysis' http://edamontology.org/operation_0255 Feature table query 'Feature table query' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0256 Sequence feature comparison 'Sequence feature comparison' SubClassOf 'Comparison' 'Sequence feature comparison' SubClassOf 'Sequence analysis' http://edamontology.org/data_2249 DTD 'DTD' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0259 Sequence alignment comparison 'Sequence alignment comparison' SubClassOf 'Sequence alignment analysis' 'Sequence alignment comparison' SubClassOf 'Comparison' http://edamontology.org/data_2245 Sequence set (bootstrapped) 'Sequence set (bootstrapped)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0250 Protein property calculation 'Protein property calculation' SubClassOf 'Prediction and recognition (protein)' 'Protein property calculation' SubClassOf 'Calculation' 'Protein property calculation' SubClassOf 'Protein analysis' http://edamontology.org/data_2247 Phylogenetic consensus tree 'Phylogenetic consensus tree' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2248 Schema 'Schema' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0253 Sequence feature detection 'Sequence feature detection' SubClassOf 'Prediction and recognition' 'Sequence feature detection' SubClassOf 'Sequence analysis' http://edamontology.org/data_2242 Phylogenetic property values 'Phylogenetic property values' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0254 Data retrieval (feature table) 'Data retrieval (feature table)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0252 Peptide immunogenicity prediction 'Peptide immunogenicity prediction' SubClassOf 'Protein property calculation (from sequence)' 'Peptide immunogenicity prediction' SubClassOf 'Protein interaction prediction' http://edamontology.org/data_2240 Heterogen annotation 'Heterogen annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1475 PDB database entry format 'PDB database entry format' SubClassOf 'Tertiary structure format' http://edamontology.org/format_1476 PDB 'PDB' SubClassOf 'PDB database entry format' 'PDB' SubClassOf 'Textual format' http://edamontology.org/format_1477 mmCIF 'mmCIF' SubClassOf 'Textual format' 'mmCIF' SubClassOf 'PDB database entry format' http://edamontology.org/operation_2008 siRNA duplex prediction 'siRNA duplex prediction' SubClassOf 'Transcription regulatory element prediction (trans)' http://edamontology.org/data_2252 XSLT stylesheet 'XSLT stylesheet' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2253 Data resource definition name 'Data resource definition name' SubClassOf 'Data resource definition ID' 'Data resource definition name' SubClassOf 'Name' http://edamontology.org/data_2254 OBO file format name 'OBO file format name' SubClassOf 'File format name' http://edamontology.org/format_3288 PED/MAP 'PED/MAP' SubClassOf 'Individual genetic data format' 'PED/MAP' SubClassOf 'Textual format' http://edamontology.org/format_3287 Individual genetic data format 'Individual genetic data format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_2250 XML Schema 'XML Schema' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2251 Relax-NG schema 'Relax-NG schema' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3284 SFF 'SFF' SubClassOf 'binary format' 'SFF' SubClassOf 'Sequence trace format' http://edamontology.org/format_3286 PED 'PED' SubClassOf 'PED/MAP' http://edamontology.org/format_3285 MAP 'MAP' SubClassOf 'PED/MAP' http://edamontology.org/operation_3349 Bibliography generation 'Bibliography generation' SubClassOf 'Generation' http://edamontology.org/operation_3348 Sequence checksum generation 'Sequence checksum generation' SubClassOf 'Generation' http://edamontology.org/format_3281 A2M 'A2M' SubClassOf 'FASTA-like (text)' 'A2M' SubClassOf 'Alignment format (text)' http://edamontology.org/operation_0288 Sequence word comparison 'Sequence word comparison' SubClassOf 'Sequence comparison' http://edamontology.org/operation_0289 Sequence distance matrix generation 'Sequence distance matrix generation' SubClassOf 'Generation' 'Sequence distance matrix generation' SubClassOf 'Sequence comparison' http://edamontology.org/operation_0282 Genetic mapping 'Genetic mapping' SubClassOf 'DNA mapping' 'Genetic mapping' SubClassOf 'Generation' http://edamontology.org/operation_0283 Linkage analysis 'Linkage analysis' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/operation_0280 Data retrieval (restriction enzyme annotation) 'Data retrieval (restriction enzyme annotation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0281 Genetic marker identification 'Genetic marker identification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0286 Codon usage analysis 'Codon usage analysis' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/operation_0287 Base position variability plotting 'Base position variability plotting' SubClassOf 'Plotting' 'Base position variability plotting' SubClassOf 'Codon usage analysis' http://edamontology.org/operation_0284 Codon usage table generation 'Codon usage table generation' SubClassOf 'Generation' 'Codon usage table generation' SubClassOf 'Codon usage table processing' http://edamontology.org/operation_0285 Codon usage table comparison 'Codon usage table comparison' SubClassOf 'Nucleic acid comparison' 'Codon usage table comparison' SubClassOf 'Codon usage table processing' http://edamontology.org/operation_0299 3D profile-to-3D profile alignment '3D profile-to-3D profile alignment' SubClassOf 'Structure alignment' http://edamontology.org/data_2289 Sequence identifier (nucleic acid) 'Sequence identifier (nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0293 Hybrid sequence alignment construction 'Hybrid sequence alignment construction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0294 Structure-based sequence alignment 'Structure-based sequence alignment' SubClassOf 'Sequence alignment' http://edamontology.org/operation_0291 Sequence clustering 'Sequence clustering' SubClassOf 'Clustering' 'Sequence clustering' SubClassOf 'Sequence comparison' 'Sequence clustering' SubClassOf 'Generation' http://edamontology.org/operation_0292 Sequence alignment 'Sequence alignment' SubClassOf 'Alignment' 'Sequence alignment' SubClassOf 'Sequence comparison' http://edamontology.org/data_2285 Gene ID (MIPS) 'Gene ID (MIPS)' SubClassOf 'Gene ID' http://edamontology.org/operation_0297 3D profile generation '3D profile generation' SubClassOf 'Structure analysis' '3D profile generation' SubClassOf 'Generation' http://edamontology.org/operation_0298 Profile-profile alignment 'Profile-profile alignment' SubClassOf 'Sequence alignment' http://edamontology.org/operation_0295 Structure alignment 'Structure alignment' SubClassOf 'Alignment' 'Structure alignment' SubClassOf 'Structure comparison' http://edamontology.org/data_2288 Sequence identifier (protein) 'Sequence identifier (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0296 Sequence profile generation 'Sequence profile generation' SubClassOf 'Sequence alignment analysis' 'Sequence profile generation' SubClassOf 'Generation' http://edamontology.org/topic_1308 Matrix/scaffold attachment sites 'Matrix/scaffold attachment sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0290 Sequence redundancy removal 'Sequence redundancy removal' SubClassOf 'Sequence comparison' http://edamontology.org/topic_1302 PolyA signal or sites 'PolyA signal or sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_1307 Splice sites 'Splice sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_1304 CpG island and isochores 'CpG island and isochores' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_1305 Restriction sites 'Restriction sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2640 Oncology 'Oncology' SubClassOf 'Medicine' http://edamontology.org/data_2296 Gene name (AceView) 'Gene name (AceView)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2297 Gene ID (ECK) 'Gene ID (ECK)' SubClassOf 'Gene ID (EcoGene)' http://edamontology.org/data_2298 Gene ID (HGNC) 'Gene ID (HGNC)' SubClassOf 'Gene ID' http://edamontology.org/data_2299 Gene name 'Gene name' SubClassOf 'Name' 'Gene name' SubClassOf 'Gene identifier' http://edamontology.org/data_2292 GenBank accession 'GenBank accession' SubClassOf 'EMBL/GenBank/DDBJ ID' http://edamontology.org/format_3244 mzML 'mzML' SubClassOf 'XML' 'mzML' SubClassOf 'Mass spectrometry data format' http://edamontology.org/data_2293 Gramene secondary identifier 'Gramene secondary identifier' SubClassOf 'Gramene identifier' http://edamontology.org/format_3243 PSI-PAR 'PSI-PAR' SubClassOf 'PSI MI XML (MIF)' http://edamontology.org/data_2294 Sequence variation ID 'Sequence variation ID' SubClassOf 'Accession' 'Sequence variation ID' SubClassOf 'Identifier (typed)' http://edamontology.org/format_3246 TraML 'TraML' SubClassOf 'XML' 'TraML' SubClassOf 'Mass spectrometry data format' http://edamontology.org/data_2295 Gene ID 'Gene ID' SubClassOf 'Gene identifier' 'Gene ID' SubClassOf 'Locus ID' http://edamontology.org/format_3245 Mass spectrometry data format 'Mass spectrometry data format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_3240 CellML 'CellML' SubClassOf 'Biological pathway or network format' 'CellML' SubClassOf 'XML' http://edamontology.org/data_2290 EMBL accession 'EMBL accession' SubClassOf 'EMBL/GenBank/DDBJ ID' http://edamontology.org/format_3242 PSI MI TAB (MITAB) 'PSI MI TAB (MITAB)' SubClassOf 'Textual format' 'PSI MI TAB (MITAB)' SubClassOf 'Protein interaction format' http://edamontology.org/data_2291 UniProt ID 'UniProt ID' SubClassOf 'Sequence name' http://edamontology.org/topic_1311 Operon 'Operon' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_1312 Promoters 'Promoters' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3248 mzQuantML 'mzQuantML' SubClassOf 'Mass spectrometry data format' 'mzQuantML' SubClassOf 'XML' http://edamontology.org/topic_1317 Structural biology 'Structural biology' SubClassOf 'Biology' http://edamontology.org/format_3247 mzIdentML 'mzIdentML' SubClassOf 'XML' 'mzIdentML' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_3249 GelML 'GelML' SubClassOf 'Experiment annotation format' 'GelML' SubClassOf 'XML' http://edamontology.org/format_3235 Cytoband format 'Cytoband format' SubClassOf 'Sequence range format' 'Cytoband format' SubClassOf 'Textual format' http://edamontology.org/operation_3359 Splitting 'Splitting' SubClassOf 'Data handling' http://edamontology.org/operation_3357 Format detection 'Format detection' SubClassOf 'Data handling' http://edamontology.org/topic_2661 Toxins and targets 'Toxins and targets' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3352 Ontology comparison 'Ontology comparison' SubClassOf 'Comparison' http://edamontology.org/operation_3351 Molecular surface analysis 'Molecular surface analysis' SubClassOf 'Structure analysis' http://edamontology.org/operation_3350 Protein quaternary structure prediction 'Protein quaternary structure prediction' SubClassOf 'Protein structure prediction' http://edamontology.org/operation_3353 Ontology comparison 'Ontology comparison' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3262 OWL/XML 'OWL/XML' SubClassOf 'OWL format' 'OWL/XML' SubClassOf 'XML' http://edamontology.org/format_3261 RDF/XML 'RDF/XML' SubClassOf 'RDF format' 'RDF/XML' SubClassOf 'XML' http://edamontology.org/topic_0003 Topic 'Topic' SubClassOf 'information content entity' http://edamontology.org/format_3255 Turtle 'Turtle' SubClassOf 'Textual format' 'Turtle' SubClassOf 'RDF format' http://edamontology.org/format_3254 KRSS2 Syntax 'KRSS2 Syntax' SubClassOf 'Ontology format' 'KRSS2 Syntax' SubClassOf 'Textual format' http://edamontology.org/format_3257 Notation3 'Notation3' SubClassOf 'RDF format' 'Notation3' SubClassOf 'Textual format' http://edamontology.org/format_3256 N-Triples 'N-Triples' SubClassOf 'Textual format' 'N-Triples' SubClassOf 'RDF format' http://edamontology.org/format_3250 spML 'spML' SubClassOf 'XML' 'spML' SubClassOf 'Experiment annotation format' http://edamontology.org/format_3253 Manchester OWL Syntax 'Manchester OWL Syntax' SubClassOf 'Textual format' 'Manchester OWL Syntax' SubClassOf 'OWL format' http://edamontology.org/format_3252 OWL Functional Syntax 'OWL Functional Syntax' SubClassOf 'OWL format' 'OWL Functional Syntax' SubClassOf 'Textual format' http://www.ebi.ac.uk/swo/algorithm/OntoDM_382176 predictive modeling algorithm 'predictive modeling algorithm' SubClassOf 'single generalization algorithm' http://edamontology.org/operation_3279 Document clustering 'Document clustering' SubClassOf 'Article comparison' 'Document clustering' SubClassOf 'Clustering' http://edamontology.org/operation_3278 Document similarity calculation 'Document similarity calculation' SubClassOf 'Article comparison' http://edamontology.org/operation_3283 Anonymisation 'Anonymisation' SubClassOf 'Operation' http://edamontology.org/operation_3289 ID retrieval 'ID retrieval' SubClassOf 'Metadata retrieval' http://edamontology.org/operation_3282 ID mapping 'ID mapping' SubClassOf 'Comparison' 'ID mapping' SubClassOf 'Mapping' http://edamontology.org/operation_3280 Named-entity and concept recognition 'Named-entity and concept recognition' SubClassOf 'Text mining' http://edamontology.org/data_1713 Fate map 'Fate map' SubClassOf 'Organism report' 'Fate map' SubClassOf 'Image' http://edamontology.org/data_1712 Chemical structure image 'Chemical structure image' SubClassOf 'Structure image' http://edamontology.org/data_1711 Sequence alignment image 'Sequence alignment image' SubClassOf 'Image' http://edamontology.org/data_1710 Structure image 'Structure image' SubClassOf 'Image' http://edamontology.org/data_1717 MeSH 'MeSH' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1716 GO 'GO' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1715 BioPax term 'BioPax term' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1714 Microarray spots image 'Microarray spots image' SubClassOf 'Raw image' 'Microarray spots image' SubClassOf 'Gene expression data' http://edamontology.org/data_1709 Protein secondary structure image 'Protein secondary structure image' SubClassOf 'Protein image' http://edamontology.org/data_1708 RNA secondary structure image 'RNA secondary structure image' SubClassOf 'Image' http://edamontology.org/data_1707 Phylogenetic tree image 'Phylogenetic tree image' SubClassOf 'Image' http://edamontology.org/data_1724 ChEBI 'ChEBI' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1723 EMAP 'EMAP' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1722 FMA 'FMA' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1721 UMLS 'UMLS' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1728 GO (molecular function) 'GO (molecular function)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1727 GO (biological process) 'GO (biological process)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1726 myGrid 'myGrid' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1725 MGED 'MGED' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1720 Plant ontology term 'Plant ontology term' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1425 Phylip tree raw 'Phylip tree raw' SubClassOf 'Phylogenetic tree format (text)' 'Phylip tree raw' SubClassOf 'Textual format' http://edamontology.org/data_1719 NCBI taxonomy vocabulary 'NCBI taxonomy vocabulary' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1718 HGNC 'HGNC' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1421 HMMER profile alignment (sequences versus HMMs) 'HMMER profile alignment (sequences versus HMMs)' SubClassOf 'Sequence-profile alignment format' 'HMMER profile alignment (sequences versus HMMs)' SubClassOf 'Textual format' http://edamontology.org/format_1422 HMMER profile alignment (HMM versus sequences) 'HMMER profile alignment (HMM versus sequences)' SubClassOf 'Textual format' 'HMMER profile alignment (HMM versus sequences)' SubClassOf 'Sequence-profile alignment format' http://edamontology.org/format_1423 Phylip distance matrix 'Phylip distance matrix' SubClassOf 'Sequence distance matrix format' 'Phylip distance matrix' SubClassOf 'Textual format' http://edamontology.org/format_1424 ClustalW dendrogram 'ClustalW dendrogram' SubClassOf 'Textual format' 'ClustalW dendrogram' SubClassOf 'Phylogenetic tree format (text)' http://edamontology.org/data_1733 Ontology concept reference 'Ontology concept reference' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1732 Ontology concept comment 'Ontology concept comment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1738 doc2loc document information 'doc2loc document information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1419 Sequence-MEME profile alignment 'Sequence-MEME profile alignment' SubClassOf 'Textual format' 'Sequence-MEME profile alignment' SubClassOf 'Sequence-profile alignment format' http://edamontology.org/data_1731 Ontology concept definition 'Ontology concept definition' SubClassOf 'Ontology concept data' http://edamontology.org/data_1730 Ontology relation type 'Ontology relation type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1729 GO (cellular component) 'GO (cellular component)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1746 Atomic z coordinate 'Atomic z coordinate' SubClassOf 'Atomic coordinate' http://edamontology.org/data_1745 Atomic y coordinate 'Atomic y coordinate' SubClassOf 'Atomic coordinate' http://edamontology.org/topic_3032 Primer or probe design 'Primer or probe design' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1744 Atomic x coordinate 'Atomic x coordinate' SubClassOf 'Atomic coordinate' http://edamontology.org/data_1743 Atomic coordinate 'Atomic coordinate' SubClassOf 'Atomic property' http://edamontology.org/data_1748 PDB atom name 'PDB atom name' SubClassOf 'Atom name' http://edamontology.org/data_1742 PDB residue number 'PDB residue number' SubClassOf 'Sequence position' http://edamontology.org/topic_3039 Nucleic acid structure 'Nucleic acid structure' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3038 Structure databases 'Structure databases' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1445 Phylip tree distance format 'Phylip tree distance format' SubClassOf 'Textual format' 'Phylip tree distance format' SubClassOf 'Phylogenetic tree report (tree distances) format' http://edamontology.org/data_1757 Atom name 'Atom name' SubClassOf 'Name' 'Atom name' SubClassOf 'Atom ID' http://edamontology.org/topic_3044 Protein interaction networks 'Protein interaction networks' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1756 Protein residue 'Protein residue' SubClassOf 'Protein structure' http://edamontology.org/topic_3043 Protein sequences 'Protein sequences' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1755 Protein atom 'Protein atom' SubClassOf 'Protein structure' http://edamontology.org/topic_3042 Nucleic acid sequences 'Nucleic acid sequences' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3041 Sequence databases 'Sequence databases' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3048 Mammals 'Mammals' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3047 Molecular biology 'Molecular biology' SubClassOf 'Biology' http://edamontology.org/data_1759 PDB model number 'PDB model number' SubClassOf 'Structure identifier' http://edamontology.org/data_1758 PDB residue name 'PDB residue name' SubClassOf 'Amino acid name (three letter)' http://edamontology.org/format_1430 Phylip continuous quantitative characters 'Phylip continuous quantitative characters' SubClassOf 'Phylogenetic continuous quantitative character format' 'Phylip continuous quantitative characters' SubClassOf 'Textual format' http://edamontology.org/format_1431 Phylogenetic property values format 'Phylogenetic property values format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1436 TreeBASE format 'TreeBASE format' SubClassOf 'Phylogenetic tree format (text)' 'TreeBASE format' SubClassOf 'Textual format' http://edamontology.org/format_1437 TreeFam format 'TreeFam format' SubClassOf 'Textual format' 'TreeFam format' SubClassOf 'Phylogenetic tree format (text)' http://edamontology.org/format_1432 Phylip character frequencies format 'Phylip character frequencies format' SubClassOf 'Textual format' 'Phylip character frequencies format' SubClassOf 'Phylogenetic continuous quantitative character format' http://edamontology.org/format_1433 Phylip discrete states format 'Phylip discrete states format' SubClassOf 'Phylogenetic discrete states format' 'Phylip discrete states format' SubClassOf 'Textual format' http://edamontology.org/format_1434 Phylip cliques format 'Phylip cliques format' SubClassOf 'Phylogenetic tree report (cliques) format' 'Phylip cliques format' SubClassOf 'Textual format' http://edamontology.org/format_1435 Phylip tree format 'Phylip tree format' SubClassOf 'Phylogenetic tree format (text)' 'Phylip tree format' SubClassOf 'Textual format' http://edamontology.org/topic_3055 Quantitative genetics 'Quantitative genetics' SubClassOf 'Genotype and phenotype' http://edamontology.org/data_1767 CATH domain sequences (COMBS) 'CATH domain sequences (COMBS)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1766 CATH domain sequences (ATOM) 'CATH domain sequences (ATOM)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3053 Genetics 'Genetics' SubClassOf 'Biology' http://edamontology.org/data_1765 CATH representative domain sequences (COMBS) 'CATH representative domain sequences (COMBS)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3052 Sequence clusters and classification 'Sequence clusters and classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3056 Population genetics 'Population genetics' SubClassOf 'Genetics' http://edamontology.org/data_1764 CATH representative domain sequences (ATOM) 'CATH representative domain sequences (ATOM)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3050 Biodiversity 'Biodiversity' SubClassOf 'Ecology' http://edamontology.org/data_1762 CATH domain report 'CATH domain report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3065 Embryology 'Embryology' SubClassOf 'Developmental biology' http://edamontology.org/topic_3064 Developmental biology 'Developmental biology' SubClassOf 'Biology' http://edamontology.org/data_1776 Protein report (function) 'Protein report (function)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3063 Medical informatics 'Medical informatics' SubClassOf 'Informatics' http://edamontology.org/topic_3068 Literature and language 'Literature and language' SubClassOf 'Topic' http://edamontology.org/topic_3067 Anatomy 'Anatomy' SubClassOf 'Biomedical science' http://edamontology.org/data_1771 Sequence version 'Sequence version' SubClassOf 'Sequence attribute' http://edamontology.org/topic_3062 Genetic organisation 'Genetic organisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3061 Documentation and help 'Documentation and help' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3060 Regulatory RNA 'Regulatory RNA' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1772 Score 'Score' SubClassOf 'Data' http://edamontology.org/topic_3077 Data acquisition 'Data acquisition' SubClassOf 'Data management' http://edamontology.org/data_1789 Gene name (TGD) 'Gene name (TGD)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1788 Gene name (SGD) 'Gene name (SGD)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3075 Biological system modelling 'Biological system modelling' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1787 Gene name (MaizeGDB) 'Gene name (MaizeGDB)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3074 Protein feature detection 'Protein feature detection' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3078 Genes and proteins resources 'Genes and proteins resources' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1786 Gene name (EcoGene primary) 'Gene name (EcoGene primary)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3073 Nucleic acid feature detection 'Nucleic acid feature detection' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1785 Gene name (dictyBase) 'Gene name (dictyBase)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3072 Sequence feature detection 'Sequence feature detection' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1784 Gene name (CGD) 'Gene name (CGD)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3071 Data management 'Data management' SubClassOf 'Informatics' http://edamontology.org/data_1783 Gene name (ASPGD) 'Gene name (ASPGD)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3070 Biology 'Biology' SubClassOf 'Topic' http://edamontology.org/topic_0804 Immunology 'Immunology' SubClassOf 'Biomedical science' http://edamontology.org/topic_0803 Human disease 'Human disease' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1799 Gene ID (GeneDB Plasmodium falciparum) 'Gene ID (GeneDB Plasmodium falciparum)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1798 Gene ID (GeneDB Leishmania major) 'Gene ID (GeneDB Leishmania major)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1793 Gene name (Bacillus subtilis) 'Gene name (Bacillus subtilis)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1792 Gene name (MGD) 'Gene name (MGD)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1791 Gene name (HGNC) 'Gene name (HGNC)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1790 Gene name (CGSC) 'Gene name (CGSC)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1797 Gene ID (GeneDB Glossina morsitans) 'Gene ID (GeneDB Glossina morsitans)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1796 Gene ID (FlyBase) 'Gene ID (FlyBase)' SubClassOf 'Gene ID' http://edamontology.org/data_1795 Gene ID (EcoGene) 'Gene ID (EcoGene)' SubClassOf 'Gene ID' http://edamontology.org/data_1794 Gene ID (PlasmoDB) 'Gene ID (PlasmoDB)' SubClassOf 'Gene ID' http://edamontology.org/data_1449 Comparison matrix (amino acid) 'Comparison matrix (amino acid)' SubClassOf 'Comparison matrix' 'Comparison matrix (amino acid)' SubClassOf 'Amino acid property' http://edamontology.org/data_1448 Comparison matrix (nucleotide) 'Comparison matrix (nucleotide)' SubClassOf 'Comparison matrix' http://edamontology.org/data_1447 Comparison matrix (floats) 'Comparison matrix (floats)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1446 Comparison matrix (integers) 'Comparison matrix (integers)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2521 Map data processing 'Map data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2777 ConsensusPathDB entity name 'ConsensusPathDB entity name' SubClassOf 'ConsensusPathDB identifier' 'ConsensusPathDB entity name' SubClassOf 'Name' http://edamontology.org/data_2778 CCAP strain number 'CCAP strain number' SubClassOf 'Strain accession' http://edamontology.org/data_2779 Stock number 'Stock number' SubClassOf 'Accession' 'Stock number' SubClassOf 'Identifier (typed)' http://edamontology.org/data_1441 Phylogenetic tree report (tree evaluation) 'Phylogenetic tree report (tree evaluation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2773 IMGT/HLA ID 'IMGT/HLA ID' SubClassOf 'Protein accession' http://edamontology.org/data_1440 Phylogenetic tree report (tree shape) 'Phylogenetic tree report (tree shape)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2774 Gene ID (JCVI) 'Gene ID (JCVI)' SubClassOf 'Gene ID' http://edamontology.org/data_2775 Kinase name 'Kinase name' SubClassOf 'Protein name' http://edamontology.org/data_2776 ConsensusPathDB entity ID 'ConsensusPathDB entity ID' SubClassOf 'Accession' 'ConsensusPathDB entity ID' SubClassOf 'ConsensusPathDB identifier' http://edamontology.org/operation_2520 DNA mapping 'DNA mapping' SubClassOf 'Mapping' http://edamontology.org/data_1444 Phylogenetic character contrasts 'Phylogenetic character contrasts' SubClassOf 'Phylogenetic data' http://edamontology.org/data_2770 HIT ID 'HIT ID' SubClassOf 'Transcript ID' http://edamontology.org/data_1443 Phylogenetic tree report (tree stratigraphic) 'Phylogenetic tree report (tree stratigraphic)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2771 HIX ID 'HIX ID' SubClassOf 'Gene ID' http://edamontology.org/data_1442 Phylogenetic tree distances 'Phylogenetic tree distances' SubClassOf 'Phylogenetic data' http://edamontology.org/data_2772 HPA antibody id 'HPA antibody id' SubClassOf 'Protein accession' http://edamontology.org/operation_2519 Structure processing (nucleic acid) 'Structure processing (nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2518 Nucleic acid structure comparison 'Nucleic acid structure comparison' SubClassOf 'Nucleic acid structure analysis' 'Nucleic acid structure comparison' SubClassOf 'Structure comparison' 'Nucleic acid structure comparison' SubClassOf 'Nucleic acid comparison' http://edamontology.org/data_1459 Nucleic acid structure 'Nucleic acid structure' SubClassOf 'Structure' http://edamontology.org/data_2788 Sequence profile data 'Sequence profile data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2789 Protein ID (TopDB) 'Protein ID (TopDB)' SubClassOf 'Protein accession' http://edamontology.org/data_1452 Amino acid comparison matrix (integers) 'Amino acid comparison matrix (integers)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2784 RNAVirusDB ID 'RNAVirusDB ID' SubClassOf 'Virus ID' http://edamontology.org/data_1451 Nucleotide comparison matrix (floats) 'Nucleotide comparison matrix (floats)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2785 Virus ID 'Virus ID' SubClassOf 'Virus identifier' 'Virus ID' SubClassOf 'Organism accession' http://edamontology.org/data_1450 Nucleotide comparison matrix (integers) 'Nucleotide comparison matrix (integers)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2786 NCBI Genome Project ID 'NCBI Genome Project ID' SubClassOf 'Genome accession' http://edamontology.org/data_2787 NCBI genome accession 'NCBI genome accession' SubClassOf 'Genome accession' http://edamontology.org/data_1456 Protein features report (membrane regions) 'Protein features report (membrane regions)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2780 Stock number (TAIR) 'Stock number (TAIR)' SubClassOf 'Stock number' http://edamontology.org/data_2781 REDIdb ID 'REDIdb ID' SubClassOf 'Sequence accession (nucleic acid)' http://edamontology.org/data_2782 SMART domain name 'SMART domain name' SubClassOf 'Protein family name' http://edamontology.org/data_1453 Amino acid comparison matrix (floats) 'Amino acid comparison matrix (floats)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2783 Protein family ID (PANTHER) 'Protein family ID (PANTHER)' SubClassOf 'Protein family accession' http://edamontology.org/format_3551 nrrd 'nrrd' SubClassOf 'Textual format' 'nrrd' SubClassOf 'Image format' http://edamontology.org/format_3554 R file format 'R file format' SubClassOf 'Textual format' http://edamontology.org/format_3550 mhd 'mhd' SubClassOf 'Image format' 'mhd' SubClassOf 'Textual format' http://edamontology.org/format_3556 MHTML 'MHTML' SubClassOf 'HTML' http://edamontology.org/format_3555 SPSS 'SPSS' SubClassOf 'Textual format' http://edamontology.org/operation_2502 Protein analysis 'Protein analysis' SubClassOf 'Analysis' http://edamontology.org/operation_2501 Nucleic acid analysis 'Nucleic acid analysis' SubClassOf 'Analysis' http://edamontology.org/data_1469 Protein structure (all atoms) 'Protein structure (all atoms)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2500 Microarray raw data analysis 'Microarray raw data analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1468 Protein domain 'Protein domain' SubClassOf 'Protein structure' http://edamontology.org/data_2799 Gene ID (MfunGD) 'Gene ID (MfunGD)' SubClassOf 'Gene ID' http://edamontology.org/operation_2506 Protein sequence alignment analysis 'Protein sequence alignment analysis' SubClassOf 'Sequence alignment analysis' 'Protein sequence alignment analysis' SubClassOf 'Prediction and recognition (protein)' 'Protein sequence alignment analysis' SubClassOf 'Protein analysis' http://edamontology.org/operation_2505 Text processing 'Text processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2504 Structural data processing 'Structural data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2503 Sequence data processing 'Sequence data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1463 Small molecule structure 'Small molecule structure' SubClassOf 'Structure' http://edamontology.org/data_2795 ORF identifier 'ORF identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_1462 Carbohydrate structure 'Carbohydrate structure' SubClassOf 'Structure' http://edamontology.org/data_2796 Linucs ID 'Linucs ID' SubClassOf 'Carbohydrate accession' http://edamontology.org/data_1461 Protein-ligand complex 'Protein-ligand complex' SubClassOf 'Protein structure' http://edamontology.org/data_2797 Protein ID (LGICdb) 'Protein ID (LGICdb)' SubClassOf 'Protein accession' http://edamontology.org/format_3590 hdf5 'hdf5' SubClassOf 'binary format' http://edamontology.org/data_1460 Protein structure 'Protein structure' SubClassOf 'Structure' http://edamontology.org/data_2798 MaizeDB ID 'MaizeDB ID' SubClassOf 'EST accession' http://edamontology.org/data_1467 Protein chain 'Protein chain' SubClassOf 'Protein structure' http://edamontology.org/data_2791 Reference map name (SWISS-2DPAGE) 'Reference map name (SWISS-2DPAGE)' SubClassOf 'Gel ID' 'Reference map name (SWISS-2DPAGE)' SubClassOf 'Name' http://edamontology.org/data_1466 tRNA structure 'tRNA structure' SubClassOf 'RNA structure' http://edamontology.org/data_2792 Protein ID (PeroxiBase) 'Protein ID (PeroxiBase)' SubClassOf 'Protein accession' http://edamontology.org/data_1465 RNA structure 'RNA structure' SubClassOf 'Nucleic acid structure' http://edamontology.org/data_2793 SISYPHUS ID 'SISYPHUS ID' SubClassOf 'Structure alignment ID' http://edamontology.org/data_1464 DNA structure 'DNA structure' SubClassOf 'Nucleic acid structure' http://edamontology.org/data_2794 ORF ID 'ORF ID' SubClassOf 'ORF identifier' 'ORF ID' SubClassOf 'Locus ID' http://edamontology.org/format_3585 bed6 'bed6' SubClassOf 'bedstrict' http://edamontology.org/format_3584 bedstrict 'bedstrict' SubClassOf 'BED format' http://edamontology.org/format_3587 chrominfo 'chrominfo' SubClassOf 'BED format' http://edamontology.org/data_2790 Gel ID 'Gel ID' SubClassOf 'Identifier (typed)' http://edamontology.org/format_3586 bed12 'bed12' SubClassOf 'bedstrict' http://edamontology.org/format_3581 arff 'arff' SubClassOf 'Textual format' http://edamontology.org/format_3580 rcc 'rcc' SubClassOf 'Textual format' 'rcc' SubClassOf 'Gene expression report format' http://edamontology.org/format_3583 bedgraph 'bedgraph' SubClassOf 'Sequence annotation track format' 'bedgraph' SubClassOf 'Textual format' http://edamontology.org/format_3582 afg 'afg' SubClassOf 'Sequence assembly format (text)' 'afg' SubClassOf 'Textual format' http://edamontology.org/format_3589 csfasta 'csfasta' SubClassOf 'FASTA-like (text)' 'csfasta' SubClassOf 'Alignment format (text)' http://edamontology.org/format_3588 customtrack 'customtrack' SubClassOf 'Textual format' 'customtrack' SubClassOf 'Sequence annotation track format' http://edamontology.org/topic_0724 Protein families 'Protein families' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0722 Nucleic acid classification 'Nucleic acid classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2513 Sequence generation (nucleic acid) 'Sequence generation (nucleic acid)' SubClassOf 'Sequence generation' http://edamontology.org/operation_2512 Sequence editing (protein) 'Sequence editing (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2511 Sequence editing (nucleic acid) 'Sequence editing (nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1479 Structure alignment (pair) 'Structure alignment (pair)' SubClassOf 'Structure alignment' http://edamontology.org/operation_2510 DNA back-translation 'DNA back-translation' SubClassOf 'Sequence conversion' http://edamontology.org/operation_2516 Protein sequence visualisation 'Protein sequence visualisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2515 Nucleic acid sequence visualisation 'Nucleic acid sequence visualisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2514 Sequence generation (protein) 'Sequence generation (protein)' SubClassOf 'Protein analysis' 'Sequence generation (protein)' SubClassOf 'Sequence generation' http://edamontology.org/data_1474 Protein domain (C-alpha atoms) 'Protein domain (C-alpha atoms)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1473 Protein domain (all atoms) 'Protein domain (all atoms)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1472 Protein chain (C-alpha atoms) 'Protein chain (C-alpha atoms)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1471 Protein chain (all atoms) 'Protein chain (all atoms)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2243 phylip property values 'phylip property values' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0736 Protein folds and structural domains 'Protein folds and structural domains' SubClassOf 'Protein structure analysis' http://edamontology.org/data_1470 C-alpha trace 'C-alpha trace' SubClassOf 'Protein structure' http://edamontology.org/operation_2509 Protein sequence comparison 'Protein sequence comparison' SubClassOf 'Sequence comparison' 'Protein sequence comparison' SubClassOf 'Protein comparison' 'Protein sequence comparison' SubClassOf 'Protein sequence analysis' http://edamontology.org/operation_2508 Nucleic acid sequence comparison 'Nucleic acid sequence comparison' SubClassOf 'Nucleic acid comparison' 'Nucleic acid sequence comparison' SubClassOf 'Nucleic acid sequence analysis' 'Nucleic acid sequence comparison' SubClassOf 'Sequence comparison' http://edamontology.org/operation_2507 Nucleic acid sequence alignment analysis 'Nucleic acid sequence alignment analysis' SubClassOf 'Prediction and recognition (nucleic acid)' 'Nucleic acid sequence alignment analysis' SubClassOf 'Nucleic acid analysis' 'Nucleic acid sequence alignment analysis' SubClassOf 'Sequence alignment analysis' http://edamontology.org/format_3578 IDAT 'IDAT' SubClassOf 'binary format' 'IDAT' SubClassOf 'Gene expression report format' http://edamontology.org/format_3579 JPG 'JPG' SubClassOf 'Image format' 'JPG' SubClassOf 'binary format' http://edamontology.org/data_1485 Structure alignment (protein all atoms) 'Structure alignment (protein all atoms)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1484 Multiple protein tertiary structure alignment 'Multiple protein tertiary structure alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1483 Structure alignment (protein pair) 'Structure alignment (protein pair)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1482 Structure alignment (nucleic acid) 'Structure alignment (nucleic acid)' SubClassOf 'Structure alignment' http://edamontology.org/data_1489 Multiple protein tertiary structure alignment (all atoms) 'Multiple protein tertiary structure alignment (all atoms)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1488 Pairwise protein tertiary structure alignment (C-alpha atoms) 'Pairwise protein tertiary structure alignment (C-alpha atoms)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1487 Pairwise protein tertiary structure alignment (all atoms) 'Pairwise protein tertiary structure alignment (all atoms)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1486 Structure alignment (protein C-alpha atoms) 'Structure alignment (protein C-alpha atoms)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0749 Transcription factors and regulatory sites 'Transcription factors and regulatory sites' SubClassOf 'DNA binding sites' 'Transcription factors and regulatory sites' SubClassOf 'Proteins' 'Transcription factors and regulatory sites' SubClassOf 'Gene expression' http://edamontology.org/topic_0747 Nucleic acid sites and features 'Nucleic acid sites and features' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0748 Protein sites and features 'Protein sites and features' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1481 Structure alignment (protein) 'Structure alignment (protein)' SubClassOf 'Protein alignment' 'Structure alignment (protein)' SubClassOf 'Structure alignment' http://edamontology.org/data_1480 Structure alignment (multiple) 'Structure alignment (multiple)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0741 Protein sequence alignment 'Protein sequence alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0740 Nucleic acid sequence alignment 'Nucleic acid sequence alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1496 Molecular similarity score 'Molecular similarity score' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1495 DaliLite hit table 'DaliLite hit table' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1494 Structural transformation matrix 'Structural transformation matrix' SubClassOf 'Matrix' http://edamontology.org/data_1493 Structure alignment (RNA) 'Structure alignment (RNA)' SubClassOf 'Structure alignment (nucleic acid)' http://edamontology.org/operation_2575 Protein binding site prediction 'Protein binding site prediction' SubClassOf 'Protein feature detection' 'Protein binding site prediction' SubClassOf 'Protein interaction prediction' http://edamontology.org/data_1499 3D-1D scoring matrix '3D-1D scoring matrix' SubClassOf 'Protein sequence-structure scoring matrix' http://edamontology.org/operation_2574 Protein hydropathy calculation 'Protein hydropathy calculation' SubClassOf 'Protein property calculation' http://edamontology.org/data_1498 Tanimoto similarity score 'Tanimoto similarity score' SubClassOf 'Structure similarity score' http://edamontology.org/data_1497 Root-mean-square deviation 'Root-mean-square deviation' SubClassOf 'Structure similarity score' http://edamontology.org/data_1492 Multiple nucleic acid tertiary structure alignment 'Multiple nucleic acid tertiary structure alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1491 Structure alignment (nucleic acid pair) 'Structure alignment (nucleic acid pair)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1490 Multiple protein tertiary structure alignment (C-alpha atoms) 'Multiple protein tertiary structure alignment (C-alpha atoms)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0753 Metabolic pathways 'Metabolic pathways' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0751 Phosphorylation sites 'Phosphorylation sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0754 Signaling pathways 'Signaling pathways' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2210 Strain data format 'Strain data format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0769 Workflows 'Workflows' SubClassOf 'Data management' http://edamontology.org/format_2211 CIP strain data format 'CIP strain data format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3549 nii 'nii' SubClassOf 'Image format' 'nii' SubClassOf 'binary format' http://edamontology.org/format_3548 DICOM format 'DICOM format' SubClassOf 'Image format' 'DICOM format' SubClassOf 'binary format' http://edamontology.org/topic_0767 Protein and peptide identification 'Protein and peptide identification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3547 Image format 'Image format' SubClassOf 'Format (by type of data)' http://edamontology.org/topic_0770 Data types and objects 'Data types and objects' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0771 Theoretical biology 'Theoretical biology' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3210 Genome index 'Genome index' SubClassOf 'Data index' http://edamontology.org/format_2200 FASTA-like (text) 'FASTA-like (text)' SubClassOf 'Textual format' 'FASTA-like (text)' SubClassOf 'FASTA-like' http://edamontology.org/format_2206 Sequence feature table format (text) 'Sequence feature table format (text)' SubClassOf 'Sequence feature table format' http://edamontology.org/format_2203 Sequence record lite format 'Sequence record lite format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2202 Sequence record full format 'Sequence record full format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0779 Mitochondria 'Mitochondria' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2205 GenBank-like format (text) 'GenBank-like format (text)' SubClassOf 'Textual format' 'GenBank-like format (text)' SubClassOf 'GenBank-like format' http://edamontology.org/format_2204 EMBL format (XML) 'EMBL format (XML)' SubClassOf 'EMBL-like (XML)' http://edamontology.org/topic_0781 Viruses 'Viruses' SubClassOf 'Model organisms' http://edamontology.org/topic_0782 Fungi 'Fungi' SubClassOf 'Eukaryotes' http://edamontology.org/topic_0780 Plants 'Plants' SubClassOf 'Eukaryotes' http://edamontology.org/topic_0786 Arabidopsis 'Arabidopsis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0783 Pathogens 'Pathogens' SubClassOf 'Model organisms' http://edamontology.org/topic_0787 Rice 'Rice' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://kt.ijs.si/panovp/OntoDM#OntoDM_731692 single generalization algorithm 'single generalization algorithm' SubClassOf 'data mining algorithm' http://edamontology.org/data_3236 Cytoband position 'Cytoband position' SubClassOf 'Sequence coordinates' http://edamontology.org/data_3238 Cell type ontology ID 'Cell type ontology ID' SubClassOf 'Cell type accession' 'Cell type ontology ID' SubClassOf 'Ontology concept ID' http://edamontology.org/data_3231 GWAS report 'GWAS report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0796 Genetic mapping and linkage 'Genetic mapping and linkage' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0797 Comparative genomics 'Comparative genomics' SubClassOf 'Genomics' http://edamontology.org/topic_0798 Mobile genetic elements 'Mobile genetic elements' SubClassOf 'Gene structure' http://edamontology.org/data_3241 Kinetic model 'Kinetic model' SubClassOf 'Mathematical model' http://edamontology.org/data_3268 Sequence feature type 'Sequence feature type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3269 Gene homology (report) 'Gene homology (report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3264 COSMIC ID 'COSMIC ID' SubClassOf 'Sequence variation ID' http://edamontology.org/data_3265 HGMD ID 'HGMD ID' SubClassOf 'Sequence variation ID' http://edamontology.org/data_3266 Sequence assembly ID 'Sequence assembly ID' SubClassOf 'Sequence set ID' http://edamontology.org/data_3275 Phenotype name 'Phenotype name' SubClassOf 'Identifier (typed)' 'Phenotype name' SubClassOf 'Name' http://edamontology.org/operation_3024 Prediction and recognition (nucleic acid) 'Prediction and recognition (nucleic acid)' SubClassOf 'Prediction and recognition' http://edamontology.org/operation_3023 Prediction and recognition (protein) 'Prediction and recognition (protein)' SubClassOf 'Prediction and recognition' http://edamontology.org/data_3271 Gene tree 'Gene tree' SubClassOf 'Phylogenetic tree' http://edamontology.org/format_3596 ppm 'ppm' SubClassOf 'binary format' 'ppm' SubClassOf 'Image format' http://edamontology.org/data_3272 Species tree 'Species tree' SubClassOf 'Phylogenetic tree' http://edamontology.org/format_3595 pcx 'pcx' SubClassOf 'binary format' 'pcx' SubClassOf 'Image format' http://edamontology.org/data_3273 Sample ID 'Sample ID' SubClassOf 'Accession' 'Sample ID' SubClassOf 'Identifier (typed)' http://edamontology.org/format_3598 xbm 'xbm' SubClassOf 'Image format' 'xbm' SubClassOf 'binary format' http://edamontology.org/data_3274 MGI accession 'MGI accession' SubClassOf 'Accession' 'MGI accession' SubClassOf 'Identifier (hybrid)' http://edamontology.org/format_3597 psd 'psd' SubClassOf 'binary format' 'psd' SubClassOf 'Image format' http://edamontology.org/format_3592 bmp 'bmp' SubClassOf 'Image format' 'bmp' SubClassOf 'binary format' http://edamontology.org/format_3591 tiff 'tiff' SubClassOf 'binary format' 'tiff' SubClassOf 'Image format' http://edamontology.org/format_3594 pcd 'pcd' SubClassOf 'Image format' 'pcd' SubClassOf 'binary format' http://edamontology.org/data_3270 Ensembl gene tree ID 'Ensembl gene tree ID' SubClassOf 'Phylogenetic tree ID' 'Ensembl gene tree ID' SubClassOf 'Ensembl ID' http://edamontology.org/format_3593 im 'im' SubClassOf 'Image format' 'im' SubClassOf 'binary format' http://edamontology.org/topic_2533 DNA mutation 'DNA mutation' SubClassOf 'DNA' 'DNA mutation' SubClassOf 'Genetic variation' http://edamontology.org/format_3599 xpm 'xpm' SubClassOf 'binary format' 'xpm' SubClassOf 'Image format' http://edamontology.org/data_0910 Km 'Km' SubClassOf 'Enzyme kinetics data' http://edamontology.org/data_0914 Codon usage data 'Codon usage data' SubClassOf 'Data' http://edamontology.org/format_1705 HET group dictionary entry format 'HET group dictionary entry format' SubClassOf 'Small molecule report format' 'HET group dictionary entry format' SubClassOf 'Textual format' http://edamontology.org/format_1704 MSDchem ligand dictionary entry format 'MSDchem ligand dictionary entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0912 Nucleic acid property 'Nucleic acid property' SubClassOf 'Molecular property' http://edamontology.org/data_0911 Nucleotide base annotation 'Nucleotide base annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1706 KEGG DRUG entry format 'KEGG DRUG entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3181 Sequence assembly report 'Sequence assembly report' SubClassOf 'Sequence alignment report' http://edamontology.org/data_0907 Protein family report 'Protein family report' SubClassOf 'Protein report' http://edamontology.org/format_1701 PubChem entry format 'PubChem entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0906 Protein interaction report 'Protein interaction report' SubClassOf 'Protein structure report' http://edamontology.org/format_1700 KEGG GLYCAN entry format 'KEGG GLYCAN entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0905 Protein interaction raw data 'Protein interaction raw data' SubClassOf 'Experimental measurement' http://edamontology.org/format_1703 ChEBI entry format 'ChEBI entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0904 Protein features (mutation) 'Protein features (mutation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1702 ChemSpider entry format 'ChemSpider entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0909 Vmax 'Vmax' SubClassOf 'Enzyme kinetics data' http://edamontology.org/data_0920 Genotype/phenotype report 'Genotype/phenotype report' SubClassOf 'Report' http://edamontology.org/data_0925 Sequence assembly 'Sequence assembly' SubClassOf 'Sequence set (nucleic acid)' http://edamontology.org/data_0924 Sequence trace 'Sequence trace' SubClassOf 'Experimental measurement' 'Sequence trace' SubClassOf 'Sequence set (nucleic acid)' http://edamontology.org/data_0923 PCR experiment report 'PCR experiment report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0922 Nucleic acid features report (primers) 'Nucleic acid features report (primers)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0918 DNA variation 'DNA variation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0917 Gene classification 'Gene classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0916 Gene report 'Gene report' SubClassOf 'Nucleic acid features' http://edamontology.org/data_0919 Chromosome report 'Chromosome report' SubClassOf 'Nucleic acid report' http://edamontology.org/data_0932 Oligonucleotide probe data 'Oligonucleotide probe data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0931 Microarray experiment report 'Microarray experiment report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0936 Sequence tag profile (with gene assignment) 'Sequence tag profile (with gene assignment)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0935 SBS experimental data 'SBS experimental data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0934 MPSS experimental data 'MPSS experimental data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0933 SAGE experimental data 'SAGE experimental data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0928 Gene expression profile 'Gene expression profile' SubClassOf 'Gene expression data' http://edamontology.org/data_0927 Genetic linkage report 'Genetic linkage report' SubClassOf 'Nucleic acid report' http://edamontology.org/data_0926 Radiation Hybrid (RH) scores 'Radiation Hybrid (RH) scores' SubClassOf 'Experimental measurement' http://edamontology.org/data_0943 Mass spectrometry spectra 'Mass spectrometry spectra' SubClassOf 'Mass spectrometry data' http://edamontology.org/data_0942 2D PAGE image '2D PAGE image' SubClassOf 'Raw image' http://edamontology.org/data_0941 Electron microscopy model 'Electron microscopy model' SubClassOf 'Structure' http://edamontology.org/data_0940 Electron microscopy volume map 'Electron microscopy volume map' SubClassOf 'Experimental measurement' http://edamontology.org/data_0947 Biological pathway map 'Biological pathway map' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0946 Pathway or network annotation 'Pathway or network annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0945 Peptide identification 'Peptide identification' SubClassOf 'Protein property' 'Peptide identification' SubClassOf 'Peptide property' http://edamontology.org/data_0944 Peptide mass fingerprint 'Peptide mass fingerprint' SubClassOf 'Mass spectrometry data' 'Peptide mass fingerprint' SubClassOf 'Peptide property' http://edamontology.org/data_0939 Protein circular dichroism (CD) spectroscopic data 'Protein circular dichroism (CD) spectroscopic data' SubClassOf 'Protein structure raw data' http://edamontology.org/data_0938 Protein NMR data 'Protein NMR data' SubClassOf 'Protein structure raw data' http://edamontology.org/data_0937 Protein X-ray crystallographic data 'Protein X-ray crystallographic data' SubClassOf 'Protein structure raw data' http://edamontology.org/data_0954 Database cross-mapping 'Database cross-mapping' SubClassOf 'Data reference' http://edamontology.org/data_0953 Version information 'Version information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0952 EMBOSS database resource definition 'EMBOSS database resource definition' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0951 Statistical estimate score 'Statistical estimate score' SubClassOf 'Score' http://edamontology.org/data_0958 Tool metadata 'Tool metadata' SubClassOf 'Resource metadata' http://edamontology.org/data_0957 Database metadata 'Database metadata' SubClassOf 'Resource metadata' http://edamontology.org/data_0956 Data index report 'Data index report' SubClassOf 'Report' http://edamontology.org/data_0955 Data index 'Data index' SubClassOf 'Data' http://edamontology.org/data_0950 Mathematical model 'Mathematical model' SubClassOf 'Data' http://edamontology.org/data_0949 Workflow metadata 'Workflow metadata' SubClassOf 'Resource metadata' http://www.ebi.ac.uk/swo/algorithm/OntoDM_175260 pattern discovery algorithm 'pattern discovery algorithm' SubClassOf 'single generalization algorithm' http://edamontology.org/data_0948 Data resource definition 'Data resource definition' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0964 Scent annotation 'Scent annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0963 Cell line report 'Cell line report' SubClassOf 'Organism report' http://edamontology.org/data_0962 Small molecule report 'Small molecule report' SubClassOf 'Structure report' http://edamontology.org/data_0968 Keyword 'Keyword' SubClassOf 'Data' http://edamontology.org/data_0967 Ontology concept data 'Ontology concept data' SubClassOf 'Ontology data' http://edamontology.org/data_0966 Ontology term 'Ontology term' SubClassOf 'Ontology concept data' http://edamontology.org/data_0960 User metadata 'User metadata' SubClassOf 'Resource metadata' http://edamontology.org/data_0959 Job metadata 'Job metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0976 Identifier (typed) 'Identifier (typed)' SubClassOf 'Identifier' http://edamontology.org/data_0975 Data resource identifier 'Data resource identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0974 Entity identifier 'Entity identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0979 Entity feature identifier 'Entity feature identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0978 Discrete entity identifier 'Discrete entity identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0977 Tool identifier 'Tool identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_0972 Text mining report 'Text mining report' SubClassOf 'Report' 'Text mining report' SubClassOf 'Text data' http://edamontology.org/data_0971 Article 'Article' SubClassOf 'Text' http://edamontology.org/data_0970 Citation 'Citation' SubClassOf 'Text data' http://edamontology.org/data_0987 Chromosome name 'Chromosome name' SubClassOf 'Molecule name' 'Chromosome name' SubClassOf 'Nucleic acid identifier' http://edamontology.org/data_0986 Chemical identifier 'Chemical identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0985 Molecule type 'Molecule type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0984 Molecule name 'Molecule name' SubClassOf 'Molecule identifier' 'Molecule name' SubClassOf 'Name' http://edamontology.org/data_0989 Protein identifier 'Protein identifier' SubClassOf 'Molecule identifier' http://edamontology.org/data_0988 Peptide identifier 'Peptide identifier' SubClassOf 'Molecule identifier' http://edamontology.org/data_0983 Atom ID 'Atom ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_0982 Molecule identifier 'Molecule identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_0981 Phenomenon identifier 'Phenomenon identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0980 Entity collection identifier 'Entity collection identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0998 Chemical name (IUPAC) 'Chemical name (IUPAC)' SubClassOf 'Compound name' http://edamontology.org/data_0997 Chemical name (ChEBI) 'Chemical name (ChEBI)' SubClassOf 'Compound name' http://edamontology.org/data_0996 Monosaccharide identifier 'Monosaccharide identifier' SubClassOf 'Compound identifier' http://edamontology.org/data_0995 Nucleotide identifier 'Nucleotide identifier' SubClassOf 'Compound identifier' http://edamontology.org/data_0999 Chemical name (INN) 'Chemical name (INN)' SubClassOf 'Compound name' http://edamontology.org/data_0990 Compound name 'Compound name' SubClassOf 'Molecule name' 'Compound name' SubClassOf 'Compound identifier' http://edamontology.org/data_0994 Amino acid identifier 'Amino acid identifier' SubClassOf 'Compound identifier' http://edamontology.org/data_0993 Drug identifier 'Drug identifier' SubClassOf 'Compound identifier' http://edamontology.org/data_0992 Ligand identifier 'Ligand identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0991 Chemical registry number 'Chemical registry number' SubClassOf 'Compound accession' http://edamontology.org/format_1782 NCBI gene report format 'NCBI gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2704 Clone ID (IMAGE) 'Clone ID (IMAGE)' SubClassOf 'Clone ID' http://edamontology.org/data_2705 GO concept ID (cellular component) 'GO concept ID (cellular component)' SubClassOf 'GO concept ID' http://edamontology.org/data_2706 Chromosome name (BioCyc) 'Chromosome name (BioCyc)' SubClassOf 'Chromosome name' http://edamontology.org/data_2700 CATH identifier 'CATH identifier' SubClassOf 'Protein domain ID' http://edamontology.org/data_2701 CATH node ID (family) 'CATH node ID (family)' SubClassOf 'CATH node ID' http://edamontology.org/data_2702 Enzyme ID (CAZy) 'Enzyme ID (CAZy)' SubClassOf 'Enzyme ID' http://edamontology.org/data_2715 Protein ID (CuticleDB) 'Protein ID (CuticleDB)' SubClassOf 'Protein accession' http://edamontology.org/data_2716 DBD ID 'DBD ID' SubClassOf 'Transcription factor accession' http://edamontology.org/data_2717 Oligonucleotide probe annotation 'Oligonucleotide probe annotation' SubClassOf 'Microarray metadata' http://edamontology.org/data_2718 Oligonucleotide ID 'Oligonucleotide ID' SubClassOf 'Molecule accession' 'Oligonucleotide ID' SubClassOf 'Nucleic acid identifier' http://edamontology.org/data_2711 Genome report 'Genome report' SubClassOf 'Organism report' http://edamontology.org/format_3508 PDF 'PDF' SubClassOf 'Document format' 'PDF' SubClassOf 'binary format' http://edamontology.org/data_2713 Protein ID (CORUM) 'Protein ID (CORUM)' SubClassOf 'Protein accession' http://edamontology.org/data_2714 CDD PSSM-ID 'CDD PSSM-ID' SubClassOf 'Sequence profile ID' http://edamontology.org/data_2710 CleanEx dataset code 'CleanEx dataset code' SubClassOf 'Experiment annotation ID' http://edamontology.org/format_3507 Document format 'Document format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_3506 docx 'docx' SubClassOf 'XML' 'docx' SubClassOf 'Document format' http://edamontology.org/data_2709 CleanEx entry name 'CleanEx entry name' SubClassOf 'Gene expression report ID' http://edamontology.org/data_2726 Inhibitor annotation 'Inhibitor annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2727 Promoter ID 'Promoter ID' SubClassOf 'Accession' 'Promoter ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2728 EST accession 'EST accession' SubClassOf 'Clone ID' http://edamontology.org/data_2729 COGEME EST ID 'COGEME EST ID' SubClassOf 'EST accession' http://edamontology.org/data_2722 Protein features report (disordered structure) 'Protein features report (disordered structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2723 Protein ID (DisProt) 'Protein ID (DisProt)' SubClassOf 'Protein accession' http://edamontology.org/data_2724 Embryo report 'Embryo report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2725 Ensembl transcript ID 'Ensembl transcript ID' SubClassOf 'Ensembl ID' 'Ensembl transcript ID' SubClassOf 'Transcript ID' http://edamontology.org/data_2720 Dinucleotide property 'Dinucleotide property' SubClassOf 'DNA base structural data' http://edamontology.org/data_2721 DiProDB ID 'DiProDB ID' SubClassOf 'Oligonucleotide ID' http://edamontology.org/data_2719 dbProbe ID 'dbProbe ID' SubClassOf 'Oligonucleotide ID' http://edamontology.org/data_1405 Gap opening penalty (float) 'Gap opening penalty (float)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2737 FIG ID 'FIG ID' SubClassOf 'Gene ID' http://edamontology.org/data_1404 Gap opening penalty (integer) 'Gap opening penalty (integer)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2738 Gene ID (Xenbase) 'Gene ID (Xenbase)' SubClassOf 'Gene ID' http://edamontology.org/data_1403 Drop off score 'Drop off score' SubClassOf 'Alignment score or penalty' http://edamontology.org/data_2739 Gene ID (Genolist) 'Gene ID (Genolist)' SubClassOf 'Gene ID' http://edamontology.org/data_1402 Mismatch penalty score 'Mismatch penalty score' SubClassOf 'Alignment score or penalty' http://edamontology.org/data_1409 Gap separation penalty (float) 'Gap separation penalty (float)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2733 Genus name (virus) 'Genus name (virus)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1408 Gap separation penalty (integer) 'Gap separation penalty (integer)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2734 Family name (virus) 'Family name (virus)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1407 Gap extension penalty (float) 'Gap extension penalty (float)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2735 Database name (SwissRegulon) 'Database name (SwissRegulon)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1406 Gap extension penalty (integer) 'Gap extension penalty (integer)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2736 Sequence feature ID (SwissRegulon) 'Sequence feature ID (SwissRegulon)' SubClassOf 'Sequence feature ID' http://edamontology.org/data_2730 COGEME unisequence ID 'COGEME unisequence ID' SubClassOf 'EST accession' http://edamontology.org/data_2731 Protein family ID (GeneFarm) 'Protein family ID (GeneFarm)' SubClassOf 'Protein family accession' http://edamontology.org/data_2732 Family name 'Family name' SubClassOf 'Taxon' http://edamontology.org/data_1401 Match reward score 'Match reward score' SubClassOf 'Alignment score or penalty' http://edamontology.org/data_1400 Terminal gap penalty 'Terminal gap penalty' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1747 PDB atom record format 'PDB atom record format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1741 OSCAR format 'OSCAR format' SubClassOf 'XML' 'OSCAR format' SubClassOf 'Annotated text format' 'OSCAR format' SubClassOf 'Textual format' http://edamontology.org/format_1740 iHOP format 'iHOP format' SubClassOf 'Text mining report format' 'iHOP format' SubClassOf 'XML' 'iHOP format' SubClassOf 'HTML' http://edamontology.org/data_1416 Sequence alignment report (site correlation) 'Sequence alignment report (site correlation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2748 Database name (Osteogenesis) 'Database name (Osteogenesis)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1415 Sequence alignment report (site conservation) 'Sequence alignment report (site conservation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2749 Genome identifier 'Genome identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_1414 Sequence alignment metadata (quality report) 'Sequence alignment metadata (quality report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1413 Sequence similarity 'Sequence similarity' SubClassOf 'Sequence similarity score' http://edamontology.org/data_2744 Locus ID (PseudoCAP) 'Locus ID (PseudoCAP)' SubClassOf 'Locus ID' http://edamontology.org/data_2745 Locus ID (UTR) 'Locus ID (UTR)' SubClassOf 'Locus ID' http://edamontology.org/format_1737 CiteXplore-all 'CiteXplore-all' SubClassOf 'Bibliographic reference format' 'CiteXplore-all' SubClassOf 'Textual format' http://edamontology.org/data_1418 Sequence-profile alignment (HMM) 'Sequence-profile alignment (HMM)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2746 MonosaccharideDB ID 'MonosaccharideDB ID' SubClassOf 'Monosaccharide accession' http://edamontology.org/data_1417 Sequence-profile alignment (Domainatrix signature) 'Sequence-profile alignment (Domainatrix signature)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2747 Database name (CMD) 'Database name (CMD)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1739 pmc 'pmc' SubClassOf 'Article format' 'pmc' SubClassOf 'Textual format' http://edamontology.org/data_2740 Gene name (Genolist) 'Gene name (Genolist)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2741 ABS ID 'ABS ID' SubClassOf 'Promoter ID' http://edamontology.org/data_2742 AraC-XylS ID 'AraC-XylS ID' SubClassOf 'Transcription factor accession' http://edamontology.org/data_2743 Gene name (HUGO) 'Gene name (HUGO)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1412 Sequence identity 'Sequence identity' SubClassOf 'Sequence similarity score' http://edamontology.org/data_1411 Terminal gap extension penalty 'Terminal gap extension penalty' SubClassOf 'Gap extension penalty' http://edamontology.org/data_1410 Terminal gap opening penalty 'Terminal gap opening penalty' SubClassOf 'Gap opening penalty' http://edamontology.org/format_1734 PubMed citation 'PubMed citation' SubClassOf 'Bibliographic reference format' 'PubMed citation' SubClassOf 'Textual format' http://edamontology.org/format_1736 CiteXplore-core 'CiteXplore-core' SubClassOf 'Bibliographic reference format' 'CiteXplore-core' SubClassOf 'Textual format' http://edamontology.org/format_1735 Medline Display Format 'Medline Display Format' SubClassOf 'Bibliographic reference format' 'Medline Display Format' SubClassOf 'Textual format' http://edamontology.org/data_1427 Phylogenetic discrete data 'Phylogenetic discrete data' SubClassOf 'Phylogenetic character data' http://edamontology.org/data_2759 Gene ID (VectorBase) 'Gene ID (VectorBase)' SubClassOf 'Gene ID' http://edamontology.org/data_1426 Phylogenetic continuous quantitative data 'Phylogenetic continuous quantitative data' SubClassOf 'Phylogenetic character data' http://edamontology.org/data_2755 Transcription factor name 'Transcription factor name' SubClassOf 'Protein name' 'Transcription factor name' SubClassOf 'Transcription factor identifier' http://edamontology.org/data_2756 TCID 'TCID' SubClassOf 'Protein accession' http://edamontology.org/data_1429 Phylogenetic invariants 'Phylogenetic invariants' SubClassOf 'Phylogenetic data' http://edamontology.org/data_2757 Pfam domain name 'Pfam domain name' SubClassOf 'Protein family name' http://edamontology.org/data_1428 Phylogenetic character cliques 'Phylogenetic character cliques' SubClassOf 'Phylogenetic data' http://edamontology.org/data_2758 Pfam clan ID 'Pfam clan ID' SubClassOf 'Protein family accession' http://edamontology.org/data_2751 GenomeReviews ID 'GenomeReviews ID' SubClassOf 'Genome accession' http://edamontology.org/data_2752 GlycoMap ID 'GlycoMap ID' SubClassOf 'Carbohydrate accession' http://edamontology.org/data_2753 Carbohydrate conformational map 'Carbohydrate conformational map' SubClassOf 'Carbohydrate property' http://edamontology.org/data_2754 Gene features report (intron) 'Gene features report (intron)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1420 Sequence-profile alignment (fingerprint) 'Sequence-profile alignment (fingerprint)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1761 CATH PDB report format 'CATH PDB report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1760 CATH chain report format 'CATH chain report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1438 Phylogenetic report 'Phylogenetic report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2766 HAMAP ID 'HAMAP ID' SubClassOf 'Protein family accession' http://edamontology.org/data_2767 Identifier with metadata 'Identifier with metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2768 Gene symbol annotation 'Gene symbol annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1439 DNA substitution model 'DNA substitution model' SubClassOf 'Mathematical model' http://edamontology.org/data_2769 Transcript ID 'Transcript ID' SubClassOf 'Molecule accession' 'Transcript ID' SubClassOf 'Nucleic acid identifier' http://edamontology.org/data_2762 Sequence signature report 'Sequence signature report' SubClassOf 'Report' http://edamontology.org/data_2763 Locus annotation 'Locus annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2764 Protein name (UniProt) 'Protein name (UniProt)' SubClassOf 'Protein name' http://edamontology.org/data_2765 Term ID list 'Term ID list' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2761 UTRSite ID 'UTRSite ID' SubClassOf 'Sequence motif identifier' http://edamontology.org/data_1567 Protein-nucleic acid interactions report 'Protein-nucleic acid interactions report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2898 Monosaccharide accession 'Monosaccharide accession' SubClassOf 'Accession' 'Monosaccharide accession' SubClassOf 'Monosaccharide identifier' http://edamontology.org/data_2899 Drug name 'Drug name' SubClassOf 'Compound name' 'Drug name' SubClassOf 'Drug identifier' http://edamontology.org/data_2894 Compound accession 'Compound accession' SubClassOf 'Compound identifier' 'Compound accession' SubClassOf 'Molecule accession' http://edamontology.org/data_1561 CATH functional category 'CATH functional category' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2895 Drug accession 'Drug accession' SubClassOf 'Drug identifier' 'Drug accession' SubClassOf 'Accession' http://edamontology.org/data_1560 CATH structurally similar group 'CATH structurally similar group' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2896 Toxin name 'Toxin name' SubClassOf 'Name' 'Toxin name' SubClassOf 'Toxin identifier' http://edamontology.org/data_2897 Toxin accession 'Toxin accession' SubClassOf 'Accession' 'Toxin accession' SubClassOf 'Toxin identifier' http://edamontology.org/data_1566 Protein-ligand interaction report 'Protein-ligand interaction report' SubClassOf 'Protein interaction report' http://edamontology.org/data_2891 Biological model accession 'Biological model accession' SubClassOf 'Accession' 'Biological model accession' SubClassOf 'Biological model ID' http://edamontology.org/data_1565 Protein-protein interaction report 'Protein-protein interaction report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1564 Protein fold recognition report 'Protein fold recognition report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2892 Cell type name 'Cell type name' SubClassOf 'Cell type identifier' 'Cell type name' SubClassOf 'Name' http://edamontology.org/data_2893 Cell type accession 'Cell type accession' SubClassOf 'Cell type identifier' 'Cell type accession' SubClassOf 'Accession' http://edamontology.org/data_1589 DNA base pair twist angle data 'DNA base pair twist angle data' SubClassOf 'DNA base structural data' http://edamontology.org/data_1584 Nucleic acid enthalpy 'Nucleic acid enthalpy' SubClassOf 'Nucleic acid thermodynamic data' http://edamontology.org/data_1583 Nucleic acid melting profile 'Nucleic acid melting profile' SubClassOf 'Nucleic acid thermodynamic data' http://edamontology.org/data_1588 DNA base pair stacking energies data 'DNA base pair stacking energies data' SubClassOf 'DNA base structural data' http://edamontology.org/data_1587 Nucleic acid stitch profile 'Nucleic acid stitch profile' SubClassOf 'Nucleic acid melting profile' http://edamontology.org/data_1586 Nucleic acid melting temperature 'Nucleic acid melting temperature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1585 Nucleic acid entropy 'Nucleic acid entropy' SubClassOf 'Nucleic acid thermodynamic data' http://edamontology.org/format_3464 JSON 'JSON' SubClassOf 'YAML' http://edamontology.org/topic_0606 Literature data resources 'Literature data resources' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0607 Laboratory information management 'Laboratory information management' SubClassOf 'Informatics' http://edamontology.org/format_3466 EPS 'EPS' SubClassOf 'PS' http://edamontology.org/topic_0605 Informatics 'Informatics' SubClassOf 'Topic' http://edamontology.org/format_3462 CRAM 'CRAM' SubClassOf 'binary format' 'CRAM' SubClassOf 'Alignment format (pair only)' http://edamontology.org/topic_0608 Cell and tissue culture 'Cell and tissue culture' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3468 xls 'xls' SubClassOf 'Document format' 'xls' SubClassOf 'XML' http://edamontology.org/topic_0602 Molecular interactions, pathways and networks 'Molecular interactions, pathways and networks' SubClassOf 'Computational biology' http://edamontology.org/format_3467 GIF 'GIF' SubClassOf 'binary format' http://edamontology.org/topic_0601 Protein modifications 'Protein modifications' SubClassOf 'Protein expression' http://edamontology.org/data_1595 Base pairing probability matrix dotplot 'Base pairing probability matrix dotplot' SubClassOf 'Plot' 'Base pairing probability matrix dotplot' SubClassOf 'DNA base structural data' http://edamontology.org/data_1594 Vienna RNA calculated energy 'Vienna RNA calculated energy' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1593 Vienna RNA concentration data 'Vienna RNA concentration data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1592 Vienna RNA structure constraints 'Vienna RNA structure constraints' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1599 Codon adaptation index 'Codon adaptation index' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1598 Genetic code 'Genetic code' SubClassOf 'Codon usage data' http://edamontology.org/data_1597 Codon usage table 'Codon usage table' SubClassOf 'Codon usage data' http://edamontology.org/data_1596 Nucleic acid folding report 'Nucleic acid folding report' SubClassOf 'Nucleic acid report' http://edamontology.org/topic_0617 Ribosomes 'Ribosomes' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0618 Scents 'Scents' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0616 Organelles 'Organelles' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1591 Vienna RNA parameters 'Vienna RNA parameters' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1590 DNA base trimer roll angles data 'DNA base trimer roll angles data' SubClassOf 'DNA base structural data' http://edamontology.org/topic_0610 Ecology 'Ecology' SubClassOf 'Biology' http://edamontology.org/topic_0613 Peptides and amino acids 'Peptides and amino acids' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0611 Electron microscopy 'Electron microscopy' SubClassOf 'Imaging' 'Electron microscopy' SubClassOf 'Structural biology' http://edamontology.org/topic_0612 Cell cycle 'Cell cycle' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0629 Gene expression and microarray 'Gene expression and microarray' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0620 Drugs and target structures 'Drugs and target structures' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0621 Model organisms 'Model organisms' SubClassOf 'Biology' http://edamontology.org/topic_0624 Chromosomes 'Chromosomes' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0625 Genotype and phenotype 'Genotype and phenotype' SubClassOf 'Genetics' http://edamontology.org/topic_0622 Genomics 'Genomics' SubClassOf 'Omics' http://edamontology.org/topic_0623 Gene and protein families 'Gene and protein families' SubClassOf 'Proteins' 'Gene and protein families' SubClassOf 'Molecular genetics' http://edamontology.org/topic_0639 Protein sequence analysis 'Protein sequence analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0637 Taxonomy 'Taxonomy' SubClassOf 'Evolutionary biology' http://edamontology.org/topic_0632 Probes and primers 'Probes and primers' SubClassOf 'Sequence analysis' http://edamontology.org/format_1697 KEGG LIGAND entry format 'KEGG LIGAND entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0635 Specific protein resources 'Specific protein resources' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1699 KEGG PLANT entry format 'KEGG PLANT entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1698 KEGG COMPOUND entry format 'KEGG COMPOUND entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0634 Pathology 'Pathology' SubClassOf 'Medicine' http://edamontology.org/operation_0004 Operation http://edamontology.org/topic_0642 Low complexity sequences 'Low complexity sequences' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0640 Nucleic acid sequence analysis 'Nucleic acid sequence analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0641 Repeat sequences 'Repeat sequences' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0644 Proteome 'Proteome' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2007 UniProt keyword 'UniProt keyword' SubClassOf 'Keyword' http://edamontology.org/data_2009 Ordered locus name 'Ordered locus name' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0659 Functional, regulatory and non-coding RNA 'Functional, regulatory and non-coding RNA' SubClassOf 'Gene structure' 'Functional, regulatory and non-coding RNA' SubClassOf 'RNA' http://edamontology.org/topic_0654 DNA 'DNA' SubClassOf 'Nucleic acids' http://edamontology.org/topic_0655 Coding RNA 'Coding RNA' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2018 Annotation 'Annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0660 rRNA 'rRNA' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2019 Map data 'Map data' SubClassOf 'Data' http://edamontology.org/data_2016 Amino acid property 'Amino acid property' SubClassOf 'Molecular property' http://edamontology.org/data_2012 Sequence coordinates 'Sequence coordinates' SubClassOf 'Map data' 'Sequence coordinates' SubClassOf 'Sequence range' 'Sequence coordinates' SubClassOf 'Sequence position' http://edamontology.org/format_2195 Ontology format 'Ontology format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2194 medline 'medline' SubClassOf 'Textual format' 'medline' SubClassOf 'Article format' http://edamontology.org/format_2197 OWL format 'OWL format' SubClassOf 'RDF format' http://edamontology.org/format_2196 OBO format 'OBO format' SubClassOf 'Ontology format' http://edamontology.org/topic_0663 tRNA 'tRNA' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2025 Michaelis Menten plot 'Michaelis Menten plot' SubClassOf 'Enzyme kinetics data' http://edamontology.org/data_3356 Hidden Markov model 'Hidden Markov model' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2026 Hanes Woolf plot 'Hanes Woolf plot' SubClassOf 'Enzyme kinetics data' http://edamontology.org/data_3358 Format identifier 'Format identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2028 Experimental data 'Experimental data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2022 Vienna RNA structural data 'Vienna RNA structural data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2023 Sequence mask parameter 'Sequence mask parameter' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3354 Transition matrix 'Transition matrix' SubClassOf 'Matrix' http://edamontology.org/data_2024 Enzyme kinetics data 'Enzyme kinetics data' SubClassOf 'Reaction data' 'Enzyme kinetics data' SubClassOf 'Protein property' http://edamontology.org/data_3355 Emission matrix 'Emission matrix' SubClassOf 'Matrix' http://edamontology.org/format_2188 UniProt format 'UniProt format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2187 UniProt-like (text) 'UniProt-like (text)' SubClassOf 'Textual format' 'UniProt-like (text)' SubClassOf 'uniprotkb-like format' http://edamontology.org/format_2189 ipi 'ipi' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2184 cdsxml 'cdsxml' SubClassOf 'EMBL format (XML)' http://edamontology.org/format_2183 EMBLXML 'EMBLXML' SubClassOf 'EMBL format (XML)' http://edamontology.org/format_2186 geneseq 'geneseq' SubClassOf 'EMBL-like (text)' http://edamontology.org/format_2185 insdxml 'insdxml' SubClassOf 'EMBL format (XML)' http://edamontology.org/topic_0694 Protein secondary structure 'Protein secondary structure' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2047 Protein sequence record (lite) 'Protein sequence record (lite)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2048 Report 'Report' SubClassOf 'Data' http://edamontology.org/data_2043 Sequence record lite 'Sequence record lite' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2044 Sequence 'Sequence' SubClassOf 'Data' http://edamontology.org/data_2046 Nucleic acid sequence record (lite) 'Nucleic acid sequence record (lite)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2041 Genome version information 'Genome version information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2042 Evidence 'Evidence' SubClassOf 'Data' http://edamontology.org/topic_0697 RNA structure 'RNA structure' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0698 Protein tertiary structure 'Protein tertiary structure' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3491 ebwtl 'ebwtl' SubClassOf 'Data index format' http://edamontology.org/data_2050 Molecular property (general) 'Molecular property (general)' SubClassOf 'Molecular property' http://edamontology.org/format_2155 Sequence features (repeats) format 'Sequence features (repeats) format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_3486 GCG format variant 'GCG format variant' SubClassOf 'Alignment format (text)' 'GCG format variant' SubClassOf 'Sequence record format (text)' 'GCG format variant' SubClassOf 'Textual format' http://edamontology.org/format_3485 RSF 'RSF' SubClassOf 'GCG format variant' http://edamontology.org/data_2053 Structural data 'Structural data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3487 BSML 'BSML' SubClassOf 'Sequence record format (XML)' 'BSML' SubClassOf 'XML' http://edamontology.org/format_3484 ebwt 'ebwt' SubClassOf 'Data index format' http://edamontology.org/format_2159 Gene features (coding region) format 'Gene features (coding region) format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2158 Nucleic acid features (restriction sites) format 'Nucleic acid features (restriction sites) format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_3475 TSV 'TSV' SubClassOf 'DSV' http://edamontology.org/format_3477 Cytoscape input file format 'Cytoscape input file format' SubClassOf 'Textual format' 'Cytoscape input file format' SubClassOf 'Gene expression report format' http://edamontology.org/format_3476 Gene expression data format 'Gene expression data format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2182 FASTQ-like format (text) 'FASTQ-like format (text)' SubClassOf 'Textual format' 'FASTQ-like format (text)' SubClassOf 'FASTQ-like format' http://edamontology.org/format_2181 EMBL-like (text) 'EMBL-like (text)' SubClassOf 'EMBL-like format' 'EMBL-like (text)' SubClassOf 'Textual format' http://edamontology.org/data_2079 Search parameter 'Search parameter' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2172 Sequence cluster format (nucleic acid) 'Sequence cluster format (nucleic acid)' SubClassOf 'Sequence cluster format' http://edamontology.org/data_2070 Sequence motif (nucleic acid) 'Sequence motif (nucleic acid)' SubClassOf 'Sequence motif' http://edamontology.org/format_2175 Gene cluster format 'Gene cluster format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2071 Sequence motif (protein) 'Sequence motif (protein)' SubClassOf 'Sequence motif' http://edamontology.org/format_2171 Sequence cluster format (protein) 'Sequence cluster format (protein)' SubClassOf 'Sequence cluster format' http://edamontology.org/format_2170 Sequence cluster format 'Sequence cluster format' SubClassOf 'Format (by type of data)' http://edamontology.org/data_2087 Molecular property 'Molecular property' SubClassOf 'Data' http://edamontology.org/data_2088 DNA base structural data 'DNA base structural data' SubClassOf 'Nucleic acid structure data' http://edamontology.org/data_2083 Alignment data 'Alignment data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2084 Nucleic acid report 'Nucleic acid report' SubClassOf 'Report' http://edamontology.org/data_2085 Structure report 'Structure report' SubClassOf 'Report' http://edamontology.org/format_3499 Ensembl variation file format 'Ensembl variation file format' SubClassOf 'Textual format' 'Ensembl variation file format' SubClassOf 'Sequence variation annotation format' http://edamontology.org/data_2086 Nucleic acid structure data 'Nucleic acid structure data' SubClassOf 'Nucleic acid property' http://edamontology.org/data_2080 Database search results 'Database search results' SubClassOf 'Data' http://edamontology.org/data_2081 Secondary structure 'Secondary structure' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2082 Matrix 'Matrix' SubClassOf 'Data' http://edamontology.org/format_2919 Sequence annotation track format 'Sequence annotation track format' SubClassOf 'Sequence feature annotation format' http://edamontology.org/topic_3656 Immunoprecipitation experiment 'Immunoprecipitation experiment' SubClassOf 'Laboratory techniques' http://edamontology.org/format_1609 Gramene gene report format 'Gramene gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1606 DragonDB gene report format 'DragonDB gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1605 CGD gene report format 'CGD gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3674 Methylated DNA immunoprecipitation 'Methylated DNA immunoprecipitation' SubClassOf 'Immunoprecipitation experiment' http://edamontology.org/format_1608 FlyBase gene report format 'FlyBase gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3673 Whole genome sequencing 'Whole genome sequencing' SubClassOf 'Sequencing' http://edamontology.org/format_1607 EcoCyc gene report format 'EcoCyc gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3679 Animal study 'Animal study' SubClassOf 'Laboratory animal science' 'Animal study' SubClassOf 'Experimental design and studies' http://edamontology.org/topic_3678 Experimental design and studies 'Experimental design and studies' SubClassOf 'Topic' http://edamontology.org/format_1604 DictyBase gene report format 'DictyBase gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1603 Ensembl gene report format 'Ensembl gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3676 Exome sequencing 'Exome sequencing' SubClassOf 'Sequencing' http://edamontology.org/format_2922 markx0 variant 'markx0 variant' SubClassOf 'Alignment format (text)' 'markx0 variant' SubClassOf 'Textual format' http://edamontology.org/format_2921 Sequence variation annotation format 'Sequence variation annotation format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_2924 Phylip format variant 'Phylip format variant' SubClassOf 'Textual format' 'Phylip format variant' SubClassOf 'Alignment format (text)' 'Phylip format variant' SubClassOf 'Sequence record format (text)' http://edamontology.org/format_2923 mega variant 'mega variant' SubClassOf 'Sequence record format (text)' 'mega variant' SubClassOf 'Alignment format (text)' 'mega variant' SubClassOf 'Textual format' http://edamontology.org/format_2920 Alignment format (pair only) 'Alignment format (pair only)' SubClassOf 'Alignment format' http://edamontology.org/topic_3697 Microbial ecology 'Microbial ecology' SubClassOf 'Microbiology' 'Microbial ecology' SubClassOf 'Ecology' http://edamontology.org/operation_3096 Editing 'Editing' SubClassOf 'Data handling' http://edamontology.org/operation_3090 Protein feature prediction (from structure) 'Protein feature prediction (from structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3095 Nucleic acid design 'Nucleic acid design' SubClassOf 'Design' 'Nucleic acid design' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/operation_3094 Protein interaction network prediction 'Protein interaction network prediction' SubClassOf 'Pathway or network prediction' http://edamontology.org/operation_3093 Database search (by sequence) 'Database search (by sequence)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3092 Protein feature detection 'Protein feature detection' SubClassOf 'Protein analysis' 'Protein feature detection' SubClassOf 'Prediction and recognition (protein)' http://edamontology.org/data_2803 Clone ID (RefSeq) 'Clone ID (RefSeq)' SubClassOf 'RefSeq accession' 'Clone ID (RefSeq)' SubClassOf 'Clone ID' http://edamontology.org/data_2804 Protein ID (ConoServer) 'Protein ID (ConoServer)' SubClassOf 'Protein accession' http://edamontology.org/data_2805 GeneSNP ID 'GeneSNP ID' SubClassOf 'Sequence variation ID' http://edamontology.org/topic_2399 Gene transcription 'Gene transcription' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2800 Orpha number 'Orpha number' SubClassOf 'Disease ID' http://edamontology.org/topic_2397 Exons 'Exons' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2802 Protein ID (EcID) 'Protein ID (EcID)' SubClassOf 'Protein accession' http://edamontology.org/operation_3088 Protein property calculation (from sequence) 'Protein property calculation (from sequence)' SubClassOf 'Protein property calculation' 'Protein property calculation (from sequence)' SubClassOf 'Protein sequence analysis' http://edamontology.org/operation_3087 Protein sequence feature detection 'Protein sequence feature detection' SubClassOf 'Sequence feature detection' 'Protein sequence feature detection' SubClassOf 'Protein sequence analysis' 'Protein sequence feature detection' SubClassOf 'Protein feature detection' http://edamontology.org/operation_3080 Structure editing 'Structure editing' SubClassOf 'Editing' http://edamontology.org/operation_3084 Protein function prediction (from sequence) 'Protein function prediction (from sequence)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3083 Pathway or network visualisation 'Pathway or network visualisation' SubClassOf 'Visualisation' 'Pathway or network visualisation' SubClassOf 'Pathway or network analysis' http://edamontology.org/operation_3081 Sequence alignment editing 'Sequence alignment editing' SubClassOf 'Editing' http://edamontology.org/data_2812 Lipid identifier 'Lipid identifier' SubClassOf 'Molecule identifier' http://edamontology.org/format_1666 BioModel mathematical model format 'BioModel mathematical model format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1651 PATIKA entry format 'PATIKA entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1650 INOH entry format 'INOH entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1653 aMAZE entry format 'aMAZE entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1652 Reactome entry format 'Reactome entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1655 Panther Pathways entry format 'Panther Pathways entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1654 CPDB entry format 'CPDB entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2836 DPVweb ID 'DPVweb ID' SubClassOf 'Virus ID' http://edamontology.org/data_1503 Amino acid pair-wise contact potentials 'Amino acid pair-wise contact potentials' SubClassOf 'Amino acid property' http://edamontology.org/data_2837 Pathway ID (BioSystems) 'Pathway ID (BioSystems)' SubClassOf 'Pathway or network accession' http://edamontology.org/data_1502 Amino acid index (chemical classes) 'Amino acid index (chemical classes)' SubClassOf 'Amino acid index' http://edamontology.org/data_2838 Experimental data (proteomics) 'Experimental data (proteomics)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1501 Amino acid index 'Amino acid index' SubClassOf 'Matrix' 'Amino acid index' SubClassOf 'Amino acid property' http://edamontology.org/data_1508 Amino acid index (van der Waals radii) 'Amino acid index (van der Waals radii)' SubClassOf 'Amino acid index' http://edamontology.org/data_2832 Web portal 'Web portal' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1507 Amino acid index (White-Wimley data) 'Amino acid index (White-Wimley data)' SubClassOf 'Amino acid index' http://edamontology.org/data_1506 Amino acid index (hydropathy) 'Amino acid index (hydropathy)' SubClassOf 'Amino acid index' http://edamontology.org/data_1505 Amino acid index (molecular weight) 'Amino acid index (molecular weight)' SubClassOf 'Amino acid index' http://edamontology.org/data_2835 Gene ID (VBASE2) 'Gene ID (VBASE2)' SubClassOf 'Gene ID' http://edamontology.org/data_2831 Databank 'Databank' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2849 Abstract 'Abstract' SubClassOf 'Text data' http://edamontology.org/data_1519 Peptide molecular weights 'Peptide molecular weights' SubClassOf 'Protein property' http://edamontology.org/data_1517 Restriction enzyme report 'Restriction enzyme report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1509 Enzyme report 'Enzyme report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1526 Protein globularity 'Protein globularity' SubClassOf 'Protein hydropathy data' http://edamontology.org/data_2858 Ontology concept 'Ontology concept' SubClassOf 'Ontology data' http://edamontology.org/data_1525 Protein crystallizability 'Protein crystallizability' SubClassOf 'Protein hydropathy data' http://edamontology.org/data_1524 Protein solubility 'Protein solubility' SubClassOf 'Protein hydropathy data' http://edamontology.org/data_1523 Protein charge plot 'Protein charge plot' SubClassOf 'Protein property' http://edamontology.org/data_2854 Position-specific scoring matrix 'Position-specific scoring matrix' SubClassOf 'Sequence profile' 'Position-specific scoring matrix' SubClassOf 'Matrix' http://edamontology.org/format_1628 ABI 'ABI' SubClassOf 'Sequence trace format' 'ABI' SubClassOf 'binary format' http://edamontology.org/data_2855 Distance matrix 'Distance matrix' SubClassOf 'Matrix' http://edamontology.org/data_1529 Protein pKa value 'Protein pKa value' SubClassOf 'Protein property' http://edamontology.org/format_1627 Primer3 primer 'Primer3 primer' SubClassOf 'Nucleic acid features (primers) format' 'Primer3 primer' SubClassOf 'Textual format' http://edamontology.org/data_1528 Protein isoelectric point 'Protein isoelectric point' SubClassOf 'Protein property' http://edamontology.org/data_2856 Structural distance matrix 'Structural distance matrix' SubClassOf 'Distance matrix' http://edamontology.org/data_1527 Protein titration curve 'Protein titration curve' SubClassOf 'Protein property' 'Protein titration curve' SubClassOf 'Plot' http://edamontology.org/data_2857 Article metadata 'Article metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1629 mira 'mira' SubClassOf 'Textual format' 'mira' SubClassOf 'Sequence trace format' http://edamontology.org/data_2850 Lipid structure 'Lipid structure' SubClassOf 'Structure' http://edamontology.org/data_2851 Drug structure 'Drug structure' SubClassOf 'Small molecule structure' http://edamontology.org/data_2852 Toxin structure 'Toxin structure' SubClassOf 'Small molecule structure' http://edamontology.org/data_1522 Protein sequence hydropathy plot 'Protein sequence hydropathy plot' SubClassOf 'Protein hydropathy data' http://edamontology.org/data_1521 Protein aliphatic index 'Protein aliphatic index' SubClassOf 'Protein hydropathy data' http://edamontology.org/data_1520 Peptide hydrophobic moment 'Peptide hydrophobic moment' SubClassOf 'Protein hydropathy data' http://edamontology.org/format_1624 HGVbase entry format 'HGVbase entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1623 OMIM entry format 'OMIM entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1626 KEGG DISEASE entry format 'KEGG DISEASE entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1625 HIVDB entry format 'HIVDB entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1620 dbSNP polymorphism report format 'dbSNP polymorphism report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1537 Protein structure report 'Protein structure report' SubClassOf 'Structure report' 'Protein structure report' SubClassOf 'Protein report' http://edamontology.org/data_2869 Nucleic acid features report (RFLP) 'Nucleic acid features report (RFLP)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1536 MHC peptide immunogenicity report 'MHC peptide immunogenicity report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1534 Peptide immunogenicity data 'Peptide immunogenicity data' SubClassOf 'Protein property' http://edamontology.org/data_2865 Codon usage bias 'Codon usage bias' SubClassOf 'Codon usage data' http://edamontology.org/format_1617 WormBase gene report format 'WormBase gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2866 Northern blot report 'Northern blot report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1616 TAIR gene report format 'TAIR gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1539 Protein structural quality report 'Protein structural quality report' SubClassOf 'Protein structure report' http://edamontology.org/data_2867 Nucleic acid features report (VNTR) 'Nucleic acid features report (VNTR)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1619 TIGR gene report format 'TIGR gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2868 Nucleic acid features report (microsatellite) 'Nucleic acid features report (microsatellite)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1618 ZFIN gene report format 'ZFIN gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1533 Protein subcellular localisation 'Protein subcellular localisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1532 Protein optical density 'Protein optical density' SubClassOf 'Protein property' http://edamontology.org/data_1531 Protein extinction coefficient 'Protein extinction coefficient' SubClassOf 'Protein property' http://edamontology.org/data_1530 Protein hydrogen exchange rate 'Protein hydrogen exchange rate' SubClassOf 'Protein property' http://edamontology.org/format_1613 RGD gene report format 'RGD gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1612 MGD gene report format 'MGD gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1615 GeneDB gene report format 'GeneDB gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1614 SGD gene report format 'SGD gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1611 MaizeGDB gene report format 'MaizeGDB gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1610 KEGG GENES gene report format 'KEGG GENES gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1548 Protein residue 3D cluster 'Protein residue 3D cluster' SubClassOf 'Protein interaction report' http://edamontology.org/data_1547 Protein contact map 'Protein contact map' SubClassOf 'Protein interaction report' http://edamontology.org/data_1546 Protein distance matrix 'Protein distance matrix' SubClassOf 'Distance matrix' 'Protein distance matrix' SubClassOf 'Protein interaction report' http://edamontology.org/data_1545 Protein dipole moment 'Protein dipole moment' SubClassOf 'Protein property' http://edamontology.org/data_2877 Protein complex 'Protein complex' SubClassOf 'Protein structure' http://edamontology.org/format_1649 HumanCyc entry format 'HumanCyc entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2878 Protein structural motif 'Protein structural motif' SubClassOf 'Protein structure' http://edamontology.org/data_1549 Protein hydrogen bonds 'Protein hydrogen bonds' SubClassOf 'Protein interaction report' http://edamontology.org/data_2879 Lipid report 'Lipid report' SubClassOf 'Structure report' http://edamontology.org/data_1540 Protein non-covalent interactions report 'Protein non-covalent interactions report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2872 ID list 'ID list' SubClassOf 'Data reference' http://edamontology.org/data_2873 Phylogenetic gene frequencies data 'Phylogenetic gene frequencies data' SubClassOf 'Phylogenetic continuous quantitative data' http://edamontology.org/data_2874 Sequence set (polymorphic) 'Sequence set (polymorphic)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2875 DRCAT resource 'DRCAT resource' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1544 Ramachandran plot 'Ramachandran plot' SubClassOf 'Protein geometry report' http://edamontology.org/data_1543 Protein surface report 'Protein surface report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1542 Protein solvent accessibility report 'Protein solvent accessibility report' SubClassOf 'Protein structure report' http://edamontology.org/data_2870 Radiation hybrid map 'Radiation hybrid map' SubClassOf 'Physical map' http://edamontology.org/data_1541 Protein flexibility or motion report 'Protein flexibility or motion report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1640 ArrayExpress entry format 'ArrayExpress entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1645 EMDB entry format 'EMDB entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1648 MetaCyc entry format 'MetaCyc entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1647 KEGG PATHWAY entry format 'KEGG PATHWAY entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1641 affymetrix-exp 'affymetrix-exp' SubClassOf 'Microarray experiment data format' 'affymetrix-exp' SubClassOf 'Textual format' http://edamontology.org/format_1644 CHP 'CHP' SubClassOf 'Gene expression report format' 'CHP' SubClassOf 'Textual format' http://edamontology.org/data_1559 CATH homologous superfamily 'CATH homologous superfamily' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1558 CATH topology 'CATH topology' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1557 CATH architecture 'CATH architecture' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1556 CATH class 'CATH class' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2887 Nucleic acid sequence record 'Nucleic acid sequence record' SubClassOf 'Sequence record' 'Nucleic acid sequence record' SubClassOf 'Nucleic acid sequence' http://edamontology.org/format_1639 affymetrix 'affymetrix' SubClassOf 'Textual format' 'affymetrix' SubClassOf 'Sequence cluster format (nucleic acid)' http://edamontology.org/data_2888 Protein sequence record (full) 'Protein sequence record (full)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1638 cel 'cel' SubClassOf 'Textual format' 'cel' SubClassOf 'Gene expression report format' http://edamontology.org/data_2889 Nucleic acid sequence record (full) 'Nucleic acid sequence record (full) ' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2883 RNA features report 'RNA features report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2884 Plot 'Plot' SubClassOf 'Data' http://edamontology.org/data_1550 Protein non-canonical interactions 'Protein non-canonical interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2885 Nucleic acid features report (polymorphism) 'Nucleic acid features report (polymorphism)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2886 Protein sequence record 'Protein sequence record' SubClassOf 'Protein sequence' 'Protein sequence record' SubClassOf 'Sequence record' http://edamontology.org/data_1555 EMBASSY domain classification 'EMBASSY domain classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1554 SCOP node 'SCOP node' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2880 Secondary structure image 'Secondary structure image' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1553 CATH node 'CATH node' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2881 Secondary structure report 'Secondary structure report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2882 DNA features 'DNA features' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1637 dat 'dat' SubClassOf 'Textual format' 'dat' SubClassOf 'Gene expression report format' http://edamontology.org/format_1631 exp 'exp' SubClassOf 'Textual format' 'exp' SubClassOf 'Sequence assembly format (text)' http://edamontology.org/format_1630 CAF 'CAF' SubClassOf 'Sequence assembly format (text)' 'CAF' SubClassOf 'Textual format' http://edamontology.org/format_1633 PHD 'PHD' SubClassOf 'Sequence trace format' 'PHD' SubClassOf 'Textual format' http://edamontology.org/format_1632 SCF 'SCF' SubClassOf 'binary format' 'SCF' SubClassOf 'Sequence trace format' http://edamontology.org/data_2539 Alignment data 'Alignment data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1205 QSAR descriptor (molecular) 'QSAR descriptor (molecular)' SubClassOf 'QSAR descriptor' http://edamontology.org/data_1204 QSAR descriptor (topological) 'QSAR descriptor (topological)' SubClassOf 'QSAR descriptor' http://edamontology.org/data_2535 Sequence tag profile 'Sequence tag profile' SubClassOf 'Gene expression profile' http://edamontology.org/data_2536 Mass spectrometry data 'Mass spectrometry data' SubClassOf 'Experimental measurement' http://edamontology.org/data_2537 Protein structure raw data 'Protein structure raw data' SubClassOf 'Experimental measurement' http://edamontology.org/data_2538 Mutation identifier 'Mutation identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2531 Experiment report 'Experiment report' SubClassOf 'Report' http://edamontology.org/data_2533 Nucleic acid features report (mutation) 'Nucleic acid features report (mutation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2534 Sequence attribute 'Sequence attribute' SubClassOf 'Data' http://edamontology.org/data_1203 QSAR descriptor (geometrical) 'QSAR descriptor (geometrical)' SubClassOf 'QSAR descriptor' http://edamontology.org/data_1202 QSAR descriptor (electronic) 'QSAR descriptor (electronic)' SubClassOf 'QSAR descriptor' http://edamontology.org/data_1201 QSAR descriptor (constitutional) 'QSAR descriptor (constitutional)' SubClassOf 'QSAR descriptor' http://edamontology.org/data_2530 Organism report 'Organism report' SubClassOf 'Report' http://edamontology.org/operation_3628 Chromatographic alignment 'Chromatographic alignment' SubClassOf 'Spectral analysis' http://edamontology.org/operation_3627 Mass spectra calibration 'Mass spectra calibration' SubClassOf 'Spectral analysis' http://edamontology.org/operation_3625 Relation inference 'Relation inference' SubClassOf 'Text mining' http://www.ifomis.org/bfo/1.1/snap#Role role http://edamontology.org/data_2540 Data index data 'Data index data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3790 SPARQL 'SPARQL' SubClassOf 'Textual format' http://edamontology.org/operation_0565 Sequence alignment visualisation 'Sequence alignment visualisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0566 Sequence cluster visualisation 'Sequence cluster visualisation' SubClassOf 'Visualisation' http://edamontology.org/operation_0563 Codon usage table formatting 'Codon usage table formatting' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0564 Sequence visualisation 'Sequence visualisation' SubClassOf 'Visualisation' 'Sequence visualisation' SubClassOf 'Sequence analysis' http://edamontology.org/operation_0569 Protein secondary structure visualisation 'Protein secondary structure visualisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0567 Phylogenetic tree visualisation 'Phylogenetic tree visualisation' SubClassOf 'Phylogenetic tree analysis' 'Phylogenetic tree visualisation' SubClassOf 'Visualisation' http://edamontology.org/operation_0568 RNA secondary structure visualisation 'RNA secondary structure visualisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0561 Sequence formatting 'Sequence formatting' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0562 Sequence alignment formatting 'Sequence alignment formatting' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0560 DNA vaccine design 'DNA vaccine design' SubClassOf 'Nucleic acid design' http://edamontology.org/topic_1811 Prokaryotes and Archaea 'Prokaryotes and Archaea' SubClassOf 'Model organisms' http://edamontology.org/data_1239 Restriction digest 'Restriction digest' SubClassOf 'Sequence set (nucleic acid)' http://edamontology.org/operation_0577 DNA linear map rendering 'DNA linear map rendering' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1238 Proteolytic digest 'Proteolytic digest' SubClassOf 'Sequence set (protein)' http://edamontology.org/operation_0574 Sequence motif rendering 'Sequence motif rendering' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1237 HMMER synthetic sequences set 'HMMER synthetic sequences set' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0575 Restriction map drawing 'Restriction map drawing' SubClassOf 'Map drawing' 'Restriction map drawing' SubClassOf 'Restriction site recognition' http://edamontology.org/operation_0578 Plasmid map drawing 'Plasmid map drawing' SubClassOf 'Map drawing' http://edamontology.org/operation_0579 Operon drawing 'Operon drawing' SubClassOf 'Map drawing' http://edamontology.org/data_2564 Amino acid name (three letter) 'Amino acid name (three letter)' SubClassOf 'Amino acid name' http://edamontology.org/data_2565 Amino acid name (full name) 'Amino acid name (full name)' SubClassOf 'Amino acid name' http://edamontology.org/data_1236 Psiblast checkpoint file 'Psiblast checkpoint file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0572 Protein interaction network rendering Protein interaction network visualisation 'Protein interaction network rendering' SubClassOf 'Pathway or network visualisation' http://edamontology.org/data_1235 Sequence cluster 'Sequence cluster' SubClassOf 'Sequence set' http://edamontology.org/operation_0573 Map drawing 'Map drawing' SubClassOf 'Visualisation' http://edamontology.org/data_1234 Sequence set (nucleic acid) 'Sequence set (nucleic acid)' SubClassOf 'Sequence set' http://edamontology.org/operation_0570 Structure visualisation 'Structure visualisation' SubClassOf 'Visualisation' 'Structure visualisation' SubClassOf 'Structure analysis' http://edamontology.org/data_1233 Sequence set (protein) 'Sequence set (protein)' SubClassOf 'Sequence set' http://edamontology.org/data_2563 Amino acid name (single letter) 'Amino acid name (single letter)' SubClassOf 'Amino acid name' http://edamontology.org/operation_0571 Microarray data rendering 'Microarray data rendering' SubClassOf 'Visualisation' 'Microarray data rendering' SubClassOf 'Plotting' 'Microarray data rendering' SubClassOf 'Gene expression analysis' http://edamontology.org/data_1249 Sequence length 'Sequence length' SubClassOf 'Sequence attribute' http://edamontology.org/data_2579 Expressed gene list 'Expressed gene list' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3659 Regression analysis 'Regression analysis' SubClassOf 'Statistical calculation' http://edamontology.org/operation_3658 Statistical inference 'Statistical inference' SubClassOf 'Statistical calculation' http://edamontology.org/data_1243 Primer3 mispriming library file 'Primer3 mispriming library file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1242 Primer3 internal oligo mishybridizing library 'Primer3 internal oligo mishybridizing library' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2576 Toxin identifier 'Toxin identifier' SubClassOf 'Compound identifier' http://edamontology.org/data_1241 vectorstrip cloning vector definition file 'vectorstrip cloning vector definition file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1240 PCR primers 'PCR primers' SubClassOf 'Sequence set (nucleic acid)' http://edamontology.org/data_2578 ArachnoServer ID 'ArachnoServer ID' SubClassOf 'Toxin accession' http://edamontology.org/data_1246 Sequence cluster (nucleic acid) 'Sequence cluster (nucleic acid)' SubClassOf 'Sequence cluster' 'Sequence cluster (nucleic acid)' SubClassOf 'Sequence set (nucleic acid)' http://edamontology.org/data_1245 Sequence cluster (protein) 'Sequence cluster (protein)' SubClassOf 'Sequence set (protein)' 'Sequence cluster (protein)' SubClassOf 'Sequence cluster' http://edamontology.org/data_1244 primersearch primer pairs sequence record 'primersearch primer pairs sequence record' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3765 KNIME datatable format 'KNIME datatable format' SubClassOf 'Workflow format' http://edamontology.org/format_3764 idXML 'idXML' SubClassOf 'Mass spectrometry data format' 'idXML' SubClassOf 'XML' http://edamontology.org/operation_3666 Molecular surface comparison 'Molecular surface comparison' SubClassOf 'Structure comparison' 'Molecular surface comparison' SubClassOf 'Molecular surface analysis' http://edamontology.org/data_1259 Sequence complexity report 'Sequence complexity report' SubClassOf 'Sequence property' http://edamontology.org/data_1254 Sequence property 'Sequence property' SubClassOf 'Sequence report' http://edamontology.org/data_2586 Northern blot image 'Northern blot image' SubClassOf 'Raw image' http://edamontology.org/operation_3660 Metabolic network modelling 'Metabolic network modelling' SubClassOf 'Network simulation' http://edamontology.org/data_1253 Sequence information report 'Sequence information report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2587 Blot ID 'Blot ID' SubClassOf 'Identifier (typed)' 'Blot ID' SubClassOf 'Accession' http://edamontology.org/data_1252 Sequence length range 'Sequence length range' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2588 BlotBase blot ID 'BlotBase blot ID' SubClassOf 'Blot ID' http://edamontology.org/data_1251 Window size 'Window size' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2589 Hierarchy 'Hierarchy' SubClassOf 'Data' http://edamontology.org/data_1258 Sequence property (nucleic acid) 'Sequence property (nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2582 GO concept ID (biological process) 'GO concept ID (biological process)' SubClassOf 'GO concept ID' http://edamontology.org/operation_3664 Statistical modelling 'Statistical modelling' SubClassOf 'Statistical calculation' http://edamontology.org/data_1257 Sequence property (protein) 'Sequence property (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2583 GO concept ID (molecular function) 'GO concept ID (molecular function)' SubClassOf 'GO concept ID' http://edamontology.org/operation_3663 Homology-based gene prediction 'Homology-based gene prediction' SubClassOf 'Gene prediction' http://edamontology.org/data_1256 Sequence features (comparative) 'Sequence features (comparative)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2584 GO concept name (cellular component) 'GO concept name (cellular component)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3662 Ab-initio gene prediction 'Ab-initio gene prediction' SubClassOf 'Gene prediction' http://edamontology.org/data_1255 Sequence features 'Sequence features' SubClassOf 'Data' http://edamontology.org/operation_3661 SNP annotation 'SNP annotation' SubClassOf 'Sequence annotation' http://edamontology.org/format_3750 YAML 'YAML' SubClassOf 'Format' http://edamontology.org/data_2580 BindingDB Monomer ID 'BindingDB Monomer ID' SubClassOf 'Compound accession' http://edamontology.org/format_3752 CSV 'CSV' SubClassOf 'DSV' http://edamontology.org/data_2581 GO concept name 'GO concept name' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3751 DSV 'DSV' SubClassOf 'Textual format' http://edamontology.org/data_1250 Word size 'Word size' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3758 SEQUEST .out file 'SEQUEST .out file' SubClassOf 'Mass spectrometry data format' 'SEQUEST .out file' SubClassOf 'Textual format' http://edamontology.org/operation_3635 Labeled quantification 'Labeled quantification' SubClassOf 'Protein quantification' http://edamontology.org/operation_3634 Label-free quantification 'Label-free quantification' SubClassOf 'Protein quantification' http://edamontology.org/operation_3633 Retention times prediction 'Retention times prediction' SubClassOf 'Calculation' http://edamontology.org/operation_3632 Isotopic distributions calculation 'Isotopic distributions calculation' SubClassOf 'Calculation' http://edamontology.org/operation_3639 iTRAQ 'iTRAQ' SubClassOf 'Labeled quantification' http://edamontology.org/operation_3638 SILAC 'SILAC' SubClassOf 'Labeled quantification' http://edamontology.org/operation_3637 Spectral counting 'Spectral counting' SubClassOf 'Label-free quantification' http://edamontology.org/operation_3636 MRM/SRM 'MRM/SRM' SubClassOf 'Protein quantification' http://edamontology.org/data_1265 Base frequencies table 'Base frequencies table' SubClassOf 'Sequence composition report' 'Base frequencies table' SubClassOf 'Matrix' http://edamontology.org/data_2597 CABRI catalogue name 'CABRI catalogue name' SubClassOf 'Name' 'CABRI catalogue name' SubClassOf 'Catalogue ID' http://edamontology.org/data_1264 Sequence composition table 'Sequence composition table' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2598 Secondary structure alignment metadata 'Secondary structure alignment metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1263 Base position variability plot 'Base position variability plot' SubClassOf 'Sequence composition report' http://edamontology.org/data_2599 Molecule interaction report 'Molecule interaction report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1262 Peptide molecular weight hits 'Peptide molecular weight hits' SubClassOf 'Sequence set (protein)' http://edamontology.org/data_1269 DAS sequence feature annotation 'DAS sequence feature annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2593 BRENDA organism ID 'BRENDA organism ID' SubClassOf 'Organism accession' http://edamontology.org/operation_3631 Peptide identification 'Peptide identification' SubClassOf 'Spectral analysis' http://edamontology.org/data_1268 Amino acid word frequencies table 'Amino acid word frequencies table' SubClassOf 'Sequence composition report' 'Amino acid word frequencies table' SubClassOf 'Matrix' http://edamontology.org/data_2594 UniGene taxon 'UniGene taxon' SubClassOf 'Taxon' http://edamontology.org/operation_3630 Protein quantification 'Protein quantification' SubClassOf 'Spectral analysis' http://edamontology.org/data_1267 Amino acid frequencies table 'Amino acid frequencies table' SubClassOf 'Matrix' 'Amino acid frequencies table' SubClassOf 'Sequence composition report' http://edamontology.org/data_2595 UTRdb taxon 'UTRdb taxon' SubClassOf 'Taxon' http://edamontology.org/data_1266 Base word frequencies table 'Base word frequencies table' SubClassOf 'Sequence composition report' 'Base word frequencies table' SubClassOf 'Matrix' http://edamontology.org/data_2596 Catalogue ID 'Catalogue ID' SubClassOf 'Identifier (typed)' http://edamontology.org/format_3783 PubTator format 'PubTator format' SubClassOf 'Textual format' 'PubTator format' SubClassOf 'Annotated text format' http://edamontology.org/data_2590 Hierarchy identifier 'Hierarchy identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3782 BioC 'BioC' SubClassOf 'XML' 'BioC' SubClassOf 'Annotated text format' http://edamontology.org/data_2591 Brite hierarchy ID 'Brite hierarchy ID' SubClassOf 'Biological model accession' http://edamontology.org/format_3785 BioNLP Shared Task format 'BioNLP Shared Task format' SubClassOf 'Annotated text format' 'BioNLP Shared Task format' SubClassOf 'Textual format' http://edamontology.org/data_2592 Cancer type 'Cancer type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3784 Open Annotation format 'Open Annotation format' SubClassOf 'Annotated text format' 'Open Annotation format' SubClassOf 'JSON-LD' http://edamontology.org/data_1261 Sequence composition report 'Sequence composition report' SubClassOf 'Sequence property' http://edamontology.org/data_1260 Sequence ambiguity report 'Sequence ambiguity report' SubClassOf 'Sequence property' http://edamontology.org/format_3781 PubAnnotation format 'PubAnnotation format' SubClassOf 'JSON' 'PubAnnotation format' SubClassOf 'Annotated text format' http://edamontology.org/format_3780 Annotated text format 'Annotated text format' SubClassOf 'Format (by type of data)' http://edamontology.org/operation_3629 Deisotoping 'Deisotoping' SubClassOf 'Spectral analysis' http://edamontology.org/format_3787 Query language 'Query language' SubClassOf 'Format (by type of data)' http://edamontology.org/format_3789 XQuery 'XQuery' SubClassOf 'Textual format' http://edamontology.org/format_3788 SQL 'SQL' SubClassOf 'Textual format' http://edamontology.org/operation_3646 Peptide database search 'Peptide database search' SubClassOf 'Peptide identification' 'Peptide database search' SubClassOf 'Database search' http://edamontology.org/operation_3645 PTM identification 'PTM identification' SubClassOf 'Peptide identification' http://edamontology.org/operation_3644 de Novo sequencing 'de Novo sequencing' SubClassOf 'Sequence generation (protein)' 'de Novo sequencing' SubClassOf 'Peptide identification' http://edamontology.org/operation_3643 Tag-based peptide identification 'Tag-based peptide identification' SubClassOf 'Peptide identification' http://edamontology.org/operation_3649 Target-Decoy 'Target-Decoy' SubClassOf 'Validation of peptide-spectrum matches' http://edamontology.org/operation_3648 Validation of peptide-spectrum matches 'Validation of peptide-spectrum matches' SubClassOf 'Validation' 'Validation of peptide-spectrum matches' SubClassOf 'Peptide database search' http://edamontology.org/operation_3647 Blind peptide database search 'Blind peptide database search' SubClassOf 'Peptide database search' http://edamontology.org/data_1276 Nucleic acid features 'Nucleic acid features' SubClassOf 'Sequence features' 'Nucleic acid features' SubClassOf 'Nucleic acid report' http://edamontology.org/data_1274 Map 'Map' SubClassOf 'Map data' http://edamontology.org/operation_3642 Dimethyl 'Dimethyl' SubClassOf 'Labeled quantification' http://edamontology.org/data_1279 Sequence map 'Sequence map' SubClassOf 'Physical map' http://edamontology.org/operation_3641 TMT-tag 'TMT-tag' SubClassOf 'Labeled quantification' http://edamontology.org/data_1278 Genetic map 'Genetic map' SubClassOf 'Map' http://edamontology.org/operation_3640 18O labeling '18O labeling' SubClassOf 'Labeled quantification' http://edamontology.org/data_1277 Protein features 'Protein features' SubClassOf 'Sequence features' 'Protein features' SubClassOf 'Protein report' http://edamontology.org/format_3772 BioJSON (BioXSD) 'BioJSON (BioXSD)' SubClassOf 'Alignment format' 'BioJSON (BioXSD)' SubClassOf 'Raw sequence format' 'BioJSON (BioXSD)' SubClassOf 'Sequence record format' 'BioJSON (BioXSD)' SubClassOf 'JSON' 'BioJSON (BioXSD)' SubClassOf 'Sequence feature annotation format' http://edamontology.org/format_3771 UniProtKB RDF 'UniProtKB RDF' SubClassOf 'RDF format' 'UniProtKB RDF' SubClassOf 'uniprotkb-like format' http://edamontology.org/format_3774 BioJSON (Jalview) 'BioJSON (Jalview)' SubClassOf 'JSON' 'BioJSON (Jalview)' SubClassOf 'Alignment format' 'BioJSON (Jalview)' SubClassOf 'Sequence feature annotation format' http://edamontology.org/format_3773 BioYAML 'BioYAML' SubClassOf 'Raw sequence format' 'BioYAML' SubClassOf 'Alignment format' 'BioYAML' SubClassOf 'Sequence feature annotation format' 'BioYAML' SubClassOf 'Sequence record format' 'BioYAML' SubClassOf 'YAML' http://edamontology.org/data_1270 Feature table 'Feature table' SubClassOf 'Sequence features' http://edamontology.org/format_3770 UniProtKB XML 'UniProtKB XML' SubClassOf 'uniprotkb-like format' 'UniProtKB XML' SubClassOf 'Sequence record format (XML)' 'UniProtKB XML' SubClassOf 'XML' http://edamontology.org/format_3776 BTrack 'BTrack' SubClassOf 'Sequence annotation track format' 'BTrack' SubClassOf 'Sequence feature table format' 'BTrack' SubClassOf 'binary format' http://edamontology.org/format_3775 GSuite 'GSuite' SubClassOf 'Textual format' 'GSuite' SubClassOf 'Sequence feature annotation format' http://edamontology.org/format_3777 MCPD 'MCPD' SubClassOf 'Textual format' 'MCPD' SubClassOf 'Biodiversity data format' http://edamontology.org/data_1286 Plasmid map 'Plasmid map' SubClassOf 'Sequence map' http://edamontology.org/data_1285 Gene map 'Gene map' SubClassOf 'Sequence map' http://edamontology.org/data_1284 DNA transduction map 'DNA transduction map' SubClassOf 'Genetic map' http://edamontology.org/data_1289 Restriction map 'Restriction map' SubClassOf 'Sequence image' 'Restriction map' SubClassOf 'Sequence map' http://edamontology.org/operation_3695 Filtering 'Filtering' SubClassOf 'Data handling' http://edamontology.org/data_1288 Genome map 'Genome map' SubClassOf 'Sequence map' http://edamontology.org/operation_3694 Mass spectrum visualisation 'Mass spectrum visualisation' SubClassOf 'Visualisation' http://edamontology.org/data_1283 Cytogenetic map 'Cytogenetic map' SubClassOf 'Physical map' http://edamontology.org/data_1281 Sequence signature map 'Sequence signature map' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1280 Physical map 'Physical map' SubClassOf 'Map' http://edamontology.org/data_1298 Sequence motif matches 'Sequence motif matches' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1299 Sequence features (repeats) 'Sequence features (repeats)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1290 InterPro compact match image 'InterPro compact match image' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1294 GlobPlot domain image 'GlobPlot domain image' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1293 SMART protein schematic 'SMART protein schematic' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1292 InterPro architecture image 'InterPro architecture image' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1291 InterPro detailed match image 'InterPro detailed match image' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3677 Differential binding analysis 'Differential binding analysis' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/operation_3675 Variant filtering 'Variant filtering' SubClassOf 'Sequencing quality control' http://edamontology.org/data_3002 Annotation track 'Annotation track' SubClassOf 'Sequence features' http://edamontology.org/operation_3672 Gene functional annotation 'Gene functional annotation' SubClassOf 'Sequence annotation' http://edamontology.org/operation_3680 RNA-Seq analysis 'RNA-Seq analysis' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/data_3026 GO concept name (biological process) 'GO concept name (biological process)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3027 GO concept name (molecular function) 'GO concept name (molecular function)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3028 Taxonomy 'Taxonomy' SubClassOf 'Data' http://edamontology.org/data_3029 Protein ID (EMBL/GenBank/DDBJ) 'Protein ID (EMBL/GenBank/DDBJ)' SubClassOf 'Protein accession' http://edamontology.org/data_3022 NCBI genetic code ID 'NCBI genetic code ID' SubClassOf 'Identifier (typed)' 'NCBI genetic code ID' SubClassOf 'Accession' http://edamontology.org/data_3025 Ontology concept identifier 'Ontology concept identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_3021 UniProt accession 'UniProt accession' SubClassOf 'Sequence accession (protein)' http://edamontology.org/topic_0594 Sequence classification 'Sequence classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0595 Protein classification 'Protein classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0593 NMR 'NMR' SubClassOf 'Structural biology' 'NMR' SubClassOf 'Imaging' http://edamontology.org/data_3034 Sequence feature identifier 'Sequence feature identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_3035 Structure identifier 'Structure identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_3036 Matrix identifier 'Matrix identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_3031 Core data 'Core data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0598 Sequence motif or profile 'Sequence motif or profile' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1197 InChI 'InChI' SubClassOf 'Textual format' 'InChI' SubClassOf 'Chemical formula format' http://edamontology.org/format_1198 mf 'mf' SubClassOf 'Textual format' 'mf' SubClassOf 'Chemical formula format' http://edamontology.org/format_1199 InChIKey 'InChIKey' SubClassOf 'Chemical formula format' 'InChIKey' SubClassOf 'Textual format' http://edamontology.org/format_1196 SMILES 'SMILES' SubClassOf 'Textual format' 'SMILES' SubClassOf 'Chemical formula format' http://edamontology.org/format_1947 GCG MSF 'GCG MSF' SubClassOf 'GCG format variant' http://edamontology.org/format_1946 mega-seq 'mega-seq' SubClassOf 'Textual format' 'mega-seq' SubClassOf 'Sequence record format (text)' http://edamontology.org/topic_3531 Protein super-secondary structure 'Protein super-secondary structure' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1949 nexus-seq 'nexus-seq' SubClassOf 'Sequence record format (text)' 'nexus-seq' SubClassOf 'Textual format' 'nexus-seq' SubClassOf 'Alignment format (text)' http://edamontology.org/topic_3530 Genetic information processing pathways 'Genetic information processing pathways' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1948 nbrf/pir 'nbrf/pir' SubClassOf 'Textual format' http://edamontology.org/format_1943 igstrict 'igstrict' SubClassOf 'Sequence record format (text)' 'igstrict' SubClassOf 'Textual format' http://edamontology.org/topic_3536 Protein cleavage sites 'Protein cleavage sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1942 ig 'ig' SubClassOf 'Textual format' 'ig' SubClassOf 'Sequence record format (text)' http://edamontology.org/topic_3535 Protein-nucleic acid binding sites 'Protein-nucleic acid binding sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1945 mase format 'mase format' SubClassOf 'Textual format' 'mase format' SubClassOf 'Sequence record format (text)' http://edamontology.org/topic_3534 Protein binding sites 'Protein binding sites' SubClassOf 'Protein sites, features and motifs' http://edamontology.org/format_1944 jackknifer 'jackknifer' SubClassOf 'Textual format' 'jackknifer' SubClassOf 'Sequence record format (text)' http://edamontology.org/topic_3533 Protein active sites 'Protein active sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3539 Protein domains 'Protein domains' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1941 hennig86 'hennig86' SubClassOf 'Sequence record format (text)' 'hennig86' SubClassOf 'Textual format' http://edamontology.org/topic_3538 Protein disordered structure 'Protein disordered structure' SubClassOf 'Protein structure analysis' http://edamontology.org/format_1940 giFASTA format 'giFASTA format' SubClassOf 'FASTA-like (text)' http://edamontology.org/topic_3537 Protein chemical modifications 'Protein chemical modifications' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1939 GFF3-seq 'GFF3-seq' SubClassOf 'GFF3' 'GFF3-seq' SubClassOf 'Sequence record format (text)' http://edamontology.org/topic_3543 Protein sequence repeats 'Protein sequence repeats' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1935 GCG 'GCG' SubClassOf 'GCG format variant' http://edamontology.org/topic_3542 Protein secondary structure 'Protein secondary structure' SubClassOf 'Protein structure analysis' http://edamontology.org/format_1938 GFF2-seq 'GFF2-seq' SubClassOf 'Sequence record format (text)' 'GFF2-seq' SubClassOf 'GFF2' http://edamontology.org/topic_3541 Protein post-translational modifications 'Protein post-translational modifications' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1937 genpept 'genpept' SubClassOf 'GenBank-like format (text)' http://edamontology.org/topic_3540 Protein key folding sites 'Protein key folding sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1932 FASTQ-sanger 'FASTQ-sanger' SubClassOf 'FASTQ-like format (text)' http://edamontology.org/format_1931 FASTQ-illumina 'FASTQ-illumina' SubClassOf 'FASTQ-like format (text)' http://edamontology.org/format_1934 fitch program 'fitch program' SubClassOf 'Sequence record format (text)' 'fitch program' SubClassOf 'Textual format' http://edamontology.org/format_1933 FASTQ-solexa 'FASTQ-solexa' SubClassOf 'FASTQ-like format (text)' http://edamontology.org/topic_3544 Protein signal peptides 'Protein signal peptides' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1930 FASTQ 'FASTQ' SubClassOf 'FASTQ-like format (text)' http://edamontology.org/format_1969 debug-seq 'debug-seq' SubClassOf 'Textual format' 'debug-seq' SubClassOf 'Sequence record format (text)' http://edamontology.org/format_1968 dasdna 'dasdna' SubClassOf 'XML' 'dasdna' SubClassOf 'Sequence record format (XML)' http://edamontology.org/format_1965 treecon sequence format 'treecon sequence format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1964 plain text format (unformatted) 'plain text format (unformatted)' SubClassOf 'Textual format' http://edamontology.org/topic_2226 Structure determination 'Structure determination' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3557 Protein interaction experiment 'Protein interaction experiment' SubClassOf 'Laboratory techniques' http://edamontology.org/format_1967 DAS format 'DAS format' SubClassOf 'XML' 'DAS format' SubClassOf 'Sequence record format (XML)' http://edamontology.org/topic_2225 Protein databases 'Protein databases' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1966 ASN.1 sequence format 'ASN.1 sequence format' SubClassOf 'Sequence record format (text)' 'ASN.1 sequence format' SubClassOf 'Textual format' http://edamontology.org/format_1961 Stockholm format 'Stockholm format' SubClassOf 'Textual format' 'Stockholm format' SubClassOf 'Alignment format (text)' http://edamontology.org/format_1960 Staden format 'Staden format' SubClassOf 'Textual format' 'Staden format' SubClassOf 'Sequence record format (text)' http://edamontology.org/format_1963 UniProtKB format 'UniProtKB format' SubClassOf 'UniProt-like (text)' http://edamontology.org/topic_2229 Cell biology 'Cell biology' SubClassOf 'Biology' http://edamontology.org/format_1962 strider format 'strider format' SubClassOf 'Sequence record format (text)' 'strider format' SubClassOf 'Textual format' http://edamontology.org/topic_2230 Classification 'Classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1958 refseqp 'refseqp' SubClassOf 'Textual format' 'refseqp' SubClassOf 'Sequence record format (text)' http://edamontology.org/format_1957 raw 'raw' SubClassOf 'Textual format' 'raw' SubClassOf 'Raw sequence format' http://edamontology.org/topic_2232 Lipoproteins 'Lipoproteins' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1959 selex sequence format 'selex sequence format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1954 Pearson format 'Pearson format' SubClassOf 'FASTA-like (text)' http://edamontology.org/topic_3569 Applied mathematics 'Applied mathematics' SubClassOf 'Mathematics' http://edamontology.org/format_1953 pdbseqres 'pdbseqres' SubClassOf 'Sequence record format (text)' 'pdbseqres' SubClassOf 'Textual format' 'pdbseqres' SubClassOf 'PDB database entry format' http://edamontology.org/format_1956 phylipnon sequence format 'phylipnon sequence format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1955 phylip sequence format 'phylip sequence format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1950 pdbatom 'pdbatom' SubClassOf 'Textual format' 'pdbatom' SubClassOf 'Sequence record format (text)' 'pdbatom' SubClassOf 'PDB database entry format' http://edamontology.org/format_1952 pdbseqresnuc 'pdbseqresnuc' SubClassOf 'Textual format' 'pdbseqresnuc' SubClassOf 'PDB database entry format' 'pdbseqresnuc' SubClassOf 'Sequence record format (text)' http://edamontology.org/format_1951 pdbatomnuc 'pdbatomnuc' SubClassOf 'Textual format' 'pdbatomnuc' SubClassOf 'PDB database entry format' 'pdbatomnuc' SubClassOf 'Sequence record format (text)' http://edamontology.org/topic_3572 Data quality management 'Data quality management' SubClassOf 'Data management' http://edamontology.org/topic_3571 Data governance 'Data governance' SubClassOf 'Data management' http://edamontology.org/topic_3570 Pure mathematics 'Pure mathematics' SubClassOf 'Mathematics' http://edamontology.org/topic_3576 Medical biotechnology 'Medical biotechnology' SubClassOf 'Biotechnology' http://edamontology.org/topic_3575 Tropical medicine 'Tropical medicine' SubClassOf 'Medicine' http://edamontology.org/topic_3574 Human genetics 'Human genetics' SubClassOf 'Genetics' http://edamontology.org/topic_3573 Freshwater biology 'Freshwater biology' SubClassOf 'Biology' http://edamontology.org/topic_3577 Personalised medicine 'Personalised medicine' SubClassOf 'Medicine' http://edamontology.org/topic_2259 Systems biology 'Systems biology' SubClassOf 'Biology' http://edamontology.org/topic_2258 Cheminformatics 'Cheminformatics' SubClassOf 'Informatics' http://edamontology.org/topic_2257 Phylogeny visualisation 'Phylogeny visualisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1928 Staden experiment format 'Staden experiment format' SubClassOf 'Sequence record format (text)' 'Staden experiment format' SubClassOf 'Textual format' http://edamontology.org/format_1925 codata 'codata' SubClassOf 'Sequence record format (text)' 'codata' SubClassOf 'Textual format' http://edamontology.org/format_1924 clustal sequence format 'clustal sequence format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1927 EMBL format 'EMBL format' SubClassOf 'EMBL-like (text)' 'EMBL format' SubClassOf 'Sequence feature table format (text)' http://edamontology.org/format_1926 dbid 'dbid' SubClassOf 'FASTA-like (text)' http://edamontology.org/format_1921 Alignment format 'Alignment format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_1920 Sequence feature annotation format 'Sequence feature annotation format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_1923 acedb 'acedb' SubClassOf 'Sequence record format (text)' http://edamontology.org/topic_2269 Statistics and probability 'Statistics and probability' SubClassOf 'Mathematics' http://edamontology.org/format_1918 Atomic data format 'Atomic data format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1919 Sequence record format 'Sequence record format' SubClassOf 'Format (by type of data)' http://edamontology.org/topic_2271 Structure database search 'Structure database search' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2278 Transmembrane protein prediction 'Transmembrane protein prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2277 SNP 'SNP' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2276 Protein function prediction 'Protein function prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1915 Format http://edamontology.org/topic_2275 Molecular modelling 'Molecular modelling' SubClassOf 'Structure prediction' http://edamontology.org/format_1912 Nexus format 'Nexus format' SubClassOf 'Phylogenetic tree format (text)' 'Nexus format' SubClassOf 'Textual format' http://edamontology.org/format_1911 TreeCon format 'TreeCon format' SubClassOf 'Phylogenetic tree format (text)' 'TreeCon format' SubClassOf 'Textual format' http://edamontology.org/operation_1831 Metal-bound cysteine detection 'Metal-bound cysteine detection' SubClassOf 'Protein cysteine and disulfide bond assignment' 'Metal-bound cysteine detection' SubClassOf 'Residue interaction calculation' http://edamontology.org/operation_0500 Secondary structure alignment generation 'Secondary structure alignment generation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1830 Free cysteine detection 'Free cysteine detection' SubClassOf 'Protein cysteine and disulfide bond assignment' http://edamontology.org/format_3729 dbGaP format 'dbGaP format' SubClassOf 'Textual format' http://edamontology.org/operation_0503 Pairwise structure alignment 'Pairwise structure alignment' SubClassOf 'Structure alignment' http://edamontology.org/operation_1835 Residue contact calculation (residue-negative ion) 'Residue contact calculation (residue-negative ion)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3728 LocARNA PP 'LocARNA PP' SubClassOf 'Textual format' http://edamontology.org/operation_0504 Multiple structure alignment 'Multiple structure alignment' SubClassOf 'Structure alignment' http://edamontology.org/operation_1834 Protein-metal contact calculation 'Protein-metal contact calculation' SubClassOf 'Residue interaction calculation' http://edamontology.org/operation_0501 Protein secondary structure alignment generation 'Protein secondary structure alignment generation' SubClassOf 'Protein secondary structure comparison' 'Protein secondary structure alignment generation' SubClassOf 'Generation' http://edamontology.org/operation_0502 RNA secondary structure alignment 'RNA secondary structure alignment' SubClassOf 'Generation' 'RNA secondary structure alignment' SubClassOf 'RNA secondary structure analysis' http://edamontology.org/operation_1832 Residue contact calculation (residue-nucleic acid) 'Residue contact calculation (residue-nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2280 Nucleic acid structure comparison 'Nucleic acid structure comparison' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3725 SBOL 'SBOL' SubClassOf 'XML' http://edamontology.org/operation_1828 Tau angle calculation 'Tau angle calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1827 Cysteine torsion angle calculation 'Cysteine torsion angle calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3727 OME-TIFF 'OME-TIFF' SubClassOf 'Image format' 'OME-TIFF' SubClassOf 'binary format' http://edamontology.org/operation_1826 Full torsion angle calculation 'Full torsion angle calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3726 PMML 'PMML' SubClassOf 'XML' http://edamontology.org/operation_1825 Backbone torsion angle calculation 'Backbone torsion angle calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1829 Cysteine bridge detection 'Cysteine bridge detection' SubClassOf 'Protein cysteine and disulfide bond assignment' http://edamontology.org/operation_0510 Global structure alignment 'Global structure alignment' SubClassOf 'Structure alignment' http://edamontology.org/operation_1842 Proline mutation value calculation 'Proline mutation value calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0511 Profile-profile alignment (pairwise) 'Profile-profile alignment (pairwise)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1841 Rotamer likelihood prediction 'Rotamer likelihood prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0514 Structural profile alignment generation (multiple) 'Structural profile alignment generation (multiple)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1846 HET group detection 'HET group detection' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0515 Data retrieval (tool metadata) 'Data retrieval (tool metadata)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1845 PDB file sequence retrieval 'PDB file sequence retrieval' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1844 Protein geometry validation 'Protein geometry validation' SubClassOf 'Protein model validation' http://edamontology.org/operation_0512 Sequence alignment generation (multiple profile) 'Sequence alignment generation (multiple profile)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0513 3D profile-to-3D profile alignment (pairwise) '3D profile-to-3D profile alignment (pairwise)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1843 Residue packing validation 'Residue packing validation' SubClassOf 'Protein model validation' http://edamontology.org/format_3714 MaxQuant APL peaklist format 'MaxQuant APL peaklist format' SubClassOf 'Mass spectrometry data format' 'MaxQuant APL peaklist format' SubClassOf 'Textual format' http://edamontology.org/operation_0507 Pairwise structure alignment generation (local) 'Pairwise structure alignment generation (local)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1839 Salt bridge calculation 'Salt bridge calculation' SubClassOf 'Residue interaction calculation' http://edamontology.org/format_3713 Mascot .dat file 'Mascot .dat file' SubClassOf 'Mass spectrometry data format' 'Mascot .dat file' SubClassOf 'Textual format' http://edamontology.org/operation_0508 Pairwise structure alignment generation (global) 'Pairwise structure alignment generation (global)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1838 Residue contact calculation (residue-ligand) 'Residue contact calculation (residue-ligand)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0505 Structure alignment (protein) 'Structure alignment (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1837 Residue symmetry contact calculation 'Residue symmetry contact calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0506 Structure alignment (RNA) 'Structure alignment (RNA)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1836 Residue bump detection 'Residue bump detection' SubClassOf 'Protein model validation' http://edamontology.org/format_3710 WIFF format 'WIFF format' SubClassOf 'Mass spectrometry data format' 'WIFF format' SubClassOf 'binary format' http://edamontology.org/format_3712 Thermo RAW 'Thermo RAW' SubClassOf 'binary format' 'Thermo RAW' SubClassOf 'Mass spectrometry data format' http://edamontology.org/operation_0509 Local structure alignment 'Local structure alignment' SubClassOf 'Structure alignment' http://edamontology.org/format_3711 X!Tandem XML 'X!Tandem XML' SubClassOf 'binary format' 'X!Tandem XML' SubClassOf 'Textual format' 'X!Tandem XML' SubClassOf 'Mass spectrometry data format' http://edamontology.org/operation_1813 Sequence retrieval 'Sequence retrieval' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1812 Loading 'Loading' SubClassOf 'Data handling' http://edamontology.org/format_3747 protXML 'protXML' SubClassOf 'Mass spectrometry data format' 'protXML' SubClassOf 'XML' http://edamontology.org/format_3746 BIOM format 'BIOM format' SubClassOf 'Textual format' 'BIOM format' SubClassOf 'Biodiversity data format' http://edamontology.org/format_3749 JSON-LD 'JSON-LD' SubClassOf 'RDF format' 'JSON-LD' SubClassOf 'JSON' http://edamontology.org/format_3748 Linked data format 'Linked data format' SubClassOf 'Format (by type of data)' http://edamontology.org/operation_1820 Protein residue surface calculation (vacuum accessible) 'Protein residue surface calculation (vacuum accessible)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1824 Protein surface calculation (accessible) 'Protein surface calculation (accessible)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1823 Protein surface calculation (accessible molecular) 'Protein surface calculation (accessible molecular)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1822 Protein residue surface calculation (vacuum molecular) 'Protein residue surface calculation (vacuum molecular)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1821 Protein residue surface calculation (accessible molecular) 'Protein residue surface calculation (accessible molecular)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1817 Protein atom surface calculation (accessible) 'Protein atom surface calculation (accessible)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1816 Surface rendering 'Surface rendering' SubClassOf 'Structure visualisation' 'Surface rendering' SubClassOf 'Molecular surface analysis' http://edamontology.org/operation_1814 Structure retrieval 'Structure retrieval' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1819 Protein residue surface calculation (accessible) 'Protein residue surface calculation (accessible)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1818 Protein atom surface calculation (accessible molecular) 'Protein atom surface calculation (accessible molecular)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0543 Phylogenetic tree construction (from polymorphism data) 'Phylogenetic tree construction (from polymorphism data)' SubClassOf 'Phylogenetic tree generation (data centric)' http://edamontology.org/operation_0544 Phylogenetic species tree construction 'Phylogenetic species tree construction' SubClassOf 'Phylogenetic tree generation (from molecular sequences)' http://edamontology.org/operation_0541 Phylogenetic tree generation (from continuous quantitative characters) 'Phylogenetic tree generation (from continuous quantitative characters)' SubClassOf 'Phylogenetic tree generation (data centric)' http://edamontology.org/operation_0542 Phylogenetic tree generation (from gene frequencies) 'Phylogenetic tree generation (from gene frequencies)' SubClassOf 'Phylogenetic tree generation (data centric)' http://edamontology.org/operation_0547 Phylogenetic tree generation (maximum likelihood and Bayesian methods) 'Phylogenetic tree generation (maximum likelihood and Bayesian methods)' SubClassOf 'Phylogenetic tree generation (method centric)' http://edamontology.org/operation_0548 Phylogenetic tree generation (quartet methods) 'Phylogenetic tree generation (quartet methods)' SubClassOf 'Phylogenetic tree generation (method centric)' http://edamontology.org/operation_0545 Phylogenetic tree generation (parsimony methods) 'Phylogenetic tree generation (parsimony methods)' SubClassOf 'Phylogenetic tree generation (method centric)' http://edamontology.org/operation_0546 Phylogenetic tree generation (minimum distance methods) 'Phylogenetic tree generation (minimum distance methods)' SubClassOf 'Phylogenetic tree generation (method centric)' http://edamontology.org/operation_0540 Phylogenetic tree generation (from molecular sequences) 'Phylogenetic tree generation (from molecular sequences)' SubClassOf 'Sequence analysis' 'Phylogenetic tree generation (from molecular sequences)' SubClassOf 'Phylogenetic tree generation (data centric)' http://edamontology.org/format_1981 GenBank feature 'GenBank feature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1980 EMBL feature 'EMBL feature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1987 markx10 'markx10' SubClassOf 'markx0 variant' http://edamontology.org/format_1986 markx1 'markx1' SubClassOf 'markx0 variant' http://edamontology.org/format_1989 markx3 'markx3' SubClassOf 'markx0 variant' http://edamontology.org/operation_0538 Phylogenetic tree generation (data centric) 'Phylogenetic tree generation (data centric)' SubClassOf 'Phylogenetic tree generation' http://edamontology.org/format_1988 markx2 'markx2' SubClassOf 'markx0 variant' http://edamontology.org/operation_0539 Phylogenetic tree generation (method centric) 'Phylogenetic tree generation (method centric)' SubClassOf 'Phylogenetic tree generation' http://edamontology.org/format_1983 debug 'debug' SubClassOf 'Alignment format (text)' 'debug' SubClassOf 'Textual format' http://edamontology.org/format_1982 ClustalW format 'ClustalW format' SubClassOf 'Alignment format (text)' 'ClustalW format' SubClassOf 'Textual format' http://edamontology.org/format_1985 markx0 'markx0' SubClassOf 'markx0 variant' http://edamontology.org/format_1984 FASTA-aln 'FASTA-aln' SubClassOf 'FASTA-like (text)' 'FASTA-aln' SubClassOf 'Alignment format (text)' http://edamontology.org/operation_0554 Phylogenetic tree analysis (natural selection) 'Phylogenetic tree analysis (natural selection)' SubClassOf 'Phylogenetic tree analysis' http://edamontology.org/operation_0555 Phylogenetic tree generation (consensus) 'Phylogenetic tree generation (consensus)' SubClassOf 'Phylogenetic tree generation' 'Phylogenetic tree generation (consensus)' SubClassOf 'Phylogenetic tree comparison' http://edamontology.org/operation_0552 Phylogenetic tree bootstrapping 'Phylogenetic tree bootstrapping' SubClassOf 'Phylogenetic tree analysis' 'Phylogenetic tree bootstrapping' SubClassOf 'Validation' http://edamontology.org/operation_0553 Phylogenetic tree analysis (gene family prediction) 'Phylogenetic tree analysis (gene family prediction)' SubClassOf 'Phylogenetic tree analysis' http://edamontology.org/operation_0558 Phylogenetic tree annotation 'Phylogenetic tree annotation' SubClassOf 'Annotation' http://edamontology.org/format_1979 debug-feat 'debug-feat' SubClassOf 'Textual format' 'debug-feat' SubClassOf 'Sequence feature annotation format' http://edamontology.org/operation_0559 Immunogenicity prediction 'Immunogenicity prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0556 Phylogenetic sub/super tree detection 'Phylogenetic sub/super tree detection' SubClassOf 'Phylogenetic tree comparison' http://edamontology.org/operation_0557 Phylogenetic tree distances calculation 'Phylogenetic tree distances calculation' SubClassOf 'Phylogenetic tree comparison' http://edamontology.org/operation_0550 DNA substitution modelling 'DNA substitution modelling' SubClassOf 'Nucleic acid sequence alignment analysis' 'DNA substitution modelling' SubClassOf 'Modelling and simulation' http://edamontology.org/operation_0551 Phylogenetic tree analysis (shape) 'Phylogenetic tree analysis (shape)' SubClassOf 'Phylogenetic tree analysis' http://edamontology.org/format_1970 jackknifernon 'jackknifernon' SubClassOf 'Sequence record format (text)' 'jackknifernon' SubClassOf 'Textual format' http://edamontology.org/format_1976 pir 'pir' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1975 GFF3 'GFF3' SubClassOf 'GFF' http://edamontology.org/format_1978 DASGFF 'DASGFF' SubClassOf 'XML' 'DASGFF' SubClassOf 'Sequence feature table format (XML)' http://edamontology.org/operation_0549 Phylogenetic tree generation (AI methods) 'Phylogenetic tree generation (AI methods)' SubClassOf 'Phylogenetic tree generation (method centric)' http://edamontology.org/format_1977 swiss feature 'swiss feature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1972 NCBI format 'NCBI format' SubClassOf 'FASTA-like (text)' http://edamontology.org/format_1971 meganon sequence format 'meganon sequence format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1974 GFF2 'GFF2' SubClassOf 'GFF' http://edamontology.org/format_1973 nexusnon 'nexusnon' SubClassOf 'Alignment format (text)' 'nexusnon' SubClassOf 'Textual format' 'nexusnon' SubClassOf 'Sequence record format (text)' http://edamontology.org/operation_0521 PCR primer design (based on gene structure) 'PCR primer design (based on gene structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0522 PCR primer design (for methylation PCRs) 'PCR primer design (for methylation PCRs)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0520 PCR primer design (for conserved primers) 'PCR primer design (for conserved primers)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1850 Protein cysteine and disulfide bond assignment 'Protein cysteine and disulfide bond assignment' SubClassOf 'Protein secondary structure assignment (from coordinate data)' http://edamontology.org/operation_0525 Genome assembly 'Genome assembly' SubClassOf 'Sequence assembly' http://edamontology.org/format_3706 Biodiversity data format 'Biodiversity data format' SubClassOf 'Format (by type of data)' http://edamontology.org/operation_0526 EST assembly 'EST assembly' SubClassOf 'Sequence assembly' http://edamontology.org/format_3709 GCT/Res format 'GCT/Res format' SubClassOf 'Textual format' 'GCT/Res format' SubClassOf 'Gene expression report format' http://edamontology.org/operation_0523 Mapping assembly 'Mapping assembly' SubClassOf 'Sequence assembly' http://edamontology.org/format_3708 ABCD format 'ABCD format' SubClassOf 'Biodiversity data format' http://edamontology.org/operation_0524 De-novo assembly 'De-novo assembly' SubClassOf 'Sequence assembly' http://edamontology.org/operation_0518 PCR primer design (for genotyping polymorphisms) 'PCR primer design (for genotyping polymorphisms)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3702 MSF 'MSF' SubClassOf 'Mass spectrometry data format' http://edamontology.org/operation_0519 PCR primer design (for gene transcription profiling) 'PCR primer design (for gene transcription profiling)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0516 Data retrieval (database metadata) 'Data retrieval (database metadata)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1848 Structure formatting 'Structure formatting' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0517 PCR primer design (for large scale sequencing) 'PCR primer design (for large scale sequencing)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1847 DSSP secondary structure assignment 'DSSP secondary structure assignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3701 Sequin format 'Sequin format' SubClassOf 'Sequence feature table format (text)' http://edamontology.org/format_3700 Tabix index file format 'Tabix index file format' SubClassOf 'Data index format' http://edamontology.org/data_2528 Molecular data 'Molecular data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0532 Gene expression profile analysis 'Gene expression profile analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2529 Molecule report 'Molecule report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0533 Gene expression profile pathway mapping 'Gene expression profile pathway mapping' SubClassOf 'Mapping' 'Gene expression profile pathway mapping' SubClassOf 'Gene expression analysis' 'Gene expression profile pathway mapping' SubClassOf 'Pathway or network analysis' http://edamontology.org/operation_0530 SBS data processing 'SBS data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0531 Heat map generation 'Heat map generation' SubClassOf 'Generation' 'Heat map generation' SubClassOf 'Microarray data rendering' http://edamontology.org/data_2524 Protein data 'Protein data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0536 Protein structure assignment (from X-ray crystallographic data) 'Protein structure assignment (from X-ray crystallographic data)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2525 Nucleic acid data 'Nucleic acid data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0537 Protein structure assignment (from NMR data) 'Protein structure assignment (from NMR data)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2526 Text data 'Text data' SubClassOf 'Data' http://edamontology.org/operation_0534 Protein secondary structure assignment (from coordinate data) 'Protein secondary structure assignment (from coordinate data)' SubClassOf 'Protein secondary structure assignment' 'Protein secondary structure assignment (from coordinate data)' SubClassOf 'Protein structure analysis' http://edamontology.org/data_2527 Parameter 'Parameter' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0535 Protein secondary structure assignment (from CD data) 'Protein secondary structure assignment (from CD data)' SubClassOf 'Protein secondary structure assignment' http://edamontology.org/data_2522 Map data 'Map data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2523 Phylogenetic data 'Phylogenetic data' SubClassOf 'Data' http://edamontology.org/format_1990 match 'match' SubClassOf 'Alignment format (text)' 'match' SubClassOf 'Textual format' http://edamontology.org/format_1992 meganon 'meganon' SubClassOf 'mega variant' http://edamontology.org/format_1991 mega 'mega' SubClassOf 'mega variant' http://edamontology.org/format_1998 phylipnon 'phylipnon' SubClassOf 'Phylip format variant' http://edamontology.org/operation_0529 MPSS data processing 'MPSS data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1997 PHYLIP format 'PHYLIP format' SubClassOf 'Phylip format variant' http://edamontology.org/operation_0527 Sequence tag mapping 'Sequence tag mapping' SubClassOf 'Annotation' 'Sequence tag mapping' SubClassOf 'DNA mapping' http://edamontology.org/format_1999 scores format 'scores format' SubClassOf 'Alignment format (text)' 'scores format' SubClassOf 'Textual format' http://edamontology.org/operation_0528 SAGE data processing 'SAGE data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1994 nexus alignment format 'nexus alignment format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1993 msf alignment format 'msf alignment format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1996 pair 'pair' SubClassOf 'Alignment format (text)' http://edamontology.org/format_1995 nexusnon alignment format 'nexusnon alignment format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1328 Protein features report (nucleic acid binding sites) 'Protein features report (nucleic acid binding sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2403 Sequence analysis 'Sequence analysis' SubClassOf 'Analysis' http://edamontology.org/data_1327 Protein features (epitopes) 'Protein features (epitopes)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1326 Protein features report (binding sites) 'Protein features report (binding sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1325 Protein features report (active sites) 'Protein features report (active sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3731 Sample comparison 'Sample comparison' SubClassOf 'Comparison' http://edamontology.org/data_2656 NeuronDB ID 'NeuronDB ID' SubClassOf 'Cell type accession' http://edamontology.org/operation_2407 Annotation processing 'Annotation processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2657 NeuroMorpho ID 'NeuroMorpho ID' SubClassOf 'Cell type accession' http://edamontology.org/operation_2406 Protein structure analysis 'Protein structure analysis' SubClassOf 'Protein analysis' 'Protein structure analysis' SubClassOf 'Structure analysis' http://edamontology.org/data_2658 Compound ID (ChemIDplus) 'Compound ID (ChemIDplus)' SubClassOf 'Compound accession' http://edamontology.org/operation_2405 Protein interaction data processing 'Protein interaction data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1329 MHC Class I epitopes report 'MHC Class I epitopes report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2659 Pathway ID (SMPDB) 'Pathway ID (SMPDB)' SubClassOf 'Pathway or network accession' http://edamontology.org/operation_2404 Sequence motif analysis 'Sequence motif analysis' SubClassOf 'Sequence analysis' http://edamontology.org/data_2652 Drug ID (PharmGKB) 'Drug ID (PharmGKB)' SubClassOf 'PharmGKB ID' 'Drug ID (PharmGKB)' SubClassOf 'Drug accession' http://edamontology.org/data_2653 Drug ID (TTD) 'Drug ID (TTD)' SubClassOf 'Drug accession' http://edamontology.org/data_2654 Target ID (TTD) 'Target ID (TTD)' SubClassOf 'Protein accession' http://edamontology.org/data_2655 Cell type identifier 'Cell type identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_1324 Protein features (post-translation modifications) 'Protein features (post-translation modifications)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3730 Cross-assembly 'Cross-assembly' SubClassOf 'Sequence assembly' http://edamontology.org/data_1323 Protein features report (cleavage sites) 'Protein features report (cleavage sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1322 Protein features report (signal peptides) 'Protein features report (signal peptides)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2650 Pathway ID (PharmGKB) 'Pathway ID (PharmGKB)' SubClassOf 'Pathway or network accession' 'Pathway ID (PharmGKB)' SubClassOf 'PharmGKB ID' http://edamontology.org/data_1321 Protein features (sites) 'Protein features (sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2651 Disease ID (PharmGKB) 'Disease ID (PharmGKB)' SubClassOf 'Disease ID' 'Disease ID (PharmGKB)' SubClassOf 'PharmGKB ID' http://edamontology.org/format_3684 PRIDE XML 'PRIDE XML' SubClassOf 'XML' 'PRIDE XML' SubClassOf 'Experiment annotation format' 'PRIDE XML' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_2352 BioXSD (XML) 'BioXSD (XML)' SubClassOf 'Sequence feature annotation format' 'BioXSD (XML)' SubClassOf 'Sequence record format' 'BioXSD (XML)' SubClassOf 'Alignment format (XML)' 'BioXSD (XML)' SubClassOf 'XML' 'BioXSD (XML)' SubClassOf 'Raw sequence format' http://edamontology.org/format_3683 qcML 'qcML' SubClassOf 'Mass spectrometry data format' 'qcML' SubClassOf 'XML' 'qcML' SubClassOf 'Experiment annotation format' http://edamontology.org/format_3686 COMBINE OMEX 'COMBINE OMEX' SubClassOf 'binary format' 'COMBINE OMEX' SubClassOf 'Biological pathway or network format' 'COMBINE OMEX' SubClassOf 'Experiment annotation format' http://edamontology.org/format_3685 SED-ML 'SED-ML' SubClassOf 'XML' 'SED-ML' SubClassOf 'Experiment annotation format' http://edamontology.org/format_3682 imzML 'imzML' SubClassOf 'Mass spectrometry data format' 'imzML' SubClassOf 'XML' 'imzML' SubClassOf 'binary format' http://edamontology.org/format_2350 Format (by type of data) 'Format (by type of data)' SubClassOf 'Format' http://edamontology.org/format_3681 mzTab 'mzTab' SubClassOf 'Mass spectrometry data format' 'mzTab' SubClassOf 'Textual format' http://edamontology.org/format_3688 SBtab 'SBtab' SubClassOf 'Biological pathway or network format' 'SBtab' SubClassOf 'Textual format' http://edamontology.org/format_3687 ISA-TAB 'ISA-TAB' SubClassOf 'Gene expression report format' 'ISA-TAB' SubClassOf 'Textual format' 'ISA-TAB' SubClassOf 'Experiment annotation format' http://edamontology.org/format_3689 BCML 'BCML' SubClassOf 'XML' 'BCML' SubClassOf 'Biological pathway or network format' http://edamontology.org/data_1339 Sequence database hits alignments list 'Sequence database hits alignments list' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2414 Protein function analysis 'Protein function analysis' SubClassOf 'Protein analysis' http://edamontology.org/operation_3745 Ancestral reconstruction 'Ancestral reconstruction' SubClassOf 'Phylogenetic tree analysis' http://edamontology.org/data_0007 Tool 'Tool' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1338 Sequence database hits scores list 'Sequence database hits scores list' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2413 Sequence profile processing 'Sequence profile processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3744 Multiple sample visualisation 'Multiple sample visualisation' SubClassOf 'Visualisation' http://edamontology.org/data_0006 Data http://edamontology.org/operation_2412 Data index processing 'Data index processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0005 Resource type 'Resource type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2411 Structural profile processing 'Structural profile processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3742 Differential gene expression analysis 'Differential gene expression analysis' SubClassOf 'Comparison' http://edamontology.org/data_2667 MMDB ID 'MMDB ID' SubClassOf 'Structure ID' http://edamontology.org/data_2668 iRefIndex ID 'iRefIndex ID' SubClassOf 'Protein interaction ID' http://edamontology.org/operation_2417 Physicochemical property data processing 'Physicochemical property data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2669 ModelDB ID 'ModelDB ID' SubClassOf 'Biological model accession' http://edamontology.org/operation_2416 Protein secondary structure analysis 'Protein secondary structure analysis' SubClassOf 'Protein analysis' http://edamontology.org/operation_2415 Protein folding analysis 'Protein folding analysis' SubClassOf 'Protein analysis' 'Protein folding analysis' SubClassOf 'Modelling and simulation' http://edamontology.org/data_1331 Protein features (PEST sites) 'Protein features (PEST sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2663 Carbohydrate identifier 'Carbohydrate identifier' SubClassOf 'Compound identifier' http://edamontology.org/data_1330 MHC Class II epitopes report 'MHC Class II epitopes report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2664 GlycomeDB ID 'GlycomeDB ID' SubClassOf 'Carbohydrate accession' http://edamontology.org/data_2665 LipidBank ID 'LipidBank ID' SubClassOf 'Lipid accession' http://edamontology.org/data_2666 CDD ID 'CDD ID' SubClassOf 'Protein domain ID' http://edamontology.org/operation_2410 Gene expression analysis 'Gene expression analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3741 Differential protein expression analysis 'Differential protein expression analysis' SubClassOf 'Differential gene expression analysis' 'Differential protein expression analysis' SubClassOf 'Protein comparison' http://edamontology.org/data_2660 BioNumbers ID 'BioNumbers ID' SubClassOf 'Accession' http://edamontology.org/data_2662 T3DB ID 'T3DB ID' SubClassOf 'Toxin accession' http://edamontology.org/format_2341 NCI-Nature pathway entry format 'NCI-Nature pathway entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2409 Data handling 'Data handling' SubClassOf 'Operation' http://edamontology.org/operation_2408 Sequence feature analysis 'Sequence feature analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1348 HMM emission and transition counts 'HMM emission and transition counts' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1347 Dirichlet distribution 'Dirichlet distribution' SubClassOf 'Mathematical model' http://edamontology.org/data_2678 Ensembl ID ('Dasypus novemcinctus') 'Ensembl ID ('Dasypus novemcinctus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2679 Ensembl ID ('Echinops telfairi') 'Ensembl ID ('Echinops telfairi')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3715 Metabolic labeling 'Metabolic labeling' SubClassOf 'Labeled quantification' http://edamontology.org/data_2674 Ensembl ID ('Cavia porcellus') 'Ensembl ID ('Cavia porcellus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2675 Ensembl ID ('Ciona intestinalis') 'Ensembl ID ('Ciona intestinalis')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1340 Sequence database hits evaluation data 'Sequence database hits evaluation data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2676 Ensembl ID ('Ciona savignyi') 'Ensembl ID ('Ciona savignyi')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2677 Ensembl ID ('Danio rerio') 'Ensembl ID ('Danio rerio')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1346 MEME motifs directive file 'MEME motifs directive file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2670 Pathway ID (DQCS) 'Pathway ID (DQCS)' SubClassOf 'Pathway or network accession' http://edamontology.org/data_1345 MEME background frequencies file 'MEME background frequencies file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2671 Ensembl ID (Homo sapiens) 'Ensembl ID (Homo sapiens)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1344 MEME motif alphabet 'MEME motif alphabet' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2672 Ensembl ID ('Bos taurus') 'Ensembl ID ('Bos taurus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2673 Ensembl ID ('Canis familiaris') 'Ensembl ID ('Canis familiaris')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2376 RDF format 'RDF format' SubClassOf 'Ontology format' 'RDF format' SubClassOf 'Linked data format' http://edamontology.org/data_1359 Prosite protein pattern 'Prosite protein pattern' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1358 Prosite nucleotide pattern 'Prosite nucleotide pattern' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2689 Ensembl ID ('Myotis lucifugus') 'Ensembl ID ('Myotis lucifugus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1353 Sequence motif 'Sequence motif' SubClassOf 'Sequence signature data' http://edamontology.org/data_2685 Ensembl ID ('Loxodonta africana') 'Ensembl ID ('Loxodonta africana')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1352 Regular expression 'Regular expression' SubClassOf 'Data' http://edamontology.org/data_2686 Ensembl ID ('Macaca mulatta') 'Ensembl ID ('Macaca mulatta')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2687 Ensembl ID ('Monodelphis domestica') 'Ensembl ID ('Monodelphis domestica')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2688 Ensembl ID ('Mus musculus') 'Ensembl ID ('Mus musculus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2681 Ensembl ID ('Felis catus') 'Ensembl ID ('Felis catus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2682 Ensembl ID ('Gallus gallus') 'Ensembl ID ('Gallus gallus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1355 Protein signature 'Protein signature' SubClassOf 'Sequence signature report' http://edamontology.org/data_2683 Ensembl ID ('Gasterosteus aculeatus') 'Ensembl ID ('Gasterosteus aculeatus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1354 Sequence profile 'Sequence profile' SubClassOf 'Sequence signature data' http://edamontology.org/data_2684 Ensembl ID ('Homo sapiens') 'Ensembl ID ('Homo sapiens')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2680 Ensembl ID ('Erinaceus europaeus') 'Ensembl ID ('Erinaceus europaeus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3696 PS 'PS' SubClassOf 'Textual format' http://edamontology.org/format_3691 BEL 'BEL' SubClassOf 'Textual format' http://edamontology.org/format_3690 BDML 'BDML' SubClassOf 'XML' http://edamontology.org/format_3693 AGP 'AGP' SubClassOf 'Textual format' 'AGP' SubClassOf 'Sequence assembly format' http://edamontology.org/format_3692 SBGN-ML 'SBGN-ML' SubClassOf 'XML' 'SBGN-ML' SubClassOf 'Biological pathway or network format' http://edamontology.org/format_3699 VDB 'VDB' SubClassOf 'binary format' http://edamontology.org/format_3698 SRA format 'SRA format' SubClassOf 'binary format' http://edamontology.org/operation_2447 Sequence processing (protein) 'Sequence processing (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3778 Text annotation 'Text annotation' SubClassOf 'Annotation' 'Text annotation' SubClassOf 'Analysis' http://edamontology.org/operation_2446 Sequence processing 'Sequence processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2445 Protein interaction network processing 'Protein interaction network processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2444 Protein secondary structure processing 'Protein secondary structure processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2448 Sequence processing (nucleic acid) 'Sequence processing (nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1364 Hidden Markov model 'Hidden Markov model' SubClassOf 'Sequence profile' 'Hidden Markov model' SubClassOf 'Mathematical model' http://edamontology.org/data_2696 Ensembl ID ('Spermophilus tridecemlineatus') 'Ensembl ID ('Spermophilus tridecemlineatus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1363 Information content matrix 'Information content matrix' SubClassOf 'Position-specific scoring matrix' http://edamontology.org/data_2697 Ensembl ID ('Takifugu rubripes') 'Ensembl ID ('Takifugu rubripes')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1362 Position weight matrix 'Position weight matrix' SubClassOf 'Position-specific scoring matrix' http://edamontology.org/data_2698 Ensembl ID ('Tupaia belangeri') 'Ensembl ID ('Tupaia belangeri')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1361 Position frequency matrix 'Position frequency matrix' SubClassOf 'Position-specific scoring matrix' http://edamontology.org/data_2699 Ensembl ID ('Xenopus tropicalis') 'Ensembl ID ('Xenopus tropicalis')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1368 Domainatrix signature 'Domainatrix signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2692 Ensembl ID ('Oryzias latipes') 'Ensembl ID ('Oryzias latipes')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2443 Phylogenetic tree processing 'Phylogenetic tree processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2693 Ensembl ID ('Otolemur garnettii') 'Ensembl ID ('Otolemur garnettii')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2442 DNA structure prediction 'DNA structure prediction' SubClassOf 'Nucleic acid structure prediction' http://edamontology.org/data_2694 Ensembl ID ('Pan troglodytes') 'Ensembl ID ('Pan troglodytes')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2441 RNA structure prediction 'RNA structure prediction' SubClassOf 'Nucleic acid structure prediction' http://edamontology.org/data_1365 Fingerprint 'Fingerprint' SubClassOf 'Position-specific scoring matrix' http://edamontology.org/data_2695 Ensembl ID ('Rattus norvegicus') 'Ensembl ID ('Rattus norvegicus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2440 Structure processing (RNA) 'Structure processing (RNA)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2690 Ensembl ID ("Ornithorhynchus anatinus") 'Ensembl ID ("Ornithorhynchus anatinus")' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2311 EMBL-HTML 'EMBL-HTML' SubClassOf 'HTML' 'EMBL-HTML' SubClassOf 'EMBL-like format' http://edamontology.org/data_2691 Ensembl ID ('Oryctolagus cuniculus') 'Ensembl ID ('Oryctolagus cuniculus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2310 FASTA-HTML 'FASTA-HTML' SubClassOf 'FASTA-like' 'FASTA-HTML' SubClassOf 'HTML' http://edamontology.org/operation_2457 GPCR coupling selectivity prediction 'GPCR coupling selectivity prediction' SubClassOf 'Protein property calculation (from sequence)' 'GPCR coupling selectivity prediction' SubClassOf 'Protein interaction prediction' 'GPCR coupling selectivity prediction' SubClassOf 'GPCR analysis' http://edamontology.org/operation_2456 GPCR classification 'GPCR classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2459 Structure processing (protein) 'Structure processing (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1375 Protein repeat signature 'Protein repeat signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1374 Protein region signature 'Protein region signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1373 Protein domain signature 'Protein domain signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1372 Protein family signature 'Protein family signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1379 Protein binding site signature 'Protein binding site signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2454 Gene prediction 'Gene prediction' SubClassOf 'Nucleic acid sequence feature detection' http://edamontology.org/data_1378 Protein active site signature 'Protein active site signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2453 Feature table processing 'Feature table processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1377 Protein conserved site signature 'Protein conserved site signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2452 Sequence cluster processing 'Sequence cluster processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1376 Protein site signature 'Protein site signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2451 Sequence comparison 'Sequence comparison' SubClassOf 'Sequence analysis' 'Sequence comparison' SubClassOf 'Comparison' http://edamontology.org/data_1371 HMMER NULL hidden Markov model 'HMMER NULL hidden Markov model' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2306 GTF 'GTF' SubClassOf 'GFF' http://edamontology.org/format_2304 STRING entry format (XML) 'STRING entry format (XML)' SubClassOf 'XML' 'STRING entry format (XML)' SubClassOf 'Protein interaction format' http://edamontology.org/format_2303 STRING entry format (HTML) 'STRING entry format (HTML)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2425 Optimisation and refinement 'Optimisation and refinement' SubClassOf 'Operation' http://edamontology.org/operation_2424 Comparison 'Comparison' SubClassOf 'Operation' http://edamontology.org/operation_3755 PTM localisation 'PTM localisation' SubClassOf 'PTM identification' http://edamontology.org/operation_2423 Prediction and recognition 'Prediction and recognition' SubClassOf 'Operation' http://edamontology.org/operation_2422 Data retrieval 'Data retrieval' SubClassOf 'Query and retrieval' http://edamontology.org/operation_2429 Mapping 'Mapping' SubClassOf 'Operation' http://edamontology.org/operation_2428 Validation 'Validation' SubClassOf 'Operation' http://edamontology.org/operation_2427 Data handling 'Data handling' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1386 Sequence alignment (nucleic acid pair) 'Sequence alignment (nucleic acid pair)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1385 Sequence alignment (hybrid) 'Sequence alignment (hybrid)' SubClassOf 'Sequence alignment' http://edamontology.org/data_1384 Sequence alignment (protein) 'Sequence alignment (protein)' SubClassOf 'Sequence alignment' 'Sequence alignment (protein)' SubClassOf 'Protein alignment' http://edamontology.org/data_1383 Sequence alignment (nucleic acid) 'Sequence alignment (nucleic acid)' SubClassOf 'Sequence alignment' http://edamontology.org/operation_2421 Database search 'Database search' SubClassOf 'Query and retrieval' http://edamontology.org/data_1389 Multiple nucleotide sequence alignment 'Multiple nucleotide sequence alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2420 Operation (typed) 'Operation (typed)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1388 Hybrid sequence alignment (pair) 'Hybrid sequence alignment (pair)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1387 Sequence alignment (protein pair) 'Sequence alignment (protein pair)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1382 Sequence alignment (multiple) 'Sequence alignment (multiple)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1381 Sequence alignment (pair) 'Sequence alignment (pair)' SubClassOf 'Sequence alignment' http://edamontology.org/data_1380 Protein post-translational modification signature 'Protein post-translational modification signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2419 Primer and probe design 'Primer and probe design' SubClassOf 'Nucleic acid design' 'Primer and probe design' SubClassOf 'Prediction and recognition (nucleic acid)' http://edamontology.org/format_2334 URI format 'URI format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3665 K-mer countgraph 'K-mer countgraph' SubClassOf 'Graph format' 'K-mer countgraph' SubClassOf 'binary format' http://edamontology.org/operation_2436 Gene-set enrichment analysis 'Gene-set enrichment analysis' SubClassOf 'Gene set testing' 'Gene-set enrichment analysis' SubClassOf 'Over-representation analysis' http://edamontology.org/operation_3767 Protein identification 'Protein identification' SubClassOf 'Protein analysis' 'Protein identification' SubClassOf 'Spectral analysis' http://edamontology.org/operation_2435 Gene expression profile processing 'Gene expression profile processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3766 Weighted correlation network analysis 'Weighted correlation network analysis' SubClassOf 'Pathway or network analysis' http://edamontology.org/operation_2434 Data retrieval (codon usage table) 'Data retrieval (codon usage table)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2433 Codon usage table processing 'Codon usage table processing' SubClassOf 'Codon usage analysis' http://edamontology.org/operation_2439 RNA secondary structure analysis 'RNA secondary structure analysis' SubClassOf 'Nucleic acid structure analysis' http://edamontology.org/operation_2438 Pathway or network processing 'Pathway or network processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2437 Gene regulatory network prediction 'Gene regulatory network prediction' SubClassOf 'Pathway or network prediction' 'Gene regulatory network prediction' SubClassOf 'Prediction and recognition (nucleic acid)' http://edamontology.org/data_1397 Gap opening penalty 'Gap opening penalty' SubClassOf 'Gap penalty' http://edamontology.org/data_1396 Aligned sequence order 'Aligned sequence order' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1395 Score end gaps control 'Score end gaps control' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1394 Alignment score or penalty 'Alignment score or penalty' SubClassOf 'Score' http://edamontology.org/operation_2432 Microarray data processing 'Microarray data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3763 Service invocation 'Service invocation' SubClassOf 'Service management' http://edamontology.org/operation_3762 Service composition 'Service composition' SubClassOf 'Service management' http://edamontology.org/data_1399 Gap separation penalty 'Gap separation penalty' SubClassOf 'Gap penalty' http://edamontology.org/operation_2430 Design 'Design' SubClassOf 'Operation' http://edamontology.org/operation_3761 Service discovery 'Service discovery' SubClassOf 'Service management' http://edamontology.org/data_1398 Gap extension penalty 'Gap extension penalty' SubClassOf 'Gap penalty' http://edamontology.org/operation_3760 Service management 'Service management' SubClassOf 'Operation' http://edamontology.org/format_3651 MGF 'MGF' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_3650 netCDF 'netCDF' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_2322 BioCyc enzyme report format 'BioCyc enzyme report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3653 pkl 'pkl' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_3652 dta 'dta' SubClassOf 'Mass spectrometry data format' http://edamontology.org/data_1390 Multiple protein sequence alignment 'Multiple protein sequence alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2328 PseudoCAP gene report format 'PseudoCAP gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2329 GeneCards gene report format 'GeneCards gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3655 pepXML 'pepXML' SubClassOf 'Mass spectrometry data format' 'pepXML' SubClassOf 'XML' http://edamontology.org/format_2323 ENZYME enzyme report format 'ENZYME enzyme report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3654 mzXML 'mzXML' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_3657 GPML 'GPML' SubClassOf 'XML' 'GPML' SubClassOf 'Biological pathway or network format' http://edamontology.org/operation_2489 Protein subcellular localisation prediction 'Protein subcellular localisation prediction' SubClassOf 'Protein function prediction' http://edamontology.org/operation_2488 Protein secondary structure comparison 'Protein secondary structure comparison' SubClassOf 'Secondary structure comparison' 'Protein secondary structure comparison' SubClassOf 'Protein secondary structure analysis' 'Protein secondary structure comparison' SubClassOf 'Protein comparison' http://edamontology.org/data_3107 Sequence feature name 'Sequence feature name' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3108 Experimental measurement 'Experimental measurement' SubClassOf 'Data' http://edamontology.org/data_3103 ATC code 'ATC code' SubClassOf 'Drug accession' http://edamontology.org/operation_2483 Structure comparison 'Structure comparison' SubClassOf 'Comparison' 'Structure comparison' SubClassOf 'Structure analysis' http://edamontology.org/data_3104 UNII 'UNII' SubClassOf 'Compound identifier' http://edamontology.org/operation_2482 Secondary structure processing 'Secondary structure processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3105 Geotemporal metadata 'Geotemporal metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2481 Nucleic acid structure analysis 'Nucleic acid structure analysis' SubClassOf 'Structure analysis' 'Nucleic acid structure analysis' SubClassOf 'Nucleic acid analysis' http://edamontology.org/data_3106 System metadata 'System metadata' SubClassOf 'Resource metadata' http://edamontology.org/operation_2480 Structure analysis 'Structure analysis' SubClassOf 'Analysis' http://edamontology.org/operation_2487 Protein structure comparison 'Protein structure comparison' SubClassOf 'Protein analysis' 'Protein structure comparison' SubClassOf 'Protein comparison' 'Protein structure comparison' SubClassOf 'Structure comparison' http://edamontology.org/operation_2486 Topology diagram drawing 'Topology diagram drawing' SubClassOf 'Structure visualisation' http://edamontology.org/data_3101 Protein domain classification node 'Protein domain classification node' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2485 Helical wheel drawing 'Helical wheel drawing' SubClassOf 'Structure visualisation' http://edamontology.org/data_3102 CAS number 'CAS number' SubClassOf 'Drug accession' http://edamontology.org/operation_2499 Splicing model analysis 'Splicing model analysis' SubClassOf 'Prediction and recognition (nucleic acid)' 'Splicing model analysis' SubClassOf 'Modelling and simulation' 'Splicing model analysis' SubClassOf 'Nucleic acid sequence comparison' http://edamontology.org/data_3118 Protein features report (topological domains) 'Protein features report (topological domains)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3119 Sequence features (compositionally-biased regions) 'Sequence features (compositionally-biased regions)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3115 Microarray metadata 'Microarray metadata' SubClassOf 'Gene expression data' http://edamontology.org/operation_2493 Codon usage data processing 'Codon usage data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3116 Microarray protocol annotation 'Microarray protocol annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2492 Protein interaction prediction 'Protein interaction prediction' SubClassOf 'Protein analysis' 'Protein interaction prediction' SubClassOf 'Prediction and recognition (protein)' http://edamontology.org/data_3117 Microarray hybridisation data 'Microarray hybridisation data' SubClassOf 'Gene expression data' http://edamontology.org/operation_2491 Hydrogen bond calculation (inter-residue) 'Hydrogen bond calculation (inter-residue)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3110 Raw microarray data 'Raw microarray data' SubClassOf 'Microarray hybridisation data' 'Raw microarray data' SubClassOf 'Experimental measurement' http://edamontology.org/operation_2498 Sequencing-based expression profile data analysis 'Sequencing-based expression profile data analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3111 Processed microarray data 'Processed microarray data' SubClassOf 'Microarray hybridisation data' http://edamontology.org/operation_2497 Pathway or network analysis 'Pathway or network analysis' SubClassOf 'Analysis' http://edamontology.org/data_3112 Gene expression matrix 'Gene expression matrix' SubClassOf 'Gene expression data' 'Gene expression matrix' SubClassOf 'Matrix' http://edamontology.org/operation_2496 Gene regulatory network processing 'Gene regulatory network processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3113 Sample annotation 'Sample annotation' SubClassOf 'Resource metadata' http://edamontology.org/operation_2495 Gene expression analysis 'Gene expression analysis' SubClassOf 'Analysis' http://edamontology.org/operation_2490 Residue contact calculation (residue-residue) 'Residue contact calculation (residue-residue)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2469 Data retrieval (protein interaction annotation) 'Data retrieval (protein interaction annotation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2468 Data retrieval (phylogenetic tree) 'Data retrieval (phylogenetic tree)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2467 Data retrieval (protein annotation) 'Data retrieval (protein annotation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2466 Map annotation 'Map annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3129 Protein features report (repeats) 'Protein features report (repeats)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_1770 Structure comparison 'Structure comparison' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3125 Nucleic acid features report (binding) 'Nucleic acid features report (binding)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2461 Protein residue surface calculation 'Protein residue surface calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3126 Nucleic acid repeats (report) 'Nucleic acid repeats (report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2460 Protein atom surface calculation 'Protein atom surface calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3127 Nucleic acid features report (replication and recombination) 'Nucleic acid features report (replication and recombination)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3128 Nucleic acid structure report 'Nucleic acid structure report' SubClassOf 'Nucleic acid report' 'Nucleic acid structure report' SubClassOf 'Structure report' http://edamontology.org/operation_2465 Structure processing 'Structure processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3122 Nucleic acid features (difference and change) 'Nucleic acid features (difference and change)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2464 Protein-protein interaction prediction 'Protein-protein interaction prediction' SubClassOf 'Protein function prediction' 'Protein-protein interaction prediction' SubClassOf 'Protein interaction prediction' http://edamontology.org/data_3123 Nucleic acid features report (expression signal) 'Nucleic acid features report (expression signal)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2463 Sequence alignment processing 'Sequence alignment processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2462 Protein surface calculation 'Protein surface calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_1775 Function analysis 'Function analysis' SubClassOf 'Computational biology' http://edamontology.org/operation_2479 Protein sequence analysis 'Protein sequence analysis' SubClassOf 'Sequence analysis' 'Protein sequence analysis' SubClassOf 'Protein analysis' http://edamontology.org/operation_2478 Nucleic acid sequence analysis 'Nucleic acid sequence analysis' SubClassOf 'Nucleic acid analysis' 'Nucleic acid sequence analysis' SubClassOf 'Sequence analysis' http://edamontology.org/operation_2472 Data retrieval (gene annotation) 'Data retrieval (gene annotation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3137 Non-coding RNA 'Non-coding RNA' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2471 Data retrieval (RNA family annotation) 'Data retrieval (RNA family annotation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3138 Transcriptional features (report) 'Transcriptional features (report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2470 Data retrieval (protein family annotation) 'Data retrieval (protein family annotation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3139 Nucleic acid features report (STS) 'Nucleic acid features report (STS)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3132 Nucleic acid features (d-loop) 'Nucleic acid features (d-loop)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2476 Molecular dynamics simulation 'Molecular dynamics simulation' SubClassOf 'Prediction and recognition' 'Molecular dynamics simulation' SubClassOf 'Modelling and simulation' 'Molecular dynamics simulation' SubClassOf 'Structure analysis' http://edamontology.org/data_3133 Nucleic acid features (stem loop) 'Nucleic acid features (stem loop)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2475 Protein architecture recognition 'Protein architecture recognition' SubClassOf 'Protein architecture analysis' 'Protein architecture recognition' SubClassOf 'Prediction and recognition (protein)' 'Protein architecture recognition' SubClassOf 'Structure classification' http://edamontology.org/data_3134 Gene transcript report 'Gene transcript report' SubClassOf 'Gene report' http://edamontology.org/operation_2474 Protein architecture comparison 'Protein architecture comparison' SubClassOf 'Protein architecture analysis' 'Protein architecture comparison' SubClassOf 'Protein secondary structure comparison' http://edamontology.org/data_3135 Nucleic acid features report (signal or transit peptide) 'Nucleic acid features report (signal or transit peptide)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2473 Data retrieval (genotype and phenotype annotation) 'Data retrieval (genotype and phenotype annotation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3130 Sequence motif matches (protein) 'Sequence motif matches (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3131 Sequence motif matches (nucleic acid) 'Sequence motif matches (nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3147 Mass spectrometry experiment 'Mass spectrometry experiment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3148 Gene family report 'Gene family report' SubClassOf 'Nucleic acid report' http://edamontology.org/data_3143 SCOP superfamily 'SCOP superfamily' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3144 SCOP family 'SCOP family' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3145 SCOP protein 'SCOP protein' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3146 SCOP species 'SCOP species' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3140 Nucleic acid features (immunoglobulin gene structure) 'Nucleic acid features (immunoglobulin gene structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3141 SCOP class 'SCOP class' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3142 SCOP fold 'SCOP fold' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3154 Protein alignment 'Protein alignment' SubClassOf 'Alignment' http://edamontology.org/data_3153 Protein image 'Protein image' SubClassOf 'Image' http://edamontology.org/topic_3500 Animals 'Animals' SubClassOf 'Eukaryotes' http://edamontology.org/topic_3510 Protein sites, features and motifs 'Protein sites, features and motifs' SubClassOf 'Sequence sites, features and motifs' 'Protein sites, features and motifs' SubClassOf 'Proteins' http://edamontology.org/data_3165 NGS experiment 'NGS experiment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3519 PCR experiment 'PCR experiment' SubClassOf 'Laboratory techniques' http://edamontology.org/topic_3514 Protein-ligand interactions 'Protein-ligand interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3512 Gene transcripts 'Gene transcripts' SubClassOf 'Gene structure' 'Gene transcripts' SubClassOf 'RNA' http://edamontology.org/topic_3511 Nucleic acid sites, features and motifs 'Nucleic acid sites, features and motifs' SubClassOf 'Nucleic acids' 'Nucleic acid sites, features and motifs' SubClassOf 'Sequence sites, features and motifs' http://edamontology.org/topic_3518 Microarray experiment 'Microarray experiment' SubClassOf 'Laboratory techniques' http://edamontology.org/topic_3517 GWAS study 'GWAS study' SubClassOf 'Experimental design and studies' http://edamontology.org/topic_3516 Genotyping experiment 'Genotyping experiment' SubClassOf 'Laboratory techniques' http://edamontology.org/topic_3515 Protein-drug interactions 'Protein-drug interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0903 Protein folding report 'Protein folding report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3521 2D PAGE experiment '2D PAGE experiment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0902 Protein architecture report 'Protein architecture report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3520 Proteomics experiment 'Proteomics experiment' SubClassOf 'Laboratory techniques' http://edamontology.org/data_0901 Protein features report (domains) 'Protein features report (domains)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0900 Protein domain classification 'Protein domain classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3525 Protein-nucleic acid interactions 'Protein-nucleic acid interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3524 Simulation experiment 'Simulation experiment' SubClassOf 'Laboratory techniques' http://edamontology.org/topic_3523 RNAi experiment 'RNAi experiment' SubClassOf 'Laboratory techniques' http://edamontology.org/topic_3522 Northern blot experiment 'Northern blot experiment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3529 Environmental information processing pathways 'Environmental information processing pathways' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3528 Disease pathways 'Disease pathways' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3527 Cellular process pathways 'Cellular process pathways' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3526 Protein-protein interactions 'Protein-protein interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3411 Gynaecology and obstetrics 'Gynaecology and obstetrics' SubClassOf 'Medicine' http://edamontology.org/topic_3410 Gender medicine 'Gender medicine' SubClassOf 'Medicine' http://edamontology.org/topic_3415 Medical toxicology 'Medical toxicology' SubClassOf 'Medicine' http://edamontology.org/topic_3414 Trauma medicine 'Trauma medicine' SubClassOf 'Medicine' http://edamontology.org/topic_3413 Infectious tropical disease 'Infectious tropical disease' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3412 Hepatic and biliary medicine 'Hepatic and biliary medicine' SubClassOf 'Medicine' http://edamontology.org/topic_3419 Psychiatry 'Psychiatry' SubClassOf 'Medicine' http://edamontology.org/topic_3418 Paediatrics 'Paediatrics' SubClassOf 'Medicine' http://edamontology.org/topic_3417 Opthalmology 'Opthalmology' SubClassOf 'Medicine' http://edamontology.org/topic_3416 Musculoskeletal medicine 'Musculoskeletal medicine' SubClassOf 'Medicine' http://edamontology.org/topic_3422 Urology and nephrology 'Urology and nephrology' SubClassOf 'Medicine' http://edamontology.org/topic_3421 Surgery 'Surgery' SubClassOf 'Medicine' http://edamontology.org/topic_3420 Reproductive health 'Reproductive health' SubClassOf 'Medicine' http://edamontology.org/format_1810 ColiCard report format 'ColiCard report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3423 Complementary medicine 'Complementary medicine' SubClassOf 'Medicine' http://edamontology.org/data_3085 Protein sequence composition 'Protein sequence composition' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3086 Nucleic acid sequence composition (report) 'Nucleic acid sequence composition (report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3444 MRI 'MRI' SubClassOf 'Imaging' http://edamontology.org/topic_3448 Neutron diffraction 'Neutron diffraction' SubClassOf 'Structural biology' 'Neutron diffraction' SubClassOf 'Imaging' http://edamontology.org/data_0832 HGNC vocabulary 'HGNC vocabulary' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0831 MeSH vocabulary 'MeSH vocabulary' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0835 UMLS vocabulary 'UMLS vocabulary' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3452 Tomography 'Tomography' SubClassOf 'Imaging' http://edamontology.org/data_0844 Molecular mass 'Molecular mass' SubClassOf 'Molecular property (general)' http://edamontology.org/data_0843 Database entry 'Database entry' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0842 Identifier 'Identifier' SubClassOf 'Data' http://edamontology.org/data_0848 Raw sequence 'Raw sequence' SubClassOf 'Sequence' http://edamontology.org/data_0847 QSAR descriptor 'QSAR descriptor' SubClassOf 'Molecular property (general)' http://edamontology.org/data_0846 Chemical formula 'Chemical formula' SubClassOf 'Molecular property (general)' http://edamontology.org/data_0845 Molecular charge 'Molecular charge' SubClassOf 'Molecular property (general)' http://edamontology.org/operation_1914 Structure retrieval (water) 'Structure retrieval (water)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1913 Residue validation 'Residue validation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0855 Sequence metadata 'Sequence metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1808 GeneIlluminator gene report format 'GeneIlluminator gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3473 Data mining 'Data mining' SubClassOf 'Computer science' http://edamontology.org/data_0854 Sequence length specification 'Sequence length specification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0853 DNA sense specification 'DNA sense specification' SubClassOf 'Sequence attribute' http://edamontology.org/data_0852 Sequence mask type 'Sequence mask type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1809 BacMap gene card format 'BacMap gene card format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0859 Sequence signature model 'Sequence signature model' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0858 Sequence signature matches 'Sequence signature matches' SubClassOf 'Sequence signature data' http://edamontology.org/data_0857 Sequence search results 'Sequence search results' SubClassOf 'Database search results' http://edamontology.org/data_0856 Sequence feature source 'Sequence feature source' SubClassOf 'Sequence features metadata' http://edamontology.org/topic_3474 Machine learning 'Machine learning' SubClassOf 'Computer science' http://edamontology.org/data_0851 Sequence mask character 'Sequence mask character' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0850 Sequence set 'Sequence set' SubClassOf 'Data' http://edamontology.org/data_0849 Sequence record 'Sequence record' SubClassOf 'Sequence' http://edamontology.org/data_0866 Sequence alignment metadata 'Sequence alignment metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0865 Sequence similarity score 'Sequence similarity score' SubClassOf 'Score' http://edamontology.org/data_0864 Sequence alignment parameter 'Sequence alignment parameter' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0863 Sequence alignment 'Sequence alignment' SubClassOf 'Alignment' http://edamontology.org/data_0869 Sequence-profile alignment 'Sequence-profile alignment' SubClassOf 'Alignment' http://edamontology.org/data_0868 Profile-profile alignment 'Profile-profile alignment' SubClassOf 'Alignment' http://edamontology.org/data_0867 Sequence alignment report 'Sequence alignment report' SubClassOf 'Report' http://edamontology.org/data_0862 Dotplot 'Dotplot' SubClassOf 'Sequence alignment report' http://edamontology.org/data_0861 Sequence alignment (words) 'Sequence alignment (words)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0860 Sequence signature data 'Sequence signature data' SubClassOf 'Data' http://edamontology.org/topic_3489 Database management 'Database management' SubClassOf 'Data management' http://edamontology.org/data_0877 Protein features report (super-secondary) 'Protein features report (super-secondary)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0876 Protein features report (secondary structure) 'Protein features report (secondary structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0875 Protein topology 'Protein topology' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0874 Comparison matrix 'Comparison matrix' SubClassOf 'Matrix' http://edamontology.org/format_3608 qualsolexa 'qualsolexa' SubClassOf 'qual' 'qualsolexa' SubClassOf 'FASTQ-solexa' http://edamontology.org/format_3607 qual 'qual' SubClassOf 'Sequence quality report format (text)' 'qual' SubClassOf 'FASTQ-like format (text)' http://edamontology.org/data_0879 Secondary structure alignment metadata (protein) 'Secondary structure alignment metadata (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0878 Secondary structure alignment (protein) 'Secondary structure alignment (protein)' SubClassOf 'Protein alignment' 'Secondary structure alignment (protein)' SubClassOf 'Secondary structure alignment' http://edamontology.org/format_3609 qualillumina 'qualillumina' SubClassOf 'FASTQ-illumina' 'qualillumina' SubClassOf 'qual' http://edamontology.org/data_0872 Phylogenetic tree 'Phylogenetic tree' SubClassOf 'Phylogenetic data' http://edamontology.org/data_0871 Phylogenetic character data 'Phylogenetic character data' SubClassOf 'Phylogenetic data' http://edamontology.org/data_0870 Sequence distance matrix 'Sequence distance matrix' SubClassOf 'Distance matrix' http://edamontology.org/format_3604 SVG 'SVG' SubClassOf 'Image format' 'SVG' SubClassOf 'XML' http://edamontology.org/format_3603 PNG 'PNG' SubClassOf 'binary format' 'PNG' SubClassOf 'Image format' http://edamontology.org/format_3606 Sequence quality report format (text) 'Sequence quality report format (text)' SubClassOf 'Format (by type of data)' 'Sequence quality report format (text)' SubClassOf 'Textual format' http://edamontology.org/format_3605 rast 'rast' SubClassOf 'binary format' 'rast' SubClassOf 'Image format' http://edamontology.org/format_3600 rgb 'rgb' SubClassOf 'binary format' 'rgb' SubClassOf 'Image format' http://edamontology.org/format_3602 pgm 'pgm' SubClassOf 'Image format' 'pgm' SubClassOf 'binary format' http://edamontology.org/format_3601 pbm 'pbm' SubClassOf 'Image format' 'pbm' SubClassOf 'binary format' http://edamontology.org/data_0888 Structure similarity score 'Structure similarity score' SubClassOf 'Score' http://edamontology.org/data_0887 Structure alignment report 'Structure alignment report' SubClassOf 'Report' http://edamontology.org/data_0886 Structure alignment 'Structure alignment' SubClassOf 'Alignment' http://edamontology.org/data_0885 Structure database search results 'Structure database search results' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0889 Structural profile 'Structural profile' SubClassOf 'Data' http://edamontology.org/data_0880 RNA secondary structure 'RNA secondary structure' SubClassOf 'RNA structure' http://edamontology.org/data_0884 Tertiary structure record 'Tertiary structure record' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0883 Structure 'Structure' SubClassOf 'Data' http://edamontology.org/data_0882 Secondary structure alignment metadata (RNA) 'Secondary structure alignment metadata (RNA)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0881 Secondary structure alignment (RNA) 'Secondary structure alignment (RNA)' SubClassOf 'Secondary structure alignment' http://edamontology.org/data_0899 Protein structural motifs and surfaces 'Protein structural motifs and surfaces' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0897 Protein property 'Protein property' SubClassOf 'Molecular property' http://edamontology.org/data_0896 Protein report 'Protein report' SubClassOf 'Report' http://edamontology.org/data_0891 Sequence-3D profile alignment 'Sequence-3D profile alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0890 Structural (3D) profile alignment 'Structural (3D) profile alignment' SubClassOf 'Alignment' http://edamontology.org/data_0895 Peptide annotation 'Peptide annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0894 Amino acid annotation 'Amino acid annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0893 Sequence-structure alignment 'Sequence-structure alignment' SubClassOf 'Alignment' http://edamontology.org/data_0892 Protein sequence-structure scoring matrix 'Protein sequence-structure scoring matrix' SubClassOf 'Matrix' http://edamontology.org/format_3620 xlsx 'xlsx' SubClassOf 'binary format' 'xlsx' SubClassOf 'Document format' http://edamontology.org/format_3626 MAT 'MAT' SubClassOf 'Matrix format' http://edamontology.org/format_3622 Gemini SQLite format 'Gemini SQLite format' SubClassOf 'Sequence variation annotation format' 'Gemini SQLite format' SubClassOf 'SQLite format' http://edamontology.org/format_3621 SQLite format 'SQLite format' SubClassOf 'binary format' http://edamontology.org/format_3624 snpeffdb 'snpeffdb' SubClassOf 'Index format' http://edamontology.org/format_3623 Index format 'Index format' SubClassOf 'Format (by type of data)' 'Index format' SubClassOf 'binary format' http://edamontology.org/data_2605 Compound ID (KEGG) 'Compound ID (KEGG)' SubClassOf 'KEGG object identifier' 'Compound ID (KEGG)' SubClassOf 'Compound accession' http://edamontology.org/data_2606 RFAM name 'RFAM name' SubClassOf 'RNA family identifier' 'RFAM name' SubClassOf 'Name' http://edamontology.org/data_2608 Reaction ID (KEGG) 'Reaction ID (KEGG)' SubClassOf 'KEGG object identifier' 'Reaction ID (KEGG)' SubClassOf 'Reaction ID' http://edamontology.org/data_2601 Small molecule data 'Small molecule data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3619 sif 'sif' SubClassOf 'Biological pathway or network format' http://edamontology.org/data_2602 Genotype and phenotype data 'Genotype and phenotype data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3618 xgmml 'xgmml' SubClassOf 'Graph format' http://edamontology.org/data_2600 Pathway or network 'Pathway or network' SubClassOf 'Data' http://edamontology.org/format_3615 bgzip 'bgzip' SubClassOf 'Image format' 'bgzip' SubClassOf 'binary format' http://edamontology.org/format_3614 ENCODE broad peak format 'ENCODE broad peak format ' SubClassOf 'ENCODE peak format' http://edamontology.org/format_3617 Graph format 'Graph format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_3616 tabix 'tabix' SubClassOf 'Image format' 'tabix' SubClassOf 'binary format' http://edamontology.org/format_3611 qual454 'qual454' SubClassOf 'qual' http://edamontology.org/format_3610 qualsolid 'qualsolid' SubClassOf 'qual' http://edamontology.org/format_3613 ENCODE narrow peak format 'ENCODE narrow peak format' SubClassOf 'ENCODE peak format' http://edamontology.org/format_3612 ENCODE peak format 'ENCODE peak format' SubClassOf 'bed6' http://edamontology.org/data_2616 DIP ID 'DIP ID' SubClassOf 'Protein interaction ID' http://edamontology.org/data_2617 Signaling Gateway protein ID 'Signaling Gateway protein ID' SubClassOf 'Protein accession' http://edamontology.org/data_2618 Protein modification ID 'Protein modification ID' SubClassOf 'Accession' 'Protein modification ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2619 RESID ID 'RESID ID' SubClassOf 'Protein modification ID' http://edamontology.org/data_2612 Sequence cluster ID (CluSTr) 'Sequence cluster ID (CluSTr)' SubClassOf 'Sequence cluster ID' http://edamontology.org/data_2613 KEGG Glycan ID 'KEGG Glycan ID' SubClassOf 'KEGG object identifier' 'KEGG Glycan ID' SubClassOf 'Carbohydrate accession' http://edamontology.org/data_2614 TCDB ID 'TCDB ID' SubClassOf 'Protein family accession' http://edamontology.org/data_2615 MINT ID 'MINT ID' SubClassOf 'Protein interaction ID' http://edamontology.org/data_2610 Ensembl ID 'Ensembl ID' SubClassOf 'Accession' 'Ensembl ID' SubClassOf 'Identifier (hybrid)' http://edamontology.org/data_2611 ICD identifier 'ICD identifier' SubClassOf 'Disease ID' http://edamontology.org/data_2609 Drug ID (KEGG) 'Drug ID (KEGG)' SubClassOf 'KEGG object identifier' 'Drug ID (KEGG)' SubClassOf 'Drug accession' http://edamontology.org/format_1861 PlasMapper TextMap 'PlasMapper TextMap' SubClassOf 'Textual format' 'PlasMapper TextMap' SubClassOf 'Map format' http://edamontology.org/data_2627 Molecular interaction ID 'Molecular interaction ID' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2628 BioGRID interaction ID 'BioGRID interaction ID' SubClassOf 'Protein interaction ID' http://edamontology.org/data_2629 Enzyme ID (MEROPS) 'Enzyme ID (MEROPS)' SubClassOf 'Enzyme ID' http://edamontology.org/operation_3705 Isotope-coded protein label 'Isotope-coded protein label' SubClassOf 'Labeled quantification' http://edamontology.org/operation_3704 Ion counting 'Ion counting' SubClassOf 'Label-free quantification' http://edamontology.org/data_2625 LIPID MAPS ID 'LIPID MAPS ID' SubClassOf 'Lipid accession' http://edamontology.org/operation_3703 Reference identification 'Reference identification' SubClassOf 'Genetic variation analysis' http://edamontology.org/data_2626 PeptideAtlas ID 'PeptideAtlas ID' SubClassOf 'Peptide ID' http://edamontology.org/data_2620 RGD ID 'RGD ID' SubClassOf 'Identifier (hybrid)' 'RGD ID' SubClassOf 'Accession' http://edamontology.org/data_2621 TAIR accession (protein) 'TAIR accession (protein)' SubClassOf 'Sequence accession (protein)' 'TAIR accession (protein)' SubClassOf 'TAIR accession' http://edamontology.org/data_2622 Compound ID (HMDB) 'Compound ID (HMDB)' SubClassOf 'Compound accession' http://edamontology.org/data_1306 Nucleosome exclusion sequences 'Nucleosome exclusion sequences' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2638 PubChem bioassay ID 'PubChem bioassay ID' SubClassOf 'PubChem ID' 'PubChem bioassay ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2639 PubChem ID 'PubChem ID' SubClassOf 'Identifier (hybrid)' 'PubChem ID' SubClassOf 'Accession' http://edamontology.org/data_1305 Nucleic acid features report (restriction sites) 'Nucleic acid features report (restriction sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1304 Nucleic acid features report (CpG island and isochore) 'Nucleic acid features report (CpG island and isochore)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1303 Nucleic acid features (quadruplexes) 'Nucleic acid features (quadruplexes)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2634 ISBN 'ISBN' SubClassOf 'Book ID' http://edamontology.org/data_1309 Gene features (exonic splicing enhancer) 'Gene features (exonic splicing enhancer)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2635 Compound ID (3DMET) 'Compound ID (3DMET)' SubClassOf 'Compound accession' http://edamontology.org/data_1308 Nucleic acid features report (matrix/scaffold attachment sites) 'Nucleic acid features report (matrix/scaffold attachment sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2636 MatrixDB interaction ID 'MatrixDB interaction ID' SubClassOf 'Protein interaction ID' http://edamontology.org/data_1307 Nucleic acid features report (splice sites) 'Nucleic acid features report (splice sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2637 cPath ID 'cPath ID' SubClassOf 'Pathway or network accession' 'cPath ID' SubClassOf 'Identifier (hybrid)' http://edamontology.org/data_2630 Mobile genetic element ID 'Mobile genetic element ID' SubClassOf 'Accession' 'Mobile genetic element ID' SubClassOf 'Identifier (typed)' http://edamontology.org/data_2631 ACLAME ID 'ACLAME ID' SubClassOf 'Mobile genetic element ID' http://edamontology.org/data_2632 SGD ID 'SGD ID' SubClassOf 'Identifier (hybrid)' 'SGD ID' SubClassOf 'Accession' http://edamontology.org/data_2633 Book ID 'Book ID' SubClassOf 'Identifier (typed)' 'Book ID' SubClassOf 'Accession' http://edamontology.org/data_1302 Nucleic acid features report (PolyA signal or site) 'Nucleic acid features report (PolyA signal or site)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1301 Mobile genetic elements 'Mobile genetic elements' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1300 Gene and transcript structure (report) 'Gene and transcript structure (report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2649 PharmGKB ID 'PharmGKB ID' SubClassOf 'Accession' 'PharmGKB ID' SubClassOf 'Identifier (hybrid)' http://edamontology.org/data_1315 Transcription factor binding sites 'Transcription factor binding sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1314 Gene features (SECIS element) 'Gene features (SECIS element)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2645 Pathway ID (Unipathway) 'Pathway ID (Unipathway)' SubClassOf 'Pathway or network accession' http://edamontology.org/data_2646 Compound ID (ChEMBL) 'Compound ID (ChEMBL)' SubClassOf 'Compound accession' http://edamontology.org/data_2647 LGICdb identifier 'LGICdb identifier' SubClassOf 'Protein accession' http://edamontology.org/data_2648 Reaction kinetics ID (SABIO-RK) 'Reaction kinetics ID (SABIO-RK)' SubClassOf 'Reaction ID (SABIO-RK)' http://edamontology.org/data_2641 Reaction ID (MACie) 'Reaction ID (MACie)' SubClassOf 'Reaction ID' http://edamontology.org/data_2642 Gene ID (miRBase) 'Gene ID (miRBase)' SubClassOf 'Gene ID' http://edamontology.org/data_2643 Gene ID (ZFIN) 'Gene ID (ZFIN)' SubClassOf 'Gene ID' http://edamontology.org/data_2644 Reaction ID (Rhea) 'Reaction ID (Rhea)' SubClassOf 'Reaction ID' http://edamontology.org/data_1313 Coding region 'Coding region' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1312 Nucleic acid features report (promoters) 'Nucleic acid features report (promoters)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1311 Gene features report (operon) 'Gene features report (operon)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1310 Nucleic acid features (microRNA) 'Nucleic acid features (microRNA)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000199 GenePix Pro 4.0 'GenePix Pro 4.0' SubClassOf 'GenePix Pro' http://www.ebi.ac.uk/swo/SWO_0000190 GeneRfold 'GeneRfold' SubClassOf 'software' 'GeneRfold' SubClassOf 'is encoded in' some 'R language' 'GeneRfold' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'PostScript')) 'GeneRfold' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GeneRfold' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000192 GeneSelector 'GeneSelector' SubClassOf 'R software' 'GeneSelector' SubClassOf 'implements' some 'Linear modelling' 'GeneSelector' SubClassOf 'implements' some 'Wilcoxon' 'GeneSelector' SubClassOf 'implements' some 'WilcEbam' 'GeneSelector' SubClassOf 'implements' some 'BaldiLongT' 'GeneSelector' SubClassOf 'software' 'GeneSelector' SubClassOf 'implements' some ''t-test'' 'GeneSelector' SubClassOf 'implements' some 'SAM' 'GeneSelector' SubClassOf 'implements' some 'Bayesian Model' 'GeneSelector' SubClassOf 'is encoded in' some 'R language' 'GeneSelector' SubClassOf 'implements' some 'FoxDimmicT' http://www.ebi.ac.uk/swo/SWO_0000191 GeneSelectMMD 'GeneSelectMMD' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GeneSelectMMD' SubClassOf 'is executed in' some 'differential expression analysis' 'GeneSelectMMD' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GeneSelectMMD' SubClassOf 'is encoded in' some 'R language' 'GeneSelectMMD' SubClassOf 'software' 'GeneSelectMMD' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'GeneSelectMMD' SubClassOf 'implements' some 'MMD' 'GeneSelectMMD' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000194 GeneSpringGX 'GeneSpringGX' SubClassOf 'GeneSpring' http://www.ebi.ac.uk/swo/SWO_0000193 GeneSpring 'GeneSpring' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GeneSpring' SubClassOf 'Agilent Technologies Software' 'GeneSpring' SubClassOf 'output of' some ('software development' and ('has participant' value 'Strand Life Sciences')) 'GeneSpring' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'GeneSpring' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) 'GeneSpring' SubClassOf 'R software' 'GeneSpring' SubClassOf 'is encoded in' some 'R language' 'GeneSpring' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000196 GeneTraffic 'GeneTraffic' SubClassOf 'is encoded in' some 'R language' 'GeneTraffic' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GeneTraffic' SubClassOf 'software' 'GeneTraffic' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000195 GeneTac Analyser 'GeneTac Analyser' SubClassOf 'software' 'GeneTac Analyser' SubClassOf 'output of' some ('software development' and ('has participant' value 'Applied Biosystems')) http://www.ontodm.com/OntoDM-core/OntoDM_000192 pattern discovery algorithm DisjointClasses: 'clustering algorithm', 'predictive modeling algorithm', 'pattern discovery algorithm' 'pattern discovery algorithm' SubClassOf 'single generalization algorithm' http://www.ebi.ac.uk/swo/data/SWO_3000069 sequence feature format 'sequence feature format' SubClassOf 'data format specification' http://www.ontodm.com/OntoDM-core/OntoDM_000160 predictive modeling algorithm DisjointClasses: 'clustering algorithm', 'predictive modeling algorithm', 'pattern discovery algorithm' 'predictive modeling algorithm' SubClassOf 'single generalization algorithm' http://purl.obolibrary.org/obo/OBI_0000011 planned process 'planned process' SubClassOf 'process' http://www.ebi.ac.uk/swo/SWO_0000165 Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA) 'Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000164 GLAD 'GLAD' SubClassOf 'implements' some 'Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)' 'GLAD' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GLAD' SubClassOf 'is encoded in' some 'R language' 'GLAD' SubClassOf 'software' 'GLAD' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'GLAD' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000167 GMS 'GMS' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000166 GLEAMS software 'GLEAMS software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Molecular Neuroscience Core, Center for Behavioral Neuroscience, Atlanta')) 'GLEAMS software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000169 Gene Recommender algorithm 'Gene Recommender algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000168 GOstats 'GOstats' SubClassOf 'implements' some 'Hypergeometric probability' 'GOstats' SubClassOf 'is encoded in' some 'R language' 'GOstats' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GOstats' SubClassOf 'software' 'GOstats' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) 'GOstats' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'GOstats' SubClassOf 'implements' some ''t-test'' 'GOstats' SubClassOf 'is executed in' some 'differential expression analysis' 'GOstats' SubClassOf 'has specified data output' some ('Gene expression data' and ('has format specification' some 'data format specification')) 'GOstats' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000163 GGtools 'GGtools' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'GGtools' SubClassOf 'R software' 'GGtools' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'rda')) 'GGtools' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GGtools' SubClassOf 'is encoded in' some 'R language' 'GGtools' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GGtools' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000176 Gene Pix 'Gene Pix' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Molecular Devices')) 'Gene Pix' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000175 GeneData Expressionist Analyst v4.0.5 'GeneData Expressionist Analyst v4.0.5' SubClassOf 'software' 'GeneData Expressionist Analyst v4.0.5' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Genedata')) http://www.ebi.ac.uk/swo/SWO_0000178 GenePix 4.1 'GenePix 4.1' SubClassOf 'Gene Pix' http://www.ebi.ac.uk/swo/SWO_0000177 GenePix 3.0.6 'GenePix 3.0.6' SubClassOf 'Gene Pix' http://www.ebi.ac.uk/swo/SWO_0000179 GenePix 4100A 'GenePix 4100A' SubClassOf 'GenePix' http://www.ebi.ac.uk/swo/SWO_0000170 GSEABase 'GSEABase' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'XML')) 'GSEABase' SubClassOf 'software' 'GSEABase' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GSEABase' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GSEABase' SubClassOf 'is encoded in' some 'R language' 'GSEABase' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000172 Gamma-Gamma hierarchical model 'Gamma-Gamma hierarchical model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000171 GSEAlm 'GSEAlm' SubClassOf 'software' 'GSEAlm' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'GSEAlm' SubClassOf 'R software' 'GSEAlm' SubClassOf 'implements' some 'Gene-Set Enrichment Analysis' 'GSEAlm' SubClassOf 'implements' some 'Linear modelling' 'GSEAlm' SubClassOf 'is executed in' some 'gene expression analysis' 'GSEAlm' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) 'GSEAlm' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GSEAlm' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000174 Gene-Set Enrichment Analysis 'Gene-Set Enrichment Analysis' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000173 Gaussian locally weighted regression 'Gaussian locally weighted regression' SubClassOf 'algorithm' http://purl.obolibrary.org/obo/IAO_0000033 directive information entity 'directive information entity' SubClassOf 'information content entity' http://www.ebi.ac.uk/swo/SWO_0000187 GenePix Pro [Axon Instruments] 'GenePix Pro [Axon Instruments]' SubClassOf 'GenePix Pro' http://www.ebi.ac.uk/swo/SWO_0000186 GenePix Pro 6 [Axon Instruments] 'GenePix Pro 6 [Axon Instruments]' SubClassOf 'GenePix Pro [Axon Instruments]' http://www.ebi.ac.uk/swo/SWO_0000189 GeneRegionScan 'GeneRegionScan' SubClassOf 'software' 'GeneRegionScan' SubClassOf 'R software' 'GeneRegionScan' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'GeneRegionScan' SubClassOf 'is encoded in' some 'R language' 'GeneRegionScan' SubClassOf 'has specified data input' some ('Image' and ('has format specification' some 'CEL binary format')) http://www.ebi.ac.uk/swo/SWO_0000188 GeneR 'GeneR' SubClassOf 'R software' 'GeneR' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GeneR' SubClassOf 'is encoded in' some 'R language' 'GeneR' SubClassOf 'software' 'GeneR' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'GeneR' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'FASTA format')) http://www.ebi.ac.uk/swo/SWO_0000181 GenePix 'GenePix' SubClassOf 'Gene Pix' http://www.ebi.ac.uk/swo/SWO_0000180 GenePix 5.0.1 'GenePix 5.0.1' SubClassOf 'Gene Pix' http://www.ebi.ac.uk/swo/SWO_0000183 GenePix Pro 3 'GenePix Pro 3' SubClassOf 'GenePix Pro' http://www.ebi.ac.uk/swo/SWO_0000182 GenePix Pro 'GenePix Pro' SubClassOf 'Gene Pix' http://www.ebi.ac.uk/swo/SWO_0000185 GenePix Pro 6.0 'GenePix Pro 6.0' SubClassOf 'GenePix Pro' http://www.ebi.ac.uk/swo/SWO_0000184 GenePix Pro 5.0 'GenePix Pro 5.0' SubClassOf 'GenePix Pro' http://purl.obolibrary.org/obo/IAO_0000028 symbol 'symbol' SubClassOf 'information content entity' http://www.ebi.ac.uk/swo/SWO_0000594 limmaGUI 'limmaGUI' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' only 'TIFF')) 'limmaGUI' SubClassOf 'software' 'limmaGUI' SubClassOf 'is published by' value 'Bioconductor' 'limmaGUI' SubClassOf 'BioConductor Software' 'limmaGUI' SubClassOf 'is encoded in' some 'R language' 'limmaGUI' SubClassOf 'R software' 'limmaGUI' SubClassOf 'implements' some 'Linear modelling' 'limmaGUI' SubClassOf 'has specified data input' some 'Text data set' http://www.ebi.ac.uk/swo/SWO_0000593 limma 'limma' SubClassOf 'BioConductor Software' 'limma' SubClassOf 'R software' 'limma' SubClassOf 'is published by' value 'Bioconductor' 'limma' SubClassOf 'is encoded in' some 'R language' 'limma' SubClassOf 'software' 'limma' SubClassOf 'has specified data input' some 'Text data set' 'limma' SubClassOf 'implements' some 'Linear modelling' 'limma' SubClassOf 'is developed by' value 'Walter and Eliza Hall Institute' 'limma' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' only 'TIFF')) http://www.ebi.ac.uk/swo/SWO_0000596 lma 'lma' SubClassOf 'binary format' http://www.ebi.ac.uk/swo/SWO_0000595 Linear modelling 'Linear modelling' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000598 log file 'log file' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000597 Local-pooled-error 'Local-pooled-error' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000599 logicFS 'logicFS' SubClassOf 'R software' 'logicFS' SubClassOf 'BioConductor Software' 'logicFS' SubClassOf 'is encoded in' some 'R language' 'logicFS' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'logicFS' SubClassOf 'implements' some 'Logic regression' 'logicFS' SubClassOf 'has specified data input' some ('has format specification' only 'logicFS dataset') 'logicFS' SubClassOf 'is published by' value 'Bioconductor' 'logicFS' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000590 keggorth 'keggorth' SubClassOf 'software' 'keggorth' SubClassOf 'BioConductor Software' 'keggorth' SubClassOf 'has specified data input' some 'Gene expression dataset' 'keggorth' SubClassOf 'is encoded in' some 'R language' 'keggorth' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'keggorth' SubClassOf 'is published by' value 'Bioconductor' 'keggorth' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000592 Likelihood method 'Likelihood method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000591 lapmix 'lapmix' SubClassOf 'has specified data input' some 'Gene expression dataset' 'lapmix' SubClassOf 'BioConductor Software' 'lapmix' SubClassOf 'is encoded in' some 'R language' 'lapmix' SubClassOf 'is published by' value 'Bioconductor' 'lapmix' SubClassOf 'R software' 'lapmix' SubClassOf 'implements' some 'Laplace mixture model' 'lapmix' SubClassOf 'software' 'lapmix' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'lapmix' SubClassOf 'is executed in' some 'differential expression analysis' http://www.ebi.ac.uk/swo/SWO_0000148 Firth's bias reduction procedure 'Firth's bias reduction procedure' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000550 gene2pathway 'gene2pathway' SubClassOf 'has specified data input' some 'Gene list' 'gene2pathway' SubClassOf 'is published by' value 'Bioconductor' 'gene2pathway' SubClassOf 'R software' 'gene2pathway' SubClassOf 'is encoded in' some 'R language' 'gene2pathway' SubClassOf 'software' 'gene2pathway' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'gene2pathway' SubClassOf 'BioConductor Software' 'gene2pathway' SubClassOf 'implements' some 'Hierarchical clustering' http://www.ebi.ac.uk/swo/SWO_0000552 Gene array analysis algorithm 'Gene array analysis algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000551 geneRecommender 'geneRecommender' SubClassOf 'software' 'geneRecommender' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'geneRecommender' SubClassOf 'has specified data input' some 'Gene list' 'geneRecommender' SubClassOf 'implements' some 'Gene Recommender algorithm' 'geneRecommender' SubClassOf 'BioConductor Software' 'geneRecommender' SubClassOf 'is executed in' some ('data normalization' and 'differential expression analysis') 'geneRecommender' SubClassOf 'is published by' value 'Bioconductor' 'geneRecommender' SubClassOf 'R software' 'geneRecommender' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000554 Gene expression dataset 'Gene expression dataset' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000553 gene expression analysis 'gene expression analysis' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_0000556 genemeta 'genemeta' SubClassOf 'is encoded in' some 'R language' 'genemeta' SubClassOf 'R software' 'genemeta' SubClassOf 'has specified data output' some 'Graph plot' 'genemeta' SubClassOf 'software' 'genemeta' SubClassOf 'has specified data input' some 'Gene expression data' 'genemeta' SubClassOf 'implements' some (''t-test'' and ''FDR'' and ('Random effects model' or 'Fixed effect model')) http://www.ebi.ac.uk/swo/SWO_0000555 genefilter 'genefilter' SubClassOf 'is encoded in' some 'R language' 'genefilter' SubClassOf 'R software' 'genefilter' SubClassOf 'is executed in' some 'differential expression analysis' 'genefilter' SubClassOf 'is published by' value 'Bioconductor' 'genefilter' SubClassOf 'has specified data input' some 'Gene expression dataset' 'genefilter' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'genefilter' SubClassOf 'BioConductor Software' 'genefilter' SubClassOf 'implements' some 'k-nearest neighbour classification' 'genefilter' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000558 genomeIntervals 'genomeIntervals' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'genomeIntervals' SubClassOf 'is published by' value 'Bioconductor' 'genomeIntervals' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'genomeIntervals' SubClassOf 'has specified data input' some ('has format specification' only ('GFF' and 'R data frame')) 'genomeIntervals' SubClassOf 'BioConductor Software' 'genomeIntervals' SubClassOf 'R software' 'genomeIntervals' SubClassOf 'is encoded in' some 'R language' 'genomeIntervals' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000557 geneplotter 'geneplotter' SubClassOf 'R software' 'geneplotter' SubClassOf 'has specified data input' some 'Gene expression dataset' 'geneplotter' SubClassOf 'software' 'geneplotter' SubClassOf 'is encoded in' some 'R language' 'geneplotter' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000561 globaltest 'globaltest' SubClassOf 'implements' some 'globaltest' 'globaltest' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'globaltest' SubClassOf 'is encoded in' some 'R language' 'globaltest' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'globaltest' SubClassOf 'R software' 'globaltest' SubClassOf 'has specified data input' some 'Gene expression dataset' 'globaltest' SubClassOf 'software' 'globaltest' SubClassOf 'is published by' value 'Bioconductor' 'globaltest' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000560 Global test 'Global test' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000563 goProfiles 'goProfiles' SubClassOf 'is encoded in' some 'R language' 'goProfiles' SubClassOf 'implements' some 'Gene-Set Enrichment Analysis' 'goProfiles' SubClassOf 'has specified data output' some 'Image' 'goProfiles' SubClassOf 'has specified data input' some 'Gene list' 'goProfiles' SubClassOf 'is executed in' some ('data visualization' and 'descriptive statistical calculation' and 'differential expression analysis') 'goProfiles' SubClassOf 'R software' 'goProfiles' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000562 gmt format 'gmt format' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000565 gpls 'gpls' SubClassOf 'BioConductor Software' 'gpls' SubClassOf 'R software' 'gpls' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'gpls' SubClassOf 'is published by' value 'Bioconductor' 'gpls' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'gpls' SubClassOf 'is encoded in' some 'R language' 'gpls' SubClassOf 'software' 'gpls' SubClassOf 'implements' some 'Iteratively ReWeighted Least Squares' http://www.ebi.ac.uk/swo/SWO_0000564 goTools 'goTools' SubClassOf 'is executed in' some 'dataset comparison' 'goTools' SubClassOf 'is encoded in' some 'R language' 'goTools' SubClassOf 'software' 'goTools' SubClassOf 'R software' 'goTools' SubClassOf 'is published by' value 'Bioconductor' 'goTools' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'goTools' SubClassOf 'BioConductor Software' 'goTools' SubClassOf 'has specified data input' some 'Gene list' http://www.ebi.ac.uk/swo/SWO_0000567 graph 'graph' SubClassOf 'R software' 'graph' SubClassOf 'implements' some 'R interface to boost graph library algorithm (RBGL)' 'graph' SubClassOf 'has specified data output' some 'Graph plot' 'graph' SubClassOf 'software' 'graph' SubClassOf 'is executed in' some ('distance calculation' and 'descriptive statistical calculation') 'graph' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'graph' SubClassOf 'is published by' value 'Bioconductor' 'graph' SubClassOf 'is encoded in' some 'R language' 'graph' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000566 gpr format 'gpr format' SubClassOf 'tab delimited file format' http://www.ebi.ac.uk/swo/SWO_0000569 gtr 'gtr' SubClassOf 'tab delimited file format' http://www.ebi.ac.uk/swo/SWO_0000572 hexbin 'hexbin' SubClassOf 'implements' some 'Hexagon binning algorithm' 'hexbin' SubClassOf 'is executed in' some ('data visualization' and 'data normalization') 'hexbin' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'hexbin' SubClassOf 'software' 'hexbin' SubClassOf 'BioConductor Software' 'hexbin' SubClassOf 'R software' 'hexbin' SubClassOf 'has specified data output' some 'Graph plot' 'hexbin' SubClassOf 'is encoded in' some 'R language' 'hexbin' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000574 hopach 'hopach' SubClassOf 'has specified data output' some ('Image' and 'Graph plot') 'hopach' SubClassOf 'implements' some 'Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm' 'hopach' SubClassOf 'is encoded in' some 'R language' 'hopach' SubClassOf 'R software' 'hopach' SubClassOf 'software' 'hopach' SubClassOf 'has specified data input' some 'Gene expression data' 'hopach' SubClassOf 'is executed in' some ('data visualization' and 'distance calculation' and 'averaging' and 'decision tree induction' and 'differential expression analysis') http://www.ebi.ac.uk/swo/SWO_0000573 Hierarchical clustering 'Hierarchical clustering' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000576 Hypergeometric enrichment 'Hypergeometric enrichment' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000575 HTML report 'HTML report' SubClassOf 'data item' 'HTML report' SubClassOf 'is encoded in' some 'HTML' http://www.ebi.ac.uk/swo/SWO_0000578 Icens 'Icens' SubClassOf 'R software' 'Icens' SubClassOf 'is encoded in' some 'R language' 'Icens' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'Icens' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'Icens' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000577 hypergraph 'hypergraph' SubClassOf 'is published by' value 'Bioconductor' 'hypergraph' SubClassOf 'is encoded in' some 'R language' 'hypergraph' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'hypergraph' SubClassOf 'R software' 'hypergraph' SubClassOf 'implements' some 'k-cores' 'hypergraph' SubClassOf 'BioConductor Software' 'hypergraph' SubClassOf 'software' 'hypergraph' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000570 gxl format 'gxl format' SubClassOf 'XML' http://www.ebi.ac.uk/swo/SWO_0000579 idiogram 'idiogram' SubClassOf 'BioConductor Software' 'idiogram' SubClassOf 'R software' 'idiogram' SubClassOf 'is encoded in' some 'R language' 'idiogram' SubClassOf 'is published by' value 'Bioconductor' 'idiogram' SubClassOf 'has specified data output' some ('Image' and 'Graph plot') 'idiogram' SubClassOf 'software' 'idiogram' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') http://www.ebi.ac.uk/swo/SWO_0000583 iterativeBMAsurv 'iterativeBMAsurv' SubClassOf 'is published by' value 'Bioconductor' 'iterativeBMAsurv' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'iterativeBMAsurv' SubClassOf 'implements' some 'Iterative Bayesian Model Averaging (BMA)' 'iterativeBMAsurv' SubClassOf 'BioConductor Software' 'iterativeBMAsurv' SubClassOf 'has specified data output' some 'Graph plot' 'iterativeBMAsurv' SubClassOf 'software' 'iterativeBMAsurv' SubClassOf 'is encoded in' some 'R language' 'iterativeBMAsurv' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000582 iterativeBMA 'iterativeBMA' SubClassOf 'has specified data output' some ('Image' and 'Graph plot') 'iterativeBMA' SubClassOf 'implements' some 'Iterative Bayesian Model Averaging (BMA)' 'iterativeBMA' SubClassOf 'R software' 'iterativeBMA' SubClassOf 'software' 'iterativeBMA' SubClassOf 'has specified data input' some 'Gene expression dataset' 'iterativeBMA' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000584 Iterative local regression and model selection 'Iterative local regression and model selection' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000587 k-cores 'k-cores' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000589 k-nearest neighbour classification 'k-nearest neighbour classification' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000588 k-means 'k-means' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000581 impute 'impute' SubClassOf 'R software' 'impute' SubClassOf 'software' 'impute' SubClassOf 'has specified data input' some 'Gene expression dataset' 'impute' SubClassOf 'implements' some 'k-nearest neighbour classification' 'impute' SubClassOf 'has specified data output' some 'Gene expression dataset' 'impute' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000510 crlmm 'crlmm' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'crlmm' SubClassOf 'is executed in' some 'data normalization' 'crlmm' SubClassOf 'BioConductor Software' 'crlmm' SubClassOf 'implements' some 'CRLMM algorithm' 'crlmm' SubClassOf 'is published by' value 'Bioconductor' 'crlmm' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'rda')) 'crlmm' SubClassOf 'software' 'crlmm' SubClassOf 'R software' 'crlmm' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000512 ctc 'ctc' SubClassOf 'is encoded in' some 'R language' 'ctc' SubClassOf 'software' 'ctc' SubClassOf 'BioConductor Software' 'ctc' SubClassOf 'R software' 'ctc' SubClassOf 'has specified data input' some 'Text data set' 'ctc' SubClassOf 'has specified data output' some ('Heat map' and ('has format specification' only ('newick' or 'cdt' or 'gtr'))) 'ctc' SubClassOf 'implements' some 'Hierarchical clustering' 'ctc' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000514 daMA 'daMA' SubClassOf 'R software' 'daMA' SubClassOf 'BioConductor Software' 'daMA' SubClassOf 'software' 'daMA' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'daMA' SubClassOf 'is executed in' some 'differential expression analysis' 'daMA' SubClassOf 'is published by' value 'Bioconductor' 'daMA' SubClassOf 'implements' some ('f-test' and ''FDR'') 'daMA' SubClassOf 'is encoded in' some 'R language' 'daMA' SubClassOf 'has specified data input' some 'Gene expression data' http://www.ebi.ac.uk/swo/SWO_0000513 dChip 'dChip' SubClassOf 'is published by' value 'Havard School of Public Health' 'dChip' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000516 .data '.data' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000518 dcf 'dcf' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_0000519 design file 'design file' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000521 'domainsignatures' ''domainsignatures'' SubClassOf 'has specified data input' some 'Gene list' ''domainsignatures'' SubClassOf 'is executed in' some 'descriptive statistical calculation' ''domainsignatures'' SubClassOf 'R software' ''domainsignatures'' SubClassOf 'has specified data output' some 'Graph plot' ''domainsignatures'' SubClassOf 'implements' some 'Gene-Set Enrichment Analysis' ''domainsignatures'' SubClassOf 'is encoded in' some 'R language' ''domainsignatures'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000520 'diffGeneAnalysis' ''diffGeneAnalysis'' SubClassOf 'has specified data output' some ('Graph plot' and 'CSV data set') ''diffGeneAnalysis'' SubClassOf 'software' ''diffGeneAnalysis'' SubClassOf 'implements' some 'Associative T method' ''diffGeneAnalysis'' SubClassOf 'is encoded in' some 'R language' ''diffGeneAnalysis'' SubClassOf 'has specified data input' some 'CSV data set' ''diffGeneAnalysis'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000523 dyebias 'dyebias' SubClassOf 'is executed in' some ('averaging' and 'correction' and 'data normalization') 'dyebias' SubClassOf 'implements' some 'GASSCO method' 'dyebias' SubClassOf 'is encoded in' some 'R language' 'dyebias' SubClassOf 'has specified data input' some (('Text data set' and ('has format specification' only 'MAGE-TAB')) or ('has format specification' only 'R data frame')) 'dyebias' SubClassOf 'R software' 'dyebias' SubClassOf 'is published by' value 'Bioconductor' 'dyebias' SubClassOf 'software' 'dyebias' SubClassOf 'has specified data output' some 'Text data set' 'dyebias' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000522 'dualKS' ''dualKS'' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') ''dualKS'' SubClassOf 'has specified data input' some 'Gene expression dataset' ''dualKS'' SubClassOf 'R software' ''dualKS'' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') ''dualKS'' SubClassOf 'is encoded in' some 'R language' ''dualKS'' SubClassOf 'implements' some ('Kolmogorov Smirnov rank-sum based algorithm' and 'Bootstrap') ''dualKS'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000525 ecolitk 'ecolitk' SubClassOf 'is encoded in' some 'R language' 'ecolitk' SubClassOf 'BioConductor Software' 'ecolitk' SubClassOf 'software' 'ecolitk' SubClassOf 'R software' 'ecolitk' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'ecolitk' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'ecolitk' SubClassOf 'is published by' value 'Bioconductor' 'ecolitk' SubClassOf 'has specified data input' some 'Meta data' http://www.ebi.ac.uk/swo/SWO_0000524 Dynamic programming algorithm 'Dynamic programming algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000527 'edgeR' ''edgeR'' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') ''edgeR'' SubClassOf 'R software' ''edgeR'' SubClassOf 'has specified data input' some 'Digital gene expression (DGE) datasets' ''edgeR'' SubClassOf 'is encoded in' some 'R language' ''edgeR'' SubClassOf 'is executed in' some 'differential expression analysis' ''edgeR'' SubClassOf 'software' ''edgeR'' SubClassOf 'implements' some ('Negative binomial distribution' and 'Empirical Bayes rule') http://www.ebi.ac.uk/swo/SWO_0000526 edd 'edd' SubClassOf 'is encoded in' some 'R language' 'edd' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'edd' SubClassOf 'BioConductor Software' 'edd' SubClassOf 'R software' 'edd' SubClassOf 'software' 'edd' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'edd' SubClassOf 'is published by' value 'Bioconductor' 'edd' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') http://www.ebi.ac.uk/swo/SWO_0000529 'explorase' ''explorase'' SubClassOf 'has specified data input' some 'CSV data set' ''explorase'' SubClassOf 'is encoded in' some 'R language' ''explorase'' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') ''explorase'' SubClassOf 'implements' some 'Linear modelling' ''explorase'' SubClassOf 'software' ''explorase'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000528 exonmap 'exonmap' SubClassOf 'BioConductor Software' 'exonmap' SubClassOf 'is encoded in' some 'R language' 'exonmap' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'exonmap' SubClassOf 'is executed in' some 'differential expression analysis' 'exonmap' SubClassOf 'implements' some ('RMA' and ''FDR'') 'exonmap' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CDF binary format' or 'CDF ASCII format' or 'CEL ASCII format')) 'exonmap' SubClassOf 'R software' 'exonmap' SubClassOf 'software' 'exonmap' SubClassOf 'is published by' value 'Bioconductor' 'exonmap' SubClassOf 'has specified data input' some ('has format specification' only 'covdesc file') http://www.ebi.ac.uk/swo/SWO_0000530 'externalVector' ''externalVector'' SubClassOf 'software' ''externalVector'' SubClassOf 'R software' ''externalVector'' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000532 factDesign 'factDesign' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'factDesign' SubClassOf 'software' 'factDesign' SubClassOf 'is encoded in' some 'R language' 'factDesign' SubClassOf 'BioConductor Software' 'factDesign' SubClassOf 'implements' some ('RMA' and 'Linear modelling' and ''ANOVA'' and ''FDR'') 'factDesign' SubClassOf 'has specified data output' some ('Heat map' and 'Graph plot' and 'Text data set') 'factDesign' SubClassOf 'R software' 'factDesign' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000531 f-test 'f-test' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000534 fdrame 'fdrame' SubClassOf 'BioConductor Software' 'fdrame' SubClassOf 'is encoded in' some 'R language' 'fdrame' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'fdrame' SubClassOf 'is executed in' some 'gene expression analysis' 'fdrame' SubClassOf 'is published by' value 'Bioconductor' 'fdrame' SubClassOf 'implements' some (''ANOVA'' and ''FDR'') 'fdrame' SubClassOf 'software' 'fdrame' SubClassOf 'has specified data output' some 'Graph plot' 'fdrame' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000533 fbat 'fbat' SubClassOf 'R software' 'fbat' SubClassOf 'BioConductor Software' 'fbat' SubClassOf 'software' 'fbat' SubClassOf 'is encoded in' some 'R language' 'fbat' SubClassOf 'implements' some ('Hardy-Weinberg equilibrium' and 'Markov Chain Monte Carlo') 'fbat' SubClassOf 'has specified data input' some ('has format specification' only 'pedigree data file') 'fbat' SubClassOf 'is published by' value 'Bioconductor' 'fbat' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') http://www.ebi.ac.uk/swo/SWO_0000536 flagme 'flagme' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'flagme' SubClassOf 'is executed in' some 'data normalization' 'flagme' SubClassOf 'has specified data input' some ('has format specification' only ('CDF binary format' or 'CDF ASCII format')) 'flagme' SubClassOf 'is encoded in' some 'R language' 'flagme' SubClassOf 'is published by' value 'Bioconductor' 'flagme' SubClassOf 'BioConductor Software' 'flagme' SubClassOf 'implements' some ('Dynamic programming algorithm' and 'AMDIS') 'flagme' SubClassOf 'software' 'flagme' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000538 flowCore 'flowCore' SubClassOf 'R software' 'flowCore' SubClassOf 'is encoded in' some 'R language' 'flowCore' SubClassOf 'BioConductor Software' 'flowCore' SubClassOf 'software' 'flowCore' SubClassOf 'has specified data input' some ('has format specification' only ('R data frame' or 'Data File Standard for Flow Cytometry')) 'flowCore' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'flowCore' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000537 flowClust 'flowClust' SubClassOf 'is encoded in' some 'R language' 'flowClust' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'flowClust' SubClassOf 'is published by' value 'Bioconductor' 'flowClust' SubClassOf 'implements' some ('Multivariate t mixture models' and 'Bayesian Model' and 'Expectation-Maximization(EM) algorithm') 'flowClust' SubClassOf 'has specified data input' some ('has format specification' only ('R data frame' or 'Data File Standard for Flow Cytometry')) 'flowClust' SubClassOf 'software' 'flowClust' SubClassOf 'R software' 'flowClust' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000539 flowFlowJo 'flowFlowJo' SubClassOf 'has specified data output' some ('has format specification' only 'Data File Standard for Flow Cytometry') 'flowFlowJo' SubClassOf 'is published by' value 'Bioconductor' 'flowFlowJo' SubClassOf 'has specified data input' some ('has format specification' only 'XML') 'flowFlowJo' SubClassOf 'is executed in' some ('parse' and 'descriptive statistical calculation') 'flowFlowJo' SubClassOf 'R software' 'flowFlowJo' SubClassOf 'is encoded in' some 'R language' 'flowFlowJo' SubClassOf 'software' 'flowFlowJo' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000541 flowStats 'flowStats' SubClassOf 'is published by' value 'Bioconductor' 'flowStats' SubClassOf 'is executed in' some 'data normalization' 'flowStats' SubClassOf 'has specified data input' some ('has format specification' only 'Data File Standard for Flow Cytometry') 'flowStats' SubClassOf 'software' 'flowStats' SubClassOf 'BioConductor Software' 'flowStats' SubClassOf 'R software' 'flowStats' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'flowStats' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000540 flowQ 'flowQ' SubClassOf 'is published by' value 'Bioconductor' 'flowQ' SubClassOf 'has specified data input' some ('has format specification' only 'Data File Standard for Flow Cytometry') 'flowQ' SubClassOf 'is encoded in' some 'R language' 'flowQ' SubClassOf 'BioConductor Software' 'flowQ' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'flowQ' SubClassOf 'R software' 'flowQ' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000543 flowViz 'flowViz' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'flowViz' SubClassOf 'software' 'flowViz' SubClassOf 'is published by' value 'Bioconductor' 'flowViz' SubClassOf 'R software' 'flowViz' SubClassOf 'is encoded in' some 'R language' 'flowViz' SubClassOf 'BioConductor Software' 'flowViz' SubClassOf 'has specified data input' some ('has format specification' only 'Data File Standard for Flow Cytometry') http://www.ebi.ac.uk/swo/SWO_0000542 flowUtils 'flowUtils' SubClassOf 'has specified data input' some ('has format specification' only 'Data File Standard for Flow Cytometry') 'flowUtils' SubClassOf 'R software' 'flowUtils' SubClassOf 'BioConductor Software' 'flowUtils' SubClassOf 'is executed in' some 'parse' 'flowUtils' SubClassOf 'has specified data output' some ('has format specification' only 'XML') 'flowUtils' SubClassOf 'is published by' value 'Bioconductor' 'flowUtils' SubClassOf 'is encoded in' some 'R language' 'flowUtils' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000545 'gaggle' ''gaggle'' SubClassOf 'R software' ''gaggle'' SubClassOf 'is encoded in' some 'R language' ''gaggle'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000544 gaga 'gaga' SubClassOf 'software' 'gaga' SubClassOf 'is published by' value 'Bioconductor' 'gaga' SubClassOf 'BioConductor Software' 'gaga' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'gaga' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'gaga' SubClassOf 'is encoded in' some 'R language' 'gaga' SubClassOf 'R software' 'gaga' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'gaga' SubClassOf 'implements' some ('Gamma-Gamma hierarchical model' and ''FDR'') http://www.ontodm.com/OntoDM-core/OntoDM_530819 ensemble algorithm 'ensemble algorithm' DisjointWith 'single generalization algorithm' 'ensemble algorithm' SubClassOf 'data mining algorithm' http://www.ebi.ac.uk/swo/SWO_0000547 gcrma 'gcrma' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'gcrma' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'gcrma' SubClassOf 'is encoded in' some 'R language' 'gcrma' SubClassOf 'is published by' value 'Bioconductor' 'gcrma' SubClassOf 'BioConductor Software' 'gcrma' SubClassOf 'R software' 'gcrma' SubClassOf 'implements' some 'RMA' 'gcrma' SubClassOf 'software' 'gcrma' SubClassOf 'is executed in' some ('correction' and 'data normalization') http://www.ebi.ac.uk/swo/SWO_0000546 gcRMA quantification 'gcRMA quantification' SubClassOf 'software' 'gcRMA quantification' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Bioconductor')) http://www.ebi.ac.uk/swo/SWO_0000549 'genArise' ''genArise'' SubClassOf 'has specified data output' some 'Graph plot' ''genArise'' SubClassOf 'software' ''genArise'' SubClassOf 'is encoded in' some 'R language' ''genArise'' SubClassOf 'has specified data input' some 'Text data set' ''genArise'' SubClassOf 'R software' ''genArise'' SubClassOf 'is executed in' some ('correction' and 'data normalization' and 'differential expression analysis') http://www.ebi.ac.uk/swo/SWO_0000548 gct 'gct' SubClassOf 'tab delimited file format' http://www.ebi.ac.uk/swo/SWO_0000501 'codelink' ''codelink'' SubClassOf 'is encoded in' some 'R language' ''codelink'' SubClassOf 'has specified data input' some ('XML' or 'Text data set') ''codelink'' SubClassOf 'software' ''codelink'' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') ''codelink'' SubClassOf 'R software' ''codelink'' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'descriptive statistical calculation' and 'differential expression analysis') http://purl.obolibrary.org/obo/OBI_0200111 data visualization 'data visualization' SubClassOf 'planned process' http://www.ebi.ac.uk/swo/SWO_0000503 Concordance 'Concordance' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000502 dataset comparison 'dataset comparison' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_0000505 copa 'copa' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'copa' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'copa' SubClassOf 'is encoded in' some 'R language' 'copa' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'copa' SubClassOf 'software' 'copa' SubClassOf 'R software' 'copa' SubClassOf 'BioConductor Software' 'copa' SubClassOf 'implements' some ('Median Average Difference Algorithm' and ''FDR'') 'copa' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000504 convert 'convert' SubClassOf 'software' 'convert' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'convert' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'convert' SubClassOf 'is encoded in' some 'R language' 'convert' SubClassOf 'BioConductor Software' 'convert' SubClassOf 'is published by' value 'Bioconductor' 'convert' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000507 cosmoGUI 'cosmoGUI' SubClassOf 'is executed in' some 'gene expression analysis' 'cosmoGUI' SubClassOf 'is encoded in' some 'R language' 'cosmoGUI' SubClassOf 'BioConductor Software' 'cosmoGUI' SubClassOf 'software' 'cosmoGUI' SubClassOf 'R software' 'cosmoGUI' SubClassOf 'implements' some 'cosmo' 'cosmoGUI' SubClassOf 'has specified data output' some ('Image' and ('HTML report' or ('has format specification' only 'R data frame'))) 'cosmoGUI' SubClassOf 'has specified data input' some ('has format specification' only ('FASTA format' or 'R data frame')) 'cosmoGUI' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000506 cosmo 'cosmo' SubClassOf 'BioConductor Software' 'cosmo' SubClassOf 'implements' some 'Cosmo' 'cosmo' SubClassOf 'is encoded in' some 'R language' 'cosmo' SubClassOf 'software' 'cosmo' SubClassOf 'is published by' value 'Bioconductor' 'cosmo' SubClassOf 'is executed in' some 'gene expression analysis' 'cosmo' SubClassOf 'R software' 'cosmo' SubClassOf 'has specified data input' some ('has format specification' only ('FASTA format' or 'R data frame')) 'cosmo' SubClassOf 'has specified data output' some ('Image' and ('HTML report' or ('has format specification' only 'R data frame'))) http://www.ebi.ac.uk/swo/SWO_0000509 database creation 'database creation' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_0000508 covdesc file 'covdesc file' SubClassOf 'data format specification' http://www.ontodm.com/OntoDM-core/OntoDM_000228 predictive model specification 'predictive model specification' SubClassOf 'single generalization specification' http://www.ontodm.com/OntoDM-core/OntoDM_000264 clustering task DisjointClasses: 'probability distribution estimation task', 'pattern discovery task', 'predictive modeling task', 'clustering task' 'clustering task' SubClassOf 'data mining task' http://www.ontodm.com/OntoDM-core/OntoDM_000253 probability distribution estimation algorithm 'probability distribution estimation algorithm' SubClassOf 'single generalization algorithm' http://www.ontodm.com/OntoDM-core/OntoDM_000235 predictive modeling task DisjointClasses: 'probability distribution estimation task', 'pattern discovery task', 'predictive modeling task', 'clustering task' 'predictive modeling task' SubClassOf 'data mining task' http://www.ontodm.com/OntoDM-core/OntoDM_000072 clustering algorithm DisjointClasses: 'clustering algorithm', 'predictive modeling algorithm', 'pattern discovery algorithm' 'clustering algorithm' SubClassOf 'single generalization algorithm' http://www.ontodm.com/OntoDM-core/OntoDM_000038 data mining algorithm 'data mining algorithm' SubClassOf 'algorithm' http://www.ontodm.com/OntoDM-core/OntoDM_000037 ensemble specification 'ensemble specification' SubClassOf 'generalization specification' http://purl.obolibrary.org/obo/IAO_0000104 plan specification 'plan specification' SubClassOf 'directive information entity' http://www.ebi.ac.uk/swo/SWO_0000275 MAVI Pro 'MAVI Pro' SubClassOf 'software' 'MAVI Pro' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'MWG Biotech')) http://www.ebi.ac.uk/swo/SWO_0000274 MATLAB language 'MATLAB language' SubClassOf 'programming language' http://www.ebi.ac.uk/swo/SWO_0000277 Markov Chain Monte Carlo 'Markov Chain Monte Carlo' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000276 Multivariate correlation estimator 'Multivariate correlation estimator' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000279 MCRestimate 'MCRestimate' SubClassOf 'software' 'MCRestimate' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'R data frame')) 'MCRestimate' SubClassOf 'is encoded in' some 'R language' 'MCRestimate' SubClassOf 'has specified data input' some ('ALL/AML data set' and ('has format specification' some 'data format specification')) 'MCRestimate' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000278 MCR algorithm 'MCR algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000271 MIcroarray Analysis Suite 'MIcroarray Analysis Suite' SubClassOf 'output of' some ('software development' and ('has participant' value 'Affymetrix')) 'MIcroarray Analysis Suite' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000270 MAQC data 'MAQC data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000272 MicroArraySuite 5.0 'MicroArraySuite 5.0' SubClassOf 'MIcroarray Analysis Suite' http://www.ebi.ac.uk/swo/SWO_0000285 MVCClass 'MVCClass' SubClassOf 'is executed in' some 'data visualization' 'MVCClass' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'MVCClass' SubClassOf 'is encoded in' some 'R language' 'MVCClass' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'MVCClass' SubClassOf 'R software' 'MVCClass' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000288 MantelCorr 'MantelCorr' SubClassOf 'R software' 'MantelCorr' SubClassOf 'is encoded in' some 'R language' 'MantelCorr' SubClassOf 'implements' some 'k-means' 'MantelCorr' SubClassOf 'software' 'MantelCorr' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'MantelCorr' SubClassOf 'has specified data output' some ('Clustered data set' and ('has format specification' some 'data format specification')) 'MantelCorr' SubClassOf 'is executed in' some 'differential expression analysis' http://www.ebi.ac.uk/swo/SWO_0000287 Mahalanobis distance 'Mahalanobis distance' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000289 MassSpecWavelet 'MassSpecWavelet' SubClassOf 'software' 'MassSpecWavelet' SubClassOf 'implements' some 'Continuous Wavelet Transform (CWT)-based peak detection algorithm' 'MassSpecWavelet' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'MassSpecWavelet' SubClassOf 'is encoded in' some 'R language' 'MassSpecWavelet' SubClassOf 'R software' 'MassSpecWavelet' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) http://www.ebi.ac.uk/swo/SWO_0000280 MEDME 'MEDME' SubClassOf 'software' 'MEDME' SubClassOf 'is encoded in' some 'R language' 'MEDME' SubClassOf 'R software' 'MEDME' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'MEDME' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'GFF')) http://www.ontodm.com/OntoDM-core/OntoDM_000098 data mining task 'data mining task' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_0000282 Mutual information matrix (MIM) 'Mutual information matrix (MIM)' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000281 'MI' ''MI'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000284 MMD 'MMD' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000283 MLInterfaces 'MLInterfaces' SubClassOf 'has specified data output' some ('ALL/AML data set' and ('has format specification' some 'data format specification')) 'MLInterfaces' SubClassOf 'is encoded in' some 'R language' 'MLInterfaces' SubClassOf 'R software' 'MLInterfaces' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'MLInterfaces' SubClassOf 'software' 'MLInterfaces' SubClassOf 'implements' some 'k-nearest neighbour classification' http://www.ebi.ac.uk/swo/SWO_0000297 MicroArraySuite 4.0 'MicroArraySuite 4.0' SubClassOf 'MIcroarray Analysis Suite' http://www.ebi.ac.uk/swo/SWO_0000296 Misclassification-Penalized Posteriors (MiPP) 'Misclassification-Penalized Posteriors (MiPP)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000298 Mixed model equations 'Mixed model equations' SubClassOf 'algorithm' http://www.ontodm.com/OntoDM-core/OntoDM_000087 probability distribution estimation task DisjointClasses: 'probability distribution estimation task', 'pattern discovery task', 'predictive modeling task', 'clustering task' 'probability distribution estimation task' SubClassOf 'data mining task' http://www.ebi.ac.uk/swo/SWO_0000293 MergeMaid 'MergeMaid' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'MergeMaid' SubClassOf 'software' 'MergeMaid' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'MergeMaid' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'MergeMaid' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'MergeMaid' SubClassOf 'R software' 'MergeMaid' SubClassOf 'is encoded in' some 'R language' 'MergeMaid' SubClassOf 'implements' some 'Regression model' 'MergeMaid' SubClassOf 'implements' some 'Logic regression' http://www.ebi.ac.uk/swo/SWO_0000292 MeasurementError.cor 'MeasurementError.cor' SubClassOf 'is encoded in' some 'R language' 'MeasurementError.cor' SubClassOf 'R software' 'MeasurementError.cor' SubClassOf 'implements' some 'Two-stage measurement error model' 'MeasurementError.cor' SubClassOf 'software' 'MeasurementError.cor' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'MeasurementError.cor' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'MeasurementError.cor' SubClassOf 'is executed in' some 'descriptive statistical calculation' http://www.ebi.ac.uk/swo/SWO_0000295 MiPP 'MiPP' SubClassOf 'is executed in' some 'data normalization' 'MiPP' SubClassOf 'has specified data input' some ('ALL/AML data set' and ('has format specification' some 'data format specification')) 'MiPP' SubClassOf 'R software' 'MiPP' SubClassOf 'implements' some 'Misclassification-Penalized Posteriors (MiPP)' 'MiPP' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'MiPP' SubClassOf 'is encoded in' some 'R language' 'MiPP' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000294 Mfuzz 'Mfuzz' SubClassOf 'implements' some 'clustering algorithm' 'Mfuzz' SubClassOf 'is encoded in' some 'R language' 'Mfuzz' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'Mfuzz' SubClassOf 'R software' 'Mfuzz' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'Mfuzz' SubClassOf 'software' 'Mfuzz' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) http://www.ontodm.com/OntoDM-core/OntoDM_000092 pattern discovery task DisjointClasses: 'probability distribution estimation task', 'pattern discovery task', 'predictive modeling task', 'clustering task' 'pattern discovery task' SubClassOf 'data mining task' http://www.ontodm.com/OntoDM-core/OntoDM_000078 pattern specification 'pattern specification' SubClassOf 'single generalization specification' http://www.ebi.ac.uk/swo/SWO_0000231 ITALICS 'ITALICS' SubClassOf 'has specified data input' some ('Image' and ('has format specification' some 'CEL binary format')) 'ITALICS' SubClassOf 'is executed in' some 'data normalization' 'ITALICS' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'ITALICS' SubClassOf 'is encoded in' some 'R language' 'ITALICS' SubClassOf 'R software' 'ITALICS' SubClassOf 'software' 'ITALICS' SubClassOf 'implements' some 'AWS algorithm' 'ITALICS' SubClassOf 'implements' some 'HaarSeg algorithm' 'ITALICS' SubClassOf 'implements' some 'Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)' http://www.ebi.ac.uk/swo/SWO_0000230 IRanges 'IRanges' SubClassOf 'is executed in' some 'data normalization' 'IRanges' SubClassOf 'R software' 'IRanges' SubClassOf 'software' 'IRanges' SubClassOf 'is executed in' some 'decision tree induction' 'IRanges' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'IRanges' SubClassOf 'is encoded in' some 'R language' 'IRanges' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) http://www.ebi.ac.uk/swo/SWO_0000233 ILLUMINA data 'ILLUMINA data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000235 ImaGene 3.0 'ImaGene 3.0' SubClassOf 'ImaGene' http://www.ebi.ac.uk/swo/SWO_0000234 ImaGene4.1 software 'ImaGene4.1 software' SubClassOf 'ImaGene' http://www.ebi.ac.uk/swo/SWO_0000237 ImageReader 'ImageReader' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000236 ImageQuant 'ImageQuant' SubClassOf 'output of' some ('software development' and ('has participant' value 'Molecular Dynamics')) 'ImageQuant' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000239 Imagene v4.0 'Imagene v4.0' SubClassOf 'ImaGene' http://www.ebi.ac.uk/swo/SWO_0000238 ImaGene 'ImaGene' SubClassOf 'output of' some ('software development' and ('has participant' value 'Bio Discovery')) 'ImaGene' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000241 Initial microarray data processing (data filtering, local normalisation and quality control) 'Initial microarray data processing (data filtering, local normalisation and quality control)' SubClassOf 'output of' some ('software development' and ('has participant' value 'Bahler Lab')) 'Initial microarray data processing (data filtering, local normalisation and quality control)' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000243 Jaccard’s index 'Jaccard’s index' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000246 KCsmart 'KCsmart' SubClassOf 'software with image input' 'KCsmart' SubClassOf 'R software' 'KCsmart' SubClassOf 'software' 'KCsmart' SubClassOf 'is executed in' some 'background correction' 'KCsmart' SubClassOf 'has specified data input' some ('Graph plot' and ('has format specification' some 'image format')) 'KCsmart' SubClassOf 'implements' some 'Gaussian locally weighted regression' 'KCsmart' SubClassOf 'is executed in' some 'data normalization' 'KCsmart' SubClassOf 'is encoded in' some 'R language' 'KCsmart' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'KCsmart' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) http://www.ebi.ac.uk/swo/SWO_0000245 Jaguar 'Jaguar' SubClassOf 'software' 'Jaguar' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Affymetrix')) http://www.ebi.ac.uk/swo/SWO_0000248 KEGGgraph 'KEGGgraph' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'KEGGgraph' SubClassOf 'is encoded in' some 'R language' 'KEGGgraph' SubClassOf 'R software' 'KEGGgraph' SubClassOf 'software' 'KEGGgraph' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'KGML')) 'KEGGgraph' SubClassOf 'implements' some 'R interface to boost graph library algorithm (RBGL)' http://www.ebi.ac.uk/swo/SWO_0000247 KEGGSOAP 'KEGGSOAP' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'KEGGSOAP' SubClassOf 'software' 'KEGGSOAP' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'KEGGSOAP' SubClassOf 'R software' 'KEGGSOAP' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000249 KGML 'KGML' SubClassOf 'XML' http://www.ebi.ac.uk/swo/SWO_0000253 LC-MS data 'LC-MS data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000252 LBE 'LBE' SubClassOf 'is executed in' some 'differential expression analysis' 'LBE' SubClassOf 'R software' 'LBE' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'LBE' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'LBE' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'LBE' SubClassOf 'software' 'LBE' SubClassOf 'implements' some ''FDR'' 'LBE' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000255 Locally Moderated Weighted-t (LMW) method 'Locally Moderated Weighted-t (LMW) method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000254 LMGene 'LMGene' SubClassOf 'is encoded in' some 'R language' 'LMGene' SubClassOf 'is executed in' some 'Linear modelling' 'LMGene' SubClassOf 'software' 'LMGene' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'LMGene' SubClassOf 'R software' 'LMGene' SubClassOf 'is executed in' some 'data normalization' 'LMGene' SubClassOf 'implements' some 'Linear modelling' 'LMGene' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) http://www.ebi.ac.uk/swo/SWO_0000257 Lognormal Normal with Modied Variance Model 'Lognormal Normal with Modied Variance Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000256 Lognormal Normal Model 'Lognormal Normal Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000259 LPEadj 'LPEadj' SubClassOf 'is executed in' some 'data normalization' 'LPEadj' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'LPEadj' SubClassOf 'is encoded in' some 'R language' 'LPEadj' SubClassOf 'is executed in' some 'differential expression analysis' 'LPEadj' SubClassOf 'software' 'LPEadj' SubClassOf 'R software' 'LPEadj' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'LPEadj' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'LPEadj' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'LPEadj' SubClassOf 'implements' some 'Local-pooled-error' 'LPEadj' SubClassOf 'implements' some ''FDR'' http://www.ebi.ac.uk/swo/SWO_0000258 LPE 'LPE' SubClassOf 'software' 'LPE' SubClassOf 'is encoded in' some 'R language' 'LPE' SubClassOf 'is executed in' some 'data normalization' 'LPE' SubClassOf 'implements' some 'Local-pooled-error' 'LPE' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'LPE' SubClassOf 'is executed in' some 'differential expression analysis' 'LPE' SubClassOf 'implements' some ''FDR'' 'LPE' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'LPE' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'LPE' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000251 Kolmogorov Smirnov rank-sum based algorithm 'Kolmogorov Smirnov rank-sum based algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000250 'KLD' ''KLD'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000264 Loess algorithm 'Loess algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000263 Library Search Algorithm 'Library Search Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000266 MAANOVA v1.2 package for MATLAB 'MAANOVA v1.2 package for MATLAB' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000265 Logic regression 'Logic regression' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000267 Median Average Difference Algorithm 'Median Average Difference Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000269 MANOR 'MANOR' SubClassOf 'implements' some 'HaarSeg algorithm' 'MANOR' SubClassOf 'is executed in' some ('data visualization' and 'data normalization') 'MANOR' SubClassOf 'implements' some 'AWS algorithm' 'MANOR' SubClassOf 'software' 'MANOR' SubClassOf 'is encoded in' some 'R language' 'MANOR' SubClassOf 'implements' some 'Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)' 'MANOR' SubClassOf 'R software' 'MANOR' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000260 publisher role 'publisher role' SubClassOf 'role' http://www.ebi.ac.uk/swo/SWO_0000262 Laplace mixture model 'Laplace mixture model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000261 Langmuir Isotherm 'Langmuir Isotherm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000671 qpcrNorm 'qpcrNorm' SubClassOf 'implements' some ('Quantile normalization' and 'Rank-invariant set normalization') 'qpcrNorm' SubClassOf 'R software' 'qpcrNorm' SubClassOf 'is executed in' some 'data normalization' 'qpcrNorm' SubClassOf 'is encoded in' some 'R language' 'qpcrNorm' SubClassOf 'has specified data input' some 'qPCR data' 'qpcrNorm' SubClassOf 'has specified data output' some 'Graph plot' 'qpcrNorm' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000670 qPCR data 'qPCR data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000673 Quantile normalization 'Quantile normalization' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000672 qpgraph 'qpgraph' SubClassOf 'is encoded in' some 'R language' 'qpgraph' SubClassOf 'has specified data input' some 'Gene expression data' 'qpgraph' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'qpgraph' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'qpgraph' SubClassOf 'is published by' value 'Bioconductor' 'qpgraph' SubClassOf 'BioConductor Software' 'qpgraph' SubClassOf 'R software' 'qpgraph' SubClassOf 'software' 'qpgraph' SubClassOf 'implements' some ('Pearson correlation estimator' and 'AvgNRRs') http://www.ebi.ac.uk/swo/SWO_0000675 quantsmooth 'quantsmooth' SubClassOf 'R software' 'quantsmooth' SubClassOf 'has specified data input' some ('ILLUMINA data' or 'Gene expression dataset') 'quantsmooth' SubClassOf 'is executed in' some 'data visualization' 'quantsmooth' SubClassOf 'software' 'quantsmooth' SubClassOf 'is encoded in' some 'R language' 'quantsmooth' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000674 Quantile regression techniques 'Quantile regression techniques' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000677 rHVDM 'rHVDM' SubClassOf 'software' 'rHVDM' SubClassOf 'is encoded in' some 'R language' 'rHVDM' SubClassOf 'implements' some 'Hidden Variable Dynamic Modelling HVDM)' 'rHVDM' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'rHVDM' SubClassOf 'R software' 'rHVDM' SubClassOf 'has specified data input' some 'Gene expression dataset' 'rHVDM' SubClassOf 'has specified data output' some 'HTML report' http://www.ebi.ac.uk/swo/SWO_0000676 qvalue 'qvalue' SubClassOf 'has specified data input' some 'Gene expression dataset' 'qvalue' SubClassOf 'R software' 'qvalue' SubClassOf 'implements' some ''FDR'' 'qvalue' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'qvalue' SubClassOf 'is encoded in' some 'R language' 'qvalue' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000679 rama 'rama' SubClassOf 'software' 'rama' SubClassOf 'has specified data input' some 'Gene expression dataset' 'rama' SubClassOf 'implements' some ('Markov Chain Monte Carlo' and 'Bayesian Model') 'rama' SubClassOf 'is encoded in' some 'R language' 'rama' SubClassOf 'is published by' value 'Bioconductor' 'rama' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'rama' SubClassOf 'is specified data input of' exactly 2 'Gene expression dataset' 'rama' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'rama' SubClassOf 'BioConductor Software' 'rama' SubClassOf 'data item' 'rama' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000678 rMAT 'rMAT' SubClassOf 'is executed in' some ('gene expression analysis' and 'parse' and 'data normalization') 'rMAT' SubClassOf 'is encoded in' some 'R language' 'rMAT' SubClassOf 'has specified data output' some ('has format specification' only ('CEL binary format' or 'BPMAP')) 'rMAT' SubClassOf 'software' 'rMAT' SubClassOf 'R software' 'rMAT' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'BPMAP')) 'rMAT' SubClassOf 'BioConductor Software' 'rMAT' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000682 .raw files '.raw files' SubClassOf 'ASCII format' http://www.ebi.ac.uk/swo/SWO_0000681 Rank product non-parametric method 'Rank product non-parametric method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000200 GenePix Pro 3.0 'GenePix Pro 3.0' SubClassOf 'GenePix Pro' http://www.ebi.ac.uk/swo/SWO_0000684 rda 'rda' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_0000683 rbsurv 'rbsurv' SubClassOf 'has specified data input' some 'Gene expression data' 'rbsurv' SubClassOf 'is published by' value 'Bioconductor' 'rbsurv' SubClassOf 'R software' 'rbsurv' SubClassOf 'software' 'rbsurv' SubClassOf 'BioConductor Software' 'rbsurv' SubClassOf 'is encoded in' some 'R language' 'rbsurv' SubClassOf 'implements' some 'Robust likelihood-based survival modeling' 'rbsurv' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') http://www.ebi.ac.uk/swo/SWO_0000202 GeneticsDesign 'GeneticsDesign' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'GeneticsDesign' SubClassOf 'software' 'GeneticsDesign' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GeneticsDesign' SubClassOf 'is encoded in' some 'R language' 'GeneticsDesign' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000686 rflowcyt 'rflowcyt' SubClassOf 'software' 'rflowcyt' SubClassOf 'is published by' value 'Bioconductor' 'rflowcyt' SubClassOf 'R software' 'rflowcyt' SubClassOf 'has specified data input' some ('has format specification' only 'Data File Standard for Flow Cytometry') 'rflowcyt' SubClassOf 'BioConductor Software' 'rflowcyt' SubClassOf 'is encoded in' some 'R language' 'rflowcyt' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') http://www.ebi.ac.uk/swo/SWO_0000201 GeneticsBase 'GeneticsBase' SubClassOf 'software' 'GeneticsBase' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'GeneticsBase' SubClassOf 'BioConductor Software' 'GeneticsBase' SubClassOf 'has specified data input' some 'CSV data set' 'GeneticsBase' SubClassOf 'is encoded in' some 'R language' 'GeneticsBase' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'GeneticsBase' SubClassOf 'has specified data input' some ('has format specification' only 'pedigree data file') 'GeneticsBase' SubClassOf 'is published by' value 'Bioconductor' 'GeneticsBase' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000685 reb 'reb' SubClassOf 'software' 'reb' SubClassOf 'has specified data output' some ('Heat map' and 'Image') 'reb' SubClassOf 'is encoded in' some 'R language' 'reb' SubClassOf 'R software' 'reb' SubClassOf 'has specified data input' some 'Gene expression dataset' http://www.ebi.ac.uk/swo/SWO_0000688 rsbml 'rsbml' SubClassOf 'R software' 'rsbml' SubClassOf 'is published by' value 'Bioconductor' 'rsbml' SubClassOf 'software' 'rsbml' SubClassOf 'has specified data input' some ('has format specification' only 'SBML') 'rsbml' SubClassOf 'is executed in' some ('parse' and 'cross validation') 'rsbml' SubClassOf 'BioConductor Software' 'rsbml' SubClassOf 'is encoded in' some 'R language' 'rsbml' SubClassOf 'has specified data output' some ('has format specification' only 'XML') http://www.ebi.ac.uk/swo/SWO_0000203 GeneticsPed 'GeneticsPed' SubClassOf 'BioConductor Software' 'GeneticsPed' SubClassOf 'implements' some 'Mixed model equations' 'GeneticsPed' SubClassOf 'is encoded in' some 'R language' 'GeneticsPed' SubClassOf 'is published by' value 'Bioconductor' 'GeneticsPed' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GeneticsPed' SubClassOf 'has specified data input' some ('has format specification' only 'pedigree data file') 'GeneticsPed' SubClassOf 'R software' 'GeneticsPed' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000687 .rma format '.rma format' SubClassOf 'audio format' http://www.ebi.ac.uk/swo/SWO_0000680 Rank-invariant set normalization 'Rank-invariant set normalization' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000206 GlobalAncova 'GlobalAncova' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GlobalAncova' SubClassOf 'software' 'GlobalAncova' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'GlobalAncova' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'GlobalAncova' SubClassOf 'is executed in' some 'differential expression analysis' 'GlobalAncova' SubClassOf 'R software' 'GlobalAncova' SubClassOf 'implements' some 'ANCOVA' 'GlobalAncova' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000205 GenomeGraphs 'GenomeGraphs' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GenomeGraphs' SubClassOf 'is encoded in' some 'R language' 'GenomeGraphs' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'GenomeGraphs' SubClassOf 'R software' 'GenomeGraphs' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000689 rtracklayer 'rtracklayer' SubClassOf 'is encoded in' some 'R language' 'rtracklayer' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'rtracklayer' SubClassOf 'is published by' value 'Bioconductor' 'rtracklayer' SubClassOf 'software' 'rtracklayer' SubClassOf 'R software' 'rtracklayer' SubClassOf 'is executed in' some 'data visualization' 'rtracklayer' SubClassOf 'BioConductor Software' 'rtracklayer' SubClassOf 'has specified data input' some ('has format specification' only ('GFF' or 'BED format')) http://www.ebi.ac.uk/swo/SWO_0000208 GraphAT 'GraphAT' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'GraphAT' SubClassOf 'R software' 'GraphAT' SubClassOf 'has specified data input' some ('Clustered data set' and ('has format specification' some 'data format specification')) 'GraphAT' SubClassOf 'implements' some 'k-means' 'GraphAT' SubClassOf 'software' 'GraphAT' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000207 GOSemSim 'GOSemSim' SubClassOf 'software' 'GOSemSim' SubClassOf 'has specified data output' some ('Clustered data set' and ('has format specification' some 'R data frame')) 'GOSemSim' SubClassOf 'R software' 'GOSemSim' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'GOSemSim' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'GOSemSim' SubClassOf 'is encoded in' some 'R language' 'GOSemSim' SubClassOf 'implements' some 'Semantic Similarity Measures' http://www.ebi.ac.uk/swo/SWO_0000209 GraphAlignment 'GraphAlignment' SubClassOf 'is encoded in' some 'R language' 'GraphAlignment' SubClassOf 'R software' 'GraphAlignment' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GraphAlignment' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GraphAlignment' SubClassOf 'software' 'GraphAlignment' SubClassOf 'implements' some 'Bayesian Model' http://www.ebi.ac.uk/swo/SWO_0000693 sigPathway 'sigPathway' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'sigPathway' SubClassOf 'software' 'sigPathway' SubClassOf 'has specified data input' some 'Gene expression data' 'sigPathway' SubClassOf 'is encoded in' some 'R language' 'sigPathway' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000692 seqLogo 'seqLogo' SubClassOf 'R software' 'seqLogo' SubClassOf 'software' 'seqLogo' SubClassOf 'BioConductor Software' 'seqLogo' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'seqLogo' SubClassOf 'is published by' value 'Bioconductor' 'seqLogo' SubClassOf 'implements' some 'Position weight matrix (PWM )' 'seqLogo' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'seqLogo' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000695 Sim method 'Sim method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000210 GridGrinder 'GridGrinder' SubClassOf 'software' 'GridGrinder' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Grid grinder')) http://www.ebi.ac.uk/swo/SWO_0000694 siggenes 'siggenes' SubClassOf 'software' 'siggenes' SubClassOf 'is encoded in' some 'R language' 'siggenes' SubClassOf 'has specified data input' some 'Text data set' 'siggenes' SubClassOf 'is executed in' some 'differential expression analysis' 'siggenes' SubClassOf 'R software' 'siggenes' SubClassOf 'has specified data output' some 'HTML report' 'siggenes' SubClassOf 'implements' some ('SAM' and 'Empirical Bayes rule' and ''FDR'') http://www.ebi.ac.uk/swo/SWO_0000213 HELP 'HELP' SubClassOf 'is executed in' some 'data normalization' 'HELP' SubClassOf 'implements' some ('RMA' and 'k-nearest neighbour classification') 'HELP' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'pair file')) 'HELP' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'HELP' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'design file')) 'HELP' SubClassOf 'is executed in' some 'data visualization' 'HELP' SubClassOf 'R software' 'HELP' SubClassOf 'software' 'HELP' SubClassOf 'is encoded in' some 'R language' 'HELP' SubClassOf 'is executed in' some 'background correction' 'HELP' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) http://www.ebi.ac.uk/swo/SWO_0000697 simulatorAPMS 'simulatorAPMS' SubClassOf 'software' 'simulatorAPMS' SubClassOf 'has specified data input' some 'AP-MS data' 'simulatorAPMS' SubClassOf 'implements' some 'Complex Estimation Algorithm' 'simulatorAPMS' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'simulatorAPMS' SubClassOf 'is encoded in' some 'R language' 'simulatorAPMS' SubClassOf 'R software' 'simulatorAPMS' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') http://www.ebi.ac.uk/swo/SWO_0000212 Hexagon binning algorithm 'Hexagon binning algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000696 simpleaffy 'simpleaffy' SubClassOf 'is encoded in' some 'R language' 'simpleaffy' SubClassOf 'BioConductor Software' 'simpleaffy' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' and 'covdesc file')) 'simpleaffy' SubClassOf 'R software' 'simpleaffy' SubClassOf 'has specified data output' some ('Heat map' and 'Graph plot' and 'Text data set') 'simpleaffy' SubClassOf 'software' 'simpleaffy' SubClassOf 'implements' some ('RMA' and ''MAS5'') 'simpleaffy' SubClassOf 'is published by' value 'Bioconductor' 'simpleaffy' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'descriptive statistical calculation') http://www.ebi.ac.uk/swo/SWO_0000215 Heterogeneous Error Model (HEM) 'Heterogeneous Error Model (HEM)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000699 xmapbridge 'xmapbridge' SubClassOf 'BioConductor Software' 'xmapbridge' SubClassOf 'software' 'xmapbridge' SubClassOf 'R software' 'xmapbridge' SubClassOf 'is published by' value 'Bioconductor' 'xmapbridge' SubClassOf 'is encoded in' some 'R language' 'xmapbridge' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'xmapbridge' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000214 HEM 'HEM' SubClassOf 'software' 'HEM' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'HEM' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'HEM' SubClassOf 'implements' some 'Empirical Bayes rule' 'HEM' SubClassOf 'is encoded in' some 'R language' 'HEM' SubClassOf 'implements' some 'Heterogeneous Error Model (HEM)' 'HEM' SubClassOf 'R software' 'HEM' SubClassOf 'implements' some ''FDR'' 'HEM' SubClassOf 'implements' some 'Markov Chain Monte Carlo' http://www.ebi.ac.uk/swo/SWO_0000698 sizepower 'sizepower' SubClassOf 'software' 'sizepower' SubClassOf 'BioConductor Software' 'sizepower' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'sizepower' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'sizepower' SubClassOf 'is published by' value 'Bioconductor' 'sizepower' SubClassOf 'R software' 'sizepower' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'differential expression analysis') 'sizepower' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000691 sagenhaft 'sagenhaft' SubClassOf 'is published by' value 'Bioconductor' 'sagenhaft' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'sagenhaft' SubClassOf 'implements' some 'Serial Analysis of Gene Expression (SAGE)' 'sagenhaft' SubClassOf 'software' 'sagenhaft' SubClassOf 'has specified data output' some 'Text data set' 'sagenhaft' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'sagenhaft' SubClassOf 'BioConductor Software' 'sagenhaft' SubClassOf 'R software' 'sagenhaft' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000690 safe 'safe' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'safe' SubClassOf 'implements' some ('Bootstrap' and 'Global test' and ''t-test'' and ''ANOVA'') 'safe' SubClassOf 'has specified data input' some 'ALL/AML data set' 'safe' SubClassOf 'BioConductor Software' 'safe' SubClassOf 'is specified data input of' exactly 3 'Text data set' 'safe' SubClassOf 'is published by' value 'Bioconductor' 'safe' SubClassOf 'is encoded in' some 'R language' 'safe' SubClassOf 'software' 'safe' SubClassOf 'data item' 'safe' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000217 Hidden Markov Model 'Hidden Markov Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000216 Hubert’s gamma 'Hubert’s gamma' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000219 Hidden Variable Dynamic Modelling HVDM) 'Hidden Variable Dynamic Modelling HVDM)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000218 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm 'Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000220 HaarSeg algorithm 'HaarSeg algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000222 Harshlight 'Harshlight' SubClassOf 'R software' 'Harshlight' SubClassOf 'is encoded in' some 'R language' 'Harshlight' SubClassOf 'implements' some 'RMA' 'Harshlight' SubClassOf 'implements' some ''MAS5'' 'Harshlight' SubClassOf 'software' 'Harshlight' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'PostScript')) 'Harshlight' SubClassOf 'has specified data input' some ('Image' and ('has format specification' some 'CEL binary format')) http://www.ebi.ac.uk/swo/SWO_0000221 Hardy-Weinberg equilibrium 'Hardy-Weinberg equilibrium' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000224 Heatplus 'Heatplus' SubClassOf 'R software' 'Heatplus' SubClassOf 'has specified data output' some ('Heat map' and ('has format specification' some 'image format')) 'Heatplus' SubClassOf 'is encoded in' some 'R language' 'Heatplus' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'Heatplus' SubClassOf 'is executed in' some 'data visualization' 'Heatplus' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000226 HilbertVisGUI 'HilbertVisGUI' SubClassOf 'R software' 'HilbertVisGUI' SubClassOf 'software' 'HilbertVisGUI' SubClassOf 'is encoded in' some 'R language' 'HilbertVisGUI' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'BED format')) 'HilbertVisGUI' SubClassOf 'is executed in' some 'data visualization' 'HilbertVisGUI' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'HilbertVisGUI' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'GFF')) http://www.ebi.ac.uk/swo/SWO_0000225 HilbertVis 'HilbertVis' SubClassOf 'software' 'HilbertVis' SubClassOf 'is encoded in' some 'R language' 'HilbertVis' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'BED format')) 'HilbertVis' SubClassOf 'is executed in' some 'data normalization' 'HilbertVis' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'HilbertVis' SubClassOf 'R software' 'HilbertVis' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'GFF')) 'HilbertVis' SubClassOf 'is executed in' some 'data visualization' http://www.ebi.ac.uk/swo/SWO_0000228 ICS-501 (version 2.3) Image Capture System 'ICS-501 (version 2.3) Image Capture System' SubClassOf 'output of' some ('software development' and ('has participant' value 'Genicon Sciences')) 'ICS-501 (version 2.3) Image Capture System' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000227 Hypergeometric probability 'Hypergeometric probability' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000229 Iteratively ReWeighted Least Squares 'Iteratively ReWeighted Least Squares' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000631 Negative binomial distribution 'Negative binomial distribution' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000630 multtest 'multtest' SubClassOf 'BioConductor Software' 'multtest' SubClassOf 'is executed in' some 'differential expression analysis' 'multtest' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'multtest' SubClassOf 'is published by' value 'Bioconductor' 'multtest' SubClassOf 'is encoded in' some 'R language' 'multtest' SubClassOf 'software' 'multtest' SubClassOf 'implements' some 'Multiple testing' 'multtest' SubClassOf 'has specified data input' some 'ALL/AML data set' 'multtest' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000633 Neural networks models 'Neural networks models' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000632 nem 'nem' SubClassOf 'R software' 'nem' SubClassOf 'is executed in' some ('data normalization' and 'decision tree induction' and 'differential expression analysis') 'nem' SubClassOf 'software' 'nem' SubClassOf 'implements' some 'Nested Effects Models' 'nem' SubClassOf 'is encoded in' some 'R language' 'nem' SubClassOf 'has specified data input' some 'Gene expression dataset' 'nem' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000635 nnNorm 'nnNorm' SubClassOf 'is published by' value 'Bioconductor' 'nnNorm' SubClassOf 'R software' 'nnNorm' SubClassOf 'has specified data input' some 'Gene expression dataset' 'nnNorm' SubClassOf 'is executed in' some 'data normalization' 'nnNorm' SubClassOf 'implements' some 'Neural networks models' 'nnNorm' SubClassOf 'BioConductor Software' 'nnNorm' SubClassOf 'has specified data output' some ('Image' or 'Graph plot' or ('has format specification' only 'R data frame')) 'nnNorm' SubClassOf 'is encoded in' some 'R language' 'nnNorm' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000637 occugene 'occugene' SubClassOf 'BioConductor Software' 'occugene' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'occugene' SubClassOf 'implements' some 'Markov Chain Monte Carlo' 'occugene' SubClassOf 'software' 'occugene' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'occugene' SubClassOf 'is encoded in' some 'R language' 'occugene' SubClassOf 'is published by' value 'Bioconductor' 'occugene' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000636 nudge 'nudge' SubClassOf 'software' 'nudge' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'nudge' SubClassOf 'is encoded in' some 'R language' 'nudge' SubClassOf 'implements' some 'Expectation-Maximization(EM) algorithm' 'nudge' SubClassOf 'BioConductor Software' 'nudge' SubClassOf 'R software' 'nudge' SubClassOf 'is published by' value 'Bioconductor' 'nudge' SubClassOf 'is executed in' some 'differential expression analysis' 'nudge' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') http://www.ebi.ac.uk/swo/SWO_0000639 oligoClasses 'oligoClasses' SubClassOf 'R software' 'oligoClasses' SubClassOf 'is encoded in' some 'R language' 'oligoClasses' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000638 oligo 'oligo' SubClassOf 'is encoded in' some 'R language' 'oligo' SubClassOf 'R software' 'oligo' SubClassOf 'implements' some ('SNPRMA algorithm' and 'CRLMM algorithm') 'oligo' SubClassOf 'BioConductor Software' 'oligo' SubClassOf 'is published by' value 'Bioconductor' 'oligo' SubClassOf 'software' 'oligo' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'oligo' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) http://www.ebi.ac.uk/swo/SWO_0000640 OMICS data 'OMICS data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000642 ontoTools 'ontoTools' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'ontoTools' SubClassOf 'is published by' value 'Bioconductor' 'ontoTools' SubClassOf 'software' 'ontoTools' SubClassOf 'R software' 'ontoTools' SubClassOf 'has specified data output' some 'Graph plot' 'ontoTools' SubClassOf 'BioConductor Software' 'ontoTools' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000641 oneChannelGUI 'oneChannelGUI' SubClassOf 'BioConductor Software' 'oneChannelGUI' SubClassOf 'R software' 'oneChannelGUI' SubClassOf 'is encoded in' some 'R language' 'oneChannelGUI' SubClassOf 'has specified data input' some ('ILLUMINA data' or 'Gene expression dataset' or ('has format specification' only ('CEL binary format' or 'GEO Matrix Series format' or 'CEL ASCII format'))) 'oneChannelGUI' SubClassOf 'implements' some ('Regression model' and 'RMA' and 'SAM' and ''FDR'') 'oneChannelGUI' SubClassOf 'software' 'oneChannelGUI' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set' and ('has format specification' only 'pdf')) 'oneChannelGUI' SubClassOf 'is executed in' some ('data visualization' and 'background correction' and 'data normalization' and 'decision tree induction' and 'descriptive statistical calculation' and 'differential expression analysis') 'oneChannelGUI' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000644 pair file 'pair file' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000646 panp 'panp' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' only ('CEL binary format' or 'CEL ASCII format'))) 'panp' SubClassOf 'has specified data output' some ('Graph plot' and 'CSV data set') 'panp' SubClassOf 'is published by' value 'Bioconductor' 'panp' SubClassOf 'implements' some 'Presence-Absence calls with Negative Probesets (PANP)' 'panp' SubClassOf 'is encoded in' some 'R language' 'panp' SubClassOf 'BioConductor Software' 'panp' SubClassOf 'R software' 'panp' SubClassOf 'is executed in' some ('gene expression analysis' and 'descriptive statistical calculation') 'panp' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000645 pamr 'pamr' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'pamr' SubClassOf 'R software' 'pamr' SubClassOf 'BioConductor Software' 'pamr' SubClassOf 'implements' some ''ANOVA'' 'pamr' SubClassOf 'is published by' value 'Bioconductor' 'pamr' SubClassOf 'has specified data input' some 'Text data set' 'pamr' SubClassOf 'software' 'pamr' SubClassOf 'is encoded in' some 'R language' 'pamr' SubClassOf 'is executed in' some 'descriptive statistical calculation' http://www.ebi.ac.uk/swo/SWO_0000648 parse 'parse' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_0000647 parody 'parody' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'parody' SubClassOf 'R software' 'parody' SubClassOf 'is published by' value 'Bioconductor' 'parody' SubClassOf 'BioConductor Software' 'parody' SubClassOf 'is encoded in' some 'R language' 'parody' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'parody' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000649 pathRender 'pathRender' SubClassOf 'is encoded in' some 'R language' 'pathRender' SubClassOf 'is executed in' some ('data visualization' and 'differential expression analysis') 'pathRender' SubClassOf 'software' 'pathRender' SubClassOf 'has specified data input' some 'Gene expression dataset' 'pathRender' SubClassOf 'has specified data output' some 'Graph plot' 'pathRender' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000651 pcot2 'pcot2' SubClassOf 'has specified data input' some 'ALL/AML data set' 'pcot2' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'JPEG')) 'pcot2' SubClassOf 'software' 'pcot2' SubClassOf 'is encoded in' some 'R language' 'pcot2' SubClassOf 'is published by' value 'Bioconductor' 'pcot2' SubClassOf 'R software' 'pcot2' SubClassOf 'BioConductor Software' 'pcot2' SubClassOf 'implements' some ''FDR'' http://www.ebi.ac.uk/swo/SWO_0000650 pcaMethods 'pcaMethods' SubClassOf 'has specified data output' some 'Graph plot' 'pcaMethods' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'pcaMethods' SubClassOf 'R software' 'pcaMethods' SubClassOf 'is published by' value 'Bioconductor' 'pcaMethods' SubClassOf 'is executed in' some ('data visualization' and 'cross validation') 'pcaMethods' SubClassOf 'BioConductor Software' 'pcaMethods' SubClassOf 'software' 'pcaMethods' SubClassOf 'is encoded in' some 'R language' 'pcaMethods' SubClassOf 'implements' some ('Nonlinear Estimation by Iterative Partial Least Squares' and 'SVDimpute algorithm' and 'Bayesian Model' and 'Expectation-Maximization(EM) algorithm') http://www.ebi.ac.uk/swo/SWO_0000653 pdInfoBuilder 'pdInfoBuilder' SubClassOf 'is published by' value 'Bioconductor' 'pdInfoBuilder' SubClassOf 'software' 'pdInfoBuilder' SubClassOf 'has specified data input' some ('Text data set' and 'CSV data set' and ('has format specification' only ('CDF binary format' or 'CDF ASCII format'))) 'pdInfoBuilder' SubClassOf 'is encoded in' some 'R language' 'pdInfoBuilder' SubClassOf 'BioConductor Software' 'pdInfoBuilder' SubClassOf 'has specified data output' some 'Text data set' 'pdInfoBuilder' SubClassOf 'is executed in' some 'data annotation' 'pdInfoBuilder' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000655 pedigree data file 'pedigree data file' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000654 pdmclass 'pdmclass' SubClassOf 'R software' 'pdmclass' SubClassOf 'implements' some 'Regression model' 'pdmclass' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'pdmclass' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'pdmclass' SubClassOf 'software' 'pdmclass' SubClassOf 'is encoded in' some 'R language' 'pdmclass' SubClassOf 'has specified data input' some 'Gene expression dataset' 'pdmclass' SubClassOf 'is published by' value 'Bioconductor' 'pdmclass' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000657 pickgene 'pickgene' SubClassOf 'software' 'pickgene' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'pickgene' SubClassOf 'is published by' value 'Bioconductor' 'pickgene' SubClassOf 'BioConductor Software' 'pickgene' SubClassOf 'implements' some ('Median Average Difference Algorithm' and 'Gene array analysis algorithm') 'pickgene' SubClassOf 'is executed in' some ('background correction' and 'descriptive statistical calculation' and 'differential expression analysis') 'pickgene' SubClassOf 'is encoded in' some 'R language' 'pickgene' SubClassOf 'has specified data input' some 'Gene expression data' 'pickgene' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000656 pgUtils 'pgUtils' SubClassOf 'has specified data output' some ('has format specification' only 'log file') 'pgUtils' SubClassOf 'is published by' value 'Bioconductor' 'pgUtils' SubClassOf 'has specified data input' some 'Text data set' 'pgUtils' SubClassOf 'BioConductor Software' 'pgUtils' SubClassOf 'is executed in' some 'database creation' 'pgUtils' SubClassOf 'software' 'pgUtils' SubClassOf 'is encoded in' some 'R language' 'pgUtils' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000659 plgem 'plgem' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'plgem' SubClassOf 'BioConductor Software' 'plgem' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'plgem' SubClassOf 'is encoded in' some 'R language' 'plgem' SubClassOf 'software' 'plgem' SubClassOf 'implements' some 'Power Law Global Error Model (PLGEM) analysis method' 'plgem' SubClassOf 'has specified data input' some 'Gene expression dataset' 'plgem' SubClassOf 'R software' 'plgem' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000658 pkgDepTools 'pkgDepTools' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'pkgDepTools' SubClassOf 'is encoded in' some 'R language' 'pkgDepTools' SubClassOf 'software' 'pkgDepTools' SubClassOf 'has specified data output' some 'Graph plot' 'pkgDepTools' SubClassOf 'is published by' value 'Bioconductor' 'pkgDepTools' SubClassOf 'BioConductor Software' 'pkgDepTools' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000660 plier 'plier' SubClassOf 'is encoded in' some 'R language' 'plier' SubClassOf 'has specified data input' some 'Gene expression dataset' 'plier' SubClassOf 'software' 'plier' SubClassOf 'R software' 'plier' SubClassOf 'implements' some 'PLIER (Probe Logarithmic Error Intensity Estimate) method' 'plier' SubClassOf 'has specified data output' some 'Gene expression dataset' http://www.ebi.ac.uk/swo/SWO_0000662 plw 'plw' SubClassOf 'R software' 'plw' SubClassOf 'BioConductor Software' 'plw' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'plw' SubClassOf 'software' 'plw' SubClassOf 'implements' some ('Locally Moderated Weighted-t (LMW) method' and 'Probe level Locally moderated Weighted median-t (PLW) method') 'plw' SubClassOf 'is published by' value 'Bioconductor' 'plw' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'plw' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'differential expression analysis') 'plw' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000661 Graph plot 'Graph plot' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000664 Position weight matrix (PWM ) 'Position weight matrix (PWM )' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000666 prada 'prada' SubClassOf 'is published by' value 'Bioconductor' 'prada' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'prada' SubClassOf 'software' 'prada' SubClassOf 'BioConductor Software' 'prada' SubClassOf 'is encoded in' some 'R language' 'prada' SubClassOf 'has specified data input' some ('FACS data' and ('has format specification' some 'FCS3.0') and ('has format specification' only 'FCS3.0')) 'prada' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000665 ppiStats 'ppiStats' SubClassOf 'has specified data input' some 'AP-MS data' 'ppiStats' SubClassOf 'is published by' value 'Bioconductor' 'ppiStats' SubClassOf 'R software' 'ppiStats' SubClassOf 'software' 'ppiStats' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'ppiStats' SubClassOf 'is encoded in' some 'R language' 'ppiStats' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000667 preprocessCore 'preprocessCore' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'preprocessCore' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'preprocessCore' SubClassOf 'R software' 'preprocessCore' SubClassOf 'BioConductor Software' 'preprocessCore' SubClassOf 'is encoded in' some 'R language' 'preprocessCore' SubClassOf 'implements' some ''PLM'' 'preprocessCore' SubClassOf 'is published by' value 'Bioconductor' 'preprocessCore' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000669 puma 'puma' SubClassOf 'is published by' value 'Bioconductor' 'puma' SubClassOf 'BioConductor Software' 'puma' SubClassOf 'implements' some ('Propagation of uncertainty in microarray analysis' and 'RMA') 'puma' SubClassOf 'is encoded in' some 'R language' 'puma' SubClassOf 'R software' 'puma' SubClassOf 'is executed in' some ('data normalization' and 'differential expression analysis') 'puma' SubClassOf 'software' 'puma' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'puma' SubClassOf 'has specified data output' some ('Graph plot' and 'CSV data set') http://www.ebi.ac.uk/swo/SWO_0000600 logicFS dataset 'logicFS dataset' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000609 made4 'made4' SubClassOf 'has specified data output' some ('Hierarchical clustering' and 'Graph plot') 'made4' SubClassOf 'software' 'made4' SubClassOf 'has specified data input' some 'Gene expression dataset' 'made4' SubClassOf 'is encoded in' some 'R language' 'made4' SubClassOf 'R software' 'made4' SubClassOf 'implements' some 'clustering algorithm' http://www.ebi.ac.uk/swo/SWO_0000602 Logit-t algorithm 'Logit-t algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000601 logitT 'logitT' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'logitT' SubClassOf 'is encoded in' some 'R language' 'logitT' SubClassOf 'implements' some ('Logit-t algorithm' and ''t-test'') 'logitT' SubClassOf 'is executed in' some 'differential expression analysis' 'logitT' SubClassOf 'is published by' value 'Bioconductor' 'logitT' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'logitT' SubClassOf 'R software' 'logitT' SubClassOf 'software' 'logitT' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000604 maCorrPlot 'maCorrPlot' SubClassOf 'software' 'maCorrPlot' SubClassOf 'is encoded in' some 'R language' 'maCorrPlot' SubClassOf 'R software' 'maCorrPlot' SubClassOf 'BioConductor Software' 'maCorrPlot' SubClassOf 'has specified data input' some ('has format specification' only ('mas5 format' or '.rma format')) 'maCorrPlot' SubClassOf 'is published by' value 'Bioconductor' 'maCorrPlot' SubClassOf 'is executed in' some ('data visualization' and 'background correction' and 'data normalization') 'maCorrPlot' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000603 lumi 'lumi' SubClassOf 'software' 'lumi' SubClassOf 'R software' 'lumi' SubClassOf 'is published by' value 'Bioconductor' 'lumi' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'lumi' SubClassOf 'has specified data input' some 'Text data set' 'lumi' SubClassOf 'implements' some 'Variance-stabilizing transformation (VST) algorithm' 'lumi' SubClassOf 'BioConductor Software' 'lumi' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000606 maSigPro 'maSigPro' SubClassOf 'is encoded in' some 'R language' 'maSigPro' SubClassOf 'is executed in' some 'differential expression analysis' 'maSigPro' SubClassOf 'has specified data input' some 'Gene expression dataset' 'maSigPro' SubClassOf 'has specified data output' some ('Heat map' and 'Gene list' and 'Graph plot') 'maSigPro' SubClassOf 'R software' 'maSigPro' SubClassOf 'software' 'maSigPro' SubClassOf 'implements' some ('Regression model' and ''FDR'') http://www.ebi.ac.uk/swo/SWO_0000605 maDB 'maDB' SubClassOf 'R software' 'maDB' SubClassOf 'is published by' value 'Bioconductor' 'maDB' SubClassOf 'BioConductor Software' 'maDB' SubClassOf 'has specified data input' some 'Gene expression data' 'maDB' SubClassOf 'is encoded in' some 'R language' 'maDB' SubClassOf 'is executed in' some ('data visualization' and 'differential expression analysis') 'maDB' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'maDB' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000608 macat 'macat' SubClassOf 'has specified data input' some 'Text data set' 'macat' SubClassOf 'R software' 'macat' SubClassOf 'software' 'macat' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'macat' SubClassOf 'is executed in' some ('data visualization' and 'distance calculation' and 'descriptive statistical calculation' and 'differential expression analysis') 'macat' SubClassOf 'is encoded in' some 'R language' 'macat' SubClassOf 'implements' some ('Radial basis function' and 'k-nearest neighbour classification' and 'Base-Pair-Distance Kernel') http://www.ebi.ac.uk/swo/SWO_0000607 maanova 'maanova' SubClassOf 'is encoded in' some 'R language' 'maanova' SubClassOf 'has specified data input' some ('R data frame' or 'Text data set') 'maanova' SubClassOf 'R software' 'maanova' SubClassOf 'software' 'maanova' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'maanova' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'maanova' SubClassOf 'implements' some ('Bootstrap' and ''ANOVA'' and 'F test' and ''FDR'') http://www.ebi.ac.uk/swo/SWO_0000611 makePlatformDesign 'makePlatformDesign' SubClassOf 'BioConductor Software' 'makePlatformDesign' SubClassOf 'is published by' value 'Bioconductor' 'makePlatformDesign' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'makePlatformDesign' SubClassOf 'software' 'makePlatformDesign' SubClassOf 'R software' 'makePlatformDesign' SubClassOf 'is encoded in' some 'R language' 'makePlatformDesign' SubClassOf 'has specified data input' some ('has format specification' only ('FASTA format' or 'CDF binary format' or 'CDF ASCII format')) http://www.ebi.ac.uk/swo/SWO_0000610 maigesPack 'maigesPack' SubClassOf 'R software' 'maigesPack' SubClassOf 'is executed in' some ('data normalization' and 'descriptive statistical calculation' and 'differential expression analysis') 'maigesPack' SubClassOf 'is encoded in' some 'R language' 'maigesPack' SubClassOf 'implements' some (''t-test'' and ''ANOVA'') 'maigesPack' SubClassOf 'has specified data output' some ('Image' and 'Clustered data set' and 'HTML report' and 'Graph plot') 'maigesPack' SubClassOf 'software' http://purl.obolibrary.org/obo/OBI_0200000 data transformation 'data transformation' SubClassOf 'planned process' http://www.ebi.ac.uk/swo/SWO_0000613 marray 'marray' SubClassOf 'implements' some 'Linear modelling' 'marray' SubClassOf 'has specified data input' some ('Gene expression dataset' and 'Text data set') 'marray' SubClassOf 'is encoded in' some 'R language' 'marray' SubClassOf 'R software' 'marray' SubClassOf 'is published by' value 'Bioconductor' 'marray' SubClassOf 'is executed in' some 'data normalization' 'marray' SubClassOf 'has specified data output' some ('Graph plot' or ('Text data set' and ('has format specification' only 'gpr format'))) 'marray' SubClassOf 'software' 'marray' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000612 makecdfenv 'makecdfenv' SubClassOf 'R software' 'makecdfenv' SubClassOf 'has specified data input' some ('has format specification' only ('CDF binary format' or 'CDF ASCII format')) 'makecdfenv' SubClassOf 'is published by' value 'Bioconductor' 'makecdfenv' SubClassOf 'software' 'makecdfenv' SubClassOf 'is encoded in' some 'R language' 'makecdfenv' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'makecdfenv' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000615 mas5 format 'mas5 format' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_0000614 'MAS5' ''MAS5'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000617 mdqc 'mdqc' SubClassOf 'has specified data output' some 'Graph plot' 'mdqc' SubClassOf 'software' 'mdqc' SubClassOf 'R software' 'mdqc' SubClassOf 'implements' some ('Multivariate correlation estimator' and 'clustering algorithm') 'mdqc' SubClassOf 'is encoded in' some 'R language' 'mdqc' SubClassOf 'has specified data input' some ('Gene expression dataset' and 'Text data set') http://www.ebi.ac.uk/swo/SWO_0000616 matchprobes 'matchprobes' SubClassOf 'has specified data output' some ('has format specification' only 'CDF binary format') 'matchprobes' SubClassOf 'is published by' value 'Bioconductor' 'matchprobes' SubClassOf 'software' 'matchprobes' SubClassOf 'R software' 'matchprobes' SubClassOf 'is encoded in' some 'R language' 'matchprobes' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'R data frame' or 'CEL ASCII format')) 'matchprobes' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000619 metaArray 'metaArray' SubClassOf 'is encoded in' some 'R language' 'metaArray' SubClassOf 'is published by' value 'Bioconductor' 'metaArray' SubClassOf 'software' 'metaArray' SubClassOf 'R software' 'metaArray' SubClassOf 'has specified data input' some 'Gene expression dataset' 'metaArray' SubClassOf 'implements' some 'Markov Chain Monte Carlo' 'metaArray' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'metaArray' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000618 M-estimation regression 'M-estimation regression' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000620 Meta data 'Meta data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000622 miRNApath 'miRNApath' SubClassOf 'is published by' value 'Bioconductor' 'miRNApath' SubClassOf 'has specified data output' some ('Heat map' and ('has format specification' only 'R data frame')) 'miRNApath' SubClassOf 'BioConductor Software' 'miRNApath' SubClassOf 'is executed in' some 'gene expression analysis' 'miRNApath' SubClassOf 'is encoded in' some 'R language' 'miRNApath' SubClassOf 'has specified data input' some 'Text data set' 'miRNApath' SubClassOf 'implements' some 'Hypergeometric enrichment' 'miRNApath' SubClassOf 'software' 'miRNApath' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000621 metahdep 'metahdep' SubClassOf 'is published by' value 'Bioconductor' 'metahdep' SubClassOf 'has specified data input' some 'Gene expression dataset' 'metahdep' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'metahdep' SubClassOf 'R software' 'metahdep' SubClassOf 'BioConductor Software' 'metahdep' SubClassOf 'implements' some 'Bayesian Model' 'metahdep' SubClassOf 'software' 'metahdep' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000623 microRNA 'microRNA' SubClassOf 'is encoded in' some 'R language' 'microRNA' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'microRNA' SubClassOf 'is published by' value 'Bioconductor' 'microRNA' SubClassOf 'R software' 'microRNA' SubClassOf 'BioConductor Software' 'microRNA' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'microRNA' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000626 mrnet algorithm 'mrnet algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000625 minet 'minet' SubClassOf 'is encoded in' some 'R language' 'minet' SubClassOf 'R software' 'minet' SubClassOf 'software' 'minet' SubClassOf 'implements' some ('mrnet algorithm' and 'ARACNE algorithm' and 'CLR algorithm') 'minet' SubClassOf 'has specified data input' some 'Gene expression data' 'minet' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'minet' SubClassOf 'has specified data output' some ('Mutual information matrix (MIM)' and 'Graph plot') http://www.ebi.ac.uk/swo/SWO_0000628 Multiple testing 'Multiple testing' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000627 Multinomial probit regression with Gaussian Process priors 'Multinomial probit regression with Gaussian Process priors' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000629 Multivariate t mixture models 'Multivariate t mixture models' SubClassOf 'algorithm' http://purl.obolibrary.org/obo/BFO_0000003 occurrent 'occurrent' SubClassOf 'entity' http://purl.obolibrary.org/obo/BFO_0000004 independent continuant 'independent continuant' SubClassOf 'continuant' http://purl.obolibrary.org/obo/BFO_0000001 entity http://purl.obolibrary.org/obo/BFO_0000002 continuant 'continuant' SubClassOf 'entity' http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant 'generically dependent continuant' SubClassOf 'continuant' http://purl.obolibrary.org/obo/BFO_0000017 realizable entity 'realizable entity' SubClassOf 'specifically dependent continuant' http://purl.obolibrary.org/obo/BFO_0000015 process 'process' SubClassOf 'occurrent' http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant 'specifically dependent continuant' SubClassOf 'continuant' http://purl.obolibrary.org/obo/BFO_0000023 role 'role' SubClassOf 'realizable entity' http://www.ontodm.com/OntoDM-core/OntoDM_000112 clustering specification 'clustering specification' SubClassOf 'single generalization specification' http://www.ebi.ac.uk/swo/SWO_0000396 software developer organization 'software developer organization' EquivalentTo 'has_role' some 'software developer role' 'software developer organization' SubClassOf 'organization' http://www.ebi.ac.uk/swo/SWO_0000398 50-50 MANOVA algorithm '50-50 MANOVA algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000397 software publisher organization 'software publisher organization' SubClassOf 'organization' 'software publisher organization' EquivalentTo 'has_role' some 'publisher role' http://www.ebi.ac.uk/swo/SWO_1100014 ARR 'ARR' SubClassOf 'XML' http://www.ebi.ac.uk/swo/SWO_1100015 AWS algorithm 'AWS algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000390 SSPA 'SSPA' SubClassOf 'has specified data input' some 'ALL/AML data set' 'SSPA' SubClassOf 'BioConductor Software' 'SSPA' SubClassOf 'is encoded in' some 'R language' 'SSPA' SubClassOf 'R software' 'SSPA' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'SSPA' SubClassOf 'is published by' value 'Bioconductor' 'SSPA' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100016 Absolute Expression Analysis 'Absolute Expression Analysis' SubClassOf 'MicroArraySuite 4.0' http://www.ebi.ac.uk/swo/SWO_1100017 Absolute Expression Analysis 'Absolute Expression Analysis' SubClassOf 'MicroArraySuite 5.0' http://www.ebi.ac.uk/swo/SWO_0000392 software developer role 'software developer role' SubClassOf 'role' http://www.ebi.ac.uk/swo/SWO_1100010 ANCOVA 'ANCOVA' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000391 SVDimpute algorithm 'SVDimpute algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100011 'ANOVA' ''ANOVA'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100012 AP-MS data 'AP-MS data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_1100013 ARACNE algorithm 'ARACNE algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100018 'AffyCompatible' ''AffyCompatible'' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'MAGE-TAB')) ''AffyCompatible'' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some 'data format specification')) ''AffyCompatible'' SubClassOf 'software' ''AffyCompatible'' SubClassOf 'R software' ''AffyCompatible'' SubClassOf 'is encoded in' some 'R language' ''AffyCompatible'' SubClassOf 'is executed in' some 'parse' http://www.ebi.ac.uk/swo/SWO_1100019 'AffyExpress' ''AffyExpress'' SubClassOf 'is executed in' some 'correction' ''AffyExpress'' SubClassOf 'implements' some ''ANOVA'' ''AffyExpress'' SubClassOf 'is executed in' some 'data normalization' ''AffyExpress'' SubClassOf 'is executed in' some 'differential expression analysis' ''AffyExpress'' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''AffyExpress'' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) ''AffyExpress'' SubClassOf 'is encoded in' some 'R language' ''AffyExpress'' SubClassOf 'R software' ''AffyExpress'' SubClassOf 'has specified data input' some ('Image' and ('has format specification' some 'CEL binary format')) ''AffyExpress'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'data format specification')) ''AffyExpress'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100003 'ACME' ''ACME'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100004 Algorithms for Calculating Microarray Enrichment 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'has specified data output' some 'Graph plot' 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'implements' some ('Algorithms for Calculating Microarray Enrichment' and 'Chi-square') 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'R software' 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'is encoded in' some 'R language' 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100005 Affymetrix Expression Console 'Affymetrix Expression Console' SubClassOf 'has specified data input' some ('Image' and ('has format specification' some 'CEL binary format')) 'Affymetrix Expression Console' SubClassOf 'implements' some 'RMA' 'Affymetrix Expression Console' SubClassOf 'implements' some 'PLIER (Probe Logarithmic Error Intensity Estimate) method' 'Affymetrix Expression Console' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Affymetrix')) 'Affymetrix Expression Console' SubClassOf 'implements' some ''MAS5'' 'Affymetrix Expression Console' SubClassOf 'software' 'Affymetrix Expression Console' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'CHP binary format')) 'Affymetrix Expression Console' SubClassOf 'output of' some ('software development' and ('has participant' value 'Affymetrix')) http://www.ebi.ac.uk/swo/SWO_1100006 AIDA 'AIDA' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Raytest')) 'AIDA' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100000 2-sample pooled t-test '2-sample pooled t-test' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100001 50-50 MANOVA '50-50 MANOVA' SubClassOf 'is encoded in' some 'MATLAB language' '50-50 MANOVA' SubClassOf 'R software' '50-50 MANOVA' SubClassOf 'is encoded in' some 'R language' '50-50 MANOVA' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Matforsk')) '50-50 MANOVA' SubClassOf 'implements' some '50-50 MANOVA algorithm' '50-50 MANOVA' SubClassOf 'software' '50-50 MANOVA' SubClassOf 'matlab software' http://www.ebi.ac.uk/swo/SWO_1100002 ABarray 'ABarray' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) 'ABarray' SubClassOf 'implements' some 'Local-pooled-error' 'ABarray' SubClassOf 'has specified data output' some ('CSV data set' and ('has format specification' some 'data format specification')) 'ABarray' SubClassOf 'is executed in' some 'gene expression analysis' 'ABarray' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some 'data format specification')) 'ABarray' SubClassOf 'is encoded in' some 'R language' 'ABarray' SubClassOf 'implements' some ''FDR'' 'ABarray' SubClassOf 'software' 'ABarray' SubClassOf 'R software' 'ABarray' SubClassOf 'implements' some ''t-test'' 'ABarray' SubClassOf 'implements' some ''ANOVA'' 'ABarray' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some 'data format specification')) http://www.ebi.ac.uk/swo/SWO_1100007 Average log expression across arrays (ALE) 'Average log expression across arrays (ALE)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100008 ALL/AML data set 'ALL/AML data set' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_1100009 AMDIS 'AMDIS' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100030 BGL 'BGL' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100031 'BGmix' ''BGmix'' SubClassOf 'software' ''BGmix'' SubClassOf 'is encoded in' some 'R language' ''BGmix'' SubClassOf 'implements' some 'Markov Chain Monte Carlo' ''BGmix'' SubClassOf 'implements' some 'Bayesian Model' ''BGmix'' SubClassOf 'R software' ''BGmix'' SubClassOf 'is executed in' some 'differential expression analysis' http://www.ebi.ac.uk/swo/SWO_1100036 BRB-ArrayTools 'BRB-ArrayTools' SubClassOf 'software' 'BRB-ArrayTools' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Biometric Research Branch')) http://www.ebi.ac.uk/swo/SWO_1100037 'BSgenome' ''BSgenome'' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'dcf')) ''BSgenome'' SubClassOf 'software' ''BSgenome'' SubClassOf 'is encoded in' some 'R language' ''BSgenome'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'FASTA format')) ''BSgenome'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100038 BZScan 'BZScan' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Technological Advances for Genomics and Clinics, France')) 'BZScan' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100039 BaldiLongT 'BaldiLongT' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100032 BLAST 'BLAST' SubClassOf 'has specified data input' some ('biological sequence data' and ('has format specification' some 'GenBank format')) 'BLAST' SubClassOf 'is executed in' some 'pairwise sequence alignment' 'BLAST' SubClassOf 'output of' some ('software development' and ('has participant' value 'NIH')) 'BLAST' SubClassOf 'has specified data input' some ('biological sequence data' and ('has format specification' some 'FASTA format')) 'BLAST' SubClassOf 'is executed in' some 'multiple sequence alignment' 'BLAST' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'NIH')) 'BLAST' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100033 Iterative Bayesian Model Averaging (BMA) 'Iterative Bayesian Model Averaging (BMA)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100034 Base-Pair-Distance Kernel 'Base-Pair-Distance Kernel' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100035 BPMAP 'BPMAP' SubClassOf 'is published by' value 'Affymetrix' 'BPMAP' SubClassOf 'binary format' http://www.ebi.ac.uk/swo/SWO_1100020 Affymetrix GCOS v1.2 'Affymetrix GCOS v1.2' SubClassOf 'Affymetrix GeneChip Operating Software' http://www.ebi.ac.uk/swo/SWO_1100025 Agilent Feature Extraction software version 7.1 'Agilent Feature Extraction software version 7.1' SubClassOf 'Agilent Feature Extraction Software' http://www.ebi.ac.uk/swo/SWO_1100026 Agilent Feature Extraction software version 7.5 'Agilent Feature Extraction software version 7.5' SubClassOf 'Agilent Feature Extraction Software' http://www.ebi.ac.uk/swo/SWO_1100027 Agilent Feature Extraction software version A.5.1.1 'Agilent Feature Extraction software version A.5.1.1' SubClassOf 'Agilent Feature Extraction Software' http://www.ebi.ac.uk/swo/SWO_1100028 ArrayVision 6.0 (Imaging Research Inc.) 'ArrayVision 6.0 (Imaging Research Inc.)' SubClassOf 'ArrayVision' http://www.ebi.ac.uk/swo/SWO_1100021 Affymetrix GeneChip Operating Software 'Affymetrix GeneChip Operating Software' SubClassOf 'software' 'Affymetrix GeneChip Operating Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Affymetrix')) http://www.ebi.ac.uk/swo/SWO_1100022 Affymetrix Software 'Affymetrix Software' SubClassOf 'software' 'Affymetrix Software' EquivalentTo 'software' and ('is published by' value 'Affymetrix') http://www.ebi.ac.uk/swo/SWO_1100023 Agi4x44PreProcess 'Agi4x44PreProcess' SubClassOf 'has specified data input' some ('Heat map' and ('has format specification' some 'image format')) 'Agi4x44PreProcess' SubClassOf 'software with image input' 'Agi4x44PreProcess' SubClassOf 'software' 'Agi4x44PreProcess' SubClassOf 'implements' some 'Loess algorithm' 'Agi4x44PreProcess' SubClassOf 'is executed in' some 'differential expression analysis' 'Agi4x44PreProcess' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'cls')) 'Agi4x44PreProcess' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'gct')) 'Agi4x44PreProcess' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'data format specification')) 'Agi4x44PreProcess' SubClassOf 'is executed in' some 'correction' 'Agi4x44PreProcess' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'Agi4x44PreProcess' SubClassOf 'is encoded in' some 'R language' 'Agi4x44PreProcess' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) 'Agi4x44PreProcess' SubClassOf 'R software' 'Agi4x44PreProcess' SubClassOf 'is executed in' some 'data normalization' http://www.ebi.ac.uk/swo/SWO_1100024 Agilent Feature Extraction 5.1.1 'Agilent Feature Extraction 5.1.1' SubClassOf 'Agilent Feature Extraction Software' http://www.ebi.ac.uk/swo/SWO_1100029 'BCRANK' ''BCRANK'' SubClassOf 'R software' ''BCRANK'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'FASTA format')) ''BCRANK'' SubClassOf 'software' ''BCRANK'' SubClassOf 'is encoded in' some 'R language' ''BCRANK'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''BCRANK'' SubClassOf 'implements' some ''BCRANK'' http://www.ebi.ac.uk/swo/SWO_0000352 RbcBook1 'RbcBook1' SubClassOf 'is encoded in' some 'R language' 'RbcBook1' SubClassOf 'software' 'RbcBook1' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100050 'BufferedMatrix' ''BufferedMatrix'' SubClassOf 'R software' ''BufferedMatrix'' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) ''BufferedMatrix'' SubClassOf 'is encoded in' some 'R language' ''BufferedMatrix'' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''BufferedMatrix'' SubClassOf 'software' ''BufferedMatrix'' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''BufferedMatrix'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'pdf')) http://www.ebi.ac.uk/swo/SWO_1100051 'BufferedMatrixMethods' ''BufferedMatrixMethods'' SubClassOf 'has specified data input' some ('Gene expression data' and ('has format specification' some 'CEL binary format')) ''BufferedMatrixMethods'' SubClassOf 'software' ''BufferedMatrixMethods'' SubClassOf 'R software' ''BufferedMatrixMethods'' SubClassOf 'is encoded in' some 'R language' ''BufferedMatrixMethods'' SubClassOf 'has specified data output' some ('Gene expression data' and ('has format specification' some 'CEL binary format')) http://www.ebi.ac.uk/swo/SWO_0000354 RdbiPgSQL 'RdbiPgSQL' SubClassOf 'BioConductor Software' 'RdbiPgSQL' SubClassOf 'has specified data output' some 'Graph plot' 'RdbiPgSQL' SubClassOf 'R software' 'RdbiPgSQL' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'RdbiPgSQL' SubClassOf 'is encoded in' some 'R language' 'RdbiPgSQL' SubClassOf 'software' 'RdbiPgSQL' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_1100052 'CALIB' ''CALIB'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) ''CALIB'' SubClassOf 'R software' ''CALIB'' SubClassOf 'is executed in' some 'differential expression analysis' ''CALIB'' SubClassOf 'is encoded in' some 'R language' ''CALIB'' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''CALIB'' SubClassOf 'software' ''CALIB'' SubClassOf 'is executed in' some 'data normalization' http://www.ebi.ac.uk/swo/SWO_0000353 Rdbi 'Rdbi' SubClassOf 'BioConductor Software' 'Rdbi' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'Rdbi' SubClassOf 'is published by' value 'Bioconductor' 'Rdbi' SubClassOf 'software' 'Rdbi' SubClassOf 'has specified data output' some 'Graph plot' 'Rdbi' SubClassOf 'is encoded in' some 'R language' 'Rdbi' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100053 'CAMERA' ''CAMERA'' SubClassOf 'R software' ''CAMERA'' SubClassOf 'is encoded in' some 'R language' ''CAMERA'' SubClassOf 'has specified data output' some ('CSV data set' and ('has format specification' some http://edamontology.org/format_2330)) ''CAMERA'' SubClassOf 'has specified data input' some ('LC-MS data' and ('has format specification' some 'data format specification')) ''CAMERA'' SubClassOf 'software' ''CAMERA'' SubClassOf 'is executed in' some 'data annotation' http://www.ebi.ac.uk/swo/SWO_0000356 RefPlus 'RefPlus' SubClassOf 'R software' 'RefPlus' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'differential expression analysis') 'RefPlus' SubClassOf 'software' 'RefPlus' SubClassOf 'has specified data output' some 'Graph plot' 'RefPlus' SubClassOf 'has specified data input' some 'Gene expression dataset' 'RefPlus' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000355 Rdisop 'Rdisop' SubClassOf 'is published by' value 'Bioconductor' 'Rdisop' SubClassOf 'software' 'Rdisop' SubClassOf 'BioConductor Software' 'Rdisop' SubClassOf 'R software' 'Rdisop' SubClassOf 'is encoded in' some 'R language' 'Rdisop' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'Rdisop' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000358 Resourcerer 'Resourcerer' SubClassOf 'has specified data output' some 'Text data set' 'Resourcerer' SubClassOf 'software' 'Resourcerer' SubClassOf 'has specified data input' some 'Annotation data packages' 'Resourcerer' SubClassOf 'is encoded in' some 'R language' 'Resourcerer' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100058 CRLMM algorithm 'CRLMM algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100059 Continuous Wavelet Transform (CWT)-based peak detection algorithm 'Continuous Wavelet Transform (CWT)-based peak detection algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100054 CDF binary format 'CDF binary format' SubClassOf 'binary format' 'CDF binary format' SubClassOf 'is published by' value 'Affymetrix' http://www.ebi.ac.uk/swo/SWO_1100055 'CMA' ''CMA'' SubClassOf 'R software' ''CMA'' SubClassOf 'is executed in' some 'descriptive statistical calculation' ''CMA'' SubClassOf 'implements' some ''CMA'' ''CMA'' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) ''CMA'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''CMA'' SubClassOf 'is encoded in' some 'R language' ''CMA'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000350 RankProd 'RankProd' SubClassOf 'implements' some 'Rank product non-parametric method' 'RankProd' SubClassOf 'software' 'RankProd' SubClassOf 'is published by' value 'Bioconductor' 'RankProd' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'RankProd' SubClassOf 'BioConductor Software' 'RankProd' SubClassOf 'has specified data input' some 'Gene expression dataset' 'RankProd' SubClassOf 'is executed in' some 'differential expression analysis' 'RankProd' SubClassOf 'is encoded in' some 'R language' 'RankProd' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100056 CMA 'CMA' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100057 'CORREP' ''CORREP'' SubClassOf 'is executed in' some 'descriptive statistical calculation' ''CORREP'' SubClassOf 'has specified data input' some ('OMICS data' and ('has format specification' some 'R data frame')) ''CORREP'' SubClassOf 'is executed in' some 'differential expression analysis' ''CORREP'' SubClassOf 'is encoded in' some 'R language' ''CORREP'' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) ''CORREP'' SubClassOf 'software' ''CORREP'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000359 Rgraphviz 'Rgraphviz' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'Rgraphviz' SubClassOf 'R software' 'Rgraphviz' SubClassOf 'BioConductor Software' 'Rgraphviz' SubClassOf 'is encoded in' some 'R language' 'Rgraphviz' SubClassOf 'is published by' value 'Bioconductor' 'Rgraphviz' SubClassOf 'has specified data output' some 'Graph plot' 'Rgraphviz' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000363 Rnw 'Rnw' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_0000362 Rmagpie 'Rmagpie' SubClassOf 'is executed in' some 'cross validation' 'Rmagpie' SubClassOf 'software' 'Rmagpie' SubClassOf 'has specified data input' some 'Gene expression dataset' 'Rmagpie' SubClassOf 'has specified data output' some 'Text data set' 'Rmagpie' SubClassOf 'R software' 'Rmagpie' SubClassOf 'implements' some 'Recursive Feature Elimination (RFE)' 'Rmagpie' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_1100040 BasReader 3.01 'BasReader 3.01' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Raytest')) 'BasReader 3.01' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000365 Rosetta Resolver 'Rosetta Resolver' SubClassOf 'software' 'Rosetta Resolver' SubClassOf 'is developed by' value 'Rosetta Biosoftware' http://www.ebi.ac.uk/swo/SWO_1100041 Bayesian Model 'Bayesian Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000364 Robust likelihood-based survival modeling 'Robust likelihood-based survival modeling' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100042 Beadstudio 'Beadstudio' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Illumina')) 'Beadstudio' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000367 RpsiXML 'RpsiXML' SubClassOf 'software' 'RpsiXML' SubClassOf 'R software' 'RpsiXML' SubClassOf 'is published by' value 'Bioconductor' 'RpsiXML' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'RpsiXML' SubClassOf 'has specified data input' some ('has format specification' only 'XML') 'RpsiXML' SubClassOf 'is executed in' some 'parse' 'RpsiXML' SubClassOf 'is encoded in' some 'R language' 'RpsiXML' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000369 Rtreemix 'Rtreemix' SubClassOf 'implements' some ('Likelihood method' or 'Sim method') 'Rtreemix' SubClassOf 'is encoded in' some 'R language' 'Rtreemix' SubClassOf 'is executed in' some 'decision tree induction' 'Rtreemix' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'Rtreemix' SubClassOf 'has specified data input' some 'Text data set' 'Rtreemix' SubClassOf 'software' 'Rtreemix' SubClassOf 'BioConductor Software' 'Rtreemix' SubClassOf 'is published by' value 'Bioconductor' 'Rtreemix' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000368 Rredland 'Rredland' SubClassOf 'BioConductor Software' 'Rredland' SubClassOf 'is encoded in' some 'R language' 'Rredland' SubClassOf 'software' 'Rredland' SubClassOf 'is published by' value 'Bioconductor' 'Rredland' SubClassOf 'has specified data input' some 'Text data set' 'Rredland' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'Rredland' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100047 BioConductor Software 'BioConductor Software' SubClassOf 'is executed in' some 'biological data processing' 'BioConductor Software' SubClassOf 'software' 'BioConductor Software' EquivalentTo 'software' and ('is published by' value 'Bioconductor') http://www.ebi.ac.uk/swo/SWO_1100048 'Biostrings' ''Biostrings'' SubClassOf 'is encoded in' some 'R language' ''Biostrings'' SubClassOf 'implements' some ''Needleman-Wunsch'' ''Biostrings'' SubClassOf 'software' ''Biostrings'' SubClassOf 'implements' some ''Smith-Waterman'' ''Biostrings'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100049 BlueFuse 'BlueFuse' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Cambridge Bluegnome')) 'BlueFuse' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100043 'BicARE' ''BicARE'' SubClassOf 'is encoded in' some 'R language' ''BicARE'' SubClassOf 'software' ''BicARE'' SubClassOf 'R software' ''BicARE'' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) http://www.ebi.ac.uk/swo/SWO_1100044 'BioMVCClass' ''BioMVCClass'' SubClassOf 'is encoded in' some 'R language' ''BioMVCClass'' SubClassOf 'R software' ''BioMVCClass'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000361 Rintact 'Rintact' SubClassOf 'has specified data input' some ('has format specification' only 'XML') 'Rintact' SubClassOf 'is executed in' some 'parse' 'Rintact' SubClassOf 'is published by' value 'Bioconductor' 'Rintact' SubClassOf 'software' 'Rintact' SubClassOf 'BioConductor Software' 'Rintact' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'Rintact' SubClassOf 'R software' 'Rintact' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_1100045 'Biobase' ''Biobase'' SubClassOf 'R software' ''Biobase'' SubClassOf 'is encoded in' some 'R language' ''Biobase'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000360 Ringo 'Ringo' SubClassOf 'has specified data input' some 'Text data set' 'Ringo' SubClassOf 'data item' 'Ringo' SubClassOf 'R software' 'Ringo' SubClassOf 'BioConductor Software' 'Ringo' SubClassOf 'is specified data input of' exactly 2 'Text data set' 'Ringo' SubClassOf 'is encoded in' some 'R language' 'Ringo' SubClassOf 'software' 'Ringo' SubClassOf 'is executed in' some ('data visualization' and 'data normalization') 'Ringo' SubClassOf 'is published by' value 'Bioconductor' 'Ringo' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'GFF')) http://www.ebi.ac.uk/swo/SWO_1100046 'BiocCaseStudies' ''BiocCaseStudies'' SubClassOf 'software' ''BiocCaseStudies'' SubClassOf 'is encoded in' some 'R language' ''BiocCaseStudies'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000374 SAM 'SAM' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100072 Chi-square 'Chi-square' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000373 SAGx 'SAGx' SubClassOf 'is encoded in' some 'R language' 'SAGx' SubClassOf 'BioConductor Software' 'SAGx' SubClassOf 'is published by' value 'Bioconductor' 'SAGx' SubClassOf 'software' 'SAGx' SubClassOf 'R software' 'SAGx' SubClassOf 'implements' some ('Linear modelling' and ''t-test'') 'SAGx' SubClassOf 'has specified data input' some ('Graph plot' and ('has format specification' only 'R data frame')) http://www.ebi.ac.uk/swo/SWO_1100073 Annotation-Driven Clustering 'Annotation-Driven Clustering' SubClassOf 'implements' some 'k-means' 'Annotation-Driven Clustering' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'Annotation-Driven Clustering' SubClassOf 'is encoded in' some 'R language' 'Annotation-Driven Clustering' SubClassOf 'R software' 'Annotation-Driven Clustering' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'Annotation-Driven Clustering' SubClassOf 'implements' some ''FDR'' 'Annotation-Driven Clustering' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) 'Annotation-Driven Clustering' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100074 distance calculation 'distance calculation' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_1100075 R software 'R software' EquivalentTo 'is encoded in' some 'R language' 'R software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000375 SAS/STAT Software, Version 8 'SAS/STAT Software, Version 8' SubClassOf 'is developed by' value 'SAS Institute Inc.' 'SAS/STAT Software, Version 8' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000378 SBMLR format 'SBMLR format' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_0000377 SBMLR 'SBMLR' SubClassOf 'is encoded in' some 'R language' 'SBMLR' SubClassOf 'has specified data output' some ('has format specification' only ('SBML' or 'SBMLR format')) 'SBMLR' SubClassOf 'has specified data input' some ('has format specification' only ('SBML' or 'SBMLR format')) 'SBMLR' SubClassOf 'BioConductor Software' 'SBMLR' SubClassOf 'R software' 'SBMLR' SubClassOf 'is published by' value 'Bioconductor' 'SBMLR' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100070 PCMG 'PCMG' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100071 Feature Extraction Software 'Feature Extraction Software' SubClassOf 'is executed in' some 'feature extraction' 'Feature Extraction Software' SubClassOf 'Affymetrix GeneChip Operating Software' http://www.ebi.ac.uk/swo/SWO_0000370 Ruuid 'Ruuid' SubClassOf 'R software' 'Ruuid' SubClassOf 'software' 'Ruuid' SubClassOf 'BioConductor Software' 'Ruuid' SubClassOf 'is published by' value 'Bioconductor' 'Ruuid' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'Ruuid' SubClassOf 'has specified data input' some 'Text data set' 'Ruuid' SubClassOf 'is encoded in' some 'R language' 'Ruuid' SubClassOf 'implements' some 'Theodore Ts’o’s' http://www.ebi.ac.uk/swo/SWO_1100076 BCRANK 'BCRANK' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100077 Cosmo 'Cosmo' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000372 Serial Analysis of Gene Expression (SAGE) 'Serial Analysis of Gene Expression (SAGE)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100078 F test 'F test' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000371 S-Score algorithm 'S-Score algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100079 MAGE-TAB inputting software 'MAGE-TAB inputting software' EquivalentTo 'has specified data input' some ('data item' and ('has format specification' some 'MAGE-TAB')) 'MAGE-TAB inputting software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000385 SMAP 'SMAP' SubClassOf 'software' 'SMAP' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'SMAP' SubClassOf 'BioConductor Software' 'SMAP' SubClassOf 'R software' 'SMAP' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'SMAP' SubClassOf 'is published by' value 'Bioconductor' 'SMAP' SubClassOf 'is executed in' some ('data visualization' and 'descriptive statistical calculation') 'SMAP' SubClassOf 'implements' some 'Hidden Markov Model' 'SMAP' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_1100061 Category analysis 'Category analysis' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000384 SLqPCR 'SLqPCR' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'SLqPCR' SubClassOf 'R software' 'SLqPCR' SubClassOf 'is encoded in' some 'R language' 'SLqPCR' SubClassOf 'is published by' value 'Bioconductor' 'SLqPCR' SubClassOf 'is executed in' some ('data normalization' and 'descriptive statistical calculation') 'SLqPCR' SubClassOf 'BioConductor Software' 'SLqPCR' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'SLqPCR' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100062 Category 'Category' SubClassOf 'R software' 'Category' SubClassOf 'BioConductor Software' 'Category' SubClassOf 'has specified data output' some ('Heat map' and ('has format specification' some 'image format')) 'Category' SubClassOf 'has specified data output' some 'Graph plot' 'Category' SubClassOf 'software' 'Category' SubClassOf 'is encoded in' some 'R language' 'Category' SubClassOf 'is executed in' some 'differential expression analysis' 'Category' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'Category' SubClassOf 'implements' some 'Category analysis' 'Category' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000387 SNPchip 'SNPchip' SubClassOf 'is published by' value 'Bioconductor' 'SNPchip' SubClassOf 'R software' 'SNPchip' SubClassOf 'is encoded in' some 'R language' 'SNPchip' SubClassOf 'BioConductor Software' 'SNPchip' SubClassOf 'software' 'SNPchip' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'SNPchip' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'SNPchip' SubClassOf 'implements' some ('data visualization' and 'data annotation' and 'descriptive statistical calculation') 'SNPchip' SubClassOf 'implements' some 'Hidden Markov Model' http://www.ebi.ac.uk/swo/SWO_1100063 'ChemmineR' ''ChemmineR'' SubClassOf 'is executed in' some 'distance calculation' ''ChemmineR'' SubClassOf 'is encoded in' some 'R language' ''ChemmineR'' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) ''ChemmineR'' SubClassOf 'software' ''ChemmineR'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'SDF format')) ''ChemmineR'' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) ''ChemmineR'' SubClassOf 'implements' some 'Binning clustering method' ''ChemmineR'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000386 SNPRMA algorithm 'SNPRMA algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100064 ChipReader 3.1 'ChipReader 3.1' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Bio-Rad Laboratories, Inc.')) 'ChipReader 3.1' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000389 Semantic Similarity Measures 'Semantic Similarity Measures' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000388 SPIA 'SPIA' SubClassOf 'R software' 'SPIA' SubClassOf 'is encoded in' some 'R language' 'SPIA' SubClassOf 'is published by' value 'Bioconductor' 'SPIA' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'SPIA' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'SPIA' SubClassOf 'has specified data input' some 'Gene expression dataset' 'SPIA' SubClassOf 'BioConductor Software' 'SPIA' SubClassOf 'implements' some 'Signaling Pathway Impact Analysis (SPIA) algorithm' 'SPIA' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100060 CARMAweb 'CARMAweb' SubClassOf 'software' 'CARMAweb' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Institute for Genomics and Bioinformatics Graz University of Technology')) http://www.ebi.ac.uk/swo/SWO_1100069 affycomp 'affycomp' SubClassOf 'implements' some ('RMA' and ''MAS5'') 'affycomp' SubClassOf 'software' 'affycomp' SubClassOf 'is encoded in' some 'R language' 'affycomp' SubClassOf 'is executed in' some ('dataset comparison' and 'correction') 'affycomp' SubClassOf 'R software' 'affycomp' SubClassOf 'has specified data input' some 'CSV data set' 'affycomp' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') http://www.ebi.ac.uk/swo/SWO_0000381 SDF format 'SDF format' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_1100065 ChipSkipper 'ChipSkipper' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'EMBL')) 'ChipSkipper' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100066 ChipSkipper V0.99 'ChipSkipper V0.99' SubClassOf 'ChipSkipper' http://www.ebi.ac.uk/swo/SWO_0000383 SLGI 'SLGI' SubClassOf 'software' 'SLGI' SubClassOf 'is encoded in' some 'R language' 'SLGI' SubClassOf 'BioConductor Software' 'SLGI' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'SLGI' SubClassOf 'is published by' value 'Bioconductor' 'SLGI' SubClassOf 'R software' 'SLGI' SubClassOf 'has specified data input' some 'Annotation data packages' http://www.ebi.ac.uk/swo/SWO_1100067 multiscan 'multiscan' SubClassOf 'has specified data output' some 'Graph plot' 'multiscan' SubClassOf 'R software' 'multiscan' SubClassOf 'software' 'multiscan' SubClassOf 'implements' some 'Non-linear functional regression model' 'multiscan' SubClassOf 'is encoded in' some 'R language' 'multiscan' SubClassOf 'has specified data input' some ('Text data set' or 'CSV data set') 'multiscan' SubClassOf 'is executed in' some 'differential expression analysis' http://www.ebi.ac.uk/swo/SWO_0000382 SIM 'SIM' SubClassOf 'software' 'SIM' SubClassOf 'R software' 'SIM' SubClassOf 'has specified data input' some 'Gene expression data' 'SIM' SubClassOf 'is encoded in' some 'R language' 'SIM' SubClassOf 'implements' some 'Global test' 'SIM' SubClassOf 'has specified data output' some ('Heat map' and 'Graph plot' and 'Text data set') http://www.ebi.ac.uk/swo/SWO_1100068 affy 'affy' SubClassOf 'implements' some ('RMA' and ''MAS5'') 'affy' SubClassOf 'R software' 'affy' SubClassOf 'has specified data input' some ('has format specification' some ('CEL binary format' or 'CDF binary format' or 'CDF ASCII format' or 'CEL ASCII format')) 'affy' SubClassOf 'is published by' value 'Bioconductor' 'affy' SubClassOf 'software' 'affy' SubClassOf 'has specified data output' some ('Image' and 'Graph plot' and 'Text data set') 'affy' SubClassOf 'BioConductor Software' 'affy' SubClassOf 'is encoded in' some 'R language' 'affy' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'differential expression analysis') http://www.ebi.ac.uk/swo/SWO_1100094 'EBImage' ''EBImage'' SubClassOf 'software' ''EBImage'' SubClassOf 'is encoded in' some 'R language' ''EBImage'' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''EBImage'' SubClassOf 'R software' ''EBImage'' SubClassOf 'has specified data input' some ('Image' and ('has format specification' some 'CEL binary format')) ''EBImage'' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) http://www.ebi.ac.uk/swo/SWO_1100095 'EBarrays' ''EBarrays'' SubClassOf 'implements' some 'Lognormal Normal with Modied Variance Model' ''EBarrays'' SubClassOf 'software' ''EBarrays'' SubClassOf 'implements' some 'Empirical Bayes rule' ''EBarrays'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''EBarrays'' SubClassOf 'implements' some 'Gamma Gamma Model' ''EBarrays'' SubClassOf 'is encoded in' some 'R language' ''EBarrays'' SubClassOf 'R software' ''EBarrays'' SubClassOf 'has specified data input' some ('Gene expression data' and ('has format specification' some 'R data frame')) ''EBarrays'' SubClassOf 'implements' some 'Lognormal Normal Model' ''EBarrays'' SubClassOf 'is executed in' some 'differential expression analysis' ''EBarrays'' SubClassOf 'has specified data output' some ('Clustered data set' and ('has format specification' some 'data format specification')) http://www.ebi.ac.uk/swo/SWO_0000310 Optiquant 'Optiquant' SubClassOf 'output of' some ('software development' and ('has participant' value 'PerkinElmer')) 'Optiquant' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100096 Expectation-Maximization(EM) algorithm 'Expectation-Maximization(EM) algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100097 Empirical Bayes rule 'Empirical Bayes rule' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000312 OutlierD 'OutlierD' SubClassOf 'has specified data input' some ('LC-MS data' and ('has format specification' some 'data format specification')) 'OutlierD' SubClassOf 'software' 'OutlierD' SubClassOf 'is encoded in' some 'R language' 'OutlierD' SubClassOf 'is executed in' some 'data normalization' 'OutlierD' SubClassOf 'R software' 'OutlierD' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'OutlierD' SubClassOf 'implements' some 'Quantile regression techniques' http://www.ebi.ac.uk/swo/SWO_1100090 Discriminant Fuzzy Pattern Algorithm 'Discriminant Fuzzy Pattern Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000311 OrderedList 'OrderedList' SubClassOf 'is encoded in' some 'R language' 'OrderedList' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'OrderedList' SubClassOf 'has specified data output' some ('Gene list' and ('has format specification' some 'data format specification')) 'OrderedList' SubClassOf 'software' 'OrderedList' SubClassOf 'is executed in' some 'differential expression analysis' 'OrderedList' SubClassOf 'R software' 'OrderedList' SubClassOf 'implements' some 'Similarity score' http://www.ebi.ac.uk/swo/SWO_1100091 DFW 'DFW' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000314 PAnnBuilder 'PAnnBuilder' SubClassOf 'software' 'PAnnBuilder' SubClassOf 'has specified data input' some ('Annotation data packages' and ('has format specification' some 'data format specification')) 'PAnnBuilder' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'PAnnBuilder' SubClassOf 'is encoded in' some 'R language' 'PAnnBuilder' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100092 Digital gene expression (DGE) datasets 'Digital gene expression (DGE) datasets' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000313 Presence-Absence calls with Negative Probesets (PANP) 'Presence-Absence calls with Negative Probesets (PANP)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100093 'DNAcopy' ''DNAcopy'' SubClassOf 'software' ''DNAcopy'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) ''DNAcopy'' SubClassOf 'is encoded in' some 'R language' ''DNAcopy'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''DNAcopy'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100098 Expert 2100 'Expert 2100' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) 'Expert 2100' SubClassOf 'Agilent Technologies Software' 'Expert 2100' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100099 FACS data 'FACS data' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000316 PCpheno 'PCpheno' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'PCpheno' SubClassOf 'implements' some 'Global test' 'PCpheno' SubClassOf 'R software' 'PCpheno' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'PCpheno' SubClassOf 'is executed in' some 'differential expression analysis' 'PCpheno' SubClassOf 'software' 'PCpheno' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'PCpheno' SubClassOf 'is encoded in' some 'R language' 'PCpheno' SubClassOf 'implements' some 'Hypergeometric enrichment' 'PCpheno' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) http://www.ebi.ac.uk/swo/SWO_0000315 Pearson correlation estimator 'Pearson correlation estimator' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000318 'PLM' ''PLM'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000317 PGSEA 'PGSEA' SubClassOf 'is encoded in' some 'R language' 'PGSEA' SubClassOf 'R software' 'PGSEA' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'PGSEA' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'data format specification')) 'PGSEA' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'PGSEA' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000319 PLPE 'PLPE' SubClassOf 'software' 'PLPE' SubClassOf 'is executed in' some 'differential expression analysis' 'PLPE' SubClassOf 'implements' some 'Statistical tests' 'PLPE' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'PLPE' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'PLPE' SubClassOf 'R software' 'PLPE' SubClassOf 'is encoded in' some 'R language' 'PLPE' SubClassOf 'has specified data input' some ('LC-MS data' and ('has format specification' some 'data format specification')) http://www.ebi.ac.uk/swo/SWO_1100083 'CoCiteStats' ''CoCiteStats'' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) ''CoCiteStats'' SubClassOf 'R software' ''CoCiteStats'' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''CoCiteStats'' SubClassOf 'is executed in' some 'descriptive statistical calculation' ''CoCiteStats'' SubClassOf 'is encoded in' some 'R language' ''CoCiteStats'' SubClassOf 'software' ''CoCiteStats'' SubClassOf 'implements' some 'Concordance' ''CoCiteStats'' SubClassOf 'implements' some 'Hubert’s gamma' ''CoCiteStats'' SubClassOf 'implements' some 'Jaccard’s index' http://www.ebi.ac.uk/swo/SWO_1100084 CodeLink Expression Analysis Software 'CodeLink Expression Analysis Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Motorola Life Sciences')) 'CodeLink Expression Analysis Software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000321 PPC algorithm 'PPC algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100085 CodeLink Expression Scanning Software 'CodeLink Expression Scanning Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Motorola Life Sciences')) 'CodeLink Expression Scanning Software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000320 Probe level Locally moderated Weighted median-t (PLW) method 'Probe level Locally moderated Weighted median-t (PLW) method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100086 Complex Estimation Algorithm 'Complex Estimation Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000323 Propagation of uncertainty in microarray analysis 'Propagation of uncertainty in microarray analysis' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000322 PROcess 'PROcess' SubClassOf 'implements' some 'k-nearest neighbour classification' 'PROcess' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'PROcess' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'PROcess' SubClassOf 'is executed in' some 'background correction' 'PROcess' SubClassOf 'is encoded in' some 'R language' 'PROcess' SubClassOf 'R software' 'PROcess' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some 'data format specification')) 'PROcess' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100080 Text data set 'Text data set' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_1100081 CSV data set 'CSV data set' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000324 Pathways 2.01 software 'Pathways 2.01 software' SubClassOf 'output of' some ('software development' and ('has participant' value 'Research Genetics')) 'Pathways 2.01 software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100082 Non-linear functional regression model 'Non-linear functional regression model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100087 Cyber-T 'Cyber-T' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'UC Irvine')) 'Cyber-T' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100088 'DEDS' ''DEDS'' SubClassOf 'is encoded in' some 'R language' ''DEDS'' SubClassOf 'is executed in' some 'differential expression analysis' ''DEDS'' SubClassOf 'implements' some ''FDR'' ''DEDS'' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) ''DEDS'' SubClassOf 'software' ''DEDS'' SubClassOf 'implements' some ''t-test'' ''DEDS'' SubClassOf 'implements' some 'SAM' ''DEDS'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''DEDS'' SubClassOf 'R software' ''DEDS'' SubClassOf 'is executed in' some 'descriptive statistical calculation' ''DEDS'' SubClassOf 'implements' some 'FC' http://www.ebi.ac.uk/swo/SWO_1100089 'DFP' ''DFP'' SubClassOf 'R software' ''DFP'' SubClassOf 'is executed in' some 'differential expression analysis' ''DFP'' SubClassOf 'is encoded in' some 'R language' ''DFP'' SubClassOf 'software' ''DFP'' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some http://edamontology.org/format_2330)) ''DFP'' SubClassOf 'implements' some 'Discriminant Fuzzy Pattern Algorithm' ''DFP'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) http://www.ebi.ac.uk/swo/SWO_0000327 Probe Cell Analysis 'Probe Cell Analysis' SubClassOf 'MicroArraySuite 5.0' http://www.ebi.ac.uk/swo/SWO_0000326 Power Law Global Error Model (PLGEM) analysis method 'Power Law Global Error Model (PLGEM) analysis method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000329 QuantArray scanner software 'QuantArray scanner software' SubClassOf 'output of' some ('software development' and ('has participant' value 'PerkinElmer')) 'QuantArray scanner software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000328 PLIER (Probe Logarithmic Error Intensity Estimate) method 'PLIER (Probe Logarithmic Error Intensity Estimate) method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000330 QuantArray, PackaardBiochip technologies 'QuantArray, PackaardBiochip technologies' SubClassOf 'QuantArray scanner software' http://www.ebi.ac.uk/swo/SWO_0000332 Radial basis function 'Radial basis function' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000331 QuantArray version 2 'QuantArray version 2' SubClassOf 'QuantArray scanner software' http://www.ebi.ac.uk/swo/SWO_0000334 R interface to boost graph library algorithm (RBGL) 'R interface to boost graph library algorithm (RBGL)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000333 RBGL 'RBGL' SubClassOf 'software' 'RBGL' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'RBGL' SubClassOf 'implements' some 'BGL' 'RBGL' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'gxl format')) 'RBGL' SubClassOf 'is executed in' some 'data visualization' 'RBGL' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'XML')) 'RBGL' SubClassOf 'R software' 'RBGL' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'RBGL' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000336 Random effects model 'Random effects model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000335 RBioinf 'RBioinf' SubClassOf 'implements' some 'Linear modelling' 'RBioinf' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) 'RBioinf' SubClassOf 'R software' 'RBioinf' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'RBioinf' SubClassOf 'software' 'RBioinf' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000338 RLMM 'RLMM' SubClassOf 'is published by' value 'Bioconductor' 'RLMM' SubClassOf 'R software' 'RLMM' SubClassOf 'has specified data input' some ('has format specification' only ('Xba.CQV and Xba.regions' and '.raw files')) 'RLMM' SubClassOf 'software' 'RLMM' SubClassOf 'implements' some 'Mahalanobis distance' 'RLMM' SubClassOf 'has specified data output' some 'Graph plot' 'RLMM' SubClassOf 'is executed in' some 'data normalization' 'RLMM' SubClassOf 'BioConductor Software' 'RLMM' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000337 Recursive Feature Elimination (RFE) 'Recursive Feature Elimination (RFE)' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000339 Regression model 'Regression model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000341 RMA+ 'RMA+' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000340 RMA 'RMA' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000343 RMAExpress 'RMAExpress' SubClassOf 'is developed by' value 'University Of California, Berkeley' 'RMAExpress' SubClassOf 'has specified data output' some 'Text data set' 'RMAExpress' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' and 'CDF binary format')) 'RMAExpress' SubClassOf 'implements' some ('background correction' and 'data normalization') 'RMAExpress' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000342 RMA++ 'RMA++' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000345 RMAExpress quantification 'RMAExpress quantification' SubClassOf 'RMAExpress' http://www.ebi.ac.uk/swo/SWO_0000344 RMAExpress 2.0 'RMAExpress 2.0' SubClassOf 'RMAExpress' http://www.ebi.ac.uk/swo/SWO_0000347 RNAither 'RNAither' SubClassOf 'R software' 'RNAither' SubClassOf 'has specified data input' some 'Text data set' 'RNAither' SubClassOf 'is executed in' some ('data normalization' and 'descriptive statistical calculation') 'RNAither' SubClassOf 'has specified data output' some 'HTML report' 'RNAither' SubClassOf 'software' 'RNAither' SubClassOf 'is encoded in' some 'R language' 'RNAither' SubClassOf 'implements' some 'Gene-Set Enrichment Analysis' http://www.ebi.ac.uk/swo/SWO_0000346 RMAGEML 'RMAGEML' SubClassOf 'BioConductor Software' 'RMAGEML' SubClassOf 'has specified data input' some ('has format specification' only 'MAGE-ML') 'RMAGEML' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' only 'R data frame')) 'RMAGEML' SubClassOf 'is encoded in' some 'R language' 'RMAGEML' SubClassOf 'software' 'RMAGEML' SubClassOf 'is published by' value 'Bioconductor' 'RMAGEML' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000349 RWebServices 'RWebServices' SubClassOf 'has specified data input' some ('has format specification' only ('R data frame' and '.data' and '.java file')) 'RWebServices' SubClassOf 'R software' 'RWebServices' SubClassOf 'BioConductor Software' 'RWebServices' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'RWebServices' SubClassOf 'is encoded in' some 'R language' 'RWebServices' SubClassOf 'is published by' value 'Bioconductor' 'RWebServices' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000348 ROC 'ROC' SubClassOf 'has specified data input' some 'Gene expression dataset' 'ROC' SubClassOf 'is published by' value 'Bioconductor' 'ROC' SubClassOf 'is encoded in' some 'R language' 'ROC' SubClassOf 'software' 'ROC' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'ROC' SubClassOf 'R software' 'ROC' SubClassOf 'BioConductor Software' http://purl.obolibrary.org/obo/SWO_1100133 Stavrox 'Stavrox' SubClassOf 'has website homepage' value "http://www.stavrox.com" 'Stavrox' SubClassOf 'software' http://purl.obolibrary.org/obo/SWO_1100134 ProteomicsTools 'ProteomicsTools' SubClassOf 'has website homepage' value "https://github.com/shengqh/RCPA.Tools/wiki" 'ProteomicsTools' SubClassOf 'software' 'ProteomicsTools' SubClassOf 'has license' some 'GNU GPL v3' http://www.ebi.ac.uk/swo/SWO_0000305 Nested Effects Models 'Nested Effects Models' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000304 'Needleman-Wunsch' ''Needleman-Wunsch'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000307 OCplus 'OCplus' SubClassOf 'software' 'OCplus' SubClassOf 'has specified data input' some ('Gene expression data' and ('has format specification' some 'data format specification')) 'OCplus' SubClassOf 'R software' 'OCplus' SubClassOf 'is encoded in' some 'R language' 'OCplus' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'OCplus' SubClassOf 'implements' some ''FDR'' 'OCplus' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) http://www.ebi.ac.uk/swo/SWO_0000306 Nonlinear Estimation by Iterative Partial Least Squares 'Nonlinear Estimation by Iterative Partial Least Squares' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000309 OLINgui 'OLINgui' SubClassOf 'is executed in' some 'background correction' 'OLINgui' SubClassOf 'software' 'OLINgui' SubClassOf 'has specified data input' some ('Gene expression data' and ('has format specification' some 'data format specification')) 'OLINgui' SubClassOf 'is encoded in' some 'R language' 'OLINgui' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'OLINgui' SubClassOf 'is executed in' some 'data normalization' 'OLINgui' SubClassOf 'R software' 'OLINgui' SubClassOf 'is executed in' some 'data visualization' 'OLINgui' SubClassOf 'implements' some 'Iterative local regression and model selection' http://www.ebi.ac.uk/swo/SWO_0000308 OLIN 'OLIN' SubClassOf 'is executed in' some 'correction' 'OLIN' SubClassOf 'is executed in' some 'data normalization' 'OLIN' SubClassOf 'implements' some 'Iterative local regression and model selection' 'OLIN' SubClassOf 'R software' 'OLIN' SubClassOf 'is encoded in' some 'R language' 'OLIN' SubClassOf 'software' 'OLIN' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'OLIN' SubClassOf 'has specified data input' some ('Gene expression data' and ('has format specification' some 'data format specification')) http://www.ebi.ac.uk/swo/SWO_0000710 sscore 'sscore' SubClassOf 'R software' 'sscore' SubClassOf 'is published by' value 'Bioconductor' 'sscore' SubClassOf 'software' 'sscore' SubClassOf 'has specified data input' some ('has format specification' only 'CEL binary format') 'sscore' SubClassOf 'implements' some 'S-Score algorithm' 'sscore' SubClassOf 'is encoded in' some 'R language' 'sscore' SubClassOf 'BioConductor Software' 'sscore' SubClassOf 'has specified data input' some 'Gene expression dataset' http://www.ebi.ac.uk/swo/SWO_0000719 topGO 'topGO' SubClassOf 'R software' 'topGO' SubClassOf 'implements' some 'Kolmogorov Smirnov rank-sum based algorithm' 'topGO' SubClassOf 'BioConductor Software' 'topGO' SubClassOf 'has specified data input' some 'Gene list' 'topGO' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'topGO' SubClassOf 'is encoded in' some 'R language' 'topGO' SubClassOf 'software' 'topGO' SubClassOf 'is published by' value 'Bioconductor' 'topGO' SubClassOf 'is executed in' some 'differential expression analysis' http://www.ebi.ac.uk/swo/SWO_0000712 stam 'stam' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'stam' SubClassOf 'R software' 'stam' SubClassOf 'is encoded in' some 'R language' 'stam' SubClassOf 'is executed in' some ('data annotation' and 'cross validation') 'stam' SubClassOf 'software' 'stam' SubClassOf 'has specified data input' some 'Gene expression data' http://www.ebi.ac.uk/swo/SWO_0000711 ssize 'ssize' SubClassOf 'software' 'ssize' SubClassOf 'implements' some 'RMA' 'ssize' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'ssize' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'ssize' SubClassOf 'is executed in' some 'data visualization' 'ssize' SubClassOf 'is published by' value 'Bioconductor' 'ssize' SubClassOf 'R software' 'ssize' SubClassOf 'is encoded in' some 'R language' 'ssize' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000714 stepNorm 'stepNorm' SubClassOf 'has specified data input' some 'Gene expression data' 'stepNorm' SubClassOf 'is executed in' some 'data normalization' 'stepNorm' SubClassOf 'has specified data output' some 'Gene expression data' 'stepNorm' SubClassOf 'R software' 'stepNorm' SubClassOf 'is encoded in' some 'R language' 'stepNorm' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000713 Statistical tests 'Statistical tests' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000716 tilingArray 'tilingArray' SubClassOf 'BioConductor Software' 'tilingArray' SubClassOf 'is published by' value 'Bioconductor' 'tilingArray' SubClassOf 'R software' 'tilingArray' SubClassOf 'software' 'tilingArray' SubClassOf 'has specified data input' some ('has format specification' only 'CEL binary format') 'tilingArray' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'tilingArray' SubClassOf 'is executed in' some ('data visualization' and 'background correction' and 'data normalization') 'tilingArray' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000715 't-test' ''t-test'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000718 tkWidgets 'tkWidgets' SubClassOf 'software' 'tkWidgets' SubClassOf 'is encoded in' some 'R language' 'tkWidgets' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000717 timecourse 'timecourse' SubClassOf 'implements' some 'RMA' 'timecourse' SubClassOf 'is encoded in' some 'R language' 'timecourse' SubClassOf 'has specified data output' some ('has format specification' only 'CEL binary format') 'timecourse' SubClassOf 'R software' 'timecourse' SubClassOf 'has specified data input' some 'Gene expression dataset' 'timecourse' SubClassOf 'BioConductor Software' 'timecourse' SubClassOf 'is published by' value 'Bioconductor' 'timecourse' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000721 twilight 'twilight' SubClassOf 'software' 'twilight' SubClassOf 'BioConductor Software' 'twilight' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'twilight' SubClassOf 'has specified data input' some 'Gene expression dataset' 'twilight' SubClassOf 'implements' some ('Pearson correlation estimator' and ''t-test'') 'twilight' SubClassOf 'is encoded in' some 'R language' 'twilight' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'twilight' SubClassOf 'R software' 'twilight' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000720 tspair 'tspair' SubClassOf 'is encoded in' some 'R language' 'tspair' SubClassOf 'is executed in' some ('cross validation' and 'descriptive statistical calculation') 'tspair' SubClassOf 'is published by' value 'Bioconductor' 'tspair' SubClassOf 'BioConductor Software' 'tspair' SubClassOf 'R software' 'tspair' SubClassOf 'has specified data input' some 'Gene expression dataset' 'tspair' SubClassOf 'software' 'tspair' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) http://www.ebi.ac.uk/swo/SWO_0000723 vbmp 'vbmp' SubClassOf 'is encoded in' some 'R language' 'vbmp' SubClassOf 'BioConductor Software' 'vbmp' SubClassOf 'implements' some 'Multinomial probit regression with Gaussian Process priors' 'vbmp' SubClassOf 'software' 'vbmp' SubClassOf 'is executed in' some 'cross validation' 'vbmp' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'vbmp' SubClassOf 'is published by' value 'Bioconductor' 'vbmp' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'vbmp' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000722 Two-stage measurement error model 'Two-stage measurement error model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000725 vsn 'vsn' SubClassOf 'software' 'vsn' SubClassOf 'has specified data input' some 'Gene expression dataset' 'vsn' SubClassOf 'is executed in' some ('correction' and 'data normalization' and 'differential expression analysis') 'vsn' SubClassOf 'R software' 'vsn' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000727 webbioc 'webbioc' SubClassOf 'is encoded in' some 'R language' 'webbioc' SubClassOf 'implements' some 'Multiple testing' 'webbioc' SubClassOf 'software' 'webbioc' SubClassOf 'R software' 'webbioc' SubClassOf 'has specified data output' some 'HTML report' 'webbioc' SubClassOf 'has specified data input' some ('has format specification' only 'CEL binary format') 'webbioc' SubClassOf 'is published by' value 'Bioconductor' 'webbioc' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000726 weaver 'weaver' SubClassOf 'is published by' value 'Bioconductor' 'weaver' SubClassOf 'has specified data input' some ('has format specification' only 'Rnw') 'weaver' SubClassOf 'R software' 'weaver' SubClassOf 'has specified data output' some ('has format specification' only 'Rnw') 'weaver' SubClassOf 'is encoded in' some 'R language' 'weaver' SubClassOf 'software' 'weaver' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000729 xcms 'xcms' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'xcms' SubClassOf 'software' 'xcms' SubClassOf 'R software' 'xcms' SubClassOf 'is published by' value 'Bioconductor' 'xcms' SubClassOf 'is encoded in' some 'R language' 'xcms' SubClassOf 'has specified data input' some 'LC-MS data' 'xcms' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000728 widgetTools 'widgetTools' SubClassOf 'is encoded in' some 'R language' 'widgetTools' SubClassOf 'R software' 'widgetTools' SubClassOf 'software' 'widgetTools' SubClassOf 'has specified data input' some 'Text data set' http://www.ebi.ac.uk/swo/SWO_0000730 xps 'xps' SubClassOf 'implements' some ('RMA' and ''MAS5'' and 'DFW' and 'FARMS') 'xps' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'xps' SubClassOf 'BioConductor Software' 'xps' SubClassOf 'is published by' value 'Bioconductor' 'xps' SubClassOf 'is encoded in' some 'R language' 'xps' SubClassOf 'has specified data input' some ('has format specification' only 'CEL binary format') 'xps' SubClassOf 'R software' 'xps' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000731 yaqcaffy 'yaqcaffy' SubClassOf 'has specified data output' some 'Graph plot' 'yaqcaffy' SubClassOf 'is encoded in' some 'R language' 'yaqcaffy' SubClassOf 'software' 'yaqcaffy' SubClassOf 'has specified data input' some 'Gene expression dataset' 'yaqcaffy' SubClassOf 'R software' http://purl.obolibrary.org/obo/SWO_1100144 FastQC 'FastQC' SubClassOf 'has website homepage' value "https://github.com/s-andrews/FastQC" 'FastQC' SubClassOf 'has license' some 'GNU GPL v2' 'FastQC' SubClassOf 'software' http://purl.obolibrary.org/obo/SWO_1100145 CutAdapt 'CutAdapt' SubClassOf 'software' 'CutAdapt' SubClassOf 'has website homepage' value "https://cutadapt.readthedocs.io/en/stable/" 'CutAdapt' SubClassOf 'has license' some 'MIT License' http://purl.obolibrary.org/obo/SWO_1100142 RSeQC 'RSeQC' SubClassOf 'software' 'RSeQC' SubClassOf 'has license' some 'GNU GPL v3' 'RSeQC' SubClassOf 'has website homepage' value "http://rseqc.sourceforge.net/" http://purl.obolibrary.org/obo/SWO_1100143 SAMtools 'SAMtools' SubClassOf 'has license' some 'MIT License' 'SAMtools' SubClassOf 'has website homepage' value "https://github.com/samtools/samtools" 'SAMtools' SubClassOf 'software' http://purl.obolibrary.org/obo/SWO_1100140 HTSeq 'HTSeq' SubClassOf 'has website homepage' value "https://htseq.readthedocs.io/en/release_0.11.1/" 'HTSeq' SubClassOf 'software' 'HTSeq' SubClassOf 'has license' some 'GNU GPL v3' http://purl.obolibrary.org/obo/SWO_1100141 RNA-SeQC 'RNA-SeQC' SubClassOf 'has license' some 'Modified BSD' 'RNA-SeQC' SubClassOf 'software' 'RNA-SeQC' SubClassOf 'has website homepage' value "https://github.com/broadinstitute/rnaseqc" http://purl.obolibrary.org/obo/SWO_1100139 PEAKS DB 'PEAKS DB' SubClassOf 'has license' some 'Proprietary commercial software license' 'PEAKS DB' SubClassOf 'has website homepage' value "http://www.bioinfor.com/peaksdb/" 'PEAKS DB' SubClassOf 'software' http://purl.obolibrary.org/obo/SWO_1100137 SWATH Software 'SWATH Software' SubClassOf 'software' 'SWATH Software' SubClassOf 'has website homepage' value "https://sciex.com/technology/swath-acquisition" 'SWATH Software' SubClassOf 'has license' some 'Proprietary commercial software license' http://purl.obolibrary.org/obo/SWO_1100138 Supernovo 'Supernovo' SubClassOf 'software' 'Supernovo' SubClassOf 'has website homepage' value "https://www.proteinmetrics.com/products/supernovo/" 'Supernovo' SubClassOf 'has license' some 'Proprietary commercial software license' http://purl.obolibrary.org/obo/SWO_1100135 Chromeleon 'Chromeleon' SubClassOf 'has license' some 'Proprietary commercial software license' 'Chromeleon' SubClassOf 'software' 'Chromeleon' SubClassOf 'has website homepage' value "https://www.thermofisher.com/order/catalog/product/CHROMELEON7#/CHROMELEON7" http://purl.obolibrary.org/obo/SWO_1100136 AnalyzerPro 'AnalyzerPro' SubClassOf 'software' 'AnalyzerPro' SubClassOf 'has license' some 'Proprietary commercial software license' 'AnalyzerPro' SubClassOf 'has website homepage' value "https://www.spectralworks.com/products/analyzerpro/" http://www.ebi.ac.uk/swo/SWO_0000709 sqlite 'sqlite' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000708 sproc 'sproc' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000701 snpMatrix 'snpMatrix' SubClassOf 'R software' 'snpMatrix' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'snpMatrix' SubClassOf 'software' 'snpMatrix' SubClassOf 'is published by' value 'Bioconductor' 'snpMatrix' SubClassOf 'BioConductor Software' 'snpMatrix' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'snpMatrix' SubClassOf 'is encoded in' some 'R language' 'snpMatrix' SubClassOf 'is executed in' some ('data visualization' and 'descriptive statistical calculation') 'snpMatrix' SubClassOf 'implements' some 'Chi-square' http://www.ebi.ac.uk/swo/SWO_0000700 snapCGH 'snapCGH' SubClassOf 'is executed in' some ('data visualization' and 'correction') 'snapCGH' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'snapCGH' SubClassOf 'BioConductor Software' 'snapCGH' SubClassOf 'R software' 'snapCGH' SubClassOf 'implements' some 'Hidden Markov Model' 'snapCGH' SubClassOf 'has specified data input' some 'Text data set' 'snapCGH' SubClassOf 'is published by' value 'Bioconductor' 'snapCGH' SubClassOf 'software' 'snapCGH' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000703 spikeLI 'spikeLI' SubClassOf 'has specified data input' some 'Gene expression dataset' 'spikeLI' SubClassOf 'software' 'spikeLI' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'spikeLI' SubClassOf 'is encoded in' some 'R language' 'spikeLI' SubClassOf 'implements' some 'Langmuir Isotherm' 'spikeLI' SubClassOf 'R software' 'spikeLI' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000705 splicegear 'splicegear' SubClassOf 'is encoded in' some 'R language' 'splicegear' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'splicegear' SubClassOf 'is published by' value 'Bioconductor' 'splicegear' SubClassOf 'software' 'splicegear' SubClassOf 'has specified data input' some ('has format specification' only 'XML') 'splicegear' SubClassOf 'R software' 'splicegear' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000704 spkTools 'spkTools' SubClassOf 'R software' 'spkTools' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'spkTools' SubClassOf 'software' 'spkTools' SubClassOf 'implements' some ('Average log expression across arrays (ALE)' and ''ANOVA'') 'spkTools' SubClassOf 'is encoded in' some 'R language' 'spkTools' SubClassOf 'has specified data input' some 'Gene expression dataset' http://www.ebi.ac.uk/swo/SWO_0000707 spotSegmentation 'spotSegmentation' SubClassOf 'is published by' value 'Bioconductor' 'spotSegmentation' SubClassOf 'implements' some 'clustering algorithm' 'spotSegmentation' SubClassOf 'software' 'spotSegmentation' SubClassOf 'is executed in' some 'background correction' 'spotSegmentation' SubClassOf 'is encoded in' some 'R language' 'spotSegmentation' SubClassOf 'BioConductor Software' 'spotSegmentation' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'spotSegmentation' SubClassOf 'R software' 'spotSegmentation' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000706 splots 'splots' SubClassOf 'is published by' value 'Bioconductor' 'splots' SubClassOf 'R software' 'splots' SubClassOf 'is encoded in' some 'R language' 'splots' SubClassOf 'has specified data output' some 'Graph plot' 'splots' SubClassOf 'software' 'splots' SubClassOf 'is executed in' some 'data visualization' 'splots' SubClassOf 'BioConductor Software' 'splots' SubClassOf 'has specified data input' some ('has format specification' only 'chamber slide format') http://www.ontodm.com/OntoDM-core/OntoDM_419460 single generalization specification 'single generalization specification' SubClassOf 'generalization specification' http://www.ebi.ac.uk/swo/SWO_0000084 CEL binary format 'CEL binary format' SubClassOf 'binary format' 'CEL binary format' SubClassOf 'is published by' value 'Affymetrix' http://www.ebi.ac.uk/swo/SWO_1100113 GGBase 'GGBase' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) 'GGBase' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'GGBase' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'rda')) 'GGBase' SubClassOf 'software' 'GGBase' SubClassOf 'is encoded in' some 'R language' 'GGBase' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GGBase' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100114 Gamma Gamma Model 'Gamma Gamma Model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100115 matlab software 'matlab software' SubClassOf 'software' 'matlab software' EquivalentTo 'is encoded in' some 'MATLAB language' http://www.ontodm.com/OntoDM-core/OntoDM_000285 probability distribution specification 'probability distribution specification' SubClassOf 'single generalization specification' http://www.ebi.ac.uk/swo/SWO_1100116 AtlasImage 'AtlasImage' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Clontech Laboratories, Inc')) 'AtlasImage' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100110 GEO data type 'GEO data type' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_1100111 GEOmetadb 'GEOmetadb' SubClassOf 'R software' 'GEOmetadb' SubClassOf 'software' 'GEOmetadb' SubClassOf 'is encoded in' some 'R language' 'GEOmetadb' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) http://www.ebi.ac.uk/swo/SWO_1100112 GEOquery 'GEOquery' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'R data frame')) 'GEOquery' SubClassOf 'software' 'GEOquery' SubClassOf 'R software' 'GEOquery' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_1100117 CBS 'CBS' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100118 CBS algorithm 'CBS algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100119 'CGHbase' ''CGHbase'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''CGHbase'' SubClassOf 'is executed in' some 'data normalization' ''CGHbase'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) ''CGHbase'' SubClassOf 'software' ''CGHbase'' SubClassOf 'is executed in' some 'averaging' ''CGHbase'' SubClassOf 'is encoded in' some 'R language' ''CGHbase'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_1100102 'FDR' ''FDR'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100103 Fixed effect model 'Fixed effect model' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100104 Agilent Feature Extraction Software 'Agilent Feature Extraction Software' SubClassOf 'software' 'Agilent Feature Extraction Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) 'Agilent Feature Extraction Software' SubClassOf 'Agilent Technologies Software' 'Agilent Feature Extraction Software' SubClassOf 'is executed in' some 'feature extraction' http://www.ebi.ac.uk/swo/SWO_1100105 Fischer's Exact Test 'Fischer's Exact Test' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100100 FARMS 'FARMS' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100101 FC 'FC' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100106 GACK 'GACK' SubClassOf 'software' 'GACK' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Stanford University')) http://www.ebi.ac.uk/swo/SWO_1100107 GASSCO method 'GASSCO method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100108 GC-RMA Quantification 'GC-RMA Quantification' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) 'GC-RMA Quantification' SubClassOf 'Agilent Technologies Software' 'GC-RMA Quantification' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100109 GEMTools 2.4 'GEMTools 2.4' SubClassOf 'software' 'GEMTools 2.4' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Incyte Genomics')) http://www.ebi.ac.uk/swo/SWO_0000032 Agilent Scan Control 'Agilent Scan Control' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) 'Agilent Scan Control' SubClassOf 'software' 'Agilent Scan Control' SubClassOf 'Agilent Technologies Software' http://www.ebi.ac.uk/swo/SWO_0000035 'AnnotationDbi' ''AnnotationDbi'' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'sqlite')) ''AnnotationDbi'' SubClassOf 'software' ''AnnotationDbi'' SubClassOf 'is encoded in' some 'R language' ''AnnotationDbi'' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some http://edamontology.org/format_2330)) ''AnnotationDbi'' SubClassOf 'has specified data output' some ('Bitmap object' and ('has format specification' some 'data format specification')) ''AnnotationDbi'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000034 Agilent Technologies Software 'Agilent Technologies Software' SubClassOf 'software' 'Agilent Technologies Software' EquivalentTo 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) http://www.ebi.ac.uk/swo/SWO_1100130 Seurat 'Seurat' SubClassOf 'has license' some 'GNU GPL v3' 'Seurat' SubClassOf 'has website homepage' value "https://satijalab.org/seurat/" 'Seurat' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000037 Applied Biosystems 1700 Expression Array System Software 'Applied Biosystems 1700 Expression Array System Software' SubClassOf 'software' 'Applied Biosystems 1700 Expression Array System Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Applied Biosystems')) http://www.ebi.ac.uk/swo/SWO_0000039 ArrayGauge 'ArrayGauge' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Fujifilm')) 'ArrayGauge' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100131 Graphpad Prism 'Graphpad Prism' SubClassOf 'has website homepage' value "https://www.graphpad.com/scientific-software/prism/" 'Graphpad Prism' SubClassOf 'has license' some 'Proprietary commercial software license' 'Graphpad Prism' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100132 Salmon 'Salmon' SubClassOf 'has website homepage' value "https://combine-lab.github.io/salmon/" 'Salmon' SubClassOf 'software' 'Salmon' SubClassOf 'has license' some 'GNU GPL v3' http://www.ebi.ac.uk/swo/SWO_0000045 Array_vision_(Interfocus) 'Array_vision_(Interfocus)' SubClassOf 'ArrayVision' http://www.ebi.ac.uk/swo/SWO_0000048 BAC 'BAC' SubClassOf 'has specified data output' some ('has format specification' some 'BED format') 'BAC' SubClassOf 'implements' some 'Bayesian Model' 'BAC' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) 'BAC' SubClassOf 'software' 'BAC' SubClassOf 'BioConductor Software' 'BAC' SubClassOf 'is encoded in' some 'R language' 'BAC' SubClassOf 'R software' 'BAC' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000047 Axon GenePix Pro 3 'Axon GenePix Pro 3' SubClassOf 'GenePix Pro [Axon Instruments]' http://www.ebi.ac.uk/swo/SWO_0000049 Binning clustering method 'Binning clustering method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100124 'DynDoc' ''DynDoc'' SubClassOf 'is encoded in' some 'R language' ''DynDoc'' SubClassOf 'R software' ''DynDoc'' SubClassOf 'software' ''DynDoc'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'Rnw')) http://www.ebi.ac.uk/swo/SWO_1100125 FoxDimmicT 'FoxDimmicT' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100126 GEO Matrix Series format 'GEO Matrix Series format' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_1100127 software before Microsoft 2007 'software before Microsoft 2007' EquivalentTo 'software' and ('has version' some ('version name' and ('followed by' value 'Microsoft 2007 version'))) 'software before Microsoft 2007' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000040 ArrayNorm 'ArrayNorm' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Institute for Genomics and Bioinformatics Graz University of Technology')) 'ArrayNorm' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100120 'CGHcall' ''CGHcall'' SubClassOf 'implements' some 'CBS algorithm' ''CGHcall'' SubClassOf 'software' ''CGHcall'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) ''CGHcall'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''CGHcall'' SubClassOf 'R software' ''CGHcall'' SubClassOf 'is executed in' some 'data normalization' ''CGHcall'' SubClassOf 'is executed in' some 'averaging' ''CGHcall'' SubClassOf 'is encoded in' some 'R language' ''CGHcall'' SubClassOf 'is executed in' some 'descriptive statistical calculation' http://www.ebi.ac.uk/swo/SWO_1100121 'CGHregions' ''CGHregions'' SubClassOf 'implements' some 'CBS algorithm' ''CGHregions'' SubClassOf 'has specified data input' some ('data item' and ('has format specification' some 'R data frame')) ''CGHregions'' SubClassOf 'R software' ''CGHregions'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''CGHregions'' SubClassOf 'software' ''CGHregions'' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000042 ArrayVision 'ArrayVision' SubClassOf 'software' 'ArrayVision' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'GE Healthcare Life Sciences')) http://www.ebi.ac.uk/swo/SWO_1100122 CHP binary format 'CHP binary format' SubClassOf 'binary format' 'CHP binary format' SubClassOf 'is published by' value 'Affymetrix' http://www.ebi.ac.uk/swo/SWO_0000041 'ArrayTools' ''ArrayTools'' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) ''ArrayTools'' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'R data frame')) ''ArrayTools'' SubClassOf 'R software' ''ArrayTools'' SubClassOf 'implements' some 'RMA' ''ArrayTools'' SubClassOf 'is encoded in' some 'R language' ''ArrayTools'' SubClassOf 'software' ''ArrayTools'' SubClassOf 'is executed in' some 'differential expression analysis' http://www.ebi.ac.uk/swo/SWO_1100123 CLR algorithm 'CLR algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_1100128 bcbio 'bcbio' SubClassOf 'has website homepage' value "https://github.com/bcbio/bcbio-nextgen" 'bcbio' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_1100129 shinyNGS 'shinyNGS' SubClassOf 'has license' some 'GNU AGPL v3' 'shinyNGS' SubClassOf 'software' 'shinyNGS' SubClassOf 'has website homepage' value "https://github.com/pinin4fjords/shinyngs" http://www.ebi.ac.uk/swo/SWO_0000473 arrayQuality 'arrayQuality' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'arrayQuality' SubClassOf 'is encoded in' some 'R language' 'arrayQuality' SubClassOf 'has specified data input' some ('Gene list' and 'Graph plot') 'arrayQuality' SubClassOf 'software' 'arrayQuality' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000472 arrayMvout 'arrayMvout' SubClassOf 'has specified data input' some 'MAQC data' 'arrayMvout' SubClassOf 'is encoded in' some 'R language' 'arrayMvout' SubClassOf 'BioConductor Software' 'arrayMvout' SubClassOf 'software' 'arrayMvout' SubClassOf 'R software' 'arrayMvout' SubClassOf 'is published by' value 'Bioconductor' 'arrayMvout' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only ('R data frame' and 'PNG'))) http://www.ebi.ac.uk/swo/SWO_0000475 arrayWoRx 2.0 'arrayWoRx 2.0' SubClassOf 'arrayWoRx' http://www.ebi.ac.uk/swo/SWO_0000474 arrayQualityMetrics 'arrayQualityMetrics' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'arrayQualityMetrics' SubClassOf 'R software' 'arrayQualityMetrics' SubClassOf 'is encoded in' some 'R language' 'arrayQualityMetrics' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'arrayQualityMetrics' SubClassOf 'BioConductor Software' 'arrayQualityMetrics' SubClassOf 'is published by' value 'Bioconductor' 'arrayQualityMetrics' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000477 Associative T method 'Associative T method' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000476 arrayWoRx 'arrayWoRx' SubClassOf 'is published by' value 'Applied Precision Life Science' 'arrayWoRx' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000479 'beadarray' ''beadarray'' SubClassOf 'R software' ''beadarray'' SubClassOf 'has specified data input' some 'Text data set' ''beadarray'' SubClassOf 'is encoded in' some 'R language' ''beadarray'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000478 AvgNRRs 'AvgNRRs' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000471 aroma.light 'aroma.light' SubClassOf 'has specified data output' some 'Graph plot' 'aroma.light' SubClassOf 'is encoded in' some 'R language' 'aroma.light' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'aroma.light' SubClassOf 'is published by' value 'Bioconductor' 'aroma.light' SubClassOf 'software' 'aroma.light' SubClassOf 'BioConductor Software' 'aroma.light' SubClassOf 'R software' 'aroma.light' SubClassOf 'is executed in' some ('averaging' and 'correction' and 'data normalization') http://www.ebi.ac.uk/swo/SWO_0000470 'apComplex' ''apComplex'' SubClassOf 'R software' ''apComplex'' SubClassOf 'software' ''apComplex'' SubClassOf 'is encoded in' some 'R language' ''apComplex'' SubClassOf 'has specified data output' some 'Graph plot' ''apComplex'' SubClassOf 'implements' some 'PCMG' ''apComplex'' SubClassOf 'has specified data input' some 'AP-MS data' http://www.ebi.ac.uk/swo/SWO_0000484 Bitmap object 'Bitmap object' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000483 bgx 'bgx' SubClassOf 'is encoded in' some 'R language' 'bgx' SubClassOf 'BioConductor Software' 'bgx' SubClassOf 'R software' 'bgx' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'bgx' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'bgx' SubClassOf 'is published by' value 'Bioconductor' 'bgx' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000486 'biocDatasets' ''biocDatasets'' SubClassOf 'is encoded in' some 'R language' ''biocDatasets'' SubClassOf 'software' ''biocDatasets'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000485 bioDist 'bioDist' SubClassOf 'implements' some (''KLD'' and ''MI'') 'bioDist' SubClassOf 'is published by' value 'Bioconductor' 'bioDist' SubClassOf 'BioConductor Software' 'bioDist' SubClassOf 'R software' 'bioDist' SubClassOf 'software' 'bioDist' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'bioDist' SubClassOf 'is encoded in' some 'R language' 'bioDist' SubClassOf 'is executed in' some 'distance calculation' http://www.ebi.ac.uk/swo/SWO_0000488 'biocViews' ''biocViews'' SubClassOf 'has specified data output' some 'HTML report' ''biocViews'' SubClassOf 'software' ''biocViews'' SubClassOf 'is encoded in' some 'R language' ''biocViews'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000487 'biocGraph' ''biocGraph'' SubClassOf 'software' ''biocGraph'' SubClassOf 'is encoded in' some 'R language' ''biocGraph'' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') ''biocGraph'' SubClassOf 'has specified data input' some 'Graph plot' ''biocGraph'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000489 biomaRT 'biomaRT' SubClassOf 'has specified data input' some ('has format specification' only 'FASTA format') 'biomaRT' SubClassOf 'BioConductor Software' 'biomaRT' SubClassOf 'software' 'biomaRT' SubClassOf 'is published by' value 'Bioconductor' 'biomaRT' SubClassOf 'R software' 'biomaRT' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000480 'beadarraySNP' ''beadarraySNP'' SubClassOf 'is encoded in' some 'R language' ''beadarraySNP'' SubClassOf 'software' ''beadarraySNP'' SubClassOf 'has specified data input' some 'Text data set' ''beadarraySNP'' SubClassOf 'has specified data output' some 'Graph plot' ''beadarraySNP'' SubClassOf 'is executed in' some 'data normalization' ''beadarraySNP'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000482 bgafun 'bgafun' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set') 'bgafun' SubClassOf 'is published by' value 'Bioconductor' 'bgafun' SubClassOf 'BioConductor Software' 'bgafun' SubClassOf 'has specified data input' some ('has format specification' only 'FASTA format') 'bgafun' SubClassOf 'R software' 'bgafun' SubClassOf 'software' 'bgafun' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000481 'betr' ''betr'' SubClassOf 'has specified data input' some 'Gene list' ''betr'' SubClassOf 'R software' ''betr'' SubClassOf 'BioConductor Software' ''betr'' SubClassOf 'is published by' value 'Bioconductor' ''betr'' SubClassOf 'implements' some 'Bayesian Model' ''betr'' SubClassOf 'is encoded in' some 'R language' ''betr'' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') ''betr'' SubClassOf 'software' ''betr'' SubClassOf 'is executed in' some 'differential expression analysis' http://www.ebi.ac.uk/swo/SWO_0000495 'cellHTS2' ''cellHTS2'' SubClassOf 'has specified data input' some 'Text data set' ''cellHTS2'' SubClassOf 'is executed in' some ('data annotation' and 'data normalization' and 'descriptive statistical calculation') ''cellHTS2'' SubClassOf 'R software' ''cellHTS2'' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') ''cellHTS2'' SubClassOf 'is encoded in' some 'R language' ''cellHTS2'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000494 'cellHTS' ''cellHTS'' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') ''cellHTS'' SubClassOf 'is encoded in' some 'R language' ''cellHTS'' SubClassOf 'R software' ''cellHTS'' SubClassOf 'has specified data input' some 'Text data set' ''cellHTS'' SubClassOf 'software' ''cellHTS'' SubClassOf 'is executed in' some ('data normalization' and 'descriptive statistical calculation') http://www.ebi.ac.uk/swo/SWO_0000497 chamber slide format 'chamber slide format' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000496 cghMCR 'cghMCR' SubClassOf 'is published by' value 'Bioconductor' 'cghMCR' SubClassOf 'R software' 'cghMCR' SubClassOf 'implements' some 'MCR algorithm' 'cghMCR' SubClassOf 'software' 'cghMCR' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'cghMCR' SubClassOf 'BioConductor Software' 'cghMCR' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'cghMCR' SubClassOf 'is executed in' some 'data normalization' 'cghMCR' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000499 'clusterStab' ''clusterStab'' SubClassOf 'software' ''clusterStab'' SubClassOf 'is encoded in' some 'R language' ''clusterStab'' SubClassOf 'has specified data output' some ('Heat map' and 'Graph plot') ''clusterStab'' SubClassOf 'R software' ''clusterStab'' SubClassOf 'implements' some 'Hierarchical clustering' ''clusterStab'' SubClassOf 'has specified data input' some 'Gene list' ''clusterStab'' SubClassOf 'is executed in' some ('decision tree induction' and 'differential expression analysis') http://www.ebi.ac.uk/swo/SWO_0000498 cls 'cls' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_0000491 'bridge' ''bridge'' SubClassOf 'software' ''bridge'' SubClassOf 'implements' some ('Markov Chain Monte Carlo' and 'Bayesian Model') ''bridge'' SubClassOf 'R software' ''bridge'' SubClassOf 'is executed in' some 'differential expression analysis' ''bridge'' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000490 Bootstrap 'Bootstrap' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000493 cdt 'cdt' SubClassOf 'tab delimited file format' http://www.ebi.ac.uk/swo/SWO_0000430 Spotfire 'Spotfire' SubClassOf 'is developed by' value 'TIBCO Software Inc' 'Spotfire' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000432 TAS Software 'TAS Software' SubClassOf 'software' 'TAS Software' SubClassOf 'Affymetrix Software' 'TAS Software' SubClassOf 'is published by' value 'Affymetrix' http://www.ebi.ac.uk/swo/SWO_0000435 TargetSearch 'TargetSearch' SubClassOf 'is encoded in' some 'R language' 'TargetSearch' SubClassOf 'has specified data input' some 'Text data set' 'TargetSearch' SubClassOf 'has specified data output' some ('Graph plot' and 'Text data set' and ('has format specification' only 'pdf')) 'TargetSearch' SubClassOf 'software' 'TargetSearch' SubClassOf 'R software' 'TargetSearch' SubClassOf 'implements' some ('Library Search Algorithm' and 'PPC algorithm') 'TargetSearch' SubClassOf 'is published by' value 'Bioconductor' 'TargetSearch' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/swo/SWO_0000437 Theodore Ts’o’s 'Theodore Ts’o’s' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000438 TypeInfo 'TypeInfo' SubClassOf 'software' 'TypeInfo' SubClassOf 'has specified data input' some ('Gene expression dataset' or ('has format specification' only 'R data frame')) 'TypeInfo' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' only 'R data frame')) 'TypeInfo' SubClassOf 'is published by' value 'Bioconductor' 'TypeInfo' SubClassOf 'BioConductor Software' 'TypeInfo' SubClassOf 'is encoded in' some 'R language' 'TypeInfo' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000442 VanillaICE 'VanillaICE' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'VanillaICE' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'VanillaICE' SubClassOf 'BioConductor Software' 'VanillaICE' SubClassOf 'implements' some 'Hidden Markov Model' 'VanillaICE' SubClassOf 'is published by' value 'Bioconductor' 'VanillaICE' SubClassOf 'R software' 'VanillaICE' SubClassOf 'is encoded in' some 'R language' 'VanillaICE' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000441 Variance-stabilizing transformation (VST) algorithm 'Variance-stabilizing transformation (VST) algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000444 WilcEbam 'WilcEbam' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000446 XDE 'XDE' SubClassOf 'is encoded in' some 'R language' 'XDE' SubClassOf 'R software' 'XDE' SubClassOf 'is published by' value 'Bioconductor' 'XDE' SubClassOf 'BioConductor Software' 'XDE' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'XDE' SubClassOf 'implements' some ('Markov Chain Monte Carlo' and 'Bayesian Model') 'XDE' SubClassOf 'is executed in' some ('cross validation' and 'differential expression analysis') 'XDE' SubClassOf 'has specified data input' some 'Gene expression dataset' 'XDE' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000445 Wilcoxon 'Wilcoxon' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000447 XDotsReader 'XDotsReader' SubClassOf 'software' 'XDotsReader' SubClassOf 'is developed by' value 'COSE, France' http://www.ebi.ac.uk/swo/SWO_0000449 Xba.CQV and Xba.regions 'Xba.CQV and Xba.regions' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000451 Acuity 'Acuity' SubClassOf 'software' 'Acuity' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Molecular Devices')) http://www.ebi.ac.uk/swo/SWO_0000450 Array Comparative Genomic Hybridization 'Array Comparative Genomic Hybridization' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'Array Comparative Genomic Hybridization' SubClassOf 'R software' 'Array Comparative Genomic Hybridization' SubClassOf 'is encoded in' some 'R language' 'Array Comparative Genomic Hybridization' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some http://edamontology.org/format_2330)) 'Array Comparative Genomic Hybridization' SubClassOf 'implements' some ''FDR'' 'Array Comparative Genomic Hybridization' SubClassOf 'has specified data output' some ('data item' and ('has format specification' some 'sproc')) 'Array Comparative Genomic Hybridization' SubClassOf 'implements' some 'Hidden Markov Model' 'Array Comparative Genomic Hybridization' SubClassOf 'implements' some ''t-test'' 'Array Comparative Genomic Hybridization' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000453 affyContam 'affyContam' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'affyContam' SubClassOf 'R software' 'affyContam' SubClassOf 'BioConductor Software' 'affyContam' SubClassOf 'software' 'affyContam' SubClassOf 'is encoded in' some 'R language' 'affyContam' SubClassOf 'is published by' value 'Bioconductor' 'affyContam' SubClassOf 'has specified data output' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) http://www.ebi.ac.uk/swo/SWO_0000452 affxparser 'affxparser' SubClassOf 'is encoded in' some 'R language' 'affxparser' SubClassOf 'R software' 'affxparser' SubClassOf 'has specified data input' only 'Affymetrix-compliant data' 'affxparser' SubClassOf 'has specified data input' some 'Affymetrix-compliant data' 'affxparser' SubClassOf 'BioConductor Software' 'affxparser' SubClassOf 'software' 'affxparser' SubClassOf 'has specified data output' some 'Text data set' 'affxparser' SubClassOf 'is executed in' some 'parse' 'affxparser' SubClassOf 'is published by' value 'Bioconductor' http://www.ebi.ac.uk/swo/SWO_0000455 'affyPLM' ''affyPLM'' SubClassOf 'is executed in' some ('correction' and 'data normalization') ''affyPLM'' SubClassOf 'implements' some (''PLM'' and 'RMA' and 'M-estimation regression') ''affyPLM'' SubClassOf 'affypdnn' ''affyPLM'' SubClassOf 'is encoded in' some 'R language' ''affyPLM'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) ''affyPLM'' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') http://www.ebi.ac.uk/swo/SWO_0000454 affyImGUI 'affyImGUI' SubClassOf 'software' 'affyImGUI' SubClassOf 'implements' some (''PLM'' or 'RMA') 'affyImGUI' SubClassOf 'BioConductor Software' 'affyImGUI' SubClassOf 'is encoded in' some 'R language' 'affyImGUI' SubClassOf 'is published by' value 'Bioconductor' 'affyImGUI' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000457 affyQCReport 'affyQCReport' SubClassOf 'R software' 'affyQCReport' SubClassOf 'BioConductor Software' 'affyQCReport' SubClassOf 'is published by' value 'Bioconductor' 'affyQCReport' SubClassOf 'is executed in' some 'differential expression analysis' 'affyQCReport' SubClassOf 'is encoded in' some 'R language' 'affyQCReport' SubClassOf 'has specified data input' some ('has format specification' some ('CEL binary format' or 'CEL ASCII format')) 'affyQCReport' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'pdf')) 'affyQCReport' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000456 affyPara 'affyPara' SubClassOf 'BioConductor Software' 'affyPara' SubClassOf 'is encoded in' some 'R language' 'affyPara' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'affyPara' SubClassOf 'is published by' value 'Bioconductor' 'affyPara' SubClassOf 'software' 'affyPara' SubClassOf 'R software' 'affyPara' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) 'affyPara' SubClassOf 'is executed in' some ('averaging' and 'correction' and 'data normalization') http://www.ebi.ac.uk/swo/SWO_0000459 'affycoretools' ''affycoretools'' SubClassOf 'has specified data input' some ('Rnw' or 'Text data set') ''affycoretools'' SubClassOf 'is encoded in' some 'R language' ''affycoretools'' SubClassOf 'R software' ''affycoretools'' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot' and 'Text data set') ''affycoretools'' SubClassOf 'implements' some ('RMA' and ''FDR'') ''affycoretools'' SubClassOf 'is executed in' some 'differential expression analysis' ''affycoretools'' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000458 affyTiling 'affyTiling' SubClassOf 'R software' 'affyTiling' SubClassOf 'has specified data output' some 'CSV data set' 'affyTiling' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' and 'BPMAP')) 'affyTiling' SubClassOf 'BioConductor Software' 'affyTiling' SubClassOf 'is published by' value 'Bioconductor' 'affyTiling' SubClassOf 'is executed in' some ('correction' and 'data normalization') 'affyTiling' SubClassOf 'implements' some 'RMA' 'affyTiling' SubClassOf 'software' 'affyTiling' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000461 affypdnn 'affypdnn' SubClassOf 'R software' 'affypdnn' SubClassOf 'has specified data output' some 'Graph plot' 'affypdnn' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some 'R data frame')) 'affypdnn' SubClassOf 'software' 'affypdnn' SubClassOf 'BioConductor Software' 'affypdnn' SubClassOf 'is published by' value 'Bioconductor' 'affypdnn' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000463 altcdfenvs 'altcdfenvs' SubClassOf 'is encoded in' some 'R language' 'altcdfenvs' SubClassOf 'is published by' value 'Bioconductor' 'altcdfenvs' SubClassOf 'has specified data input' some ('has format specification' only 'FASTA format') 'altcdfenvs' SubClassOf 'BioConductor Software' 'altcdfenvs' SubClassOf 'R software' 'altcdfenvs' SubClassOf 'software' 'altcdfenvs' SubClassOf 'has specified data output' some 'Graph plot' http://www.ebi.ac.uk/swo/SWO_0000466 'annotate' ''annotate'' SubClassOf 'has specified data output' some 'HTML report' ''annotate'' SubClassOf 'software' ''annotate'' SubClassOf 'has specified data input' some 'CSV data set' ''annotate'' SubClassOf 'is encoded in' some 'R language' ''annotate'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/SWO_0000465 annaffy 'annaffy' SubClassOf 'is published by' value 'Bioconductor' 'annaffy' SubClassOf 'R software' 'annaffy' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'annaffy' SubClassOf 'is encoded in' some 'R language' 'annaffy' SubClassOf 'software' 'annaffy' SubClassOf 'BioConductor Software' 'annaffy' SubClassOf 'has specified data output' some 'HTML report' http://www.ebi.ac.uk/swo/SWO_0000468 annotationTools 'annotationTools' SubClassOf 'is encoded in' some 'R language' 'annotationTools' SubClassOf 'is published by' value 'Bioconductor' 'annotationTools' SubClassOf 'R software' 'annotationTools' SubClassOf 'BioConductor Software' 'annotationTools' SubClassOf 'is executed in' some ('data annotation' and 'gene expression analysis') 'annotationTools' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'annotationTools' SubClassOf 'has specified data input' some 'CSV data set' 'annotationTools' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000467 data annotation 'data annotation' SubClassOf 'data transformation' http://www.ebi.ac.uk/swo/SWO_0000460 affyio 'affyio' SubClassOf 'R software' 'affyio' SubClassOf 'BioConductor Software' 'affyio' SubClassOf 'is encoded in' some 'R language' 'affyio' SubClassOf 'is published by' value 'Bioconductor' 'affyio' SubClassOf 'is executed in' some 'parse' 'affyio' SubClassOf 'has specified data input' some ('has format specification' only ('CEL binary format' or 'CDF binary format' or 'CDF ASCII format' or 'CEL ASCII format')) 'affyio' SubClassOf 'software' 'affyio' SubClassOf 'has specified data output' some ('has format specification' only ('CEL binary format' or 'CDF binary format' or 'CDF ASCII format' or 'CEL ASCII format')) http://www.ebi.ac.uk/swo/SWO_0000469 Annotation data packages 'Annotation data packages' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000406 Gene list 'Gene list' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000405 ArrayExpress Bioconductor 'ArrayExpress Bioconductor' SubClassOf 'is encoded in' some 'R language' 'ArrayExpress Bioconductor' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'MAGE-TAB')) 'ArrayExpress Bioconductor' SubClassOf 'R software' 'ArrayExpress Bioconductor' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Bioconductor')) 'ArrayExpress Bioconductor' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'R data frame')) 'ArrayExpress Bioconductor' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'European Bioinformatics Institute')) 'ArrayExpress Bioconductor' SubClassOf 'software' 'ArrayExpress Bioconductor' SubClassOf 'MAGE-TAB inputting software' 'ArrayExpress Bioconductor' SubClassOf 'output of' some ('software development' and ('has participant' value 'European Bioinformatics Institute')) http://www.ebi.ac.uk/swo/SWO_0000408 Clustered data set 'Clustered data set' SubClassOf 'data item' http://www.ebi.ac.uk/swo/SWO_0000409 R data frame 'R data frame' SubClassOf http://edamontology.org/format_2330 http://www.ebi.ac.uk/swo/SWO_0000415 R language 'R language' SubClassOf 'programming language' http://www.ebi.ac.uk/swo/SWO_0000417 ScanAlyze 'ScanAlyze' SubClassOf 'software' 'ScanAlyze' SubClassOf 'is developed by' value 'obsolete_Stanford University' http://www.ebi.ac.uk/swo/SWO_0000416 ScISI 'ScISI' SubClassOf 'is encoded in' some 'R language' 'ScISI' SubClassOf 'R software' 'ScISI' SubClassOf 'is published by' value 'Bioconductor' 'ScISI' SubClassOf 'BioConductor Software' 'ScISI' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'ScISI' SubClassOf 'software' 'ScISI' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'ScISI' SubClassOf 'is executed in' some ('data annotation' and 'descriptive statistical calculation') http://www.ebi.ac.uk/swo/SWO_0000419 ScanArray v3.1 software 'ScanArray v3.1 software' SubClassOf 'ScanArray' http://www.ebi.ac.uk/swo/SWO_0000418 ScanArray 'ScanArray' SubClassOf 'software' 'ScanArray' SubClassOf 'is developed by' value 'PerkinElmer' http://www.ebi.ac.uk/swo/SWO_0000420 scanning software 'scanning software' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000422 ShortRead 'ShortRead' SubClassOf 'R software' 'ShortRead' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'ShortRead' SubClassOf 'has specified data input' some 'Text data set' 'ShortRead' SubClassOf 'is published by' value 'Bioconductor' 'ShortRead' SubClassOf 'software' 'ShortRead' SubClassOf 'BioConductor Software' 'ShortRead' SubClassOf 'is encoded in' some 'R language' http://www.ebi.ac.uk/swo/SWO_0000421 Scanning software G2565AA version A6.3.1 'Scanning software G2565AA version A6.3.1' SubClassOf 'scanning software' 'Scanning software G2565AA version A6.3.1' SubClassOf 'is developed by' value 'Agilent Technologies' http://www.ebi.ac.uk/swo/SWO_0000424 Silicon Genetics Genespring 'Silicon Genetics Genespring' SubClassOf 'is developed by' value 'Agilent Technologies' 'Silicon Genetics Genespring' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000423 Signaling Pathway Impact Analysis (SPIA) algorithm 'Signaling Pathway Impact Analysis (SPIA) algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000426 'Smith-Waterman' ''Smith-Waterman'' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000425 Similarity score 'Similarity score' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/SWO_0000428 Spot quantification 'Spot quantification' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000429 Spotfinder [TIGR] 'Spotfinder [TIGR]' SubClassOf 'software' 'Spotfinder [TIGR]' SubClassOf 'is developed by' value 'Dana-Farber Cancer Institute and Harvard School of Public Health' 'Spotfinder [TIGR]' SubClassOf 'is developed by' value 'J. Craig Venter Institute' http://www.ontodm.com/OntoDM-core/OntoDM_731692 single generalization algorithm 'ensemble algorithm' DisjointWith 'single generalization algorithm' 'single generalization algorithm' SubClassOf 'data mining algorithm'