2188 361 2 http://edamontology.org/operation_0345 Sequence retrieval (by keyword) 'Sequence retrieval (by keyword)' SubClassOf 'Obsolete concept (EDAM)' '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 'Database search' 'Sequence similarity search' SubClassOf 'Structure database search' 'Sequence similarity search' SubClassOf 'Sequence database search' http://edamontology.org/operation_0343 Transmembrane protein database search 'Transmembrane protein database search' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence retrieval (by code)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0347 Sequence database search (by motif or pattern) 'Sequence database search (by motif or pattern)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence database search (by isoelectric point)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0357 Structure retrieval (by code) 'Structure retrieval (by code)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Structure retrieval (by keyword)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2307 Virus annotation 'Virus annotation' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Gene name (NCBI)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence database search (by sequence using profile-based methods)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0323 Phylogenetic tree generation 'Phylogenetic tree generation' SubClassOf 'has topic' some 'Sequence analysis' 'Phylogenetic tree generation' SubClassOf 'has output' some 'Phylogenetic tree' 'Phylogenetic tree generation' SubClassOf 'Phylogenetic tree processing' 'Phylogenetic tree generation' SubClassOf 'Phylogenetic tree analysis' http://edamontology.org/operation_0324 Phylogenetic tree analysis 'Phylogenetic tree analysis' SubClassOf 'Phylogenetic tree processing' 'Phylogenetic tree analysis' SubClassOf 'has output' some 'Phylogenetic data' 'Phylogenetic tree analysis' SubClassOf 'has input' some 'Phylogenetic tree' 'Phylogenetic tree analysis' SubClassOf 'Analysis' http://edamontology.org/operation_0321 Protein model validation 'Protein model validation' SubClassOf 'has topic' some 'Molecular modelling' 'Protein model validation' SubClassOf 'has output' some 'Protein structural quality report' 'Protein model validation' SubClassOf 'has topic' some 'Protein structure prediction' http://edamontology.org/operation_0327 Phylogenetic footprinting / shadowing 'Phylogenetic footprinting / shadowing' SubClassOf 'has topic' some 'Phylogenomics' http://edamontology.org/operation_0325 Phylogenetic tree comparison 'Phylogenetic tree comparison' SubClassOf 'Phylogenetic tree processing' 'Phylogenetic tree comparison' SubClassOf 'Phylogenetic tree analysis' http://edamontology.org/operation_0326 Phylogenetic tree editing 'Phylogenetic tree editing' SubClassOf 'has output' some 'Phylogenetic tree' 'Phylogenetic tree editing' SubClassOf 'Phylogenetic tree processing' 'Phylogenetic tree editing' SubClassOf 'has input' some 'Phylogenetic tree' 'Phylogenetic tree editing' SubClassOf 'Phylogenetic tree analysis' http://edamontology.org/operation_0320 Protein structure assignment 'Protein structure assignment' SubClassOf 'Protein analysis' 'Protein structure assignment' SubClassOf 'has topic' some 'Structural biology' 'Protein structure assignment' SubClassOf 'has output' some 'Protein structure' 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://edamontology.org/operation_0318 Structural genomics target selection 'Structural genomics target selection' SubClassOf 'Obsolete concept (EDAM)' '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 'has topic' some 'Structural biology' 'Protein secondary structure assignment' SubClassOf 'has topic' some 'Protein structure analysis' 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 'has specified data input' some ('DNA nucleotide sequence' and ('has format specification' some 'FASTA format')) http://edamontology.org/operation_0334 Enzyme kinetics calculation 'Enzyme kinetics calculation' SubClassOf 'has topic' some 'Enzymes' 'Enzyme kinetics calculation' SubClassOf 'has output' some 'Enzyme kinetics data' http://edamontology.org/operation_0332 Immunogen design 'Immunogen design' SubClassOf 'Obsolete concept (EDAM)' 'Immunogen design' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0333 Zinc finger prediction 'Zinc finger prediction' SubClassOf 'has topic' some 'Protein folding, stability and design' 'Zinc finger prediction' SubClassOf 'has output' some 'Protein interaction report' http://edamontology.org/operation_0338 Sequence database search 'Sequence database search' SubClassOf 'has output' some 'Sequence search results' 'Sequence database search' SubClassOf 'has topic' some 'Sequence comparison' http://edamontology.org/operation_0339 Structure database search 'Structure database search' SubClassOf 'has topic' some 'Structure analysis' http://edamontology.org/operation_0336 Format validation 'Format validation' SubClassOf 'Utility operation' http://edamontology.org/operation_0337 Visualisation 'Visualisation' SubClassOf 'information processing' 'Visualisation' SubClassOf 'has input' some 'data' 'Visualisation' SubClassOf 'has topic' some 'Data visualisation' 'Visualisation' SubClassOf 'has output' some 'Image' 'Visualisation' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/operation_0330 Protein SNP mapping 'Protein SNP mapping' SubClassOf 'Protein modelling (mutation)' 'Protein SNP mapping' SubClassOf 'has topic' some 'SNP' 'Protein SNP mapping' SubClassOf '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 'Obsolete concept (EDAM)' '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 'has topic' some 'Genetic variation' 'Protein modelling (mutation)' SubClassOf 'Prediction and recognition (protein)' 'Protein modelling (mutation)' SubClassOf 'has topic' some 'Protein folding, stability and design' http://edamontology.org/operation_2990 Classification 'Classification' SubClassOf 'Analysis' 'Classification' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/format_1391 HMMER-aln 'HMMER-aln' SubClassOf 'Textual format' 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://edamontology.org/operation_0389 Protein-nucleic acid binding site analysis 'Protein-nucleic acid binding site analysis' SubClassOf 'has topic' some 'Protein interactions' http://edamontology.org/data_1008 Polypeptide chain ID 'Polypeptide chain ID' SubClassOf 'is identifier of' some 'Protein chain' http://edamontology.org/operation_0387 Protein surface and interior calculation 'Protein surface and interior calculation' SubClassOf 'Protein solvent accessibility calculation' 'Protein surface and interior calculation' SubClassOf 'has topic' some 'Protein structural motifs and surfaces' 'Protein surface and interior calculation' SubClassOf 'Protein surface analysis' http://edamontology.org/operation_0388 Protein binding site prediction (from structure) 'Protein binding site prediction (from structure)' SubClassOf 'Protein structural motif recognition' 'Protein binding site prediction (from structure)' SubClassOf 'Protein binding site prediction' '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 'data' 'Resource metadata' SubClassOf 'Report' http://edamontology.org/data_2338 Ontology identifier 'Ontology identifier' SubClassOf 'is identifier of' some 'Ontology' http://edamontology.org/operation_0385 Protein hydropathy cluster calculation 'Protein hydropathy cluster calculation' SubClassOf 'Protein hydropathy calculation (from structure)' 'Protein hydropathy cluster calculation' SubClassOf 'Protein residue cluster calculation' 'Protein hydropathy cluster calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0386 Protein dipole moment calculation 'Protein dipole moment calculation' SubClassOf 'has output' some 'Protein dipole moment' http://edamontology.org/operation_0383 Protein hydropathy calculation (from structure) 'Protein hydropathy calculation (from structure)' SubClassOf 'Protein hydropathy calculation' 'Protein hydropathy calculation (from structure)' SubClassOf 'Protein structure analysis' 'Protein hydropathy calculation (from structure)' SubClassOf 'Protein property calculation (from structure)' 'Protein hydropathy calculation (from structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0384 Protein solvent accessibility calculation 'Protein solvent accessibility calculation' SubClassOf 'Protein property calculation (from structure)' 'Protein solvent accessibility calculation' SubClassOf 'has output' some 'Protein solvent accessibility' 'Protein solvent accessibility calculation' SubClassOf 'has topic' some 'Protein properties' 'Protein solvent accessibility calculation' SubClassOf 'Protein surface analysis' http://edamontology.org/data_1019 Protein feature identifier 'Protein feature identifier' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'has topic' some 'Proteomics' 'Protein molecular weight calculation' SubClassOf 'has output' some 'Peptide molecular weights' http://edamontology.org/operation_0399 Protein extinction coefficient calculation 'Protein extinction coefficient calculation' SubClassOf 'has output' some 'Protein extinction coefficient' http://edamontology.org/operation_3429 Generation 'Generation' SubClassOf 'Analysis' 'Generation' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/operation_0392 Protein contact map calculation 'Protein contact map calculation' SubClassOf 'has output' some 'Protein contact map' 'Protein contact map calculation' SubClassOf 'Residue contact calculation (residue-residue)' 'Protein contact map calculation' SubClassOf 'Protein distance matrix calculation' http://edamontology.org/operation_0393 Protein residue cluster calculation 'Protein residue cluster calculation' SubClassOf 'Residue contact calculation (residue-residue)' 'Protein residue cluster calculation' SubClassOf 'has output' some 'Protein residue 3D cluster' 'Protein residue cluster calculation' SubClassOf 'Residue contact calculation' http://edamontology.org/operation_0391 Protein distance matrix calculation 'Protein distance matrix calculation' SubClassOf 'has output' some 'Protein distance matrix' 'Protein distance matrix calculation' SubClassOf 'Residue interaction calculation' 'Protein distance matrix calculation' SubClassOf 'Residue contact calculation' http://edamontology.org/operation_0396 Ramachandran plot calculation 'Ramachandran plot calculation' SubClassOf 'has output' some 'Ramachandran plot' http://edamontology.org/operation_0397 Ramachandran plot validation 'Ramachandran plot validation' SubClassOf 'has input' some 'Ramachandran plot' 'Ramachandran plot validation' SubClassOf 'has output' some 'Protein structural quality report' http://edamontology.org/data_1014 Sequence position specification 'Sequence position specification' SubClassOf 'Obsolete concept (EDAM)' 'Sequence position specification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0394 Hydrogen bond calculation 'Hydrogen bond calculation' SubClassOf 'has output' some 'Protein hydrogen bonds' http://edamontology.org/operation_0395 Residue non-canonical interaction detection 'Residue non-canonical interaction detection' SubClassOf 'Protein model validation' 'Residue non-canonical interaction detection' SubClassOf 'Residue interaction calculation' 'Residue non-canonical interaction detection' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://purl.obolibrary.org/obo/BFO_0000040 material entity 'material entity' DisjointWith 'Obsolete concept (EDAM)' http://edamontology.org/data_1029 Gene identifier (NCBI UniGene) 'Gene identifier (NCBI UniGene)' SubClassOf 'Obsolete concept (EDAM)' '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 'has output' some 'Restriction digest' http://edamontology.org/data_1028 Gene identifier (NCBI RefSeq) 'Gene identifier (NCBI RefSeq)' SubClassOf 'Obsolete concept (EDAM)' '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 'has output' some 'Proteolytic digest' 'Protein sequence cleavage' SubClassOf 'has topic' some 'Proteomics' http://edamontology.org/data_2359 Domain-domain interactions 'Domain-domain interactions' SubClassOf 'Obsolete concept (EDAM)' 'Domain-domain interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2355 RNA family identifier 'RNA family identifier' SubClassOf 'is identifier of' some 'RNA family report' http://edamontology.org/data_1022 Sequence feature label 'Sequence feature label' SubClassOf 'Sequence feature identifier' 'Sequence feature label' SubClassOf 'Name' http://edamontology.org/operation_0360 Structural similarity search 'Structural similarity search' SubClassOf 'has topic' some 'Structure comparison' http://edamontology.org/data_2357 Protein signature type 'Protein signature type' SubClassOf 'Obsolete concept (EDAM)' 'Protein signature type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2358 Domain-nucleic acid interaction report 'Domain-nucleic acid interaction report' SubClassOf 'Obsolete concept (EDAM)' 'Domain-nucleic acid interaction report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2353 Ontology data 'Ontology data' SubClassOf 'has topic' some 'Ontology and terminology' 'Ontology data' SubClassOf 'data' 'Ontology data' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_1025 Gene identifier 'Gene identifier' SubClassOf 'is identifier of' some 'Gene report' http://edamontology.org/operation_0361 Sequence annotation 'Sequence annotation' SubClassOf 'has input' some 'Sequence record' 'Sequence annotation' SubClassOf 'has output' some 'Sequence record' http://edamontology.org/data_1024 Codon name 'Codon name' SubClassOf 'Obsolete concept (EDAM)' 'Codon name' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://purl.obolibrary.org/obo/IAO_0000030 information content entity 'information content entity' DisjointWith 'Obsolete concept (EDAM)' http://edamontology.org/operation_0378 Sequence composition calculation (protein) 'Sequence composition calculation (protein)' SubClassOf 'Obsolete concept (EDAM)' 'Sequence composition calculation (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0377 Sequence composition calculation (nucleic acid) 'Sequence composition calculation (nucleic acid)' SubClassOf 'Obsolete concept (EDAM)' 'Sequence composition calculation (nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0371 DNA translation 'DNA translation' SubClassOf 'has topic' some 'Protein expression' http://edamontology.org/data_1038 Protein domain ID 'Protein domain ID' SubClassOf 'is identifier of' some 'Protein domain' http://edamontology.org/data_2362 Sequence accession (hybrid) 'Sequence accession (hybrid)' SubClassOf 'is identifier of' some 'Sequence record' http://edamontology.org/data_2363 2D PAGE data '2D PAGE data' SubClassOf 'Obsolete concept (EDAM)' '2D PAGE data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2364 2D PAGE report '2D PAGE report' SubClassOf 'Obsolete concept (EDAM)' '2D PAGE report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0372 DNA transcription 'DNA transcription' SubClassOf 'has topic' some 'Gene expression' http://purl.obolibrary.org/obo/IAO_0000027 data 'data' SubClassOf 'is encoded in' some 'data format specification' 'data' DisjointWith 'data format specification' 'data' DisjointWith http://www.w3.org/2002/07/owl#DeprecatedClass 'Topic' DisjointWith 'data' 'data' DisjointWith 'information processing' http://edamontology.org/data_2360 Domain-domain interaction (indirect) 'Domain-domain interaction (indirect)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Gene identifier (Entrez)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2953 Nucleic acid design 'Nucleic acid design' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid design' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3459 Functional clustering 'Functional clustering' SubClassOf 'has topic' some 'Function analysis' http://edamontology.org/operation_3457 Single particle analysis 'Single particle analysis' SubClassOf 'has topic' some 'Structural biology' http://edamontology.org/operation_2120 Listfile processing 'Listfile processing' SubClassOf 'Obsolete concept (EDAM)' 'Listfile processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2378 Protein-motif interaction 'Protein-motif interaction' SubClassOf 'Obsolete concept (EDAM)' 'Protein-motif interaction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3450 Neurite measurement 'Neurite measurement' SubClassOf 'has topic' some 'Cell biology' http://edamontology.org/data_1048 Database ID 'Database ID' SubClassOf 'is identifier of' some 'Database metadata' http://edamontology.org/operation_2123 Small molecule data processing 'Small molecule data processing' SubClassOf 'Obsolete concept (EDAM)' 'Small molecule data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2122 Sequence alignment file processing 'Sequence alignment file processing' SubClassOf 'Obsolete concept (EDAM)' 'Sequence alignment file processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2121 Sequence file editing 'Sequence file editing' SubClassOf 'Sequence analysis' http://edamontology.org/format_3167 Experiment annotation format 'Experiment annotation format' SubClassOf 'is format of' some 'Experiment report' http://edamontology.org/format_3166 Biological pathway or network report format 'Biological pathway or network report format' SubClassOf 'is format of' some 'Pathway or network report' http://edamontology.org/data_2372 2D PAGE spot report '2D PAGE spot report' SubClassOf 'Obsolete concept (EDAM)' '2D PAGE spot report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3162 MAGE-TAB 'MAGE-TAB' SubClassOf 'Textual format' 'MAGE-TAB' SubClassOf 'Microarray experiment data format' http://edamontology.org/format_3164 GTrack 'GTrack' SubClassOf 'Sequence feature table format (text)' http://edamontology.org/operation_3469 RNA structure covariance model generation 'RNA structure covariance model generation' SubClassOf 'has topic' some 'Nucleic acid structure analysis' http://edamontology.org/operation_3461 Virulence prediction 'Virulence prediction' SubClassOf 'has topic' some 'Microbiology' http://edamontology.org/format_3161 MAGE-ML 'MAGE-ML' SubClassOf 'Microarray experiment data format' http://edamontology.org/data_1057 Sequence database name 'Sequence database name' SubClassOf 'Obsolete concept (EDAM)' '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 http://edamontology.org/operation_3465 http://edamontology.org/data_2381 Experiment report (genotyping) 'Experiment report (genotyping)' SubClassOf 'Obsolete concept (EDAM)' 'Experiment report (genotyping)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2382 Genotype experiment ID 'Genotype experiment ID' SubClassOf 'is identifier of' some 'Experiment report' http://edamontology.org/data_1051 Ontology name 'Ontology name' SubClassOf 'is identifier of' some 'Ontology' http://edamontology.org/operation_3435 Standardization and normalization 'Standardization and normalization' SubClassOf 'Analysis' 'Standardization and normalization' SubClassOf 'Statistical calculation' http://edamontology.org/operation_3434 Conversion 'Conversion' SubClassOf 'Utility operation' 'Conversion' SubClassOf http://edamontology.org/operation_0004 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')) http://edamontology.org/operation_3439 Pathway or network prediction 'Pathway or network prediction' SubClassOf 'Pathway or network processing' 'Pathway or network prediction' SubClassOf 'Pathway or network analysis' 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' 'Entrez' SubClassOf 'search engine' http://edamontology.org/operation_3438 Calculation 'Calculation' SubClassOf 'Analysis' 'Calculation' SubClassOf http://edamontology.org/operation_0004 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' 'NONMEM' SubClassOf 'software with command line interface' http://edamontology.org/data_1067 Phylogenetic distance matrix identifier 'Phylogenetic distance matrix identifier' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'is identifier of' some 'Sequence alignment' http://edamontology.org/data_1065 Sequence signature identifier 'Sequence signature identifier' SubClassOf 'Obsolete concept (EDAM)' 'Sequence signature identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1064 Sequence set ID 'Sequence set ID' SubClassOf 'is identifier of' some 'Sequence set' http://edamontology.org/data_2395 Fungi annotation 'Fungi annotation' SubClassOf 'Obsolete concept (EDAM)' 'Fungi annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3433 Assembly 'Assembly' SubClassOf 'Analysis' 'Assembly' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/data_2396 Fungi annotation (anamorph) 'Fungi annotation (anamorph)' SubClassOf 'Obsolete concept (EDAM)' 'Fungi annotation (anamorph)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3432 Clustering 'Clustering' SubClassOf 'Analysis' 'Clustering' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/data_1069 Comparison matrix identifier 'Comparison matrix identifier' SubClassOf 'is identifier of' some 'Comparison matrix' http://edamontology.org/data_2397 Gene features report (exon) 'Gene features report (exon)' SubClassOf 'Obsolete concept (EDAM)' 'Gene features report (exon)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3431 Deposition 'Deposition' SubClassOf 'information processing' 'Deposition' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/data_1068 Phylogenetic tree ID 'Phylogenetic tree ID' SubClassOf 'is identifier of' some 'Phylogenetic tree' http://edamontology.org/data_1063 Sequence identifier 'Sequence identifier' SubClassOf 'is identifier of' some 'Sequence' http://edamontology.org/data_1062 Database entry identifier 'Database entry identifier' SubClassOf 'Obsolete concept (EDAM)' 'Database entry identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1061 QSAR descriptor name 'QSAR descriptor name' SubClassOf 'is identifier of' some 'QSAR descriptor' 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://edamontology.org/operation_3446 Cell migration analysis 'Cell migration analysis' SubClassOf 'has topic' some 'Cell biology' 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 '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 output' some ('data' and ('has format specification' some 'BED format')) 'Segway 1.2' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'genomedata format')) 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://edamontology.org/data_1078 Microarray experiment annotation ID 'Microarray experiment annotation ID' SubClassOf 'is identifier of' some 'Experiment report' http://edamontology.org/operation_3440 Genome assembly 'Genome assembly' SubClassOf 'Sequence assembly' 'Genome assembly' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1077 Transcription factor identifier 'Transcription factor identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_1076 Codon usage table name 'Codon usage table name' SubClassOf 'is identifier of' some 'Codon usage table' 'Codon usage table name' SubClassOf 'is identifier of' some 'Genetic code' http://edamontology.org/data_1075 Protein family identifier 'Protein family identifier' SubClassOf 'is identifier of' some 'Protein family report' http://edamontology.org/operation_3443 Image analysis 'Image analysis' SubClassOf 'Operation (typed)' 'Image analysis' SubClassOf 'has topic' some 'Imaging' 'Image analysis' SubClassOf 'Analysis' 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://edamontology.org/data_1079 Electron microscopy model ID 'Electron microscopy model ID' SubClassOf 'is identifier of' some 'Electron microscopy model' http://edamontology.org/operation_3441 Plotting 'Plotting' SubClassOf 'Analysis' 'Plotting' SubClassOf http://edamontology.org/operation_0004 http://www.ebi.ac.uk/swo/SWO_0000140 search engine 'search engine' EquivalentTo 'software' and ('is executed in' some 'web content search') http://edamontology.org/data_1074 Protein interaction ID 'Protein interaction ID' SubClassOf 'is identifier of' some 'Protein interaction report' http://edamontology.org/data_1073 Amino acid index ID 'Amino acid index ID' SubClassOf 'is identifier of' some 'Amino acid index' http://edamontology.org/data_1072 Structure alignment ID 'Structure alignment ID' SubClassOf 'is identifier of' some 'Structure alignment' http://edamontology.org/data_1071 Structural (3D) profile ID 'Structural (3D) profile ID' SubClassOf 'is identifier of' some 'Structural profile' http://edamontology.org/data_1088 Article ID 'Article ID' SubClassOf 'is identifier of' some 'Article' http://edamontology.org/data_1086 Compound identifier 'Compound identifier' SubClassOf 'is identifier of' some 'Small molecule report' http://edamontology.org/data_1081 Genotype and phenotype annotation ID 'Genotype and phenotype annotation ID' SubClassOf 'is identifier of' some 'Genotype/phenotype report' http://edamontology.org/data_1080 Gene expression report ID 'Gene expression report ID' SubClassOf 'is identifier of' some 'Processed microarray data' http://edamontology.org/data_1085 Biological model ID 'Biological model ID' SubClassOf 'is identifier of' some 'Mathematical model' http://edamontology.org/data_1082 Pathway or network identifier 'Pathway or network identifier' SubClassOf 'is identifier of' some 'Pathway or network' http://edamontology.org/data_1099 UniProt accession (extended) 'UniProt accession (extended)' SubClassOf 'Obsolete concept (EDAM)' 'UniProt accession (extended)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1097 Sequence accession (nucleic acid) 'Sequence accession (nucleic acid)' SubClassOf 'is identifier of' some 'Nucleic acid sequence' http://edamontology.org/data_1096 Sequence accession (protein) 'Sequence accession (protein)' SubClassOf 'is identifier of' some 'Protein sequence' http://edamontology.org/data_1094 Sequence type 'Sequence type' SubClassOf 'Obsolete concept (EDAM)' 'Sequence type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3478 Phylogenetic tree reconstruction 'Phylogenetic tree reconstruction' SubClassOf 'has topic' some 'Phylogeny' http://edamontology.org/operation_3482 Antimicrobial resistance prediction 'Antimicrobial resistance prediction' SubClassOf 'has topic' some 'Microbiology' http://edamontology.org/topic_3301 Microbiology 'Microbiology' SubClassOf 'Biomedical science' 'Microbiology' SubClassOf 'Biology' http://edamontology.org/topic_3307 Computational biology 'Computational biology' SubClassOf 'Computer science' 'Computational biology' SubClassOf 'Biology' 'Computational biology' SubClassOf 'Topic' http://edamontology.org/topic_3323 Metabolic disease 'Metabolic disease' SubClassOf 'Obsolete concept (EDAM)' 'Metabolic disease' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3321 Molecular genetics 'Molecular genetics' SubClassOf 'Computational biology' http://edamontology.org/topic_3320 RNA splicing 'RNA splicing' SubClassOf 'Molecular genetics' 'RNA splicing' SubClassOf 'Gene expression' http://edamontology.org/data_1801 Gene ID (GeneDB Trypanosoma brucei) 'Gene ID (GeneDB Trypanosoma brucei)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Gene ID (GeneDB Schizosaccharomyces pombe)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3344 Biomedical science 'Biomedical science' SubClassOf 'Biology' 'Biomedical science' SubClassOf 'Medicine' 'Biomedical science' SubClassOf 'Topic' http://edamontology.org/data_1806 Gene synonym 'Gene synonym' SubClassOf 'Obsolete concept (EDAM)' 'Gene synonym' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3346 Sequence search 'Sequence search' SubClassOf 'Sequence analysis' 'Sequence search' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3097 Protein domain classification format 'Protein domain classification format' SubClassOf 'is format of' some 'Protein family report' http://purl.obolibrary.org/obo/IAO_0000098 data format specification 'Topic' DisjointWith 'data format specification' 'data format specification' DisjointWith 'information processing' 'data' DisjointWith 'data format specification' 'data format specification' DisjointWith http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3379 Preclinical and clinical studies 'Preclinical and clinical studies' SubClassOf http://edamontology.org/topic_3678 http://edamontology.org/operation_2931 Secondary structure comparison 'Secondary structure comparison' SubClassOf 'has topic' some 'Structure comparison' http://edamontology.org/operation_2930 Protein property comparison 'Protein property comparison' SubClassOf 'has output' some 'Protein property' http://edamontology.org/data_1853 Chromosome annotation (aberration) 'Chromosome annotation (aberration)' SubClassOf 'Obsolete concept (EDAM)' 'Chromosome annotation (aberration)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2932 Hopp and Woods plotting 'Hopp and Woods plotting' SubClassOf 'Peptide immunogenicity prediction' 'Hopp and Woods plotting' SubClassOf 'Plotting' 'Hopp and Woods plotting' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1852 Sequence assembly component 'Sequence assembly component' SubClassOf 'Obsolete concept (EDAM)' 'Sequence assembly component' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2928 Alignment 'Alignment' SubClassOf 'has output' some 'Alignment' 'Alignment' SubClassOf 'Analysis' http://kt.ijs.si/panovp/OntoDM#OntoDM_000087 probability distribution estimation task DisjointClasses: 'probability distribution estimation task', 'pattern discovery task', 'predictive modeling task', 'clustering task' http://edamontology.org/data_1866 Map type 'Map type' SubClassOf 'Obsolete concept (EDAM)' 'Map type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1865 Map feature 'Map feature' SubClassOf 'Obsolete concept (EDAM)' 'Map feature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://kt.ijs.si/panovp/OntoDM#OntoDM_000092 pattern discovery task DisjointClasses: 'probability distribution estimation task', 'pattern discovery task', 'predictive modeling task', 'clustering task' http://edamontology.org/data_1869 Organism identifier 'Organism identifier' SubClassOf 'is identifier of' some 'Organism report' http://edamontology.org/topic_3391 Omics 'Omics' SubClassOf 'Biology' 'Omics' SubClassOf 'Topic' http://edamontology.org/data_1878 Misspelling 'Misspelling' SubClassOf 'Obsolete concept (EDAM)' 'Misspelling' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1877 Synonym 'Synonym' SubClassOf 'Obsolete concept (EDAM)' 'Synonym' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1879 Acronym 'Acronym' SubClassOf 'Obsolete concept (EDAM)' 'Acronym' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1316 est2genome format 'est2genome format' SubClassOf 'Gene features (coding region) format' 'est2genome format' SubClassOf 'Gene annotation format' http://edamontology.org/data_1889 Gene name (DragonDB) 'Gene name (DragonDB)' SubClassOf 'Obsolete concept (EDAM)' '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 'has input' some 'Structural profile' 'Sequence-to-3D-profile alignment' SubClassOf 'has output' some 'Sequence-structure alignment' http://edamontology.org/operation_2964 Codon usage fraction calculation 'Codon usage fraction calculation' SubClassOf 'has output' some 'Codon usage fraction difference' http://edamontology.org/data_1888 Gene ID (MIPS Medicago) 'Gene ID (MIPS Medicago)' SubClassOf 'Obsolete concept (EDAM)' 'Gene ID (MIPS Medicago)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0302 Protein threading 'Protein threading' SubClassOf 'has input' some 'Protein structure' 'Protein threading' SubClassOf 'has output' some 'Sequence-structure alignment' http://edamontology.org/operation_2963 Codon usage bias plotting 'Codon usage bias plotting' SubClassOf 'has output' some 'Codon usage bias plot' http://edamontology.org/data_1887 Gene ID (MIPS Maize) 'Gene ID (MIPS Maize)' SubClassOf 'Obsolete concept (EDAM)' '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 'has output' some 'Codon usage bias' http://edamontology.org/operation_0300 Sequence-to-profile alignment 'Sequence-to-profile alignment' SubClassOf 'has topic' some 'Sequence sites, features and motifs' 'Sequence-to-profile alignment' SubClassOf 'has input' some 'Sequence profile' 'Sequence-to-profile alignment' SubClassOf 'has output' some 'Sequence-profile alignment' http://edamontology.org/operation_0305 Literature search 'Literature search' SubClassOf 'has topic' some 'Literature and reference' 'Literature search' SubClassOf 'has output' some 'Citation' http://edamontology.org/operation_0306 Text mining 'Text mining' SubClassOf 'has input' some 'Report' 'Text mining' SubClassOf 'has topic' some 'Data mining' 'Text mining' SubClassOf 'has output' some 'Text mining report' 'Text mining' SubClassOf 'Prediction and recognition' http://edamontology.org/operation_0303 Protein fold recognition 'Protein fold recognition' SubClassOf 'has topic' some 'Protein fold recognition' http://edamontology.org/operation_0304 Metadata retrieval 'Metadata retrieval' SubClassOf 'has output' some 'Resource metadata' http://edamontology.org/data_1880 Misnomer 'Misnomer' SubClassOf 'Obsolete concept (EDAM)' 'Misnomer' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1884 UniProt keywords 'UniProt keywords' SubClassOf 'Obsolete concept (EDAM)' 'UniProt keywords' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0312 Sequencing-based expression profile data processing 'Sequencing-based expression profile data processing' SubClassOf 'Obsolete concept (EDAM)' 'Sequencing-based expression profile data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0313 Gene expression profile clustering 'Gene expression profile clustering' SubClassOf 'has output' some 'Processed microarray data' http://edamontology.org/operation_0310 Sequence assembly 'Sequence assembly' SubClassOf 'has topic' some 'Sequence assembly' 'Sequence assembly' SubClassOf 'has output' some 'Sequence assembly' http://edamontology.org/operation_0311 Microarray data standardization and normalization 'Microarray data standardization and normalization' SubClassOf 'has output' some 'Microarray hybridisation data' 'Microarray data standardization and normalization' SubClassOf 'Standardization and normalization' 'Microarray data standardization and normalization' SubClassOf 'has input' some 'Microarray hybridisation data' 'Microarray data standardization and normalization' SubClassOf 'Gene expression data analysis' 'Microarray data standardization and normalization' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0316 Functional profiling 'Functional profiling' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'has output' some 'Gene expression profile' http://edamontology.org/operation_0315 Gene expression profile comparison 'Gene expression profile comparison' SubClassOf 'has output' some 'Processed microarray data' http://edamontology.org/data_1892 Gene name (GeneFarm) 'Gene name (GeneFarm)' SubClassOf 'Obsolete concept (EDAM)' 'Gene name (GeneFarm)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1890 Gene name (Arabidopsis) 'Gene name (Arabidopsis)' SubClassOf 'Obsolete concept (EDAM)' 'Gene name (Arabidopsis)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1893 Locus ID 'Locus ID' SubClassOf 'is identifier of' some 'Sequence coordinates' http://edamontology.org/operation_0309 Microarray probe design 'Microarray probe design' SubClassOf 'has output' some 'Oligonucleotide probe annotation' 'Microarray probe design' SubClassOf 'has topic' some 'Gene expression' 'Microarray probe design' SubClassOf 'Design' 'Microarray probe design' SubClassOf 'has topic' some 'Sequence design' 'Microarray probe design' SubClassOf 'has input' some 'Nucleic acid sequence' http://edamontology.org/operation_0307 Virtual PCR 'Virtual PCR' SubClassOf 'has topic' some 'Nucleic acids' http://edamontology.org/operation_0308 PCR primer design 'PCR primer design' SubClassOf 'has topic' some 'Sequence design' 'PCR primer design' SubClassOf 'has input' some 'Nucleic acid sequence' 'PCR primer design' SubClassOf 'has output' some 'PCR primers' http://edamontology.org/operation_2946 Alignment analysis 'Alignment analysis' SubClassOf 'Obsolete concept (EDAM)' 'Alignment analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2945 Analysis 'Analysis' SubClassOf 'information processing' 'Analysis' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/operation_2944 Physical mapping 'Physical mapping' SubClassOf 'has topic' some 'Mapping' 'Physical mapping' SubClassOf 'has output' some 'Physical map' http://edamontology.org/operation_2952 Structure alignment processing 'Structure alignment processing' SubClassOf 'Obsolete concept (EDAM)' 'Structure alignment processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2951 Alignment processing 'Alignment processing' SubClassOf 'Obsolete concept (EDAM)' 'Alignment processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0583 Directory metadata 'Directory metadata' SubClassOf 'Obsolete concept (EDAM)' 'Directory metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0582 Ontology 'Ontology' SubClassOf 'has topic' some 'Ontology and terminology' 'Ontology' SubClassOf 'Ontology data' http://edamontology.org/data_0581 Database 'Database' SubClassOf 'Obsolete concept (EDAM)' 'Database' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2949 Protein interaction analysis 'Protein interaction analysis' SubClassOf 'has output' some 'Protein interaction report' 'Protein interaction analysis' SubClassOf 'has topic' some 'Protein interactions' http://edamontology.org/operation_2948 Molecular interaction analysis 'Molecular interaction analysis' SubClassOf 'Obsolete concept (EDAM)' 'Molecular interaction analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2947 Article analysis 'Article analysis' SubClassOf 'has topic' some 'Literature and reference' 'Article analysis' SubClassOf 'Text mining' 'Article analysis' SubClassOf 'has output' some 'Article data' 'Article analysis' SubClassOf 'has input' some 'Article' 'Article analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0464 tRNA gene prediction 'tRNA gene prediction' SubClassOf 'Whole gene prediction' 'tRNA gene prediction' SubClassOf 'has topic' some 'Functional, regulatory and non-coding RNA' 'tRNA gene prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_0465 siRNA binding specificity prediction 'siRNA binding specificity prediction' SubClassOf 'has topic' some 'Functional, regulatory and non-coding RNA' http://edamontology.org/operation_0460 Nucleic acid temperature profile plotting 'Nucleic acid temperature profile plotting' SubClassOf 'has output' some 'Nucleic acid temperature profile' http://edamontology.org/operation_0461 Nucleic acid curvature calculation 'Nucleic acid curvature calculation' SubClassOf 'has output' some 'Nucleic acid property' http://www.ebi.ac.uk/swo/maturity/SWO_9000073 Maintained 'Obsolete' DisjointWith 'Maintained' http://edamontology.org/operation_0477 Protein modelling 'Protein modelling' SubClassOf 'has topic' some 'Molecular modelling' http://edamontology.org/operation_0478 Molecular docking 'Molecular docking' SubClassOf 'has output' some 'Protein-ligand complex' 'Molecular docking' SubClassOf 'has output' some 'Protein complex' 'Molecular docking' SubClassOf 'has topic' some 'Molecular docking' http://edamontology.org/operation_3502 Chemical class enrichment 'Chemical class enrichment' SubClassOf 'Gene expression data analysis' 'Chemical class enrichment' SubClassOf 'has topic' some 'Function analysis' http://edamontology.org/operation_0475 Nucleic acid structure prediction 'Nucleic acid structure prediction' SubClassOf 'has topic' some 'Nucleic acid structure analysis' 'Nucleic acid structure prediction' SubClassOf 'has output' some 'Nucleic acid structure' http://edamontology.org/operation_3501 Enrichment 'Enrichment' SubClassOf 'has topic' some 'Function analysis' 'Enrichment' SubClassOf 'Gene expression data analysis' http://edamontology.org/operation_0473 GPCR analysis 'GPCR analysis' SubClassOf 'has topic' some 'Membrane and lipoproteins' http://edamontology.org/operation_0474 Protein structure prediction 'Protein structure prediction' SubClassOf 'Protein analysis' 'Protein structure prediction' SubClassOf 'has output' some 'Protein structure' 'Protein structure prediction' SubClassOf 'has topic' some 'Protein structure prediction' http://purl.obolibrary.org/obo/IAO_0000129 version name 'version name' SubClassOf 'is version of' only ('programming language' or 'algorithm' or 'data format specification' or 'software' or 'software license') http://edamontology.org/operation_1774 Annotation retrieval 'Annotation retrieval' SubClassOf 'Obsolete concept (EDAM)' 'Annotation retrieval' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0443 Transcription regulatory element prediction (trans) 'Transcription regulatory element prediction (trans)' SubClassOf 'has topic' some 'Functional, regulatory and non-coding RNA' http://edamontology.org/operation_0449 Sequence alignment analysis (site correlation) 'Sequence alignment analysis (site correlation)' SubClassOf 'Correlation' 'Sequence alignment analysis (site correlation)' SubClassOf http://edamontology.org/operation_3465 http://edamontology.org/operation_1778 Protein function comparison 'Protein function comparison' SubClassOf 'has topic' some 'Function analysis' http://edamontology.org/operation_0446 Exonic splicing enhancer prediction 'Exonic splicing enhancer prediction' SubClassOf 'has topic' some 'Gene structure' http://edamontology.org/operation_1777 Protein function prediction 'Protein function prediction' SubClassOf 'has topic' some 'Function analysis' http://edamontology.org/data_1100 PIR identifier 'PIR identifier' SubClassOf 'is identifier of' some 'Sequence record' http://edamontology.org/data_1101 TREMBL accession 'TREMBL accession' SubClassOf 'Obsolete concept (EDAM)' 'TREMBL accession' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/algorithm/OntoDM_170075 clustering algorithm DisjointClasses: 'clustering algorithm', 'pattern discovery algorithm', 'predictive modeling algorithm' http://edamontology.org/operation_0439 Translation initiation site prediction 'Translation initiation site prediction' SubClassOf 'has topic' some 'Protein expression' http://edamontology.org/operation_0455 Nucleic acid thermodynamic property calculation 'Nucleic acid thermodynamic property calculation' SubClassOf 'has output' some 'Nucleic acid thermodynamic data' http://edamontology.org/data_1118 HMMER hidden Markov model ID 'HMMER hidden Markov model ID' SubClassOf 'is identifier of' some 'Hidden Markov model' http://edamontology.org/operation_0456 Nucleic acid melting profile plotting 'Nucleic acid melting profile plotting' SubClassOf 'has output' some 'Nucleic acid melting profile' http://edamontology.org/operation_0453 Nucleosome formation potential prediction 'Nucleosome formation potential prediction' SubClassOf 'Obsolete concept (EDAM)' 'Nucleosome formation potential prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0459 Nucleic acid probability profile plotting 'Nucleic acid probability profile plotting' SubClassOf 'has output' some 'Nucleic acid probability profile' http://edamontology.org/operation_0457 Nucleic acid stitch profile plotting 'Nucleic acid stitch profile plotting' SubClassOf 'has output' some 'Nucleic acid stitch profile' http://edamontology.org/operation_0458 Nucleic acid melting curve plotting 'Nucleic acid melting curve plotting' SubClassOf 'has output' some 'Nucleic acid melting curve' http://edamontology.org/data_1111 EMBOSS listfile 'EMBOSS listfile' SubClassOf 'Obsolete concept (EDAM)' 'EMBOSS listfile' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1110 EMBOSS sequence type 'EMBOSS sequence type' SubClassOf 'Obsolete concept (EDAM)' 'EMBOSS sequence type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1115 Sequence profile ID 'Sequence profile ID' SubClassOf 'is identifier of' some 'Sequence profile' http://edamontology.org/data_1114 Sequence motif identifier 'Sequence motif identifier' SubClassOf 'is identifier of' some 'Sequence motif' http://edamontology.org/operation_0452 Indel detection 'Indel detection' SubClassOf 'Mutation detection' http://edamontology.org/operation_1781 Gene regulatory network analysis 'Gene regulatory network analysis' SubClassOf 'has topic' some 'Gene regulatory networks' http://edamontology.org/data_1112 Sequence cluster ID 'Sequence cluster ID' SubClassOf 'is identifier of' some 'Sequence cluster' http://edamontology.org/operation_1780 Sequence submission 'Sequence submission' SubClassOf 'Obsolete concept (EDAM)' 'Sequence submission' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/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 'has specified data input' some ('has format specification' only 'R data frame') 'spotSegmentation' SubClassOf 'has specified data output' some 'Graph plot' 'spotSegmentation' SubClassOf 'BioConductor Software' 'spotSegmentation' SubClassOf 'R software' 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 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/maturity/SWO_9000065 Live DisjointClasses: 'alpha', 'beta', 'Release candidate', 'Live', 'Obsolete' http://www.ebi.ac.uk/efo/swo/SWO_0000706 splots 'splots' SubClassOf 'is published by' value 'Bioconductor' '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 'has specified data input' some ('has format specification' only 'chamber slide format') 'splots' SubClassOf 'R software' 'splots' SubClassOf 'BioConductor 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 spikeLI 'spikeLI' SubClassOf 'has specified data input' some 'Gene expression dataset' 'spikeLI' SubClassOf 'software' 'spikeLI' SubClassOf 'is encoded in' some 'R language' 'spikeLI' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'spikeLI' SubClassOf 'implements' some 'Langmuir Isotherm' 'spikeLI' SubClassOf 'has specified data output' some 'Graph plot' 'spikeLI' SubClassOf '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 spkTools 'spkTools' SubClassOf 'has specified data output' some ('Text data set' and 'Graph plot') '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' 'spkTools' SubClassOf '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 snpMatrix '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 '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' 'snpMatrix' SubClassOf 'R software' 'snpMatrix' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 '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' 'snapCGH' SubClassOf 'BioConductor Software' 'snapCGH' SubClassOf 'R software' http://edamontology.org/data_1122 Phylogenetic tree type 'Phylogenetic tree type' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'BLAST sequence alignment type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1120 Sequence alignment type 'Sequence alignment type' SubClassOf 'Obsolete concept (EDAM)' 'Sequence alignment type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1126 Comparison matrix name 'Comparison matrix name' SubClassOf 'is identifier of' some 'Comparison matrix' http://edamontology.org/data_1125 Comparison matrix type 'Comparison matrix type' SubClassOf 'Obsolete concept (EDAM)' 'Comparison matrix type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2807 Tool topic 'Tool topic' SubClassOf 'Obsolete concept (EDAM)' 'Tool topic' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2809 Study topic 'Study topic' SubClassOf 'Obsolete concept (EDAM)' 'Study topic' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000718 tkWidgets 'tkWidgets' SubClassOf 'software' 'tkWidgets' SubClassOf 'is encoded in' some 'R language' 'tkWidgets' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000719 topGO 'topGO' SubClassOf 'has specified data input' some 'Gene list' 'topGO' SubClassOf 'implements' some 'Kolmogorov Smirnov rank-sum based algorithm' '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' 'topGO' SubClassOf 'R software' 'topGO' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000716 tilingArray 'tilingArray' SubClassOf 'is published by' value 'Bioconductor' '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' 'tilingArray' SubClassOf 'BioConductor Software' 'tilingArray' SubClassOf 'R software' http://edamontology.org/format_1228 UniGene entry format 'UniGene entry format' SubClassOf 'Obsolete concept (EDAM)' 'UniGene entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000717 timecourse 'timecourse' SubClassOf 'implements' some 'RMA' 'timecourse' SubClassOf 'has specified data output' some ('has format specification' only 'CEL binary format') 'timecourse' SubClassOf 'is encoded in' some 'R language' 'timecourse' SubClassOf 'has specified data input' some 'Gene expression dataset' 'timecourse' SubClassOf 'is published by' value 'Bioconductor' 'timecourse' SubClassOf 'software' 'timecourse' SubClassOf 'R software' 'timecourse' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'is encoded in' some 'R language' 'stepNorm' SubClassOf 'software' 'stepNorm' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000712 stam 'stam' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') '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' 'stam' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000710 sscore '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 'has specified data input' some 'Gene expression dataset' 'sscore' SubClassOf 'R software' 'sscore' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'is published by' value 'Bioconductor' 'ssize' SubClassOf 'is executed in' some 'data visualization' 'ssize' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'ssize' SubClassOf 'is encoded in' some 'R language' 'ssize' SubClassOf 'R software' 'ssize' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'has specified data input' some 'Gene expression dataset' 'tspair' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'tspair' SubClassOf 'software' 'tspair' SubClassOf 'BioConductor Software' 'tspair' SubClassOf 'R software' http://edamontology.org/operation_3545 Mathematical modelling 'Mathematical modelling' SubClassOf 'Modelling and simulation' 'Mathematical modelling' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1133 InterPro accession 'InterPro accession' SubClassOf 'is identifier of' some 'Protein signature' http://edamontology.org/data_1132 InterPro entry name 'InterPro entry name' SubClassOf 'is identifier of' some 'Protein signature' http://edamontology.org/data_1134 InterPro secondary accession 'InterPro secondary accession' SubClassOf 'is identifier of' some 'Protein signature' http://edamontology.org/topic_2817 Yeast 'Yeast' SubClassOf 'Obsolete concept (EDAM)' 'Yeast' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2542 Protein features (domains) format 'Protein features (domains) format' SubClassOf 'Obsolete concept (EDAM)' 'Protein features (domains) format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2816 Gene resources 'Gene resources' SubClassOf 'Obsolete concept (EDAM)' 'Gene resources' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2815 Humans 'Humans' SubClassOf 'Obsolete concept (EDAM)' 'Humans' SubClassOf 'Vertebrates' http://www.ebi.ac.uk/efo/swo/SWO_0000729 xcms 'xcms' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'xcms' SubClassOf 'software' 'xcms' SubClassOf 'is encoded in' some 'R language' 'xcms' SubClassOf 'is published by' value 'Bioconductor' 'xcms' SubClassOf 'has specified data input' some 'LC-MS data' 'xcms' SubClassOf 'R software' 'xcms' SubClassOf 'BioConductor Software' http://edamontology.org/format_2548 Sequence feature table format 'Sequence feature table format' SubClassOf 'is format of' some 'Sequence features' http://www.ebi.ac.uk/efo/swo/SWO_0000727 webbioc 'webbioc' SubClassOf 'is encoded in' some 'R language' 'webbioc' SubClassOf 'implements' some 'Multiple testing' 'webbioc' SubClassOf '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 'R software' 'webbioc' SubClassOf 'BioConductor Software' http://edamontology.org/format_2547 uniprotkb-like format 'uniprotkb-like format' SubClassOf 'Sequence feature table format (text)' 'uniprotkb-like format' SubClassOf 'Sequence feature table format' http://www.ebi.ac.uk/efo/swo/SWO_0000728 widgetTools 'widgetTools' SubClassOf 'is encoded in' some 'R language' 'widgetTools' SubClassOf 'software' 'widgetTools' SubClassOf 'has specified data input' some 'Text data set' 'widgetTools' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'is encoded in' some 'R language' 'vsn' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'has specified data output' some ('has format specification' only 'Rnw') 'weaver' SubClassOf 'software' 'weaver' SubClassOf 'is encoded in' some 'R language' 'weaver' SubClassOf 'R software' 'weaver' SubClassOf 'BioConductor Software' http://edamontology.org/topic_2814 Protein structure analysis 'Protein structure analysis' SubClassOf 'Proteins' http://www.ebi.ac.uk/efo/swo/SWO_0000723 vbmp 'vbmp' SubClassOf 'is encoded in' some 'R language' '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 'BioConductor Software' 'vbmp' SubClassOf 'R software' http://edamontology.org/topic_2813 Disease genes and proteins 'Disease genes and proteins' SubClassOf 'Obsolete concept (EDAM)' 'Disease genes and proteins' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000721 twilight 'twilight' SubClassOf '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 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'twilight' SubClassOf 'is encoded in' some 'R language' 'twilight' SubClassOf 'is published by' value 'Bioconductor' 'twilight' SubClassOf 'BioConductor Software' 'twilight' SubClassOf 'R software' http://edamontology.org/topic_2811 Nomenclature 'Nomenclature' SubClassOf 'Obsolete concept (EDAM)' 'Nomenclature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0488 Linkage disequilibrium calculation 'Linkage disequilibrium calculation' SubClassOf 'has output' some 'Genetic linkage report' http://www.ebi.ac.uk/efo/swo/SWO_0000730 xps '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 'implements' some ('DFW' and 'FARMS' and 'RMA' and ''MAS5'') 'xps' SubClassOf 'software' 'xps' SubClassOf 'has specified data output' some ('Text data set' and 'Graph plot') 'xps' SubClassOf 'BioConductor Software' 'xps' SubClassOf 'R software' http://edamontology.org/operation_0489 Genetic code prediction 'Genetic code prediction' SubClassOf 'has output' some 'Genetic code' http://www.ebi.ac.uk/efo/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://edamontology.org/operation_0486 Functional mapping 'Functional mapping' SubClassOf 'Obsolete concept (EDAM)' 'Functional mapping' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0487 Haplotype mapping 'Haplotype mapping' SubClassOf 'has output' some 'Haplotype map' http://edamontology.org/operation_0484 SNP detection 'SNP detection' SubClassOf 'Nucleic acid sequence feature detection' http://edamontology.org/operation_0485 Radiation Hybrid Mapping 'Radiation Hybrid Mapping' SubClassOf 'has output' some 'Radiation hybrid map' http://edamontology.org/operation_0482 Protein-ligand docking 'Protein-ligand docking' SubClassOf 'has output' some 'Protein-ligand complex' 'Protein-ligand docking' SubClassOf 'has topic' some 'Protein interactions' http://edamontology.org/operation_0483 Structured RNA prediction and optimisation 'Structured RNA prediction and optimisation' SubClassOf 'has topic' some 'Nucleic acid structure prediction' 'Structured RNA prediction and optimisation' SubClassOf 'has output' some 'Sequence set (nucleic acid)' http://edamontology.org/topic_2829 Ontologies, nomenclature and classification 'Ontologies, nomenclature and classification' SubClassOf 'Obsolete concept (EDAM)' 'Ontologies, nomenclature and classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2826 Protein structure alignment 'Protein structure alignment' SubClassOf 'Obsolete concept (EDAM)' 'Protein structure alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2571 Raw sequence format 'Raw sequence format' SubClassOf 'is format of' some 'Raw sequence' http://edamontology.org/format_1247 COG sequence cluster format 'COG sequence cluster format' SubClassOf 'Obsolete concept (EDAM)' 'COG sequence cluster format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0499 Tree-based sequence alignment 'Tree-based sequence alignment' SubClassOf 'has topic' some 'Phylogeny' http://edamontology.org/operation_0498 Consensus-based sequence alignment 'Consensus-based sequence alignment' SubClassOf 'Sequence alignment generation' 'Consensus-based sequence alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0491 Pairwise sequence alignment 'Pairwise sequence alignment' SubClassOf 'Multiple sequence alignment' 'Pairwise sequence alignment' SubClassOf 'has output' some 'Sequence alignment (pair)' 'Pairwise sequence alignment' SubClassOf 'Sequence alignment generation' http://edamontology.org/data_1152 HIVDB identifier 'HIVDB identifier' SubClassOf 'Obsolete concept (EDAM)' 'HIVDB identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0490 Dotplot plotting 'Dotplot plotting' SubClassOf 'Sequence alignment visualisation' 'Dotplot plotting' SubClassOf 'has output' some 'Dotplot' 'Dotplot plotting' SubClassOf 'Sequence visualisation' http://edamontology.org/operation_0493 Pairwise sequence alignment generation (local) 'Pairwise sequence alignment generation (local)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Amino acid identifier format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2839 Molecules 'Molecules' SubClassOf 'Obsolete concept (EDAM)' 'Molecules' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1150 Disease ID 'Disease ID' SubClassOf 'is identifier of' some 'Disease report' 'Disease ID' SubClassOf 'Identifier (typed)' 'Disease ID' SubClassOf 'Accession' 'Disease ID' SubClassOf http://edamontology.org/data_3667 http://edamontology.org/format_2560 STRING entry format 'STRING entry format' SubClassOf 'Obsolete concept (EDAM)' 'STRING entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2830 Immunoproteins, genes and antigens 'Immunoproteins, genes and antigens' SubClassOf 'Protein families' 'Immunoproteins, genes and antigens' SubClassOf 'Gene families' http://edamontology.org/operation_2246 Demonstration 'Demonstration' SubClassOf 'Obsolete concept (EDAM)' 'Demonstration' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2241 Transmembrane protein visualisation 'Transmembrane protein visualisation' SubClassOf 'Protein secondary structure rendering' 'Transmembrane protein visualisation' SubClassOf 'has output' some 'Protein structure image' 'Transmembrane protein visualisation' SubClassOf 'Structure visualisation' http://edamontology.org/data_1164 MIRIAM URI 'MIRIAM URI' SubClassOf 'is identifier of' some 'Database metadata' http://edamontology.org/data_1163 MIRIAM data type name 'MIRIAM data type name' SubClassOf 'is identifier of' some 'Database metadata' http://edamontology.org/correlation_3465 Correlation 'Correlation' SubClassOf 'Analysis' 'Correlation' SubClassOf 'has topic' some 'Proteomics' http://edamontology.org/data_1162 MIRIAM identifier 'MIRIAM identifier' SubClassOf 'is identifier of' some 'Database metadata' http://edamontology.org/topic_2842 High-throughput sequencing 'High-throughput sequencing' SubClassOf 'Obsolete concept (EDAM)' 'High-throughput sequencing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2847 Disease (specific) 'Disease (specific)' SubClassOf 'Obsolete concept (EDAM)' 'Disease (specific)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2846 Gene regulatory networks 'Gene regulatory networks' SubClassOf 'Gene regulation' 'Gene regulatory networks' SubClassOf 'Molecular interactions, pathways and networks' 'Gene regulatory networks' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2844 Structural clustering 'Structural clustering' SubClassOf 'Obsolete concept (EDAM)' 'Structural clustering' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3033 Matrix format 'Matrix format' SubClassOf 'is format of' some 'Matrix' http://edamontology.org/operation_2224 Data retrieval (ontology concept) 'Data retrieval (ontology concept)' SubClassOf 'Obsolete concept (EDAM)' 'Data retrieval (ontology concept)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2222 Data retrieval (ontology annotation) 'Data retrieval (ontology annotation)' SubClassOf 'Obsolete concept (EDAM)' 'Data retrieval (ontology annotation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0203 Gene expression 'Gene expression' SubClassOf 'Genetics' 'Gene expression' SubClassOf 'Molecular genetics' http://edamontology.org/topic_0200 Microarrays 'Microarrays' SubClassOf 'Obsolete concept (EDAM)' 'Microarrays' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2869 RFLP 'RFLP' SubClassOf 'DNA polymorphism' 'RFLP' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2868 Microsatellites 'Microsatellites' SubClassOf 'DNA polymorphism' 'Microsatellites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2867 VNTR 'VNTR' SubClassOf 'DNA polymorphism' 'VNTR' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2237 Data retrieval (sequence profile) 'Data retrieval (sequence profile)' SubClassOf 'Obsolete concept (EDAM)' 'Data retrieval (sequence profile)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0210 Fish 'Fish' SubClassOf 'Obsolete concept (EDAM)' '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 'has topic' some 'Structure comparison' '3D-1D scoring matrix generation' SubClassOf 'has output' some '3D-1D scoring matrix' http://edamontology.org/operation_2234 Structure file processing 'Structure file processing' SubClassOf 'Obsolete concept (EDAM)' 'Structure file processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2233 Representative sequence identification 'Representative sequence identification' SubClassOf 'has topic' some 'Sequence comparison' http://edamontology.org/topic_0213 Mice or rats 'Mice or rats' SubClassOf 'Obsolete concept (EDAM)' 'Mice or rats' SubClassOf 'Vertebrates' http://edamontology.org/topic_0211 Flies 'Flies' SubClassOf 'Obsolete concept (EDAM)' 'Flies' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0217 Literature analysis 'Literature analysis' SubClassOf 'Obsolete concept (EDAM)' 'Literature analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0218 Data mining 'Data mining' SubClassOf 'Computer science' http://edamontology.org/topic_0215 Worms 'Worms' SubClassOf 'Obsolete concept (EDAM)' 'Worms' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0220 File management 'File management' SubClassOf 'Data management' 'File management' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0221 Sequence annotation 'Sequence annotation' SubClassOf 'Obsolete concept (EDAM)' 'Sequence annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0222 Genome annotation 'Genome annotation' SubClassOf 'Obsolete concept (EDAM)' 'Genome annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2265 Data retrieval (identifier) 'Data retrieval (identifier)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Data retrieval (pathway or network)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0143 Protein structure comparison 'Protein structure comparison' SubClassOf 'Obsolete concept (EDAM)' 'Protein structure comparison' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0144 Protein residue interactions 'Protein residue interactions' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Protein-protein interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0148 Protein-ligand interactions 'Protein-ligand interactions' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Protein-nucleic acid interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0150 Protein design 'Protein design' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'G protein-coupled receptors (GPCR)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0154 Small molecules 'Small molecules' SubClassOf 'Biochemistry' 'Small molecules' SubClassOf 'Structure analysis' http://edamontology.org/topic_0152 Carbohydrates 'Carbohydrates' SubClassOf 'Biochemistry' 'Carbohydrates' SubClassOf 'Structure analysis' http://edamontology.org/topic_0153 Lipids 'Lipids' SubClassOf 'Biochemistry' 'Lipids' SubClassOf 'Structure analysis' http://edamontology.org/topic_0158 Sequence motifs 'Sequence motifs' SubClassOf 'Obsolete concept (EDAM)' 'Sequence motifs' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0159 Sequence comparison 'Sequence comparison' SubClassOf 'Sequence analysis' 'Sequence comparison' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0156 Sequence editing 'Sequence editing' SubClassOf 'Obsolete concept (EDAM)' 'Sequence editing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0160 Sequence sites, features and motifs 'Sequence sites, features and motifs' SubClassOf 'Sequence analysis' 'Sequence sites, features and motifs' SubClassOf 'Computational biology' http://edamontology.org/topic_0166 Protein structural motifs and surfaces 'Protein structural motifs and surfaces' SubClassOf 'Protein sites, features and motifs' http://edamontology.org/topic_0163 Sequence database search 'Sequence database search' SubClassOf 'Obsolete concept (EDAM)' 'Sequence database search' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0164 Sequence clustering 'Sequence clustering' SubClassOf 'Obsolete concept (EDAM)' 'Sequence clustering' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0167 Structural (3D) profiles 'Structural (3D) profiles' SubClassOf 'Obsolete concept (EDAM)' 'Structural (3D) profiles' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0172 Protein structure prediction 'Protein structure prediction' SubClassOf 'Structure prediction' 'Protein structure prediction' SubClassOf 'Protein structure analysis' '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 'Structure prediction' 'Nucleic acid structure prediction' SubClassOf 'Nucleic acid structure analysis' 'Nucleic acid structure prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0177 Molecular docking 'Molecular docking' SubClassOf 'Structure prediction' '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 'Obsolete concept (EDAM)' 'Ab initio structure prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0175 Homology modelling 'Homology modelling' SubClassOf 'Obsolete concept (EDAM)' 'Homology modelling' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1906 Quantitative trait locus 'Quantitative trait locus' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Protein secondary structure prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0179 Protein tertiary structure prediction 'Protein tertiary structure prediction' SubClassOf 'Obsolete concept (EDAM)' 'Protein tertiary structure prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0183 Structure alignment 'Structure alignment' SubClassOf 'Obsolete concept (EDAM)' 'Structure alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0184 Threading 'Threading' SubClassOf 'Obsolete concept (EDAM)' 'Threading' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0182 Sequence alignment 'Sequence alignment' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Structure prediction' 'Protein fold recognition' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1916 Alignment 'Alignment' SubClassOf 'data' 'Alignment' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/topic_0195 Virtual PCR 'Virtual PCR' SubClassOf 'Obsolete concept (EDAM)' 'Virtual PCR' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0199 Genetic variation 'Genetic variation' SubClassOf 'Nucleic acid sites, features and motifs' 'Genetic variation' SubClassOf 'Genotype and phenotype' 'Genetic variation' SubClassOf 'Molecular genetics' http://edamontology.org/topic_0191 Phylogeny reconstruction 'Phylogeny reconstruction' SubClassOf 'Obsolete concept (EDAM)' 'Phylogeny reconstruction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/software_before_Microsoft_2007 software before Microsoft 2007 'software before Microsoft 2007' EquivalentTo 'software' and ('has version' some ('version name' and ('followed by' value 'Microsoft 2007 version'))) http://purl.obolibrary.org/obo/BFO_0000007 process 'process' DisjointWith 'Obsolete concept (EDAM)' http://edamontology.org/operation_0422 Protein cleavage site prediction 'Protein cleavage site prediction' SubClassOf 'has topic' some 'Proteomics' http://edamontology.org/operation_0423 Epitope mapping (MHC Class I) 'Epitope mapping (MHC Class I)' SubClassOf 'Obsolete concept (EDAM)' 'Epitope mapping (MHC Class I)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0420 Protein-nucleic acid binding prediction 'Protein-nucleic acid binding prediction' SubClassOf 'Protein binding site prediction (from sequence)' 'Protein-nucleic acid binding prediction' SubClassOf 'Protein binding site prediction' http://edamontology.org/topic_3295 Epigenetics 'Epigenetics' SubClassOf 'Molecular genetics' 'Epigenetics' SubClassOf 'Genetics' http://edamontology.org/operation_0426 Gene component prediction 'Gene component prediction' SubClassOf 'Gene prediction' 'Gene component prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0424 Epitope mapping (MHC Class II) 'Epitope mapping (MHC Class II)' SubClassOf 'Obsolete concept (EDAM)' 'Epitope mapping (MHC Class II)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0425 Whole gene prediction 'Whole gene prediction' SubClassOf 'Gene prediction' 'Whole gene prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3298 Phenomics 'Phenomics' SubClassOf 'Omics' http://edamontology.org/operation_0419 Protein binding site prediction (from sequence) 'Protein binding site prediction (from sequence)' SubClassOf 'Protein binding site prediction' 'Protein binding site prediction (from sequence)' SubClassOf 'Protein sequence feature detection' '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 'has topic' some 'Protein modifications' http://edamontology.org/operation_0418 Protein signal peptide detection 'Protein signal peptide detection' SubClassOf 'has topic' some 'Protein targeting and localization' http://edamontology.org/operation_0433 Splice site prediction 'Splice site prediction' SubClassOf 'has topic' some 'Gene structure' http://edamontology.org/operation_0434 Integrated gene prediction 'Integrated gene prediction' SubClassOf 'Whole gene prediction' 'Integrated gene prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_0431 Restriction site recognition 'Restriction site recognition' SubClassOf 'has topic' some 'Sequence sites, features and motifs' http://edamontology.org/operation_0437 Selenocysteine insertion sequence (SECIS) prediction 'Selenocysteine insertion sequence (SECIS) prediction' SubClassOf 'Gene component prediction' 'Selenocysteine insertion sequence (SECIS) prediction' SubClassOf 'has output' some 'Gene report' 'Selenocysteine insertion sequence (SECIS) prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_0438 Regulatory element prediction 'Regulatory element prediction' SubClassOf 'has topic' some 'Transcription factors and regulatory sites' 'Regulatory element prediction' SubClassOf 'Gene component prediction' 'Regulatory element prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_1768 Nucleic acid folding family identification 'Nucleic acid folding family identification' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid folding family identification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0435 Operon prediction 'Operon prediction' SubClassOf 'Whole gene prediction' 'Operon prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_0436 Coding region prediction 'Coding region prediction' SubClassOf 'Gene component prediction' 'Coding region prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_0430 CpG island and isochore detection 'CpG island and isochore detection' SubClassOf 'has topic' some 'Sequence composition, complexity and repeats' http://edamontology.org/operation_0429 Quadruplex formation site detection 'Quadruplex formation site detection' SubClassOf 'has topic' some 'Nucleic acid structure prediction' 'Quadruplex formation site detection' SubClassOf 'has output' some 'Nucleic acid structure report' http://edamontology.org/operation_0400 Protein pH-dependent property calculation 'Protein pH-dependent property calculation' SubClassOf 'has output' some 'Protein property' 'Protein pH-dependent property calculation' SubClassOf 'has topic' some 'Protein properties' http://edamontology.org/operation_0401 Protein hydropathy calculation (from sequence) 'Protein hydropathy calculation (from sequence)' SubClassOf 'Protein sequence analysis' 'Protein hydropathy calculation (from sequence)' SubClassOf 'Protein hydropathy calculation' 'Protein hydropathy calculation (from sequence)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0404 Protein hydrogen exchange rate calculation 'Protein hydrogen exchange rate calculation' SubClassOf 'has output' some 'Protein hydrogen exchange rate' http://edamontology.org/operation_0405 Protein hydrophobic region calculation 'Protein hydrophobic region calculation' SubClassOf 'Protein hydropathy calculation (from sequence)' 'Protein hydrophobic region calculation' SubClassOf 'Protein hydropathy calculation' http://edamontology.org/operation_0402 Protein titration curve plotting 'Protein titration curve plotting' SubClassOf 'has output' some 'Protein titration curve' http://edamontology.org/operation_0403 Protein isoelectric point calculation 'Protein isoelectric point calculation' SubClassOf 'has output' some 'Protein isoelectric point' http://edamontology.org/operation_0410 Protein crystallizability prediction 'Protein crystallizability prediction' SubClassOf 'has output' some 'Protein crystallizability' 'Protein crystallizability prediction' SubClassOf 'Protein hydropathy calculation (from sequence)' 'Protein crystallizability prediction' SubClassOf 'Protein hydropathy calculation' http://edamontology.org/operation_0415 Nucleic acid feature detection 'Nucleic acid feature detection' SubClassOf 'has output' some 'Nucleic acid features' 'Nucleic acid feature detection' SubClassOf 'has topic' some 'Sequence sites, features and motifs' http://edamontology.org/operation_0416 Epitope mapping 'Epitope mapping' SubClassOf 'has topic' some 'Immunology' http://edamontology.org/operation_0413 MHC peptide immunogenicity prediction 'MHC peptide immunogenicity prediction' SubClassOf 'Peptide immunogenicity prediction' 'MHC peptide immunogenicity prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0414 Protein feature prediction (from sequence) 'Protein feature prediction (from sequence)' SubClassOf 'Obsolete concept (EDAM)' 'Protein feature prediction (from sequence)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2400 Toxin annotation 'Toxin annotation' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Protein report (membrane protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2402 Protein-drug interaction report 'Protein-drug interaction report' SubClassOf 'Protein structure report' 'Protein-drug interaction report' SubClassOf 'Protein-ligand interaction report' 'Protein-drug interaction report' SubClassOf 'Drug report' 'Protein-drug interaction report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0408 Protein globularity prediction 'Protein globularity prediction' SubClassOf 'has output' some 'Protein globularity' 'Protein globularity prediction' SubClassOf 'Protein hydropathy calculation (from sequence)' 'Protein globularity prediction' SubClassOf 'Protein hydropathy calculation' http://edamontology.org/operation_0409 Protein solubility prediction 'Protein solubility prediction' SubClassOf 'has output' some 'Protein solubility' 'Protein solubility prediction' SubClassOf 'Protein hydropathy calculation (from sequence)' 'Protein solubility prediction' SubClassOf 'Protein hydropathy calculation' http://edamontology.org/operation_0406 Protein aliphatic index calculation 'Protein aliphatic index calculation' SubClassOf 'Protein hydropathy calculation (from sequence)' 'Protein aliphatic index calculation' SubClassOf 'has output' some 'Protein aliphatic index' '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 (from sequence)' 'Protein hydrophobic moment plotting' SubClassOf 'has output' some 'Peptide hydrophobic moment' 'Protein hydrophobic moment plotting' SubClassOf 'Protein hydropathy calculation' http://edamontology.org/data_1688 EMBOSS vectorstrip log file 'EMBOSS vectorstrip log file' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'NACCESS log file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1680 STRIDE log file 'STRIDE log file' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'EMBOSS sites log file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3327 BAI 'BAI' SubClassOf 'is format of' some 'Data index' http://edamontology.org/format_3326 Data index format 'Data index format' SubClassOf 'is format of' some 'Data index' http://edamontology.org/data_1694 Number of output entities 'Number of output entities' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Number of iterations' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1696 Drug report 'Drug report' SubClassOf 'has topic' some 'Drugs and target structures' http://edamontology.org/data_1695 Hit sort order 'Hit sort order' SubClassOf 'Obsolete concept (EDAM)' 'Hit sort order' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2014 Sequence-profile alignment format 'Sequence-profile alignment format' SubClassOf 'is format of' some 'Sequence-profile alignment' http://edamontology.org/format_2013 Biological pathway or network format 'Biological pathway or network format' SubClassOf 'is format of' some 'Pathway or network' http://edamontology.org/format_2015 Sequence-profile alignment (HMM) format 'Sequence-profile alignment (HMM) format' SubClassOf 'Obsolete concept (EDAM)' '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 'is format of' some 'Amino acid index' http://edamontology.org/format_2006 Phylogenetic tree format 'Phylogenetic tree format' SubClassOf 'is format of' some 'Phylogenetic tree' http://edamontology.org/data_3426 Proteomics experiment report 'Proteomics experiment report' SubClassOf 'Obsolete concept (EDAM)' 'Proteomics experiment report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3427 RNAi report 'RNAi report' SubClassOf 'Obsolete concept (EDAM)' 'RNAi report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3428 Simulation experiment report 'Simulation experiment report' SubClassOf 'Obsolete concept (EDAM)' 'Simulation experiment report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1580 ProDom entry format 'ProDom entry format' SubClassOf 'Obsolete concept (EDAM)' 'ProDom entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1581 FSSP entry format 'FSSP entry format' SubClassOf 'Obsolete concept (EDAM)' 'FSSP entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2106 Reaction ID (BioCyc) 'Reaction ID (BioCyc)' SubClassOf 'has topic' some 'Peptides and amino acids' http://edamontology.org/data_2108 Reaction ID 'Reaction ID' SubClassOf 'is identifier of' some 'Reaction data' http://edamontology.org/data_2103 Gene name (KEGG GENES) 'Gene name (KEGG GENES)' SubClassOf 'Obsolete concept (EDAM)' 'Gene name (KEGG GENES)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2100 Type 'Type' SubClassOf 'Obsolete concept (EDAM)' 'Type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1571 InterPro entry abstract format 'InterPro entry abstract format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Gene3D entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1573 PIRSF entry format 'PIRSF entry format' SubClassOf 'Obsolete concept (EDAM)' 'PIRSF entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1574 PRINTS entry format 'PRINTS entry format' SubClassOf 'Obsolete concept (EDAM)' 'PRINTS entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000608 macat 'macat' SubClassOf 'has specified data input' some 'Text data set' 'macat' 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some ('has format specification' only 'R data frame') 'nudge' SubClassOf 'BioConductor Software' 'nudge' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'has specified data output' some 'Graph plot' 'ontoTools' SubClassOf 'is encoded in' some 'R language' 'ontoTools' SubClassOf 'R software' 'ontoTools' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000641 oneChannelGUI '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 'software' 'oneChannelGUI' SubClassOf 'implements' 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data set' and 'Graph plot') 'simpleaffy' SubClassOf 'implements' some ('RMA' and ''MAS5'') 'simpleaffy' SubClassOf 'software' 'simpleaffy' SubClassOf 'is published by' value 'Bioconductor' 'simpleaffy' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'descriptive statistical calculation') 'simpleaffy' SubClassOf 'BioConductor Software' 'simpleaffy' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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_0000694 siggenes 'siggenes' SubClassOf 'has specified data input' some 'Text data set' 'siggenes' SubClassOf 'software' 'siggenes' SubClassOf 'is encoded in' some 'R language' 'siggenes' SubClassOf 'is executed in' some 'differential expression analysis' 'siggenes' SubClassOf 'implements' some ('Empirical Bayes rule' and ''FDR'' and 'SAM') 'siggenes' SubClassOf 'has specified data output' some 'HTML report' 'siggenes' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'is encoded in' some 'R language' 'sagenhaft' SubClassOf 'BioConductor Software' 'sagenhaft' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000692 seqLogo 'seqLogo' SubClassOf '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' 'seqLogo' SubClassOf 'R software' 'seqLogo' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000690 safe 'safe' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'safe' SubClassOf 'has specified data input' some 'ALL/AML data set' 'safe' SubClassOf 'is specified data input of' exactly 3 'Text data set' 'safe' SubClassOf 'is published by' value 'Bioconductor' 'safe' SubClassOf 'implements' some (''ANOVA'' and 'Bootstrap' and 'Global test' and ''t-test'') 'safe' SubClassOf 'is encoded in' some 'R language' 'safe' SubClassOf 'software' 'safe' SubClassOf 'BioConductor Software' 'safe' SubClassOf 'data' 'safe' SubClassOf 'R software' http://edamontology.org/format_2060 Map format 'Map format' SubClassOf 'is format of' some 'Map' http://edamontology.org/data_2198 Gene cluster 'Gene cluster' SubClassOf 'Obsolete concept (EDAM)' 'Gene cluster' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3232 Gene expression QTL analysis 'Gene expression QTL analysis' SubClassOf 'has output' some 'Pathway or network report' http://edamontology.org/format_2056 Microarray experiment data format 'Microarray experiment data format' SubClassOf 'Format (typed)' 'Microarray experiment data format' SubClassOf 'Experiment annotation format' http://edamontology.org/format_2055 Sequence assembly format 'Sequence assembly format' SubClassOf 'is format of' some 'Sequence assembly' http://edamontology.org/format_2058 Gene expression report format 'Gene expression report format' SubClassOf 'Gene annotation format' 'Gene expression report format' SubClassOf 'is format of' some 'Processed microarray data' 'Gene expression report format' SubClassOf 'Format (typed)' http://edamontology.org/format_2057 Sequence trace format 'Sequence trace format' SubClassOf 'is format of' some 'Sequence trace' http://edamontology.org/format_2052 Protein family report format 'Protein family report format' SubClassOf 'is format of' some 'Protein family report' http://edamontology.org/format_2051 Polymorphism report format 'Polymorphism report format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'is format of' some 'Protein interaction report' http://edamontology.org/data_2192 Error 'Error' SubClassOf 'Obsolete concept (EDAM)' 'Error' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_1456 Protein membrane regions 'Protein membrane regions' SubClassOf 'Protein domains and folds' 'Protein membrane regions' SubClassOf 'Protein domains' 'Protein membrane regions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2059 Genotype and phenotype annotation format 'Genotype and phenotype annotation format' SubClassOf 'Obsolete concept (EDAM)' 'Genotype and phenotype annotation format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000699 xmapbridge 'xmapbridge' SubClassOf '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' 'xmapbridge' SubClassOf 'BioConductor Software' 'xmapbridge' SubClassOf 'R software' http://edamontology.org/topic_0133 Two-dimensional gel electrophoresis 'Two-dimensional gel electrophoresis' SubClassOf 'Obsolete concept (EDAM)' 'Two-dimensional gel electrophoresis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2045 Electron microscopy model format 'Electron microscopy model format' SubClassOf 'Obsolete concept (EDAM)' '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 'is format of' some 'Phylogenetic invariants' http://edamontology.org/topic_0137 Protein hydropathy 'Protein hydropathy' SubClassOf 'Obsolete concept (EDAM)' 'Protein hydropathy' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0134 Mass spectrometry 'Mass spectrometry' SubClassOf 'Proteomics experiment' 'Mass spectrometry' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0135 Protein microarrays 'Protein microarrays' SubClassOf 'Obsolete concept (EDAM)' '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 'is format of' some 'Phylogenetic tree distances' http://www.ebi.ac.uk/efo/swo/SWO_0000599 logicFS 'logicFS' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'logicFS' SubClassOf 'is encoded in' some 'R language' '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' 'logicFS' SubClassOf 'BioConductor Software' 'logicFS' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'is encoded in' some 'R language' 'limmaGUI' SubClassOf 'has specified data input' some 'Text data set' 'limmaGUI' SubClassOf 'implements' some 'Linear modelling' 'limmaGUI' SubClassOf 'BioConductor Software' 'limmaGUI' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000593 limma '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')) 'limma' SubClassOf 'BioConductor Software' 'limma' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000590 keggorth 'keggorth' SubClassOf '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 'BioConductor Software' 'keggorth' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000591 lapmix 'lapmix' SubClassOf 'has specified data input' some 'Gene expression dataset' 'lapmix' SubClassOf 'is encoded in' some 'R language' 'lapmix' SubClassOf 'is published by' value 'Bioconductor' 'lapmix' SubClassOf 'software' 'lapmix' SubClassOf 'implements' some 'Laplace mixture model' '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' 'lapmix' SubClassOf 'BioConductor Software' 'lapmix' SubClassOf 'R software' http://kt.ijs.si/panovp/OntoDM#OntoDM_000235 predictive modeling task DisjointClasses: 'probability distribution estimation task', 'pattern discovery task', 'predictive modeling task', 'clustering task' http://edamontology.org/data_2090 Database entry version information 'Database entry version information' SubClassOf 'Obsolete concept (EDAM)' 'Database entry version information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2092 SNP 'SNP' SubClassOf 'Obsolete concept (EDAM)' 'SNP' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2093 Data reference 'Data reference' SubClassOf 'data' 'Data reference' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/operation_3187 Sequence contamination filtering 'Sequence contamination filtering' SubClassOf 'has topic' some 'Nucleic acids' http://edamontology.org/operation_3185 Base-calling 'Base-calling' SubClassOf 'has topic' some 'Sequencing' http://edamontology.org/operation_3189 Trim ends 'Trim ends' SubClassOf 'Sequence trimming' 'Trim ends' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3180 Sequence assembly validation 'Sequence assembly validation' SubClassOf 'has output' some 'Sequence assembly report' 'Sequence assembly validation' SubClassOf 'has input' some 'Sequence assembly' 'Sequence assembly validation' SubClassOf 'has topic' some 'Sequence assembly' http://kt.ijs.si/panovp/OntoDM#OntoDM_000264 clustering task DisjointClasses: 'probability distribution estimation task', 'pattern discovery task', 'predictive modeling task', 'clustering task' http://edamontology.org/topic_0077 Nucleic acids 'Nucleic acids' SubClassOf 'Biochemistry' 'Nucleic acids' SubClassOf 'Computational biology' http://edamontology.org/topic_0078 Proteins 'Proteins' SubClassOf 'Biochemistry' 'Proteins' SubClassOf 'Computational biology' http://www.ebi.ac.uk/swo/SWO_9000090 Dropbox 'Dropbox' SubClassOf 'has license' some 'Proprietary commercial software license' 'Dropbox' SubClassOf 'output of' some ('software development process' 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 'has website homepage' value "www.dropbox.com"^^http://www.w3.org/2001/XMLSchema#string 'Dropbox' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Dropbox')) 'Dropbox' SubClassOf 'software with command line interface' 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 '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')) 'EMBOSS package' SubClassOf 'software with command line interface' http://www.ebi.ac.uk/swo/SWO_9000091 Eclipse 'Eclipse' SubClassOf 'has interface' some 'graphical user interface' 'Eclipse' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'Textual format')) 'Eclipse' SubClassOf 'has website homepage' value "http://www.eclipse.org" 'Eclipse' SubClassOf 'has license' some 'EPL v1' 'Eclipse' SubClassOf 'output of' some ('software development process' and ('has participant' value 'Eclipse Foundation')) 'Eclipse' SubClassOf 'has version' value 'Helios Service Release 2' '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 'has specified data output' some ('data' and ('has format specification' some 'XML')) 'Grimoires' SubClassOf 'software' 'Grimoires' SubClassOf 'software with command line interface' 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://edamontology.org/topic_0079 Metabolites 'Metabolites' SubClassOf 'Small molecules' 'Metabolites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0084 Phylogeny 'Phylogeny' SubClassOf 'Computational biology' http://edamontology.org/data_2914 Sequence features metadata 'Sequence features metadata' SubClassOf 'Parameter' 'Sequence features metadata' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/topic_0083 Alignment 'Alignment' SubClassOf 'Obsolete concept (EDAM)' 'Alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0089 Ontology and terminology 'Ontology and terminology' SubClassOf 'Data management' 'Ontology and terminology' SubClassOf 'Informatics' http://edamontology.org/data_2911 Transcription factor accession 'Transcription factor accession' SubClassOf 'Accession' http://edamontology.org/data_2912 Strain accession 'Strain accession' SubClassOf 'is identifier of' some 'Cell line report' http://edamontology.org/operation_3195 Sequencing error detection 'Sequencing error detection' SubClassOf 'has topic' some 'Sequencing' http://edamontology.org/operation_3190 Trim vector 'Trim vector' SubClassOf 'Sequence trimming' 'Trim vector' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3191 Trim to reference 'Trim to reference' SubClassOf 'Sequence trimming' 'Trim to reference' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3118 Protein topological domains 'Protein topological domains' SubClassOf 'Protein domains' 'Protein topological domains' SubClassOf 'Protein domains and folds' 'Protein topological domains' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2925 Sequence data 'Sequence data' SubClassOf 'Obsolete concept (EDAM)' 'Sequence data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3120 Protein variants 'Protein variants' SubClassOf 'Protein structure analysis' 'Protein variants' SubClassOf 'Protein expression' http://edamontology.org/data_2927 Codon usage 'Codon usage' SubClassOf 'Obsolete concept (EDAM)' 'Codon usage' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0094 Nucleic acid thermodynamics 'Nucleic acid thermodynamics' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid thermodynamics' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0097 Nucleic acid structure analysis 'Nucleic acid structure analysis' SubClassOf 'Nucleic acids' http://edamontology.org/topic_3123 Expression signals 'Expression signals' SubClassOf 'Gene structure' 'Expression signals' SubClassOf 'Gene expression' 'Expression signals' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.geneontology.org/formats/oboInOwl#ObsoleteClass obsolete SWO class Obsolete concept (EDAM) 'Obsolete concept (EDAM)' SubClassOf 'Obsolete concept (EDAM)' 'process' DisjointWith 'Obsolete concept (EDAM)' 'material entity' DisjointWith 'Obsolete concept (EDAM)' 'Obsolete concept (EDAM)' DisjointWith 'role' 'information content entity' DisjointWith 'Obsolete concept (EDAM)' http://edamontology.org/topic_0091 Bioinformatics 'Bioinformatics' SubClassOf 'Computer science' 'Bioinformatics' SubClassOf 'Biology' 'Bioinformatics' SubClassOf 'Informatics' http://edamontology.org/topic_0092 Data visualisation 'Data visualisation' SubClassOf 'Data management' 'Data visualisation' SubClassOf 'Computer science' http://edamontology.org/topic_0090 Data search, query and retrieval 'Data search, query and retrieval' SubClassOf 'Data management' 'Data search, query and retrieval' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3127 DNA replication and recombination 'DNA replication and recombination' SubClassOf 'DNA binding sites' 'DNA replication and recombination' SubClassOf 'DNA' http://edamontology.org/topic_3126 Nucleic acid repeats 'Nucleic acid repeats' SubClassOf 'Nucleic acid sites, features and motifs' 'Nucleic acid repeats' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1601 Nc statistic 'Nc statistic' SubClassOf 'Obsolete concept (EDAM)' 'Nc statistic' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3135 Signal or transit peptide 'Signal or transit peptide' SubClassOf 'Gene transcript features' '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 'Nucleic acid sites, features and motifs' 'Sequence tagged sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1622 Disease report 'Disease report' SubClassOf 'has topic' some 'Pathology' http://edamontology.org/data_2954 Article report 'Article report' SubClassOf 'Obsolete concept (EDAM)' 'Article report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_9000081 BioPerl 'BioPerl' SubClassOf 'has website homepage' value "http://www.bioperl.org"^^http://www.w3.org/2001/XMLSchema#string 'BioPerl' SubClassOf 'is executed in' some 'biological data processing' 'BioPerl' SubClassOf 'has license' some 'Artistic License v1.0' '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 specified data input' some ('data' and ('has format specification' some 'tab delimited file format')) 'DNDC' SubClassOf 'has interface' some 'graphical user interface' 'DNDC' SubClassOf 'is executed in' some 'modelling' 'DNDC' SubClassOf 'software' 'DNDC' SubClassOf 'has website homepage' value "http://ecobas.org/www-server/rem/mdb/dndc.html"^^http://www.w3.org/2001/XMLSchema#string 'DNDC' SubClassOf 'has interface' some 'command-line interface' 'DNDC' SubClassOf 'has website homepage' value "http://www.dndc.sr.unh.edu/"^^http://www.w3.org/2001/XMLSchema#string 'DNDC' SubClassOf 'output of' some ('software development process' and ('has participant' value 'University of New Hampshire')) 'DNDC' SubClassOf 'software with command line interface' 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/"^^http://www.w3.org/2001/XMLSchema#string 'DROID' SubClassOf 'has version' value '6.02' 'DROID' SubClassOf 'has interface' some 'command-line interface' 'DROID' SubClassOf 'software with command line interface' http://edamontology.org/format_1563 SMART domain assignment report format 'SMART domain assignment report format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'BIND entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1569 IntAct entry format 'IntAct entry format' SubClassOf 'Obsolete concept (EDAM)' 'IntAct entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1636 Heatmap Heat map 'Heatmap' SubClassOf 'data' 'Heatmap' SubClassOf 'Gene expression data' 'Heatmap' SubClassOf http://edamontology.org/data_3768 http://edamontology.org/data_2968 Image 'Image' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_1634 Linkage disequilibrium (report) 'Linkage disequilibrium (report)' SubClassOf 'Obsolete concept (EDAM)' 'Linkage disequilibrium (report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3169 ChIP-seq 'ChIP-seq' SubClassOf 'Obsolete concept (EDAM)' 'ChIP-seq' SubClassOf 'Sequencing' 'ChIP-seq' SubClassOf http://edamontology.org/topic_3656 http://edamontology.org/data_2965 2D PAGE gel report '2D PAGE gel report' SubClassOf 'Obsolete concept (EDAM)' '2D PAGE gel report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2966 Oligonucleotide probe sets annotation 'Oligonucleotide probe sets annotation' SubClassOf 'Oligonucleotide probe annotation' 'Oligonucleotide probe sets annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2967 Microarray image 'Microarray image' SubClassOf 'Obsolete concept (EDAM)' 'Microarray image' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2961 Gene regulatory network report 'Gene regulatory network report' SubClassOf 'Obsolete concept (EDAM)' 'Gene regulatory network report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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 output' some ('data' and ('has format specification' some 'XLS spreadsheet')) 'Microsoft Excel' SubClassOf 'is executed in' some 'spreadsheet editing' 'Microsoft Excel' SubClassOf 'output of' some ('software development process' and ('has participant' value 'Microsoft')) 'Microsoft Excel' SubClassOf 'has interface' some 'graphical user interface' 'Microsoft Excel' SubClassOf 'has license' some 'Proprietary commercial software license' 'Microsoft Excel' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'XLS spreadsheet')) 'Microsoft Excel' SubClassOf 'software' 'Microsoft Excel' SubClassOf 'Microsoft developed software' http://www.ebi.ac.uk/swo/SWO_9000072 Microsoft Windows 'Microsoft Windows' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Microsoft')) 'Microsoft Windows' SubClassOf 'output of' some ('software development 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' 'Microsoft Windows' SubClassOf 'operating system' 'Microsoft Windows' SubClassOf 'Microsoft developed software' 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 declared status' some 'Live' 'Microsoft Excel for Windows 2010' SubClassOf 'has release date' value "2010-06-15T0:00:00"^^http://www.w3.org/2001/XMLSchema#string '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"^^http://www.w3.org/2001/XMLSchema#string '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 release date' value "2006-11-08T0:00:00"^^http://www.w3.org/2001/XMLSchema#string 'Windows Vista' SubClassOf 'has version' value 'Windows 6.0' 'Windows Vista' SubClassOf 'directly preceded by' some 'Windows XP' 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_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' 'Microsoft Office 2001' SubClassOf 'software suite' http://www.ebi.ac.uk/swo/SWO_9000078 Annotare 'Annotare' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'MAGE-TAB')) 'Annotare' SubClassOf 'is executed in' some 'annotation editing' 'Annotare' SubClassOf 'has license' some 'MIT License' 'Annotare' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'MAGE-TAB')) 'Annotare' SubClassOf 'has declared status' some 'Latest release' 'Annotare' SubClassOf 'has website homepage' value "http://code.google.com/p/annotare/"^^http://www.w3.org/2001/XMLSchema#string 'Annotare' SubClassOf 'has interface' some 'graphical user interface' 'Annotare' SubClassOf 'output of' some ('software development process' and ('has participant' value 'Stanford University')) 'Annotare' SubClassOf 'software' 'Annotare' SubClassOf 'has version' value '1' 'Annotare' SubClassOf '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 'has website homepage' value "http://get.adobe.com/reader/"^^http://www.w3.org/2001/XMLSchema#string 'Adobe Acrobat Reader' SubClassOf 'is executed in' some 'file rendering' 'Adobe Acrobat Reader' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'pdf')) 'Adobe Acrobat Reader' SubClassOf 'has license' some 'Proprietary commercial software license' '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 'output of' some ('software development process' and ('has participant' value 'The Community')) 'BioJava' SubClassOf 'has interface' some 'application programming interface' 'BioJava' SubClassOf 'has license' some 'lGPL' 'BioJava' SubClassOf 'has website homepage' value "http://biojava.org"^^http://www.w3.org/2001/XMLSchema#string 'BioJava' SubClassOf 'is executed in' some 'biological data processing' http://edamontology.org/data_1646 Molecular weights standard fingerprint 'Molecular weights standard fingerprint' SubClassOf 'Peptide mass fingerprint' 'Molecular weights standard fingerprint' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3175 Structural variation 'Structural variation' SubClassOf 'Chromosomes' 'Structural variation' SubClassOf 'DNA' http://edamontology.org/topic_3179 ChIP-on-chip 'ChIP-on-chip' SubClassOf 'Obsolete concept (EDAM)' 'ChIP-on-chip' SubClassOf http://edamontology.org/topic_3656 http://edamontology.org/topic_3178 RNA-Seq alignment 'RNA-Seq alignment' SubClassOf 'Obsolete concept (EDAM)' 'RNA-Seq alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2978 Reaction data 'Reaction data' SubClassOf 'data' 'Reaction data' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/topic_3177 DNA-Seq 'DNA-Seq' SubClassOf 'Obsolete concept (EDAM)' 'DNA-Seq' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2971 Workflow data 'Workflow data' SubClassOf 'Obsolete concept (EDAM)' 'Workflow data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2972 Workflow 'Workflow' SubClassOf 'Obsolete concept (EDAM)' 'Workflow' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2973 Secondary structure data 'Secondary structure data' SubClassOf 'Obsolete concept (EDAM)' 'Secondary structure data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1643 Affymetrix probe sets information library file 'Affymetrix probe sets information library file' SubClassOf 'Obsolete concept (EDAM)' 'Affymetrix probe sets information library file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1642 Affymetrix probe sets library file 'Affymetrix probe sets library file' SubClassOf 'Obsolete concept (EDAM)' 'Affymetrix probe sets library file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3171 DNA methylation 'DNA methylation' SubClassOf 'Obsolete concept (EDAM)' 'DNA methylation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3170 RNA-Seq 'RNA-Seq' SubClassOf 'Obsolete concept (EDAM)' 'RNA-Seq' SubClassOf 'Sequencing' 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://edamontology.org/format_1500 Domainatrix 3D-1D scoring matrix format 'Domainatrix 3D-1D scoring matrix format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Metabolic pathway report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2986 Nucleic acid classification 'Nucleic acid classification' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2987 Classification report 'Classification report' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Report' 'Pathway or network report' SubClassOf 'has topic' some 'Molecular interactions, pathways and networks' 'Pathway or network report' SubClassOf http://edamontology.org/data_3753 http://edamontology.org/data_2980 Protein classification 'Protein classification' SubClassOf 'Obsolete concept (EDAM)' 'Protein classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2981 Sequence motif data 'Sequence motif data' SubClassOf 'Obsolete concept (EDAM)' 'Sequence motif data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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 derivative software not allowed 'derivative software not allowed' DisjointWith 'derivative software allowed' http://www.ebi.ac.uk/swo/SWO_9000017 Restrictions on derivative software 'No restrictions on derivatives' DisjointWith 'Restrictions on derivative software' http://kt.ijs.si/panovp/OntoDM#OntoDM_530819 ensemble algorithm 'ensemble algorithm' DisjointWith 'single generalization algorithm' http://edamontology.org/data_1661 Disease pathway or network report 'Disease pathway or network report' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Cellular process pathways report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1664 MIRIAM datatype 'MIRIAM datatype' SubClassOf 'Obsolete concept (EDAM)' 'MIRIAM datatype' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2991 Protein torsion angle data 'Protein torsion angle data' SubClassOf 'Protein property' 'Protein torsion angle data' SubClassOf 'Protein structure report' http://edamontology.org/data_1663 Protein interaction networks 'Protein interaction networks' SubClassOf 'Obsolete concept (EDAM)' 'Protein interaction networks' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0922 Primers 'Primers' SubClassOf 'Gene transcription features' 'Primers' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1679 DaliLite log file 'DaliLite log file' SubClassOf 'Obsolete concept (EDAM)' 'DaliLite log file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1678 Tool log 'Tool log' SubClassOf 'Obsolete concept (EDAM)' 'Tool log' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1677 Job type 'Job type' SubClassOf 'Obsolete concept (EDAM)' 'Job type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2848 Bibliographic reference format 'Bibliographic reference format' SubClassOf 'is format of' some 'Abstract' 'Bibliographic reference format' SubClassOf 'is format of' some 'Citation' http://edamontology.org/data_1672 CATH version information 'CATH version information' SubClassOf 'Obsolete concept (EDAM)' 'CATH version information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1671 Tool version information 'Tool version information' SubClassOf 'Obsolete concept (EDAM)' 'Tool version information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1670 Database version information 'Database version information' SubClassOf 'Obsolete concept (EDAM)' 'Database version information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1676 Job ID 'Job ID' SubClassOf 'Obsolete concept (EDAM)' 'Job ID' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1675 Job status 'Job status' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence database cross-references' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_9000030 Usage unrestricted 'Usage unrestricted' DisjointWith 'Usage restricted' http://edamontology.org/data_1673 Swiss-Prot to PDB mapping 'Swiss-Prot to PDB mapping' SubClassOf 'Obsolete concept (EDAM)' 'Swiss-Prot to PDB mapping' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_9000031 Usage restricted 'Usage unrestricted' DisjointWith 'Usage restricted' http://edamontology.org/format_1513 KEGG REACTION enzyme report format 'KEGG REACTION enzyme report format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'BRENDA enzyme report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0224 Query and retrieval 'Query and retrieval' SubClassOf 'has output' some 'data' 'Query and retrieval' SubClassOf 'information processing' 'Query and retrieval' SubClassOf 'has topic' some 'Data search, query and retrieval' 'Query and retrieval' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/operation_0225 Data retrieval (database cross-reference) 'Data retrieval (database cross-reference)' SubClassOf 'Obsolete concept (EDAM)' 'Data retrieval (database cross-reference)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0228 Data index analysis 'Data index analysis' SubClassOf 'Obsolete concept (EDAM)' 'Data index analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0229 Annotation retrieval (sequence) 'Annotation retrieval (sequence)' SubClassOf 'Obsolete concept (EDAM)' 'Annotation retrieval (sequence)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0226 Annotation 'Annotation' SubClassOf 'Analysis' 'Annotation' SubClassOf 'has topic' some 'Ontology and terminology' 'Annotation' SubClassOf 'has input' some 'Ontology' 'Annotation' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/operation_0227 Indexing 'Indexing' SubClassOf 'Utility operation' 'Indexing' SubClassOf 'has output' some 'Data index' 'Indexing' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/topic_0820 Membrane and lipoproteins 'Membrane and lipoproteins' SubClassOf 'Protein families' 'Membrane and lipoproteins' SubClassOf 'Proteins' http://edamontology.org/topic_0821 Enzymes 'Enzymes' SubClassOf 'Protein families' 'Enzymes' SubClassOf 'Proteins' http://edamontology.org/operation_0235 Sequence ambiguity calculation 'Sequence ambiguity calculation' SubClassOf 'has topic' some 'Sequence composition, complexity and repeats' 'Sequence ambiguity calculation' SubClassOf 'has output' some 'Sequence ambiguity report' http://edamontology.org/operation_0236 Sequence composition calculation 'Sequence composition calculation' SubClassOf 'has output' some 'Sequence composition report' 'Sequence composition calculation' SubClassOf 'has topic' some 'Sequence composition, complexity and repeats' http://edamontology.org/operation_0234 Sequence complexity calculation 'Sequence complexity calculation' SubClassOf 'has output' some 'Sequence complexity report' 'Sequence complexity calculation' SubClassOf 'has topic' some 'Sequence composition, complexity and repeats' http://edamontology.org/operation_0239 Sequence signature recognition 'Sequence signature recognition' SubClassOf 'has output' some 'Sequence signature matches' 'Sequence signature recognition' SubClassOf 'has topic' some 'Sequence sites, features and motifs' 'Sequence signature recognition' SubClassOf 'Sequence motif processing' http://edamontology.org/operation_0237 Repeat sequence analysis 'Repeat sequence analysis' SubClassOf 'has topic' some 'Sequence composition, complexity and repeats' http://edamontology.org/operation_0238 Sequence motif discovery 'Sequence motif discovery' SubClassOf 'has topic' some 'Sequence sites, features and motifs' 'Sequence motif discovery' SubClassOf 'has output' some 'Sequence signature matches' 'Sequence motif discovery' SubClassOf 'Sequence motif processing' http://edamontology.org/data_2201 Sequence record full 'Sequence record full' SubClassOf 'Obsolete concept (EDAM)' '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 'has output' some 'Sequence map' http://edamontology.org/operation_0268 Protein super-secondary structure prediction 'Protein super-secondary structure prediction' SubClassOf 'has output' some 'Protein features' http://edamontology.org/operation_0267 Protein secondary structure prediction 'Protein secondary structure prediction' SubClassOf 'Prediction and recognition (protein)' 'Protein secondary structure prediction' SubClassOf 'has topic' some 'Protein structure prediction' http://edamontology.org/data_2217 Tumor annotation 'Tumor annotation' SubClassOf 'Obsolete concept (EDAM)' 'Tumor annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2218 Server metadata 'Server metadata' SubClassOf 'Obsolete concept (EDAM)' 'Server metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2212 Mutation annotation (basic) 'Mutation annotation (basic)' SubClassOf 'Obsolete concept (EDAM)' 'Mutation annotation (basic)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2213 Mutation annotation (prevalence) 'Mutation annotation (prevalence)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Mutation annotation (prognostic)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2215 Mutation annotation (functional) 'Mutation annotation (functional)' SubClassOf 'Obsolete concept (EDAM)' 'Mutation annotation (functional)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0264 Splice transcript prediction 'Splice transcript prediction' SubClassOf 'has topic' some 'Gene structure' http://edamontology.org/operation_0265 Frameshift detection 'Frameshift detection' SubClassOf 'has topic' some 'Sequencing' http://edamontology.org/operation_0262 Nucleic acid property calculation 'Nucleic acid property calculation' SubClassOf 'has output' some 'Nucleic acid property' http://edamontology.org/operation_0279 Nucleic acid folding prediction 'Nucleic acid folding prediction' SubClassOf 'has topic' some 'Nucleic acid structure prediction' 'Nucleic acid folding prediction' SubClassOf 'has output' some 'Nucleic acid folding report' http://edamontology.org/operation_0278 RNA secondary structure prediction 'RNA secondary structure prediction' SubClassOf 'has topic' some 'Nucleic acid structure prediction' 'RNA secondary structure prediction' SubClassOf 'has output' some 'RNA secondary structure' http://edamontology.org/data_2223 Ontology metadata 'Ontology metadata' SubClassOf 'has topic' some 'Ontology and terminology' http://edamontology.org/operation_0271 Structure prediction 'Structure prediction' SubClassOf 'has topic' some 'Structure prediction' 'Structure prediction' SubClassOf 'has output' some 'Structure' http://edamontology.org/operation_0272 Residue interaction prediction 'Residue interaction prediction' SubClassOf 'has topic' some 'Protein folding, stability and design' http://edamontology.org/operation_0270 Transmembrane protein analysis 'Transmembrane protein analysis' SubClassOf 'has topic' some 'Membrane and lipoproteins' http://edamontology.org/operation_0275 Protein-protein interaction prediction (from protein structure) 'Protein-protein interaction prediction (from protein structure)' SubClassOf 'Protein-protein interaction prediction' 'Protein-protein interaction prediction (from protein structure)' SubClassOf 'Protein feature detection' 'Protein-protein interaction prediction (from protein structure)' SubClassOf 'Protein structure analysis' 'Protein-protein interaction prediction (from protein structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0276 Protein interaction network analysis 'Protein interaction network analysis' SubClassOf 'has output' some 'Pathway or network report' 'Protein interaction network analysis' SubClassOf 'has topic' some 'Protein interactions' http://edamontology.org/operation_0273 Protein interaction raw data analysis 'Protein interaction raw data analysis' SubClassOf 'has input' some 'Protein interaction raw data' 'Protein interaction raw data analysis' SubClassOf 'has topic' some 'Protein interactions' http://edamontology.org/operation_0274 Protein-protein interaction prediction (from protein sequence) 'Protein-protein interaction prediction (from protein sequence)' SubClassOf 'Protein-protein interaction prediction' 'Protein-protein interaction prediction (from protein sequence)' SubClassOf 'Protein function prediction' '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 'Textual format' http://edamontology.org/operation_0246 Protein domain recognition 'Protein domain recognition' SubClassOf 'has topic' some 'Protein domains and folds' http://edamontology.org/operation_0245 Protein structural motif recognition 'Protein structural motif recognition' SubClassOf 'has topic' some 'Protein structural motifs and surfaces' http://edamontology.org/operation_0248 Residue interaction calculation 'Residue interaction calculation' SubClassOf 'has output' some 'Protein residue interactions' 'Residue interaction calculation' SubClassOf 'has topic' some 'Protein folding, stability and design' http://edamontology.org/operation_0249 Torsion angle calculation 'Torsion angle calculation' SubClassOf 'has output' some 'Protein torsion angle data' http://edamontology.org/data_2235 Raw SCOP domain classification 'Raw SCOP domain classification' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Raw CATH domain classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0242 Conserved transcription regulatory sequence identification 'Conserved transcription regulatory sequence identification' SubClassOf 'Nucleic acid sequence feature detection' http://edamontology.org/operation_0243 Protein property calculation (from structure) 'Protein property calculation (from structure)' SubClassOf 'has topic' some 'Protein structure analysis' 'Protein property calculation (from structure)' SubClassOf 'has output' some 'Protein property' http://edamontology.org/operation_0240 Sequence motif comparison 'Sequence motif comparison' SubClassOf 'has topic' some 'Sequence sites, features and motifs' 'Sequence motif comparison' SubClassOf 'has output' some 'Sequence signature matches' 'Sequence motif comparison' SubClassOf 'Sequence motif processing' http://edamontology.org/operation_0241 Transcription regulatory sequence analysis 'Transcription regulatory sequence analysis' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'has input' some 'Sequence alignment' http://edamontology.org/operation_0255 Feature table query 'Feature table query' SubClassOf 'Obsolete concept (EDAM)' 'Feature table query' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0256 Sequence feature comparison 'Sequence feature comparison' SubClassOf 'has topic' some 'Sequence sites, features and motifs' 'Sequence feature comparison' SubClassOf 'has input' some 'Feature table' 'Sequence feature comparison' SubClassOf 'has input' some 'Sequence record' http://edamontology.org/data_2249 DTD 'DTD' SubClassOf 'Obsolete concept (EDAM)' 'DTD' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2245 Sequence set (bootstrapped) 'Sequence set (bootstrapped)' SubClassOf 'Obsolete concept (EDAM)' 'Sequence set (bootstrapped)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0250 Protein property calculation 'Protein property calculation' SubClassOf 'has topic' some 'Protein properties' 'Protein property calculation' SubClassOf 'has output' some 'Protein property' http://edamontology.org/data_2247 Phylogenetic consensus tree 'Phylogenetic consensus tree' SubClassOf 'Obsolete concept (EDAM)' 'Phylogenetic consensus tree' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2248 Schema 'Schema' SubClassOf 'Obsolete concept (EDAM)' 'Schema' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0253 Sequence feature detection 'Sequence feature detection' SubClassOf 'has output' some 'Sequence features' 'Sequence feature detection' SubClassOf 'has topic' some 'Sequence sites, features and motifs' http://edamontology.org/data_2242 Phylogenetic property values 'Phylogenetic property values' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'has topic' some 'Immunology' 'Peptide immunogenicity prediction' SubClassOf 'has output' some 'Peptide immunogenicity data' http://edamontology.org/data_2240 Heterogen annotation 'Heterogen annotation' SubClassOf 'Obsolete concept (EDAM)' '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 'is format of' some 'Structure' http://www.ebi.ac.uk/efo/swo/SWO_0000507 cosmoGUI 'cosmoGUI' SubClassOf 'is executed in' some 'gene expression analysis' 'cosmoGUI' SubClassOf 'is encoded in' some 'R language' 'cosmoGUI' SubClassOf 'software' 'cosmoGUI' SubClassOf 'implements' some 'cosmo' 'cosmoGUI' SubClassOf 'has specified data input' some ('has format specification' only ('FASTA format' or 'R data frame')) 'cosmoGUI' SubClassOf 'has specified data output' some ('Image' and ('HTML report' or ('has format specification' only 'R data frame'))) 'cosmoGUI' SubClassOf 'is published by' value 'Bioconductor' 'cosmoGUI' SubClassOf 'BioConductor Software' 'cosmoGUI' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000505 copa 'copa' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'copa' SubClassOf 'is encoded in' some 'R language' 'copa' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'copa' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'copa' SubClassOf 'software' 'copa' SubClassOf 'implements' some (''FDR'' and 'Median Average Difference Algorithm') 'copa' SubClassOf 'is published by' value 'Bioconductor' 'copa' SubClassOf 'R software' 'copa' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000506 cosmo '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 'has specified data output' some ('Image' and ('HTML report' or ('has format specification' only 'R data frame'))) 'cosmo' SubClassOf 'has specified data input' some ('has format specification' only ('FASTA format' or 'R data frame')) 'cosmo' SubClassOf 'BioConductor Software' 'cosmo' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'is published by' value 'Bioconductor' 'convert' SubClassOf 'BioConductor Software' 'convert' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 ('Text data set' and 'Graph plot') ''codelink'' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'descriptive statistical calculation' and 'differential expression analysis') ''codelink'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 '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 'is encoded in' some 'R language' 'crlmm' SubClassOf 'BioConductor Software' 'crlmm' SubClassOf 'R software' http://edamontology.org/operation_2008 siRNA duplex prediction 'siRNA duplex prediction' SubClassOf 'has topic' some 'Functional, regulatory and non-coding RNA' http://edamontology.org/data_2252 XSLT stylesheet 'XSLT stylesheet' SubClassOf 'Obsolete concept (EDAM)' 'XSLT stylesheet' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2250 XML Schema 'XML Schema' SubClassOf 'Obsolete concept (EDAM)' 'XML Schema' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2251 Relax-NG schema 'Relax-NG schema' SubClassOf 'Obsolete concept (EDAM)' 'Relax-NG schema' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000514 daMA 'daMA' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'daMA' SubClassOf 'software' 'daMA' SubClassOf 'is executed in' some 'differential expression analysis' 'daMA' SubClassOf 'is published by' value 'Bioconductor' 'daMA' SubClassOf 'is encoded in' some 'R language' 'daMA' SubClassOf 'implements' some (''FDR'' and 'f-test') 'daMA' SubClassOf 'has specified data input' some 'Gene expression data' 'daMA' SubClassOf 'R software' 'daMA' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000512 ctc 'ctc' SubClassOf 'is encoded in' some 'R language' 'ctc' SubClassOf 'software' 'ctc' SubClassOf 'has specified data output' some ('Heatmap' and ('has format specification' only ('newick' or 'cdt' or 'gtr'))) 'ctc' SubClassOf 'has specified data input' some 'Text data set' 'ctc' SubClassOf 'implements' some 'Hierarchical clustering' 'ctc' SubClassOf 'is published by' value 'Bioconductor' 'ctc' SubClassOf 'R software' 'ctc' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000513 dChip 'dChip' SubClassOf 'is published by' value 'Havard School of Public Health' http://edamontology.org/operation_3349 Bibliography generation 'Bibliography generation' SubClassOf 'has output' some 'Bibliography' http://www.ebi.ac.uk/efo/swo/SWO_0000521 'domainsignatures' ''domainsignatures'' SubClassOf 'has specified data input' some 'Gene list' ''domainsignatures'' SubClassOf 'is executed in' some 'descriptive statistical calculation' ''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' ''domainsignatures'' SubClassOf 'R software' http://edamontology.org/operation_3348 Sequence checksum generation 'Sequence checksum generation' SubClassOf 'has topic' some 'Data acquisition' 'Sequence checksum generation' SubClassOf 'has input' some 'Sequence' http://www.ebi.ac.uk/efo/swo/SWO_0000522 'dualKS' ''dualKS'' SubClassOf 'has specified data input' some 'Gene expression dataset' ''dualKS'' SubClassOf 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') ''dualKS'' SubClassOf 'is encoded in' some 'R language' ''dualKS'' SubClassOf 'implements' some ('Kolmogorov Smirnov rank-sum based algorithm' and 'Bootstrap') ''dualKS'' SubClassOf 'software' ''dualKS'' SubClassOf 'has specified data output' some ('Text data set' and 'Graph plot') ''dualKS'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000520 'diffGeneAnalysis' ''diffGeneAnalysis'' SubClassOf 'software' ''diffGeneAnalysis'' SubClassOf 'has specified data output' some ('CSV data set' and 'Graph plot') ''diffGeneAnalysis'' SubClassOf 'implements' some 'Associative T method' ''diffGeneAnalysis'' SubClassOf 'has specified data input' some 'CSV data set' ''diffGeneAnalysis'' SubClassOf 'is encoded in' some 'R language' ''diffGeneAnalysis'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 ('Text data set' and 'Graph plot') ''explorase'' SubClassOf 'implements' some 'Linear modelling' ''explorase'' SubClassOf 'software' ''explorase'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000527 'edgeR' ''edgeR'' SubClassOf 'has specified data output' some ('Text data set' and 'Graph plot') ''edgeR'' SubClassOf 'implements' some ('Empirical Bayes rule' and 'Negative binomial distribution') ''edgeR'' SubClassOf 'has specified data input' some 'Digital gene expression (DGE) datasets' ''edgeR'' SubClassOf 'is executed in' some 'differential expression analysis' ''edgeR'' SubClassOf 'software' ''edgeR'' SubClassOf 'is encoded in' some 'R language' ''edgeR'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000528 exonmap '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 (''FDR'' and 'RMA') 'exonmap' SubClassOf 'software' 'exonmap' SubClassOf 'has specified data input' some ('has format specification' only ('CDF binary format' or 'CEL binary format' or 'CDF ASCII format' or 'CEL ASCII format')) 'exonmap' SubClassOf 'is published by' value 'Bioconductor' 'exonmap' SubClassOf 'has specified data input' some ('has format specification' only 'covdesc file') 'exonmap' SubClassOf 'BioConductor Software' 'exonmap' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000525 ecolitk 'ecolitk' SubClassOf 'is encoded in' some 'R language' 'ecolitk' SubClassOf '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' 'ecolitk' SubClassOf 'BioConductor Software' 'ecolitk' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 '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') 'edd' SubClassOf 'BioConductor Software' 'edd' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'is published by' value 'Bioconductor' 'dyebias' SubClassOf 'software' 'dyebias' SubClassOf 'has specified data output' some 'Text data set' 'dyebias' SubClassOf 'R software' 'dyebias' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'has specified data output' some ('Heatmap' and 'Text data set' and 'Graph plot') 'factDesign' SubClassOf 'implements' some (''ANOVA'' and ''FDR'' and 'RMA' and 'Linear modelling') 'factDesign' SubClassOf 'is published by' value 'Bioconductor' 'factDesign' SubClassOf 'BioConductor Software' 'factDesign' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000533 fbat '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') 'fbat' SubClassOf 'BioConductor Software' 'fbat' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000530 'externalVector' ''externalVector'' SubClassOf 'software' ''externalVector'' SubClassOf 'is encoded in' some 'R language' ''externalVector'' SubClassOf 'R software' http://edamontology.org/operation_0289 Sequence distance matrix generation 'Sequence distance matrix generation' SubClassOf 'has output' some 'Sequence distance matrix' 'Sequence distance matrix generation' SubClassOf 'has topic' some 'Phylogeny' http://edamontology.org/operation_0282 Genetic mapping 'Genetic mapping' SubClassOf 'has output' some 'Genetic map' http://edamontology.org/operation_0283 Linkage analysis 'Linkage analysis' SubClassOf 'has output' some 'Genetic linkage report' 'Linkage analysis' SubClassOf 'has topic' some 'Mapping' http://edamontology.org/operation_0280 Data retrieval (restriction enzyme annotation) 'Data retrieval (restriction enzyme annotation)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Genetic marker identification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0286 Codon usage analysis 'Codon usage analysis' SubClassOf 'has output' some 'Codon usage data' 'Codon usage analysis' SubClassOf 'has topic' some 'Gene expression' 'Codon usage analysis' SubClassOf 'has input' some 'Codon usage table' 'Codon usage analysis' SubClassOf 'has input' some 'Nucleic acid sequence' 'Codon usage analysis' SubClassOf 'has output' some 'Codon usage table' http://edamontology.org/operation_0287 Base position variability plotting 'Base position variability plotting' SubClassOf 'has output' some 'Base position variability plot' 'Base position variability plotting' SubClassOf 'has topic' some 'Gene structure' http://edamontology.org/operation_0284 Codon usage table generation 'Codon usage table generation' SubClassOf 'has output' some 'Codon usage table' http://www.ebi.ac.uk/efo/swo/SWO_0000538 flowCore 'flowCore' SubClassOf 'is encoded in' some 'R language' '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' 'flowCore' SubClassOf 'R software' 'flowCore' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'is executed in' some ('parse' and 'descriptive statistical calculation') 'flowFlowJo' SubClassOf 'has specified data input' some ('has format specification' only 'XML') 'flowFlowJo' SubClassOf 'is encoded in' some 'R language' 'flowFlowJo' SubClassOf 'software' 'flowFlowJo' SubClassOf 'R software' 'flowFlowJo' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'implements' some ('AMDIS' and 'Dynamic programming algorithm') 'flagme' SubClassOf 'software' 'flagme' SubClassOf 'BioConductor Software' 'flagme' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'has specified data input' some ('has format specification' only ('R data frame' or 'Data File Standard for Flow Cytometry')) 'flowClust' SubClassOf 'software' 'flowClust' SubClassOf 'implements' some ('Bayesian Model' and 'Expectation-Maximization(EM) algorithm' and 'Multivariate t mixture models') 'flowClust' SubClassOf 'R software' 'flowClust' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000534 fdrame '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 'BioConductor Software' 'fdrame' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000543 flowViz 'flowViz' SubClassOf 'has specified data output' some ('Text data set' and 'Graph plot') 'flowViz' SubClassOf 'software' 'flowViz' SubClassOf 'is published by' value 'Bioconductor' 'flowViz' SubClassOf 'is encoded in' some 'R language' 'flowViz' SubClassOf 'has specified data input' some ('has format specification' only 'Data File Standard for Flow Cytometry') 'flowViz' SubClassOf 'R software' 'flowViz' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000544 gaga 'gaga' SubClassOf 'software' 'gaga' SubClassOf 'implements' some (''FDR'' and 'Gamma-Gamma hierarchical model') 'gaga' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'gaga' SubClassOf 'is published by' value 'Bioconductor' '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 'is executed in' some ('descriptive statistical calculation' and 'differential expression analysis') 'gaga' SubClassOf 'BioConductor Software' 'gaga' SubClassOf 'R software' http://edamontology.org/operation_0299 3D profile-to-3D profile alignment '3D profile-to-3D profile alignment' SubClassOf 'Alignment' '3D profile-to-3D profile alignment' SubClassOf 'has input' some 'Structural profile' '3D profile-to-3D profile alignment' SubClassOf 'has output' some 'Structural (3D) profile alignment' http://www.ebi.ac.uk/efo/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 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'flowStats' SubClassOf 'is encoded in' some 'R language' 'flowStats' SubClassOf 'BioConductor Software' 'flowStats' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000542 flowUtils 'flowUtils' SubClassOf 'has specified data input' some ('has format specification' only 'Data File Standard for Flow Cytometry') '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' 'flowUtils' SubClassOf 'R software' 'flowUtils' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000540 flowQ 'flowQ' SubClassOf 'is published by' value 'Bioconductor' 'flowQ' SubClassOf 'is encoded in' some 'R language' 'flowQ' SubClassOf 'has specified data input' some ('has format specification' only 'Data File Standard for Flow Cytometry') 'flowQ' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'flowQ' SubClassOf 'software' 'flowQ' SubClassOf 'BioConductor Software' 'flowQ' SubClassOf 'R software' http://edamontology.org/data_2289 Sequence identifier (nucleic acid) 'Sequence identifier (nucleic acid)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Hybrid sequence alignment construction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0291 Sequence clustering 'Sequence clustering' SubClassOf 'has output' some 'Sequence cluster' 'Sequence clustering' SubClassOf 'has topic' some 'Sequence comparison' http://edamontology.org/operation_0292 Sequence alignment generation 'Sequence alignment generation' SubClassOf 'has output' some 'Sequence alignment' 'Sequence alignment generation' SubClassOf 'Sequence analysis' http://edamontology.org/operation_0297 3D profile generation '3D profile generation' SubClassOf 'has output' some 'Structural profile' '3D profile generation' SubClassOf 'has input' some 'Structure alignment' '3D profile generation' SubClassOf 'has input' some 'Structure' http://edamontology.org/operation_0298 Profile-to-profile alignment 'Profile-to-profile alignment' SubClassOf 'has output' some 'Sequence profile alignment' 'Profile-to-profile alignment' SubClassOf 'has input' some 'Sequence profile' 'Profile-to-profile alignment' SubClassOf 'has topic' some 'Sequence sites, features and motifs' http://edamontology.org/operation_0295 Structure alignment 'Structure alignment' SubClassOf 'has output' some 'Structure alignment' 'Structure alignment' SubClassOf 'Structure analysis' http://edamontology.org/data_2288 Sequence identifier (protein) 'Sequence identifier (protein)' SubClassOf 'Obsolete concept (EDAM)' 'Sequence identifier (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0296 Sequence profile generation 'Sequence profile generation' SubClassOf 'has input' some 'Sequence alignment' 'Sequence profile generation' SubClassOf 'has topic' some 'Sequence sites, features and motifs' 'Sequence profile generation' SubClassOf 'has output' some 'Sequence profile' http://edamontology.org/topic_1308 Matrix/scaffold attachment sites 'Matrix/scaffold attachment sites' SubClassOf 'Gene transcription features' '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 'has output' some 'Sequence' http://edamontology.org/topic_1302 PolyA signal or sites 'PolyA signal or sites' SubClassOf 'Gene transcript features' 'PolyA signal or sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000549 'genArise' ''genArise'' SubClassOf 'has specified data output' some 'Graph plot' ''genArise'' SubClassOf 'software' ''genArise'' SubClassOf 'has specified data input' some 'Text data set' ''genArise'' SubClassOf 'is encoded in' some 'R language' ''genArise'' SubClassOf 'is executed in' some ('correction' and 'data normalization' and 'differential expression analysis') ''genArise'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'implements' some 'RMA' 'gcrma' SubClassOf 'software' 'gcrma' SubClassOf 'is executed in' some ('correction' and 'data normalization') 'gcrma' SubClassOf 'BioConductor Software' 'gcrma' SubClassOf 'R software' http://edamontology.org/topic_1307 Splice sites 'Splice sites' SubClassOf 'Gene transcript features' 'Splice sites' SubClassOf 'RNA splicing' '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 'Gene transcription features' 'CpG island and isochores' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000545 'gaggle' ''gaggle'' SubClassOf 'is encoded in' some 'R language' ''gaggle'' SubClassOf 'software' ''gaggle'' SubClassOf 'R software' http://edamontology.org/topic_1305 Restriction sites 'Restriction sites' SubClassOf 'DNA binding sites' 'Restriction sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000546 gcRMA quantification 'gcRMA quantification' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Bioconductor')) http://www.ebi.ac.uk/efo/swo/SWO_0000555 genefilter 'genefilter' SubClassOf 'is encoded in' some 'R language' '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 'implements' some 'k-nearest neighbour classification' 'genefilter' SubClassOf 'software' 'genefilter' SubClassOf 'R software' 'genefilter' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000550 gene2pathway 'gene2pathway' SubClassOf 'has specified data input' some 'Gene list' 'gene2pathway' SubClassOf 'is published by' value 'Bioconductor' '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 'implements' some 'Hierarchical clustering' 'gene2pathway' SubClassOf 'R software' 'gene2pathway' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'is executed in' some ('data normalization' and 'differential expression analysis') 'geneRecommender' SubClassOf 'is published by' value 'Bioconductor' 'geneRecommender' SubClassOf 'is encoded in' some 'R language' 'geneRecommender' SubClassOf 'BioConductor Software' 'geneRecommender' SubClassOf 'R software' http://edamontology.org/data_2296 Gene name (AceView) 'Gene name (AceView)' SubClassOf 'Obsolete concept (EDAM)' 'Gene name (AceView)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3245 Mass spectrometry data format 'Mass spectrometry data format' SubClassOf 'is format of' some 'Mass spectrometry data' http://edamontology.org/data_2291 UniProt ID 'UniProt ID' SubClassOf 'is identifier of' some 'Sequence record' http://edamontology.org/topic_1311 Operon 'Operon' SubClassOf 'Gene structure' 'Operon' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_1312 Promoters 'Promoters' SubClassOf 'Gene transcription features' 'Promoters' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/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 'is encoded in' some 'R language' 'genomeIntervals' SubClassOf 'software' 'genomeIntervals' SubClassOf 'BioConductor Software' 'genomeIntervals' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000556 genemeta 'genemeta' SubClassOf 'is encoded in' some 'R language' '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 (''FDR'' and ''t-test'' and ('Fixed effect model' or 'Random effects model')) 'genemeta' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000557 geneplotter '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' 'geneplotter' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000565 gpls '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' 'gpls' SubClassOf 'BioConductor Software' 'gpls' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'software' 'goProfiles' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'is published by' value 'Bioconductor' 'goTools' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'goTools' SubClassOf 'has specified data input' some 'Gene list' 'goTools' SubClassOf 'R software' 'goTools' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'has specified data input' some 'Gene expression dataset' 'globaltest' SubClassOf 'software' 'globaltest' SubClassOf 'is published by' value 'Bioconductor' 'globaltest' SubClassOf 'R software' 'globaltest' SubClassOf 'BioConductor Software' http://edamontology.org/format_3235 Cytoband format 'Cytoband format' SubClassOf 'is format of' some 'Cytoband position' http://www.ebi.ac.uk/efo/swo/SWO_0000567 graph '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 'R software' 'graph' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'implements' some 'k-cores' 'hypergraph' SubClassOf 'has specified data output' some 'Graph plot' 'hypergraph' SubClassOf 'software' 'hypergraph' SubClassOf 'R software' 'hypergraph' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'is executed in' some ('distance calculation' and 'data visualization' and 'averaging' and 'decision tree induction' and 'differential expression analysis') 'hopach' SubClassOf 'software' 'hopach' SubClassOf 'has specified data input' some 'Gene expression data' 'hopach' SubClassOf 'R software' http://edamontology.org/operation_3357 Format detection 'Format detection' SubClassOf 'has input' some 'data' 'Format detection' SubClassOf 'has output' some 'Format identifier' http://www.ebi.ac.uk/efo/swo/SWO_0000575 HTML report 'HTML report' SubClassOf 'is encoded in' some 'HTML' http://www.ebi.ac.uk/efo/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 'has specified data output' some 'Graph plot' 'hexbin' SubClassOf 'is encoded in' some 'R language' 'hexbin' SubClassOf 'is published by' value 'Bioconductor' 'hexbin' SubClassOf 'BioConductor Software' 'hexbin' SubClassOf 'R software' http://edamontology.org/topic_2661 Toxins and targets 'Toxins and targets' SubClassOf 'Small molecules' 'Toxins and targets' SubClassOf 'Toxicology' 'Toxins and targets' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3351 Protein surface analysis 'Protein surface analysis' SubClassOf 'Protein property calculation (from structure)' 'Protein surface analysis' SubClassOf 'Structure analysis' http://edamontology.org/operation_3353 Ontology comparison 'Ontology comparison' SubClassOf 'Comparison' 'Ontology comparison' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3261 RDF/XML 'RDF/XML' SubClassOf 'OWL format' http://edamontology.org/topic_0003 Topic 'Topic' DisjointWith 'data format specification' 'Topic' DisjointWith http://www.w3.org/2002/07/owl#DeprecatedClass 'Topic' DisjointWith 'data' 'Topic' DisjointWith 'information processing' http://www.ebi.ac.uk/efo/swo/SWO_0000578 Icens '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' and ('has format specification' some 'R data frame')) 'Icens' SubClassOf 'software' 'Icens' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000579 idiogram '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') 'idiogram' SubClassOf 'BioConductor Software' 'idiogram' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'has specified data output' some 'Graph plot' 'iterativeBMAsurv' SubClassOf 'software' 'iterativeBMAsurv' SubClassOf 'is encoded in' some 'R language' 'iterativeBMAsurv' SubClassOf 'BioConductor Software' 'iterativeBMAsurv' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000581 impute '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' 'impute' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'software' 'iterativeBMA' SubClassOf 'is encoded in' some 'R language' 'iterativeBMA' SubClassOf 'has specified data input' some 'Gene expression dataset' 'iterativeBMA' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000476 arrayWoRx 'arrayWoRx' SubClassOf 'is published by' value 'Applied Precision Life Science' http://www.ebi.ac.uk/efo/swo/SWO_0000473 arrayQuality 'arrayQuality' SubClassOf 'is encoded in' some 'R language' 'arrayQuality' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'arrayQuality' SubClassOf 'has specified data input' some ('Gene list' and 'Graph plot') 'arrayQuality' SubClassOf 'software' 'arrayQuality' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000474 arrayQualityMetrics 'arrayQualityMetrics' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'arrayQualityMetrics' SubClassOf 'is encoded in' some 'R language' 'arrayQualityMetrics' SubClassOf 'has specified data output' some ('HTML report' and 'Graph plot') 'arrayQualityMetrics' SubClassOf 'is published by' value 'Bioconductor' 'arrayQualityMetrics' SubClassOf 'software' 'arrayQualityMetrics' SubClassOf 'R software' 'arrayQualityMetrics' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'is executed in' some ('averaging' and 'correction' and 'data normalization') 'aroma.light' SubClassOf 'BioConductor Software' 'aroma.light' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000472 arrayMvout 'arrayMvout' SubClassOf 'has specified data input' some 'MAQC data' 'arrayMvout' SubClassOf 'is encoded in' some 'R language' 'arrayMvout' SubClassOf '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'))) 'arrayMvout' SubClassOf 'BioConductor Software' 'arrayMvout' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000470 'apComplex' ''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' ''apComplex'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000479 'beadarray' ''beadarray'' SubClassOf 'has specified data input' some 'Text data set' ''beadarray'' SubClassOf 'is encoded in' some 'R language' ''beadarray'' SubClassOf 'software' ''beadarray'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/algorithm/OntoDM_382176 predictive modeling algorithm DisjointClasses: 'clustering algorithm', 'pattern discovery algorithm', 'predictive modeling algorithm' http://www.ebi.ac.uk/efo/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/efo/swo/SWO_0000489 biomaRT 'biomaRT' SubClassOf 'has specified data input' some ('has format specification' only 'FASTA format') 'biomaRT' SubClassOf 'software' 'biomaRT' SubClassOf 'is published by' value 'Bioconductor' 'biomaRT' SubClassOf 'is encoded in' some 'R language' 'biomaRT' SubClassOf 'BioConductor Software' 'biomaRT' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000486 'biocDatasets' ''biocDatasets'' SubClassOf 'is encoded in' some 'R language' ''biocDatasets'' SubClassOf 'software' ''biocDatasets'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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/efo/swo/SWO_0000485 bioDist 'bioDist' SubClassOf 'implements' some (''KLD'' and ''MI'') 'bioDist' SubClassOf 'is published by' value 'Bioconductor' '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' 'bioDist' SubClassOf 'BioConductor Software' 'bioDist' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000482 bgafun 'bgafun' SubClassOf 'has specified data output' some ('Text data set' and 'Graph plot') 'bgafun' SubClassOf 'is published by' value 'Bioconductor' 'bgafun' SubClassOf 'has specified data input' some ('has format specification' only 'FASTA format') 'bgafun' SubClassOf 'software' 'bgafun' SubClassOf 'is encoded in' some 'R language' 'bgafun' SubClassOf 'BioConductor Software' 'bgafun' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000483 bgx 'bgx' SubClassOf 'is encoded in' some 'R language' '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' 'bgx' SubClassOf 'BioConductor Software' 'bgx' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000480 'beadarraySNP' ''beadarraySNP'' SubClassOf 'software' ''beadarraySNP'' SubClassOf 'is encoded in' some 'R language' ''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/efo/swo/SWO_0000481 'betr' ''betr'' SubClassOf 'has specified data input' some 'Gene list' ''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 'is executed in' some 'differential expression analysis' ''betr'' SubClassOf 'software' ''betr'' SubClassOf 'R software' ''betr'' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000499 'clusterStab' ''clusterStab'' SubClassOf 'software' ''clusterStab'' SubClassOf 'is encoded in' some 'R language' ''clusterStab'' SubClassOf 'has specified data output' some ('Heatmap' and 'Graph plot') ''clusterStab'' SubClassOf 'implements' some 'Hierarchical clustering' ''clusterStab'' SubClassOf 'is executed in' some ('decision tree induction' and 'differential expression analysis') ''clusterStab'' SubClassOf 'has specified data input' some 'Gene list' ''clusterStab'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'has specified data output' some ('HTML report' and 'Graph plot') ''cellHTS2'' SubClassOf 'is encoded in' some 'R language' ''cellHTS2'' SubClassOf 'software' ''cellHTS2'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000496 cghMCR 'cghMCR' SubClassOf 'implements' some 'MCR algorithm' 'cghMCR' SubClassOf 'is published by' value 'Bioconductor' 'cghMCR' SubClassOf 'software' 'cghMCR' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'cghMCR' SubClassOf 'is executed in' some 'data normalization' 'cghMCR' SubClassOf 'is encoded in' some 'R language' 'cghMCR' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'cghMCR' SubClassOf 'R software' 'cghMCR' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'has specified data input' some 'Text data set' ''cellHTS'' SubClassOf 'software' ''cellHTS'' SubClassOf 'is executed in' some ('data normalization' and 'descriptive statistical calculation') ''cellHTS'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000491 'bridge' ''bridge'' SubClassOf 'software' ''bridge'' SubClassOf 'is executed in' some 'differential expression analysis' ''bridge'' SubClassOf 'is encoded in' some 'R language' ''bridge'' SubClassOf 'implements' some ('Bayesian Model' and 'Markov Chain Monte Carlo') ''bridge'' SubClassOf 'R software' http://edamontology.org/operation_3283 Anonymisation 'Anonymisation' SubClassOf 'Utility operation' 'Anonymisation' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/operation_3289 ID retrieval 'ID retrieval' SubClassOf 'has output' some 'Identifier' http://edamontology.org/operation_3280 Named entity recognition 'Named entity recognition' SubClassOf 'Prediction and recognition' http://edamontology.org/data_1713 Fate map 'Fate map' SubClassOf 'has topic' some 'Embryology' http://edamontology.org/data_1717 MeSH 'MeSH' SubClassOf 'Obsolete concept (EDAM)' 'MeSH' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1716 GO 'GO' SubClassOf 'Obsolete concept (EDAM)' 'GO' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1715 BioPax term 'BioPax term' SubClassOf 'Obsolete concept (EDAM)' 'BioPax term' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1724 ChEBI 'ChEBI' SubClassOf 'Obsolete concept (EDAM)' 'ChEBI' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1723 EMAP 'EMAP' SubClassOf 'Obsolete concept (EDAM)' 'EMAP' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1722 FMA 'FMA' SubClassOf 'Obsolete concept (EDAM)' 'FMA' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1721 UMLS 'UMLS' SubClassOf 'Obsolete concept (EDAM)' 'UMLS' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1728 GO (molecular function) 'GO (molecular function)' SubClassOf 'Obsolete concept (EDAM)' 'GO (molecular function)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1727 GO (biological process) 'GO (biological process)' SubClassOf 'Obsolete concept (EDAM)' 'GO (biological process)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1726 myGrid 'myGrid' SubClassOf 'Obsolete concept (EDAM)' 'myGrid' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1725 MGED 'MGED' SubClassOf 'Obsolete concept (EDAM)' 'MGED' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1720 Plant ontology term 'Plant ontology term' SubClassOf 'Obsolete concept (EDAM)' 'Plant ontology term' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1719 NCBI taxonomy vocabulary 'NCBI taxonomy vocabulary' SubClassOf 'Obsolete concept (EDAM)' 'NCBI taxonomy vocabulary' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1718 HGNC 'HGNC' SubClassOf 'Obsolete concept (EDAM)' 'HGNC' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1733 Ontology concept reference 'Ontology concept reference' SubClassOf 'Obsolete concept (EDAM)' 'Ontology concept reference' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1732 Ontology concept comment 'Ontology concept comment' SubClassOf 'Obsolete concept (EDAM)' 'Ontology concept comment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1738 doc2loc document information 'doc2loc document information' SubClassOf 'Obsolete concept (EDAM)' 'doc2loc document information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1730 Ontology relation type 'Ontology relation type' SubClassOf 'Obsolete concept (EDAM)' 'Ontology relation type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1729 GO (cellular component) 'GO (cellular component)' SubClassOf 'Obsolete concept (EDAM)' 'GO (cellular component)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3032 Primer or probe design 'Primer or probe design' SubClassOf 'Obsolete concept (EDAM)' 'Primer or probe design' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3039 Nucleic acid structure 'Nucleic acid structure' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid structure' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3038 Structure databases 'Structure databases' SubClassOf 'Obsolete concept (EDAM)' 'Structure databases' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3044 Protein interaction networks 'Protein interaction networks' SubClassOf 'Obsolete concept (EDAM)' 'Protein interaction networks' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3043 Protein sequences 'Protein sequences' SubClassOf 'Obsolete concept (EDAM)' 'Protein sequences' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3042 Nucleic acid sequences 'Nucleic acid sequences' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid sequences' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3041 Sequence databases 'Sequence databases' SubClassOf 'Obsolete concept (EDAM)' 'Sequence databases' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3048 Mammals 'Mammals' SubClassOf 'Obsolete concept (EDAM)' 'Mammals' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1431 Phylogenetic property values format 'Phylogenetic property values format' SubClassOf 'Obsolete concept (EDAM)' 'Phylogenetic property values format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1767 CATH domain sequences (COMBS) 'CATH domain sequences (COMBS)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'CATH domain sequences (ATOM)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1765 CATH representative domain sequences (COMBS) 'CATH representative domain sequences (COMBS)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence clusters and classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1764 CATH representative domain sequences (ATOM) 'CATH representative domain sequences (ATOM)' SubClassOf 'Obsolete concept (EDAM)' 'CATH representative domain sequences (ATOM)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1762 CATH domain report 'CATH domain report' SubClassOf 'Obsolete concept (EDAM)' 'CATH domain report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1776 Protein report (function) 'Protein report (function)' SubClassOf 'Obsolete concept (EDAM)' 'Protein report (function)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3063 Medical informatics 'Medical informatics' SubClassOf 'Medicine' 'Medical informatics' SubClassOf 'Computer science' 'Medical informatics' SubClassOf 'Informatics' http://edamontology.org/topic_3062 Genetic organisation 'Genetic organisation' SubClassOf 'Obsolete concept (EDAM)' 'Genetic organisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3061 Documentation and help 'Documentation and help' SubClassOf 'Literature and reference' 'Documentation and help' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3060 Regulatory RNA 'Regulatory RNA' SubClassOf 'Obsolete concept (EDAM)' 'Regulatory RNA' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1772 Score 'Score' SubClassOf 'data' 'Score' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_1789 Gene name (TGD) 'Gene name (TGD)' SubClassOf 'Obsolete concept (EDAM)' 'Gene name (TGD)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1788 Gene name (SGD) 'Gene name (SGD)' SubClassOf 'Obsolete concept (EDAM)' 'Gene name (SGD)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3075 Biological system modelling 'Biological system modelling' SubClassOf 'Obsolete concept (EDAM)' 'Biological system modelling' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1787 Gene name (MaizeGDB) 'Gene name (MaizeGDB)' SubClassOf 'Obsolete concept (EDAM)' 'Gene name (MaizeGDB)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3074 Protein feature detection 'Protein feature detection' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Gene name (dictyBase)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3072 Sequence feature detection 'Sequence feature detection' SubClassOf 'Obsolete concept (EDAM)' 'Sequence feature detection' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1784 Gene name (CGD) 'Gene name (CGD)' SubClassOf 'Obsolete concept (EDAM)' 'Gene name (CGD)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3071 Data management 'Data management' SubClassOf 'Topic' 'Data management' SubClassOf 'Informatics' http://edamontology.org/data_1783 Gene name (ASPGD) 'Gene name (ASPGD)' SubClassOf 'Obsolete concept (EDAM)' 'Gene name (ASPGD)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0803 Human disease 'Human disease' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Gene name (MGD)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1791 Gene name (HGNC) 'Gene name (HGNC)' SubClassOf 'Obsolete concept (EDAM)' 'Gene name (HGNC)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1790 Gene name (CGSC) 'Gene name (CGSC)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Gene ID (GeneDB Glossina morsitans)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1447 Comparison matrix (floats) 'Comparison matrix (floats)' SubClassOf 'Obsolete concept (EDAM)' 'Comparison matrix (floats)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1446 Comparison matrix (integers) 'Comparison matrix (integers)' SubClassOf 'Obsolete concept (EDAM)' 'Comparison matrix (integers)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2521 Map data processing 'Map data processing' SubClassOf 'Obsolete concept (EDAM)' 'Map data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1441 Phylogenetic tree report (tree evaluation) 'Phylogenetic tree report (tree evaluation)' SubClassOf 'Obsolete concept (EDAM)' 'Phylogenetic tree report (tree evaluation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1440 Phylogenetic tree report (tree shape) 'Phylogenetic tree report (tree shape)' SubClassOf 'Obsolete concept (EDAM)' 'Phylogenetic tree report (tree shape)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2520 DNA mapping 'DNA mapping' SubClassOf 'has topic' some 'Mapping' 'DNA mapping' SubClassOf 'has output' some 'Map' 'DNA mapping' SubClassOf 'has topic' some 'Sequence assembly' http://edamontology.org/data_1443 Phylogenetic tree report (tree stratigraphic) 'Phylogenetic tree report (tree stratigraphic)' SubClassOf 'Obsolete concept (EDAM)' 'Phylogenetic tree report (tree stratigraphic)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2519 Structure processing (nucleic acid) 'Structure processing (nucleic acid)' SubClassOf 'Obsolete concept (EDAM)' 'Structure processing (nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1459 Nucleic acid structure 'Nucleic acid structure' SubClassOf 'has topic' some 'Nucleic acid structure analysis' http://edamontology.org/data_2788 Sequence profile data 'Sequence profile data' SubClassOf 'Obsolete concept (EDAM)' 'Sequence profile data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1452 Amino acid comparison matrix (integers) 'Amino acid comparison matrix (integers)' SubClassOf 'Obsolete concept (EDAM)' 'Amino acid comparison matrix (integers)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1451 Nucleotide comparison matrix (floats) 'Nucleotide comparison matrix (floats)' SubClassOf 'Obsolete concept (EDAM)' 'Nucleotide comparison matrix (floats)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1450 Nucleotide comparison matrix (integers) 'Nucleotide comparison matrix (integers)' SubClassOf 'Obsolete concept (EDAM)' 'Nucleotide comparison matrix (integers)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1456 Protein features report (membrane regions) 'Protein features report (membrane regions)' SubClassOf 'Obsolete concept (EDAM)' 'Protein features report (membrane regions)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1453 Amino acid comparison matrix (floats) 'Amino acid comparison matrix (floats)' SubClassOf 'Obsolete concept (EDAM)' 'Amino acid comparison matrix (floats)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2502 Protein analysis 'Protein analysis' SubClassOf 'Operation (typed)' 'Protein analysis' SubClassOf 'has topic' some 'Proteins' 'Protein analysis' SubClassOf 'Analysis' http://edamontology.org/operation_2501 Nucleic acid analysis 'Nucleic acid analysis' SubClassOf 'has topic' some 'Nucleic acids' 'Nucleic acid analysis' SubClassOf 'Operation (typed)' 'Nucleic acid analysis' SubClassOf 'Analysis' http://edamontology.org/data_1469 Protein structure (all atoms) 'Protein structure (all atoms)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Microarray raw data analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1468 Protein domain 'Protein domain' SubClassOf 'has topic' some 'Protein domains and folds' http://edamontology.org/operation_2506 Protein sequence alignment analysis 'Protein sequence alignment analysis' SubClassOf 'has input' some 'Sequence alignment (protein)' http://edamontology.org/operation_2505 Text processing 'Text processing' SubClassOf 'Obsolete concept (EDAM)' 'Text processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2504 Structural data processing 'Structural data processing' SubClassOf 'Obsolete concept (EDAM)' 'Structural data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2503 Sequence data processing 'Sequence data processing' SubClassOf 'Obsolete concept (EDAM)' 'Sequence data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1463 Small molecule structure 'Small molecule structure' SubClassOf 'has topic' some 'Small molecules' http://edamontology.org/data_1462 Carbohydrate structure 'Carbohydrate structure' SubClassOf 'has topic' some 'Lipids' 'Carbohydrate structure' SubClassOf 'has topic' some 'Carbohydrates' http://edamontology.org/data_1460 Protein structure 'Protein structure' SubClassOf 'has topic' some 'Protein structure analysis' http://edamontology.org/data_1465 RNA structure 'RNA structure' SubClassOf 'has topic' some 'Nucleic acid structure analysis' http://edamontology.org/topic_0724 Protein families 'Protein families' SubClassOf 'Proteins' 'Protein families' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0722 Nucleic acid classification 'Nucleic acid classification' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2512 Sequence editing (protein) 'Sequence editing (protein)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence editing (nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2510 DNA back-translation 'DNA back-translation' SubClassOf 'has topic' some 'Protein expression' http://edamontology.org/operation_2516 Protein sequence visualisation 'Protein sequence visualisation' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Nucleic acid sequence visualisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1474 Protein domain (C-alpha atoms) 'Protein domain (C-alpha atoms)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'phylip property values' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2507 Nucleic acid sequence alignment analysis 'Nucleic acid sequence alignment analysis' SubClassOf 'has input' some 'Sequence alignment (nucleic acid)' http://edamontology.org/data_1485 Structure alignment (protein all atoms) 'Structure alignment (protein all atoms)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Structure alignment (pair)' 'Structure alignment (protein pair)' SubClassOf 'Structure alignment (protein)' 'Structure alignment (protein pair)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1489 Multiple protein tertiary structure alignment (all atoms) 'Multiple protein tertiary structure alignment (all atoms)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Promoters' 'Transcription factors and regulatory sites' SubClassOf 'Protein families' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Protein sites and features' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1480 Structure alignment (multiple) 'Structure alignment (multiple)' SubClassOf 'Obsolete concept (EDAM)' 'Structure alignment (multiple)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0741 Protein sequence alignment 'Protein sequence alignment' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Molecular similarity score' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1495 DaliLite hit table 'DaliLite hit table' SubClassOf 'Obsolete concept (EDAM)' 'DaliLite hit table' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2575 Protein binding site prediction 'Protein binding site prediction' SubClassOf 'has topic' some 'Protein interactions' 'Protein binding site prediction' SubClassOf 'Protein feature detection' http://edamontology.org/operation_2574 Protein hydropathy calculation 'Protein hydropathy calculation' SubClassOf 'has topic' some 'Protein properties' 'Protein hydropathy calculation' SubClassOf 'has output' some 'Protein hydropathy data' http://edamontology.org/data_1492 Multiple nucleic acid tertiary structure alignment 'Multiple nucleic acid tertiary structure alignment' SubClassOf 'Obsolete concept (EDAM)' '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 'Structure alignment (pair)' 'Structure alignment (nucleic acid pair)' SubClassOf 'Structure alignment (nucleic acid)' '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 'Obsolete concept (EDAM)' '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 'Molecular interactions, pathways and networks' 'Metabolic pathways' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0751 Phosphorylation sites 'Phosphorylation sites' SubClassOf 'Obsolete concept (EDAM)' 'Phosphorylation sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0754 Signaling pathways 'Signaling pathways' SubClassOf 'Molecular interactions, pathways and networks' 'Signaling pathways' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2210 Strain data format 'Strain data format' SubClassOf 'Obsolete concept (EDAM)' 'Strain data format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0769 Workflows 'Workflows' SubClassOf 'Obsolete concept (EDAM)' 'Workflows' SubClassOf 'Data management' http://edamontology.org/format_2211 CIP strain data format 'CIP strain data format' SubClassOf 'Obsolete concept (EDAM)' 'CIP strain data format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0767 Protein and peptide identification 'Protein and peptide identification' SubClassOf 'Obsolete concept (EDAM)' 'Protein and peptide identification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0770 Data types and objects 'Data types and objects' SubClassOf 'Obsolete concept (EDAM)' 'Data types and objects' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0771 Theoretical biology 'Theoretical biology' SubClassOf 'Obsolete concept (EDAM)' 'Theoretical biology' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2203 Sequence record lite format 'Sequence record lite format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence record full format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0779 Mitochondria 'Mitochondria' SubClassOf 'Obsolete concept (EDAM)' 'Mitochondria' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0786 Arabidopsis 'Arabidopsis' SubClassOf 'Obsolete concept (EDAM)' 'Arabidopsis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0787 Rice 'Rice' SubClassOf 'Obsolete concept (EDAM)' 'Rice' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://kt.ijs.si/panovp/OntoDM#OntoDM_731692 single generalization algorithm 'ensemble algorithm' DisjointWith 'single generalization algorithm' http://edamontology.org/data_3231 GWAS report 'GWAS report' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Genetic mapping and linkage' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/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 'output of' some ('software development process' and ('has participant' value 'European Bioinformatics Institute')) '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 'R software' 'ArrayExpress Bioconductor' SubClassOf 'MAGE-TAB inputting software' http://edamontology.org/topic_0798 Mobile genetic elements 'Mobile genetic elements' SubClassOf 'Genetics' 'Mobile genetic elements' SubClassOf 'Nucleic acid sites, features and motifs' 'Mobile genetic elements' SubClassOf 'Gene structure' http://www.ebi.ac.uk/efo/swo/SWO_0000417 ScanAlyze 'ScanAlyze' SubClassOf 'is developed by' value 'obsolete_Stanford University' http://www.ebi.ac.uk/efo/swo/SWO_0000418 ScanArray 'ScanArray' SubClassOf 'is developed by' value 'PerkinElmer' http://www.ebi.ac.uk/efo/swo/SWO_0000416 ScISI 'ScISI' SubClassOf 'is encoded in' some 'R language' 'ScISI' SubClassOf 'is published by' value 'Bioconductor' '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') 'ScISI' SubClassOf 'R software' 'ScISI' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000422 ShortRead '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 'is encoded in' some 'R language' 'ShortRead' SubClassOf 'R software' 'ShortRead' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000421 Scanning software G2565AA version A6.3.1 'Scanning software G2565AA version A6.3.1' SubClassOf 'is developed by' value 'Agilent Technologies' http://www.ebi.ac.uk/efo/swo/SWO_0000429 Spotfinder [TIGR] '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_0000424 Silicon Genetics Genespring 'Silicon Genetics Genespring' SubClassOf 'is developed by' value 'Agilent Technologies' http://www.ebi.ac.uk/efo/swo/SWO_0000432 TAS Software 'TAS Software' SubClassOf 'software' 'TAS Software' SubClassOf 'is published by' value 'Affymetrix' 'TAS Software' SubClassOf 'Affymetrix Software' http://www.ebi.ac.uk/efo/swo/SWO_0000430 Spotfire 'Spotfire' SubClassOf 'is developed by' value 'TIBCO Software Inc' http://edamontology.org/data_3268 Sequence feature type 'Sequence feature type' SubClassOf 'Obsolete concept (EDAM)' 'Sequence feature type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3269 Gene homology (report) 'Gene homology (report)' SubClassOf 'Obsolete concept (EDAM)' 'Gene homology (report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/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 'is encoded in' some 'R language' 'TypeInfo' SubClassOf 'BioConductor Software' 'TypeInfo' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000435 TargetSearch 'TargetSearch' SubClassOf 'has specified data output' some ('Text data set' and 'Graph plot' and ('has format specification' only 'pdf')) 'TargetSearch' SubClassOf 'is encoded in' some 'R language' 'TargetSearch' SubClassOf 'has specified data input' some 'Text data set' 'TargetSearch' SubClassOf 'software' 'TargetSearch' SubClassOf 'implements' some ('Library Search Algorithm' and 'PPC algorithm') 'TargetSearch' SubClassOf 'is published by' value 'Bioconductor' 'TargetSearch' SubClassOf 'R software' 'TargetSearch' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'implements' some 'Hidden Markov Model' 'VanillaICE' SubClassOf 'is published by' value 'Bioconductor' 'VanillaICE' SubClassOf 'is encoded in' some 'R language' 'VanillaICE' SubClassOf 'software' 'VanillaICE' SubClassOf 'BioConductor Software' 'VanillaICE' SubClassOf 'R software' http://edamontology.org/data_3273 Sample ID 'Sample ID' SubClassOf 'is identifier of' some 'Sample annotation' http://www.ebi.ac.uk/efo/swo/SWO_0000446 XDE 'XDE' SubClassOf 'is encoded in' some 'R language' 'XDE' SubClassOf 'is published by' value 'Bioconductor' 'XDE' SubClassOf 'implements' some ('Bayesian Model' and 'Markov Chain Monte Carlo') 'XDE' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'XDE' SubClassOf 'has specified data input' some 'Gene expression dataset' 'XDE' SubClassOf 'software' 'XDE' SubClassOf 'is executed in' some ('cross validation' and 'differential expression analysis') 'XDE' SubClassOf 'R software' 'XDE' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000447 XDotsReader 'XDotsReader' SubClassOf 'is developed by' value 'COSE, France' http://www.ebi.ac.uk/efo/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 '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 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'R language' 'affyContam' SubClassOf 'has specified data output' some ('has format specification' only ('CEL binary format' or 'CEL ASCII format')) 'affyContam' SubClassOf 'R software' 'affyContam' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000454 affyImGUI 'affyImGUI' SubClassOf 'software' 'affyImGUI' SubClassOf 'implements' some (''PLM'' or 'RMA') 'affyImGUI' SubClassOf 'is encoded in' some 'R language' 'affyImGUI' SubClassOf 'is published by' value 'Bioconductor' 'affyImGUI' SubClassOf 'BioConductor Software' 'affyImGUI' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000451 Acuity 'Acuity' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Molecular Devices')) http://www.ebi.ac.uk/efo/swo/SWO_0000452 affxparser 'affxparser' SubClassOf 'is encoded in' some 'R language' 'affxparser' SubClassOf 'has specified data input' only 'Affymetrix-compliant data' 'affxparser' SubClassOf 'has specified data input' some 'Affymetrix-compliant data' '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' 'affxparser' SubClassOf 'R software' 'affxparser' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'is encoded in' some 'R language' 'Array Comparative Genomic Hybridization' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'sproc')) 'Array Comparative Genomic Hybridization' SubClassOf 'implements' some ''FDR'' 'Array Comparative Genomic Hybridization' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some 'Textual format')) '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' 'Array Comparative Genomic Hybridization' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000459 'affycoretools' ''affycoretools'' SubClassOf 'has specified data output' some ('Text data set' and 'HTML report' and 'Graph plot') ''affycoretools'' SubClassOf 'is encoded in' some 'R language' ''affycoretools'' SubClassOf 'has specified data input' some ('Text data set' or 'Rnw') ''affycoretools'' SubClassOf 'is executed in' some 'differential expression analysis' ''affycoretools'' SubClassOf 'software' ''affycoretools'' SubClassOf 'implements' some (''FDR'' and 'RMA') ''affycoretools'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000457 affyQCReport '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' 'affyQCReport' SubClassOf 'R software' 'affyQCReport' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000458 affyTiling 'affyTiling' SubClassOf 'has specified data output' some 'CSV data set' 'affyTiling' SubClassOf 'is published by' value 'Bioconductor' 'affyTiling' SubClassOf 'is executed in' some ('correction' and 'data normalization') 'affyTiling' SubClassOf 'implements' some 'RMA' 'affyTiling' SubClassOf 'has specified data input' some ('has format specification' only ('BPMAP' and 'CEL binary format')) 'affyTiling' SubClassOf 'software' 'affyTiling' SubClassOf 'is encoded in' some 'R language' 'affyTiling' SubClassOf 'R software' 'affyTiling' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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_0000465 annaffy 'annaffy' SubClassOf 'is published by' value 'Bioconductor' '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 'has specified data output' some 'HTML report' 'annaffy' SubClassOf 'R software' 'annaffy' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/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 'software' 'altcdfenvs' SubClassOf 'has specified data output' some 'Graph plot' 'altcdfenvs' SubClassOf 'BioConductor Software' 'altcdfenvs' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000460 affyio '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 ('CDF binary format' or 'CEL binary format' or 'CDF ASCII format' or 'CEL ASCII format')) 'affyio' SubClassOf 'has specified data output' some ('has format specification' only ('CDF binary format' or 'CEL binary format' or 'CDF ASCII format' or 'CEL ASCII format')) 'affyio' SubClassOf 'software' 'affyio' SubClassOf 'R software' 'affyio' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000461 affypdnn '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 'is published by' value 'Bioconductor' 'affypdnn' SubClassOf 'is encoded in' some 'R language' 'affypdnn' SubClassOf 'R software' 'affypdnn' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000468 annotationTools 'annotationTools' SubClassOf 'is encoded in' some 'R language' 'annotationTools' SubClassOf 'is published by' value 'Bioconductor' '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 'software' 'annotationTools' SubClassOf 'has specified data input' some 'CSV data set' 'annotationTools' SubClassOf 'R software' 'annotationTools' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000356 RefPlus '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' 'RefPlus' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000354 RdbiPgSQL 'RdbiPgSQL' SubClassOf 'has specified data output' some 'Graph plot' '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' 'RdbiPgSQL' SubClassOf 'BioConductor Software' 'RdbiPgSQL' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000355 Rdisop 'Rdisop' SubClassOf 'is published by' value 'Bioconductor' 'Rdisop' SubClassOf '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' 'Rdisop' SubClassOf 'BioConductor Software' 'Rdisop' SubClassOf 'R software' http://edamontology.org/data_0914 Codon usage data 'Codon usage data' SubClassOf 'data' 'Codon usage data' SubClassOf 'has topic' some 'Gene expression' 'Codon usage data' SubClassOf http://edamontology.org/data_0006 http://www.ebi.ac.uk/efo/swo/SWO_0000352 RbcBook1 'RbcBook1' SubClassOf 'is encoded in' some 'R language' 'RbcBook1' SubClassOf 'software' 'RbcBook1' SubClassOf 'R software' http://edamontology.org/format_1704 MSDchem ligand dictionary entry format 'MSDchem ligand dictionary entry format' SubClassOf 'Obsolete concept (EDAM)' 'MSDchem ligand dictionary entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000353 Rdbi '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 'BioConductor Software' 'Rdbi' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 '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 'BioConductor Software' 'RankProd' SubClassOf 'R software' http://edamontology.org/data_0911 Nucleotide base annotation 'Nucleotide base annotation' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'KEGG DRUG entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0907 Protein family report 'Protein family report' SubClassOf 'has topic' some 'Protein families' http://edamontology.org/format_1701 PubChem entry format 'PubChem entry format' SubClassOf 'Obsolete concept (EDAM)' 'PubChem entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0906 Protein interaction report 'Protein interaction report' SubClassOf 'has topic' some 'Protein interactions' 'Protein interaction report' SubClassOf 'Protein report' 'Protein interaction report' SubClassOf 'Protein structure report' http://edamontology.org/format_1700 KEGG GLYCAN entry format 'KEGG GLYCAN entry format' SubClassOf 'Obsolete concept (EDAM)' 'KEGG GLYCAN entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1703 ChEBI entry format 'ChEBI entry format' SubClassOf 'Obsolete concept (EDAM)' 'ChEBI entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0904 Protein features (mutation) 'Protein features (mutation)' SubClassOf 'Obsolete concept (EDAM)' 'Protein features (mutation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1702 ChemSpider entry format 'ChemSpider entry format' SubClassOf 'Obsolete concept (EDAM)' 'ChemSpider entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/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/efo/swo/SWO_0000359 Rgraphviz 'Rgraphviz' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') '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' 'Rgraphviz' SubClassOf 'R software' 'Rgraphviz' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000367 RpsiXML 'RpsiXML' SubClassOf '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 'R software' 'RpsiXML' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000368 Rredland 'Rredland' SubClassOf 'is encoded in' some 'R language' 'Rredland' SubClassOf 'software' 'Rredland' SubClassOf 'is published by' value 'Bioconductor' 'Rredland' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'Rredland' SubClassOf 'has specified data input' some 'Text data set' 'Rredland' SubClassOf 'BioConductor Software' 'Rredland' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000365 Rosetta Resolver 'Rosetta Resolver' SubClassOf 'is developed by' value 'Rosetta Biosoftware' http://edamontology.org/data_0923 PCR experiment report 'PCR experiment report' SubClassOf 'Obsolete concept (EDAM)' 'PCR experiment report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/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 'has specified data output' some ('has format specification' only 'R data frame') 'Rintact' SubClassOf 'is encoded in' some 'R language' 'Rintact' SubClassOf 'BioConductor Software' 'Rintact' SubClassOf 'R software' http://edamontology.org/data_0922 Nucleic acid features report (primers) 'Nucleic acid features report (primers)' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid features report (primers)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/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 'implements' some 'Recursive Feature Elimination (RFE)' 'Rmagpie' SubClassOf 'is encoded in' some 'R language' 'Rmagpie' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000360 Ringo 'Ringo' SubClassOf 'has specified data input' some 'Text data set' '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')) 'Ringo' SubClassOf 'R software' 'Ringo' SubClassOf 'BioConductor Software' 'Ringo' SubClassOf 'data' http://edamontology.org/data_0918 DNA variation 'DNA variation' SubClassOf 'Obsolete concept (EDAM)' 'DNA variation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0917 Gene classification 'Gene classification' SubClassOf 'Obsolete concept (EDAM)' 'Gene classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000369 Rtreemix 'Rtreemix' SubClassOf 'implements' some ('Likelihood method' or 'Sim method') 'Rtreemix' SubClassOf 'is encoded in' some 'R language' 'Rtreemix' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'Rtreemix' SubClassOf 'is executed in' some 'decision tree induction' 'Rtreemix' SubClassOf 'has specified data input' some 'Text data set' 'Rtreemix' SubClassOf 'software' 'Rtreemix' SubClassOf 'is published by' value 'Bioconductor' 'Rtreemix' SubClassOf 'BioConductor Software' 'Rtreemix' SubClassOf 'R software' http://edamontology.org/data_0919 Chromosome report 'Chromosome report' SubClassOf 'has topic' some 'Chromosomes' http://edamontology.org/data_0932 Oligonucleotide probe data 'Oligonucleotide probe data' SubClassOf 'Obsolete concept (EDAM)' 'Oligonucleotide probe data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0931 Microarray experiment report 'Microarray experiment report' SubClassOf 'Obsolete concept (EDAM)' 'Microarray experiment report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000377 SBMLR 'SBMLR' SubClassOf 'is encoded in' some 'R language' 'SBMLR' SubClassOf 'has specified data input' some ('has format specification' only ('SBML' or 'SBMLR format')) 'SBMLR' SubClassOf 'has specified data output' some ('has format specification' only ('SBML' or 'SBMLR format')) 'SBMLR' SubClassOf 'is published by' value 'Bioconductor' 'SBMLR' SubClassOf 'software' 'SBMLR' SubClassOf 'BioConductor Software' 'SBMLR' SubClassOf 'R software' http://edamontology.org/data_0936 Sequence tag profile (with gene assignment) 'Sequence tag profile (with gene assignment)' SubClassOf 'Sequence tag profile' '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 'Obsolete concept (EDAM)' 'SBS experimental data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000375 SAS/STAT Software, Version 8 'SAS/STAT Software, Version 8' SubClassOf 'is developed by' value 'SAS Institute Inc.' http://edamontology.org/data_0934 MPSS experimental data 'MPSS experimental data' SubClassOf 'Obsolete concept (EDAM)' 'MPSS experimental data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0933 SAGE experimental data 'SAGE experimental data' SubClassOf 'Obsolete concept (EDAM)' 'SAGE experimental data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000373 SAGx 'SAGx' SubClassOf 'is encoded in' some 'R language' 'SAGx' SubClassOf 'is published by' value 'Bioconductor' 'SAGx' SubClassOf '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')) 'SAGx' SubClassOf 'BioConductor Software' 'SAGx' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000370 Ruuid 'Ruuid' SubClassOf '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' 'Ruuid' SubClassOf 'R software' 'Ruuid' SubClassOf 'BioConductor Software' http://edamontology.org/data_0943 Mass spectrometry spectra 'Mass spectrometry spectra' SubClassOf 'has topic' some 'Proteomics' http://edamontology.org/data_0942 2D PAGE image '2D PAGE image' SubClassOf 'has topic' some 'Proteomics' http://edamontology.org/data_0941 Electron microscopy model 'Electron microscopy model' SubClassOf 'has topic' some 'Structural biology' http://www.ebi.ac.uk/efo/swo/SWO_0000387 SNPchip 'SNPchip' SubClassOf 'is published by' value 'Bioconductor' 'SNPchip' SubClassOf 'is encoded in' some 'R language' 'SNPchip' SubClassOf 'software' 'SNPchip' SubClassOf 'implements' some ('data annotation' and 'data visualization' and 'descriptive statistical calculation') 'SNPchip' SubClassOf 'has specified data output' some ('Text data set' and 'Graph plot') 'SNPchip' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'SNPchip' SubClassOf 'implements' some 'Hidden Markov Model' 'SNPchip' SubClassOf 'R software' 'SNPchip' SubClassOf 'BioConductor Software' http://edamontology.org/data_0940 Electron microscopy volume map 'Electron microscopy volume map' SubClassOf 'has topic' some 'Structural biology' http://www.ebi.ac.uk/efo/swo/SWO_0000388 SPIA '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 'implements' some 'Signaling Pathway Impact Analysis (SPIA) algorithm' 'SPIA' SubClassOf 'software' 'SPIA' SubClassOf 'R software' 'SPIA' SubClassOf 'BioConductor Software' http://edamontology.org/data_0947 Biological pathway map 'Biological pathway map' SubClassOf 'Obsolete concept (EDAM)' 'Biological pathway map' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000385 SMAP 'SMAP' SubClassOf 'software' 'SMAP' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'SMAP' SubClassOf 'is published by' value 'Bioconductor' 'SMAP' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'SMAP' SubClassOf 'implements' some 'Hidden Markov Model' 'SMAP' SubClassOf 'is executed in' some ('data visualization' and 'descriptive statistical calculation') 'SMAP' SubClassOf 'is encoded in' some 'R language' 'SMAP' SubClassOf 'BioConductor Software' 'SMAP' SubClassOf 'R software' http://edamontology.org/data_0946 Pathway or network annotation 'Pathway or network annotation' SubClassOf 'Obsolete concept (EDAM)' 'Pathway or network annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0945 Peptide identification 'Peptide identification' SubClassOf 'has topic' some 'Proteomics' 'Peptide identification' SubClassOf 'Protein property' http://www.ebi.ac.uk/efo/swo/SWO_0000383 SLGI 'SLGI' SubClassOf 'software' 'SLGI' SubClassOf 'is encoded in' some 'R language' 'SLGI' SubClassOf 'is published by' value 'Bioconductor' 'SLGI' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) 'SLGI' SubClassOf 'has specified data input' some 'Annotation data packages' 'SLGI' SubClassOf 'BioConductor Software' 'SLGI' SubClassOf 'R software' http://edamontology.org/data_0944 Peptide mass fingerprint 'Peptide mass fingerprint' SubClassOf 'has topic' some 'Proteomics' http://www.ebi.ac.uk/efo/swo/SWO_0000384 SLqPCR 'SLqPCR' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' only 'R data frame')) '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 'software' 'SLqPCR' SubClassOf 'has specified data input' some ('has format specification' only 'R data frame') 'SLqPCR' SubClassOf 'R software' 'SLqPCR' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000382 SIM 'SIM' SubClassOf 'software' 'SIM' SubClassOf 'has specified data output' some ('Heatmap' and 'Text data set' and 'Graph plot') '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 'R software' http://www.ebi.ac.uk/swo/license/SWO_10000037 Distribution unrestricted 'Distribution restricted' DisjointWith 'Distribution unrestricted' http://edamontology.org/data_0953 Version information 'Version information' SubClassOf 'Obsolete concept (EDAM)' 'Version information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/license/SWO_10000038 derivative software allowed 'derivative software not allowed' DisjointWith 'derivative software allowed' http://edamontology.org/data_0952 EMBOSS database resource definition 'EMBOSS database resource definition' SubClassOf 'Obsolete concept (EDAM)' 'EMBOSS database resource definition' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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 software developer organization 'software developer organization' EquivalentTo 'has_role' some 'software developer role' http://www.ebi.ac.uk/efo/swo/SWO_0000397 software publisher organization 'software publisher organization' EquivalentTo 'has_role' some 'publisher role' http://edamontology.org/data_0956 Data index report 'Data index report' SubClassOf 'has topic' some 'File management' http://edamontology.org/data_0955 Data index 'Data index' SubClassOf 'has topic' some 'File management' 'Data index' SubClassOf 'data' 'Data index' SubClassOf http://edamontology.org/data_0006 http://www.ebi.ac.uk/efo/swo/SWO_0000390 SSPA 'SSPA' SubClassOf 'has specified data input' some 'ALL/AML data set' 'SSPA' SubClassOf 'is encoded in' some 'R language' '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' 'SSPA' SubClassOf 'BioConductor Software' 'SSPA' SubClassOf 'R software' http://edamontology.org/data_0950 Mathematical model 'Mathematical model' SubClassOf 'data' 'Mathematical model' SubClassOf 'has topic' some 'Computational biology' 'Mathematical model' SubClassOf http://edamontology.org/data_0006 http://www.ebi.ac.uk/swo/algorithm/OntoDM_175260 pattern discovery algorithm DisjointClasses: 'clustering algorithm', 'pattern discovery algorithm', 'predictive modeling algorithm' http://edamontology.org/data_0948 Data resource definition 'Data resource definition' SubClassOf 'Obsolete concept (EDAM)' 'Data resource definition' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0964 Scent annotation 'Scent annotation' SubClassOf 'Obsolete concept (EDAM)' 'Scent annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0962 Small molecule report 'Small molecule report' SubClassOf 'has topic' some 'Small molecules' http://edamontology.org/data_0968 Keyword 'Keyword' SubClassOf 'data' 'Keyword' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_0959 Job metadata 'Job metadata' SubClassOf 'Obsolete concept (EDAM)' 'Job metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0975 Data resource identifier 'Data resource identifier' SubClassOf 'Obsolete concept (EDAM)' 'Data resource identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0974 Entity identifier 'Entity identifier' SubClassOf 'Obsolete concept (EDAM)' 'Entity identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0979 Entity feature identifier 'Entity feature identifier' SubClassOf 'Obsolete concept (EDAM)' 'Entity feature identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0978 Discrete entity identifier 'Discrete entity identifier' SubClassOf 'Obsolete concept (EDAM)' 'Discrete entity identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0972 Text mining report 'Text mining report' SubClassOf 'Report' http://edamontology.org/data_0971 Article 'Article' SubClassOf 'has topic' some 'Literature and reference' 'Article' SubClassOf 'data' 'Article' SubClassOf http://edamontology.org/data_3671 http://edamontology.org/data_0987 Chromosome name 'Chromosome name' SubClassOf 'is identifier of' some 'Chromosome report' http://edamontology.org/data_0986 Chemical identifier 'Chemical identifier' SubClassOf 'Obsolete concept (EDAM)' 'Chemical identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0985 Molecule type 'Molecule type' SubClassOf 'Obsolete concept (EDAM)' 'Molecule type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0989 Protein identifier 'Protein identifier' SubClassOf 'is identifier of' some 'Protein report' http://edamontology.org/data_0981 Phenomenon identifier 'Phenomenon identifier' SubClassOf 'Obsolete concept (EDAM)' 'Phenomenon identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0980 Entity collection identifier 'Entity collection identifier' SubClassOf 'Obsolete concept (EDAM)' 'Entity collection identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0994 Amino acid identifier 'Amino acid identifier' SubClassOf 'is identifier of' some 'Amino acid property' http://edamontology.org/data_0993 Drug identifier 'Drug identifier' SubClassOf 'is identifier of' some 'Drug structure' http://edamontology.org/data_0992 Ligand identifier 'Ligand identifier' SubClassOf 'Obsolete concept (EDAM)' 'Ligand identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1782 NCBI gene report format 'NCBI gene report format' SubClassOf 'Obsolete concept (EDAM)' 'NCBI gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2717 Oligonucleotide probe annotation 'Oligonucleotide probe annotation' SubClassOf 'has topic' some 'Sequence design' http://edamontology.org/data_2726 Inhibitor annotation 'Inhibitor annotation' SubClassOf 'Obsolete concept (EDAM)' 'Inhibitor annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2722 Protein features report (disordered structure) 'Protein features report (disordered structure)' SubClassOf 'Obsolete concept (EDAM)' 'Protein features report (disordered structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2724 Embryo report 'Embryo report' SubClassOf 'Obsolete concept (EDAM)' 'Embryo report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1405 Gap opening penalty (float) 'Gap opening penalty (float)' SubClassOf 'Obsolete concept (EDAM)' 'Gap opening penalty (float)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1404 Gap opening penalty (integer) 'Gap opening penalty (integer)' SubClassOf 'Obsolete concept (EDAM)' 'Gap opening penalty (integer)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1409 Gap separation penalty (float) 'Gap separation penalty (float)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Gap extension penalty (integer)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1400 Terminal gap penalty 'Terminal gap penalty' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'PDB atom record format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1741 Oscar3 'Oscar3' SubClassOf 'Text mining report format' 'Oscar3' SubClassOf 'XML' 'Oscar3' SubClassOf http://edamontology.org/format_3780 http://edamontology.org/format_1740 iHOP text mining abstract format 'iHOP text mining abstract format' SubClassOf 'Textual format' 'iHOP text mining abstract format' SubClassOf 'XML' 'iHOP text mining abstract format' SubClassOf 'HTML' http://edamontology.org/data_1416 Sequence alignment report (site correlation) 'Sequence alignment report (site correlation)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence alignment report (site conservation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1414 Sequence alignment metadata (quality report) 'Sequence alignment metadata (quality report)' SubClassOf 'Obsolete concept (EDAM)' 'Sequence alignment metadata (quality report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1418 Sequence-profile alignment (HMM) 'Sequence-profile alignment (HMM)' SubClassOf 'Obsolete concept (EDAM)' 'Sequence-profile alignment (HMM)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1417 Sequence-profile alignment (Domainatrix signature) 'Sequence-profile alignment (Domainatrix signature)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Database name (CMD)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2740 Gene name (Genolist) 'Gene name (Genolist)' SubClassOf 'Obsolete concept (EDAM)' 'Gene name (Genolist)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2743 Gene name (HUGO) 'Gene name (HUGO)' SubClassOf 'Obsolete concept (EDAM)' 'Gene name (HUGO)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1429 Phylogenetic invariants 'Phylogenetic invariants' SubClassOf 'has topic' some 'Genetic variation' http://edamontology.org/data_2754 Gene features report (intron) 'Gene features report (intron)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'CATH chain report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1438 Phylogenetic report 'Phylogenetic report' SubClassOf 'Obsolete concept (EDAM)' 'Phylogenetic report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2767 Identifier with metadata 'Identifier with metadata' SubClassOf 'Identifier' 'Identifier with metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2768 Gene symbol annotation 'Gene symbol annotation' SubClassOf 'Obsolete concept (EDAM)' 'Gene symbol annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2769 Transcript ID 'Transcript ID' SubClassOf 'is identifier of' some 'Nucleic acid features' http://edamontology.org/data_2762 Sequence signature report 'Sequence signature report' SubClassOf 'has topic' some 'Sequence sites, features and motifs' http://edamontology.org/data_2763 Locus annotation 'Locus annotation' SubClassOf 'Obsolete concept (EDAM)' 'Locus annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2765 Term ID list 'Term ID list' SubClassOf 'Obsolete concept (EDAM)' 'Term ID list' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1567 Protein-nucleic acid interactions report 'Protein-nucleic acid interactions report' SubClassOf 'Obsolete concept (EDAM)' 'Protein-nucleic acid interactions report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1561 CATH functional category 'CATH functional category' SubClassOf 'Obsolete concept (EDAM)' 'CATH functional category' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1560 CATH structurally similar group 'CATH structurally similar group' SubClassOf 'Obsolete concept (EDAM)' 'CATH structurally similar group' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1565 Protein-protein interaction report 'Protein-protein interaction report' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Protein fold recognition report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1586 Nucleic acid melting temperature 'Nucleic acid melting temperature' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid melting temperature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3464 JSON 'JSON' SubClassOf 'Textual format' 'JSON' SubClassOf http://edamontology.org/format_3750 http://edamontology.org/topic_0606 Literature data resources 'Literature data resources' SubClassOf 'Obsolete concept (EDAM)' 'Literature data resources' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0607 Laboratory information management 'Laboratory information management' SubClassOf 'Data management' 'Laboratory information management' SubClassOf 'Informatics' http://edamontology.org/format_3466 EPS 'EPS' SubClassOf 'Textual format' 'EPS' SubClassOf http://edamontology.org/format_3696 http://edamontology.org/topic_0605 Informatics 'Informatics' SubClassOf 'Obsolete concept (EDAM)' 'Informatics' SubClassOf 'Topic' http://edamontology.org/topic_0608 Cell and tissue culture 'Cell and tissue culture' SubClassOf 'Obsolete concept (EDAM)' 'Cell and tissue culture' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0602 Molecular interactions, pathways and networks 'Molecular interactions, pathways and networks' SubClassOf 'Biology' 'Molecular interactions, pathways and networks' SubClassOf 'Computational biology' http://edamontology.org/data_1594 Vienna RNA calculated energy 'Vienna RNA calculated energy' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Codon adaptation index' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1597 Codon usage table 'Codon usage table' SubClassOf 'data' 'Codon usage table' SubClassOf 'has topic' some 'Gene expression' 'Codon usage table' SubClassOf 'Codon usage data' http://edamontology.org/topic_0617 Ribosomes 'Ribosomes' SubClassOf 'Obsolete concept (EDAM)' 'Ribosomes' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0618 Scents 'Scents' SubClassOf 'Obsolete concept (EDAM)' 'Scents' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0616 Organelles 'Organelles' SubClassOf 'Obsolete concept (EDAM)' 'Organelles' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1591 Vienna RNA parameters 'Vienna RNA parameters' SubClassOf 'Obsolete concept (EDAM)' 'Vienna RNA parameters' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0613 Peptides and amino acids 'Peptides and amino acids' SubClassOf 'Small molecules' 'Peptides and amino acids' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0612 Cell cycle 'Cell cycle' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Drug discovery' 'Drugs and target structures' SubClassOf 'Small molecules' 'Drugs and target structures' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0624 Chromosomes 'Chromosomes' SubClassOf 'DNA' 'Chromosomes' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0623 Gene families 'Gene families' SubClassOf 'Genetics' 'Gene families' SubClassOf 'Molecular genetics' 'Gene families' SubClassOf 'Proteins' http://edamontology.org/topic_0639 Protein sequence analysis 'Protein sequence analysis' SubClassOf 'Obsolete concept (EDAM)' 'Protein sequence analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1697 KEGG LIGAND entry format 'KEGG LIGAND entry format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'KEGG COMPOUND entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0642 Low complexity sequences 'Low complexity sequences' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Nucleic acid sequence analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0641 Repeat sequences 'Repeat sequences' SubClassOf 'Obsolete concept (EDAM)' 'Repeat sequences' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0644 Proteome 'Proteome' SubClassOf 'Obsolete concept (EDAM)' 'Proteome' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2009 Ordered locus name 'Ordered locus name' SubClassOf 'Obsolete concept (EDAM)' 'Ordered locus name' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0655 Coding RNA 'Coding RNA' SubClassOf 'Gene transcript features' 'Coding RNA' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2018 Annotation 'Annotation' SubClassOf 'Obsolete concept (EDAM)' 'Annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0660 rRNA 'rRNA' SubClassOf 'Obsolete concept (EDAM)' 'rRNA' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2019 Map data 'Map data' SubClassOf 'has topic' some 'Mapping' 'Map data' SubClassOf 'data' 'Map data' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/format_2195 Ontology format 'Ontology format' SubClassOf 'is format of' some 'Ontology' http://edamontology.org/format_2197 OWL format 'OWL format' SubClassOf 'XML' 'OWL format' SubClassOf 'Ontology format' 'OWL format' SubClassOf 'RDF format' http://edamontology.org/topic_0663 tRNA 'tRNA' SubClassOf 'Obsolete concept (EDAM)' 'tRNA' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3356 Hidden Markov model 'Hidden Markov model' SubClassOf 'Mathematical model' 'Hidden Markov model' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2028 Experimental data 'Experimental data' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence mask parameter' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2188 UniProt format 'UniProt format' SubClassOf 'Obsolete concept (EDAM)' 'UniProt format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2189 ipi 'ipi' SubClassOf 'Obsolete concept (EDAM)' 'ipi' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0694 Protein secondary structure 'Protein secondary structure' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Protein sequence record (lite)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2048 Report 'Identifier' DisjointWith 'Report' 'Report' SubClassOf 'data' 'Report' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_2043 Sequence record lite 'Sequence record lite' SubClassOf 'Obsolete concept (EDAM)' 'Sequence record lite' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2044 Sequence 'Sequence' SubClassOf 'has topic' some 'Sequence analysis' 'Sequence' SubClassOf 'data' 'Sequence' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_2046 Nucleic acid sequence record (lite) 'Nucleic acid sequence record (lite)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Genome version information' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2042 Evidence 'Evidence' SubClassOf 'data' 'Evidence' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/topic_0697 RNA structure 'RNA structure' SubClassOf 'Obsolete concept (EDAM)' 'RNA structure' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/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 'implements' some 'Iterative local regression and model selection' 'OLINgui' SubClassOf 'is executed in' some 'data visualization' 'OLINgui' SubClassOf 'R software' http://edamontology.org/topic_0698 Protein tertiary structure 'Protein tertiary structure' SubClassOf 'Obsolete concept (EDAM)' 'Protein tertiary structure' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/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 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) '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 'R software' http://www.ebi.ac.uk/efo/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 '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')) 'OLIN' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'OutlierD' SubClassOf 'is encoded in' some 'R language' 'OutlierD' SubClassOf 'is executed in' some 'data normalization' 'OutlierD' SubClassOf 'implements' some 'Quantile regression techniques' 'OutlierD' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000310 Optiquant 'Optiquant' SubClassOf 'output of' some ('software development process' and ('has participant' value 'PerkinElmer')) http://www.ebi.ac.uk/efo/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 'implements' some 'Similarity score' 'OrderedList' SubClassOf 'R software' http://edamontology.org/format_3491 ebwtl 'ebwtl' SubClassOf 'is format of' some 'Genome index' http://edamontology.org/data_2053 Structural data 'Structural data' SubClassOf 'Obsolete concept (EDAM)' 'Structural data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3484 ebwt 'ebwt' SubClassOf 'is format of' some 'Genome index' http://www.ebi.ac.uk/efo/swo/SWO_0000319 PLPE 'PLPE' SubClassOf 'software' 'PLPE' SubClassOf 'implements' some 'Statistical tests' 'PLPE' SubClassOf 'is executed in' some 'differential expression analysis' 'PLPE' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'PLPE' SubClassOf 'is executed in' some 'descriptive statistical calculation' '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')) 'PLPE' SubClassOf 'R software' http://edamontology.org/format_2159 Gene features (coding region) format 'Gene features (coding region) format' SubClassOf 'Gene annotation format' 'Gene features (coding region) format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000316 PCpheno 'PCpheno' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'PCpheno' SubClassOf 'implements' some 'Global test' 'PCpheno' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) '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 'is encoded in' some 'R language' 'PCpheno' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'PCpheno' SubClassOf 'implements' some 'Hypergeometric enrichment' 'PCpheno' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000317 PGSEA 'PGSEA' SubClassOf 'is encoded in' some 'R language' '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' 'PGSEA' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000314 PAnnBuilder 'PAnnBuilder' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some 'Textual format')) 'PAnnBuilder' SubClassOf 'software' 'PAnnBuilder' SubClassOf 'has specified data input' some ('Annotation data packages' and ('has format specification' some 'data format specification')) 'PAnnBuilder' SubClassOf 'is encoded in' some 'R language' 'PAnnBuilder' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000324 Pathways 2.01 software 'Pathways 2.01 software' SubClassOf 'output of' some ('software development process' and ('has participant' value 'Research Genetics')) http://www.ebi.ac.uk/efo/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 'software' 'PROcess' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some 'data format specification')) 'PROcess' SubClassOf 'R software' http://edamontology.org/format_3475 TSV 'TSV' SubClassOf 'Textual format' 'TSV' SubClassOf http://edamontology.org/format_3751 http://edamontology.org/format_3477 Cytoscape input file format 'Cytoscape input file format' SubClassOf 'Gene expression data format' 'Cytoscape input file format' SubClassOf 'Gene expression report format' http://edamontology.org/format_3476 Gene expression data format 'Gene expression data format' SubClassOf 'is format of' some 'Gene expression data' 'Gene expression data format' SubClassOf 'Format (typed)' 'Gene expression data format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000329 QuantArray scanner software 'QuantArray scanner software' SubClassOf 'output of' some ('software development process' and ('has participant' value 'PerkinElmer')) http://www.ebi.ac.uk/efo/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 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'RBioinf' SubClassOf 'software' 'RBioinf' SubClassOf 'is encoded in' some 'R language' 'RBioinf' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000333 RBGL 'RBGL' SubClassOf 'software' 'RBGL' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'gxl format')) 'RBGL' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'RBGL' SubClassOf 'implements' some 'BGL' 'RBGL' SubClassOf 'is executed in' some 'data visualization' 'RBGL' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'RBGL' SubClassOf 'is encoded in' some 'R language' 'RBGL' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'XML')) 'RBGL' SubClassOf 'R software' http://edamontology.org/data_2079 Search parameter 'Search parameter' SubClassOf 'Obsolete concept (EDAM)' 'Search parameter' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2175 Gene cluster format 'Gene cluster format' SubClassOf 'Obsolete concept (EDAM)' 'Gene cluster format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000338 RLMM 'RLMM' SubClassOf 'is published by' value 'Bioconductor' 'RLMM' SubClassOf 'has specified data input' some ('has format specification' only ('Xba.CQV and Xba.regions' and '.raw files')) 'RLMM' SubClassOf 'software' 'RLMM' SubClassOf 'has specified data output' some 'Graph plot' 'RLMM' SubClassOf 'implements' some 'Mahalanobis distance' 'RLMM' SubClassOf 'is executed in' some 'data normalization' 'RLMM' SubClassOf 'is encoded in' some 'R language' 'RLMM' SubClassOf 'R software' 'RLMM' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000346 RMAGEML '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 'BioConductor Software' 'RMAGEML' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 ('CDF binary format' and 'CEL binary format')) 'RMAExpress' SubClassOf 'implements' some ('background correction' and 'data normalization') http://edamontology.org/format_2170 Sequence cluster format 'Sequence cluster format' SubClassOf 'is format of' some 'Sequence cluster' http://edamontology.org/data_2087 Molecular property 'Molecular property' SubClassOf 'data' 'Molecular property' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_2083 Alignment data 'Alignment data' SubClassOf 'Obsolete concept (EDAM)' 'Alignment data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2080 Database search results 'Database search results' SubClassOf 'data' 'Database search results' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_2081 Secondary structure 'Secondary structure' SubClassOf 'Obsolete concept (EDAM)' 'Secondary structure' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2082 Matrix 'Matrix' SubClassOf 'data' 'Matrix' SubClassOf http://edamontology.org/data_0006 http://www.ebi.ac.uk/efo/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 'is encoded in' some 'R language' 'RWebServices' SubClassOf 'has specified data output' some ('has format specification' only 'R data frame') 'RWebServices' SubClassOf 'is published by' value 'Bioconductor' 'RWebServices' SubClassOf 'software' 'RWebServices' SubClassOf 'R software' 'RWebServices' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000347 RNAither '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' 'RNAither' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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://edamontology.org/format_2919 Sequence annotation track format 'Sequence annotation track format' SubClassOf 'is format of' some 'Annotation track' http://www.ebi.ac.uk/efo/swo/SWO_0000236 ImageQuant 'ImageQuant' SubClassOf 'output of' some ('software development process' and ('has participant' value 'Molecular Dynamics')) http://www.ebi.ac.uk/efo/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 '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)' 'ITALICS' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000230 IRanges 'IRanges' SubClassOf 'is executed in' some 'data normalization' 'IRanges' SubClassOf 'software' 'IRanges' SubClassOf 'is executed in' some 'decision tree induction' 'IRanges' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'IRanges' SubClassOf 'is encoded in' some 'R language' 'IRanges' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'IRanges' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000238 ImaGene 'ImaGene' SubClassOf 'output of' some ('software development process' and ('has participant' value 'Bio Discovery')) http://www.ebi.ac.uk/efo/swo/SWO_0000246 KCsmart 'KCsmart' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'KCsmart' SubClassOf 'software' 'KCsmart' SubClassOf 'is executed in' some 'background correction' 'KCsmart' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some 'Textual format')) '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 'software with image input' 'KCsmart' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'Textual format')) 'KEGGSOAP' SubClassOf 'is encoded in' some 'R language' 'KEGGSOAP' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000245 Jaguar 'Jaguar' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Affymetrix')) http://www.ebi.ac.uk/efo/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 process' and ('has participant' value 'Bahler Lab')) http://www.ebi.ac.uk/efo/swo/SWO_0000248 KEGGgraph 'KEGGgraph' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'KGML')) '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 'software' 'KEGGgraph' SubClassOf 'implements' some 'R interface to boost graph library algorithm (RBGL)' 'KEGGgraph' SubClassOf 'R software' http://edamontology.org/format_1609 Gramene gene report format 'Gramene gene report format' SubClassOf 'Obsolete concept (EDAM)' 'Gramene gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000258 LPE 'LPE' SubClassOf 'software' 'LPE' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) '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 'R software' http://edamontology.org/format_1606 DragonDB gene report format 'DragonDB gene report format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'CGD gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/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 'is executed in' some 'data normalization' 'LMGene' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'LMGene' SubClassOf 'implements' some 'Linear modelling' 'LMGene' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'LMGene' SubClassOf 'R software' http://edamontology.org/format_1608 FlyBase gene report format 'FlyBase gene report format' SubClassOf 'Obsolete concept (EDAM)' 'FlyBase gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1607 EcoCyc gene report format 'EcoCyc gene report format' SubClassOf 'Obsolete concept (EDAM)' 'EcoCyc gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000252 LBE 'LBE' SubClassOf 'is executed in' some 'differential expression analysis' 'LBE' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) '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 'software' 'LBE' SubClassOf 'implements' some ''FDR'' 'LBE' SubClassOf 'is encoded in' some 'R language' 'LBE' SubClassOf 'R software' http://edamontology.org/format_1604 DictyBase gene report format 'DictyBase gene report format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Ensembl gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/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 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'LPEadj' SubClassOf 'software' 'LPEadj' SubClassOf 'has specified data input' some ('data' 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'' 'LPEadj' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'implements' some 'Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)' 'MANOR' SubClassOf 'is encoded in' some 'R language' 'MANOR' SubClassOf 'software' 'MANOR' SubClassOf 'has specified data output' some 'Graph plot' 'MANOR' SubClassOf 'R software' http://edamontology.org/format_2921 Sequence variation annotation format 'Sequence variation annotation format' SubClassOf 'is format of' some 'Sequence variations' http://edamontology.org/format_2920 Alignment format (pair only) 'Alignment format (pair only)' SubClassOf 'is format of' some 'Sequence alignment (pair)' http://www.ebi.ac.uk/efo/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/efo/swo/SWO_0000275 MAVI Pro 'MAVI Pro' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'MWG Biotech')) http://www.ebi.ac.uk/efo/swo/SWO_0000271 MIcroarray Analysis Suite 'MIcroarray Analysis Suite' SubClassOf 'output of' some ('software development process' and ('has participant' value 'Affymetrix')) http://edamontology.org/operation_3090 Protein feature prediction (from structure) 'Protein feature prediction (from structure)' SubClassOf 'Obsolete concept (EDAM)' 'Protein feature prediction (from structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3094 Protein interaction network prediction 'Protein interaction network prediction' SubClassOf 'has topic' some 'Protein interactions' 'Protein interaction network prediction' SubClassOf 'has output' some 'Protein interaction report' http://edamontology.org/operation_3093 Database search (by sequence) 'Database search (by sequence)' SubClassOf 'Obsolete concept (EDAM)' '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 'has topic' some 'Sequence sites, features and motifs' 'Protein feature detection' SubClassOf 'has output' some 'Protein features' http://www.ebi.ac.uk/efo/swo/SWO_0000288 MantelCorr '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' 'MantelCorr' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000289 MassSpecWavelet 'MassSpecWavelet' SubClassOf 'software' 'MassSpecWavelet' SubClassOf 'implements' some 'Continuous Wavelet Transform (CWT)-based peak detection algorithm' 'MassSpecWavelet' SubClassOf 'is encoded in' some 'R language' 'MassSpecWavelet' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'MassSpecWavelet' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'MassSpecWavelet' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000285 MVCClass 'MVCClass' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'MVCClass' SubClassOf 'is executed in' some 'data visualization' 'MVCClass' SubClassOf 'is encoded in' some 'R language' 'MVCClass' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'MVCClass' SubClassOf 'software' 'MVCClass' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 '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' 'MLInterfaces' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000280 MEDME 'MEDME' SubClassOf 'software' 'MEDME' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'GFF')) 'MEDME' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'MEDME' SubClassOf 'is encoded in' some 'R language' 'MEDME' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'is encoded in' some 'R language' 'MiPP' SubClassOf 'implements' some 'Misclassification-Penalized Posteriors (MiPP)' 'MiPP' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'MiPP' SubClassOf 'software' 'MiPP' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000293 MergeMaid '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 'has specified data output' some ('Text data set' and ('has format specification' some 'Textual format')) 'MergeMaid' SubClassOf 'is encoded in' some 'R language' 'MergeMaid' SubClassOf 'implements' some 'Logic regression' 'MergeMaid' SubClassOf 'implements' some 'Regression model' 'MergeMaid' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'has specified data output' some ('Text data set' and ('has format specification' some 'Textual format')) 'Mfuzz' SubClassOf 'software' 'Mfuzz' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'Mfuzz' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000292 MeasurementError.cor 'MeasurementError.cor' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'MeasurementError.cor' SubClassOf 'is encoded in' some 'R language' 'MeasurementError.cor' SubClassOf 'implements' some 'Two-stage measurement error model' 'MeasurementError.cor' SubClassOf 'software' 'MeasurementError.cor' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'MeasurementError.cor' SubClassOf 'is executed in' some 'descriptive statistical calculation' 'MeasurementError.cor' SubClassOf 'R software' http://edamontology.org/topic_2399 Gene transcription features 'Gene transcription features' SubClassOf 'Gene structure' 'Gene transcription features' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2800 Orpha number 'Orpha number' SubClassOf 'is identifier of' some 'Disease report' http://edamontology.org/topic_2397 Exons 'Exons' SubClassOf 'Coding RNA' 'Exons' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3080 Structure editing 'Structure editing' SubClassOf 'has input' some 'Structure' http://edamontology.org/operation_3084 Protein function prediction (from sequence) 'Protein function prediction (from sequence)' SubClassOf 'Obsolete concept (EDAM)' '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 'has input' some 'Pathway or network' 'Pathway or network visualisation' SubClassOf 'Pathway or network processing' 'Pathway or network visualisation' SubClassOf 'Pathway or network analysis' http://edamontology.org/data_2812 Lipid identifier 'Lipid identifier' SubClassOf 'is identifier of' some 'Lipid structure' 'Lipid identifier' SubClassOf 'is identifier of' some 'Lipid report' http://edamontology.org/format_1666 BioModel mathematical model format 'BioModel mathematical model format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'PATIKA entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1650 INOH entry format 'INOH entry format' SubClassOf 'Obsolete concept (EDAM)' 'INOH entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1653 aMAZE entry format 'aMAZE entry format' SubClassOf 'Obsolete concept (EDAM)' 'aMAZE entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1652 Reactome entry format 'Reactome entry format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'CPDB entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2838 Experimental data (proteomics) 'Experimental data (proteomics)' SubClassOf 'Obsolete concept (EDAM)' 'Experimental data (proteomics)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2832 Web portal 'Web portal' SubClassOf 'Obsolete concept (EDAM)' 'Web portal' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2831 Databank 'Databank' SubClassOf 'Obsolete concept (EDAM)' 'Databank' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1517 Restriction enzyme report 'Restriction enzyme report' SubClassOf 'Obsolete concept (EDAM)' 'Restriction enzyme report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1509 Enzyme report 'Enzyme report' SubClassOf 'Obsolete concept (EDAM)' 'Enzyme report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2857 Article metadata 'Article metadata' SubClassOf 'Obsolete concept (EDAM)' 'Article metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1624 HGVbase entry format 'HGVbase entry format' SubClassOf 'Obsolete concept (EDAM)' 'HGVbase entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1623 OMIM entry format 'OMIM entry format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'dbSNP polymorphism report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2869 Nucleic acid features report (RFLP) 'Nucleic acid features report (RFLP)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'MHC peptide immunogenicity report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1617 WormBase gene report format 'WormBase gene report format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'TAIR gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2867 Nucleic acid features report (VNTR) 'Nucleic acid features report (VNTR)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'ZFIN gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1533 Protein subcellular localization 'Protein subcellular localization' SubClassOf 'Obsolete concept (EDAM)' 'Protein subcellular localization' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1613 RGD gene report format 'RGD gene report format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 residue interactions' 'Protein residue 3D cluster' SubClassOf 'Protein interaction report' http://edamontology.org/data_1547 Protein contact map 'Protein contact map' SubClassOf 'Protein residue interactions' 'Protein contact map' SubClassOf 'Protein interaction report' http://edamontology.org/data_1546 Protein distance matrix 'Protein distance matrix' SubClassOf 'Protein residue interactions' 'Protein distance matrix' SubClassOf 'Distance matrix' 'Protein distance matrix' SubClassOf 'Protein interaction report' http://edamontology.org/format_1649 HumanCyc entry format 'HumanCyc entry format' SubClassOf 'Obsolete concept (EDAM)' 'HumanCyc entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1549 Protein hydrogen bonds 'Protein hydrogen bonds' SubClassOf 'Protein residue interactions' 'Protein hydrogen bonds' SubClassOf 'Protein interaction report' http://edamontology.org/data_1540 Protein residue interactions 'Protein residue interactions' SubClassOf 'has topic' some 'Protein folding, stability and design' 'Protein residue interactions' SubClassOf 'Protein property' 'Protein residue interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2874 Sequence set (polymorphic) 'Sequence set (polymorphic)' SubClassOf 'Obsolete concept (EDAM)' 'Sequence set (polymorphic)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2875 DRCAT resource 'DRCAT resource' SubClassOf 'Obsolete concept (EDAM)' 'DRCAT resource' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1543 Protein surface report 'Protein surface report' SubClassOf 'Obsolete concept (EDAM)' 'Protein surface report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1542 Protein solvent accessibility 'Protein solvent accessibility' SubClassOf 'Protein residue interactions' 'Protein solvent accessibility' SubClassOf 'Protein structure report' http://edamontology.org/data_1541 Protein flexibility or motion report 'Protein flexibility or motion report' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'ArrayExpress entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1645 EMDB entry format 'EMDB entry format' SubClassOf 'Obsolete concept (EDAM)' 'EMDB entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1648 MetaCyc entry format 'MetaCyc entry format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'KEGG PATHWAY entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1644 CHP 'CHP' SubClassOf 'is format of' some 'Processed microarray data' http://edamontology.org/data_1559 CATH homologous superfamily 'CATH homologous superfamily' SubClassOf 'Obsolete concept (EDAM)' 'CATH homologous superfamily' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1558 CATH topology 'CATH topology' SubClassOf 'Obsolete concept (EDAM)' 'CATH topology' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1557 CATH architecture 'CATH architecture' SubClassOf 'Obsolete concept (EDAM)' 'CATH architecture' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1556 CATH class 'CATH class' SubClassOf 'Obsolete concept (EDAM)' 'CATH class' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2888 Protein sequence record (full) 'Protein sequence record (full)' SubClassOf 'Obsolete concept (EDAM)' 'Protein sequence record (full)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1638 cel 'cel' SubClassOf 'is format of' some 'Raw microarray data' http://edamontology.org/data_2889 Nucleic acid sequence record (full) 'Nucleic acid sequence record (full) ' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'RNA features report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2884 Plot 'Plot' SubClassOf 'data' 'Plot' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_1550 Protein non-canonical interactions 'Protein non-canonical interactions' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Nucleic acid features report (polymorphism)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1555 EMBASSY domain classification 'EMBASSY domain classification' SubClassOf 'Obsolete concept (EDAM)' 'EMBASSY domain classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1554 SCOP node 'SCOP node' SubClassOf 'Obsolete concept (EDAM)' 'SCOP node' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2880 Secondary structure image 'Secondary structure image' SubClassOf 'Obsolete concept (EDAM)' 'Secondary structure image' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1553 CATH node 'CATH node' SubClassOf 'Obsolete concept (EDAM)' 'CATH node' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2881 Secondary structure report 'Secondary structure report' SubClassOf 'Obsolete concept (EDAM)' 'Secondary structure report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2882 DNA features 'DNA features' SubClassOf 'Obsolete concept (EDAM)' 'DNA features' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1637 dat 'dat' SubClassOf 'is format of' some 'Microarray spots image' http://edamontology.org/data_2539 Alignment data 'Alignment data' SubClassOf 'Obsolete concept (EDAM)' 'Alignment data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2533 Nucleic acid features report (mutation) 'Nucleic acid features report (mutation)' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid features report (mutation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2534 Sequence attribute 'Sequence attribute' SubClassOf 'Parameter' 'Sequence attribute' SubClassOf http://edamontology.org/data_0006 http://www.ifomis.org/bfo/1.1/snap#Role role 'Obsolete concept (EDAM)' DisjointWith 'role' http://edamontology.org/data_2540 Data index data 'Data index data' SubClassOf 'Obsolete concept (EDAM)' 'Data index data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0565 Sequence alignment visualisation 'Sequence alignment visualisation' SubClassOf 'has input' some 'Sequence alignment' 'Sequence alignment visualisation' SubClassOf 'Visualisation' 'Sequence alignment visualisation' SubClassOf 'Sequence analysis' 'Sequence alignment visualisation' SubClassOf 'has output' some 'Sequence alignment image' 'Sequence alignment visualisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0566 Sequence cluster visualisation 'Sequence cluster visualisation' SubClassOf 'has topic' some 'Sequence comparison' 'Sequence cluster visualisation' SubClassOf 'has input' some 'Sequence cluster' http://edamontology.org/operation_0563 Codon usage table formatting 'Codon usage table formatting' SubClassOf 'Codon usage table processing' 'Codon usage table formatting' SubClassOf 'has output' some 'Codon usage table' 'Codon usage table formatting' SubClassOf 'Formatting' 'Codon usage table formatting' SubClassOf 'has input' some 'Codon usage table' 'Codon usage table formatting' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0564 Sequence visualisation 'Sequence visualisation' SubClassOf 'has output' some 'Sequence image' 'Sequence visualisation' SubClassOf 'has input' some 'Sequence' http://edamontology.org/operation_0569 Protein secondary structure rendering Protein secondary structure visualisation 'Protein secondary structure rendering' SubClassOf 'has topic' some 'Protein structure analysis' 'Protein secondary structure rendering' SubClassOf 'Visualisation' 'Protein secondary structure rendering' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0567 Phylogenetic tree visualisation 'Phylogenetic tree visualisation' SubClassOf 'has output' some 'Phylogenetic tree' 'Phylogenetic tree visualisation' SubClassOf 'Phylogenetic tree processing' 'Phylogenetic tree visualisation' SubClassOf 'Phylogenetic tree analysis' http://edamontology.org/operation_0568 RNA secondary structure visualisation 'RNA secondary structure visualisation' SubClassOf 'has input' some 'RNA secondary structure' 'RNA secondary structure visualisation' SubClassOf 'RNA secondary structure analysis' 'RNA secondary structure visualisation' SubClassOf 'Visualisation' 'RNA secondary structure visualisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0561 Sequence formatting 'Sequence formatting' SubClassOf 'Formatting' 'Sequence formatting' SubClassOf 'has output' some 'Sequence' 'Sequence formatting' SubClassOf 'has input' some 'Sequence' 'Sequence formatting' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0562 Sequence alignment formatting 'Sequence alignment formatting' SubClassOf 'has output' some 'Sequence alignment' 'Sequence alignment formatting' SubClassOf 'has input' some 'Sequence alignment' 'Sequence alignment formatting' SubClassOf '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 'has topic' some 'Nucleic acid structure prediction' 'DNA vaccine design' SubClassOf 'Design' 'DNA vaccine design' SubClassOf 'has topic' some 'Immunology' http://edamontology.org/operation_0577 DNA linear map rendering 'DNA linear map rendering' SubClassOf 'Obsolete concept (EDAM)' 'DNA linear map rendering' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1238 Proteolytic digest 'Proteolytic digest' SubClassOf 'has topic' some 'Proteomics' http://edamontology.org/operation_0574 Sequence motif rendering 'Sequence motif rendering' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'has output' some 'Restriction map' http://edamontology.org/operation_0579 Operon drawing 'Operon drawing' SubClassOf 'has topic' some 'Gene structure' http://edamontology.org/data_1236 Psiblast checkpoint file 'Psiblast checkpoint file' SubClassOf 'Obsolete concept (EDAM)' '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 'has topic' some 'Protein interactions' http://edamontology.org/data_1235 Sequence cluster 'Sequence cluster' SubClassOf 'has topic' some 'Protein families' 'Sequence cluster' SubClassOf 'has topic' some 'Sequence comparison' http://edamontology.org/operation_0573 Map drawing 'Map drawing' SubClassOf 'has input' some 'Map' http://edamontology.org/operation_0570 Structure visualisation 'Structure visualisation' SubClassOf 'has input' some 'Structure' 'Structure visualisation' SubClassOf 'has output' some 'Structure image' http://edamontology.org/operation_0571 Microarray data rendering 'Microarray data rendering' SubClassOf 'has input' some 'Microarray hybridisation data' http://edamontology.org/data_2579 Expressed gene list 'Expressed gene list' SubClassOf 'Obsolete concept (EDAM)' 'Expressed gene list' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1243 Primer3 mispriming library file 'Primer3 mispriming library file' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Primer3 internal oligo mishybridizing library' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2576 Toxin identifier 'Toxin identifier' SubClassOf 'is identifier of' some 'Toxin structure' http://edamontology.org/data_1241 vectorstrip cloning vector definition file 'vectorstrip cloning vector definition file' SubClassOf 'Obsolete concept (EDAM)' 'vectorstrip cloning vector definition file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1244 primersearch primer pairs sequence record 'primersearch primer pairs sequence record' SubClassOf 'Obsolete concept (EDAM)' 'primersearch primer pairs sequence record' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1253 Sequence information report 'Sequence information report' SubClassOf 'Obsolete concept (EDAM)' 'Sequence information report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1252 Sequence length range 'Sequence length range' SubClassOf 'Obsolete concept (EDAM)' 'Sequence length range' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1251 Window size 'Window size' SubClassOf 'Obsolete concept (EDAM)' 'Window size' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2589 Hierarchy 'Hierarchy' SubClassOf 'data' 'Hierarchy' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_1258 Sequence property (nucleic acid) 'Sequence property (nucleic acid)' SubClassOf 'Obsolete concept (EDAM)' 'Sequence property (nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1257 Sequence property (protein) 'Sequence property (protein)' SubClassOf 'Obsolete concept (EDAM)' 'Sequence property (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1256 Sequence features (comparative) 'Sequence features (comparative)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'GO concept name (cellular component)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1255 Sequence features 'Sequence features' SubClassOf 'data' 'Sequence features' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_2581 GO concept name 'GO concept name' SubClassOf 'Obsolete concept (EDAM)' 'GO concept name' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1250 Word size 'Word size' SubClassOf 'Obsolete concept (EDAM)' 'Word size' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1264 Sequence composition table 'Sequence composition table' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Secondary structure alignment metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2599 Molecule interaction report 'Molecule interaction report' SubClassOf 'Obsolete concept (EDAM)' 'Molecule interaction report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1269 DAS sequence feature annotation 'DAS sequence feature annotation' SubClassOf 'Obsolete concept (EDAM)' 'DAS sequence feature annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2590 Hierarchy identifier 'Hierarchy identifier' SubClassOf 'Obsolete concept (EDAM)' 'Hierarchy identifier' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2592 Cancer type 'Cancer type' SubClassOf 'Obsolete concept (EDAM)' 'Cancer type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1274 Map 'Map' SubClassOf 'data' 'Map' SubClassOf 'has topic' some 'Mapping' 'Map' SubClassOf 'Map data' http://edamontology.org/data_1281 Sequence signature map 'Sequence signature map' SubClassOf 'Obsolete concept (EDAM)' 'Sequence signature map' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1298 Sequence motif matches 'Sequence motif matches' SubClassOf 'Obsolete concept (EDAM)' 'Sequence motif matches' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1299 Sequence features (repeats) 'Sequence features (repeats)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'GlobPlot domain image' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1293 SMART protein schematic 'SMART protein schematic' SubClassOf 'Obsolete concept (EDAM)' 'SMART protein schematic' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1292 InterPro architecture image 'InterPro architecture image' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'InterPro detailed match image' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3026 GO concept name (biological process) 'GO concept name (biological process)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'GO concept name (molecular function)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3028 Taxonomy 'Taxonomy' SubClassOf 'data' 'Taxonomy' SubClassOf 'has topic' some 'Phylogeny' 'Taxonomy' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_3025 Ontology concept identifier 'Ontology concept identifier' SubClassOf 'is identifier of' some 'Ontology concept' http://edamontology.org/data_3021 UniProt accession 'UniProt accession' SubClassOf 'is identifier of' some 'Sequence record' http://www.ebi.ac.uk/efo/swo/SWO_0000202 GeneticsDesign 'GeneticsDesign' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'GeneticsDesign' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some 'Textual format')) 'GeneticsDesign' SubClassOf 'software' 'GeneticsDesign' SubClassOf 'is encoded in' some 'R language' 'GeneticsDesign' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000203 GeneticsPed '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' and ('has format specification' some 'R data frame')) 'GeneticsPed' SubClassOf 'has specified data input' some ('has format specification' only 'pedigree data file') 'GeneticsPed' SubClassOf 'software' 'GeneticsPed' SubClassOf 'BioConductor Software' 'GeneticsPed' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000201 GeneticsBase 'GeneticsBase' SubClassOf 'software' 'GeneticsBase' SubClassOf 'has specified data input' some 'CSV data set' 'GeneticsBase' SubClassOf 'is encoded in' some 'R language' 'GeneticsBase' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some 'Textual format')) 'GeneticsBase' SubClassOf 'is published by' value 'Bioconductor' 'GeneticsBase' SubClassOf 'has specified data input' some ('has format specification' only 'pedigree data file') 'GeneticsBase' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some 'Textual format')) 'GeneticsBase' SubClassOf 'BioConductor Software' 'GeneticsBase' SubClassOf 'R software' http://edamontology.org/topic_0594 Sequence classification 'Sequence classification' SubClassOf 'Sequence analysis' 'Sequence classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_0595 Protein classification 'Protein classification' SubClassOf 'Obsolete concept (EDAM)' 'Protein classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3034 Sequence feature identifier 'Sequence feature identifier' SubClassOf 'is identifier of' some 'Sequence features' http://edamontology.org/data_3035 Structure identifier 'Structure identifier' SubClassOf 'is identifier of' some 'Structure' http://edamontology.org/data_3036 Matrix identifier 'Matrix identifier' SubClassOf 'is identifier of' some 'Matrix' http://edamontology.org/data_3031 Core data 'Core data' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence motif or profile' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000208 GraphAT 'GraphAT' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'GraphAT' SubClassOf 'implements' some 'k-means' 'GraphAT' SubClassOf 'has specified data input' some ('Clustered data set' and ('has format specification' some 'data format specification')) 'GraphAT' SubClassOf 'software' 'GraphAT' SubClassOf 'is encoded in' some 'R language' 'GraphAT' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000209 GraphAlignment 'GraphAlignment' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'GraphAlignment' SubClassOf 'is encoded in' some 'R language' 'GraphAlignment' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'GraphAlignment' SubClassOf 'software' 'GraphAlignment' SubClassOf 'implements' some 'Bayesian Model' 'GraphAlignment' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'implements' some 'ANCOVA' 'GlobalAncova' SubClassOf 'is encoded in' some 'R language' 'GlobalAncova' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 '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' 'GOSemSim' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 'software' 'GenomeGraphs' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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' 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 'is executed in' some 'data visualization' 'HELP' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'design file')) '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')) 'HELP' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000214 HEM 'HEM' SubClassOf 'software' '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 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'HEM' SubClassOf 'implements' some ''FDR'' 'HEM' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'HEM' SubClassOf 'implements' some 'Markov Chain Monte Carlo' 'HEM' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000210 GridGrinder 'GridGrinder' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Grid grinder')) http://www.ebi.ac.uk/efo/swo/SWO_0000224 Heatplus 'Heatplus' SubClassOf 'has specified data output' some ('Heatmap' and ('has format specification' some 'image format')) 'Heatplus' SubClassOf 'is encoded in' some 'R language' 'Heatplus' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'Heatplus' SubClassOf 'is executed in' some 'data visualization' 'Heatplus' SubClassOf 'software' 'Heatplus' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000225 HilbertVis 'HilbertVis' SubClassOf 'is encoded in' some 'R language' 'HilbertVis' SubClassOf 'software' 'HilbertVis' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'GFF')) '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 'has specified data input' some ('data' and ('has format specification' some 'BED format')) 'HilbertVis' SubClassOf 'is executed in' some 'data visualization' 'HilbertVis' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000222 Harshlight '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 input' some ('Image' and ('has format specification' some 'CEL binary format')) 'Harshlight' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'PostScript')) 'Harshlight' SubClassOf 'R software' http://www.ebi.ac.uk/efo/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 process' and ('has participant' value 'Genicon Sciences')) http://www.ebi.ac.uk/efo/swo/SWO_0000226 HilbertVisGUI 'HilbertVisGUI' SubClassOf 'software' 'HilbertVisGUI' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'BED format')) 'HilbertVisGUI' SubClassOf 'is encoded in' some 'R language' 'HilbertVisGUI' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'GFF')) '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 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000115 MAGE-TAB inputting software 'MAGE-TAB inputting software' EquivalentTo 'has specified data input' some ('data' and ('has format specification' some 'MAGE-TAB')) http://edamontology.org/topic_3531 Protein super-secondary structure 'Protein super-secondary structure' SubClassOf 'Protein structural motifs and surfaces' 'Protein super-secondary structure' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000111 R software 'R software' EquivalentTo 'is encoded in' some 'R language' http://edamontology.org/topic_3530 Genetic information processing pathways 'Genetic information processing pathways' SubClassOf 'Molecular interactions, pathways and networks' 'Genetic information processing pathways' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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 '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 'Number of users unrestricted' 'MIT License' SubClassOf 'has clause' some 'derivative software allowed' 'MIT License' SubClassOf 'GNU Copyleft Software License Type' http://edamontology.org/topic_3536 Protein cleavage sites 'Protein cleavage sites' SubClassOf 'Protein sites, features and motifs' 'Protein cleavage sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3535 Protein-nucleic acid binding sites 'Protein-nucleic acid binding sites' SubClassOf 'Protein structural motifs and surfaces' 'Protein-nucleic acid binding sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3534 Protein binding sites 'Protein binding sites' SubClassOf 'Protein structural motifs and surfaces' 'Protein binding sites' SubClassOf 'Protein sites, features and motifs' http://edamontology.org/topic_3533 Protein active sites 'Protein active sites' SubClassOf 'Protein structural motifs and surfaces' 'Protein active sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3539 Protein domains 'Protein domains' SubClassOf 'Protein domains and folds' 'Protein domains' SubClassOf 'Protein sites, features and motifs' 'Protein domains' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3538 Protein disordered structure 'Protein disordered structure' SubClassOf 'Protein sites, features and motifs' 'Protein disordered structure' SubClassOf 'Protein structure analysis' http://edamontology.org/topic_3537 Protein chemical modifications 'Protein chemical modifications' SubClassOf 'Protein sites, features and motifs' 'Protein chemical modifications' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000125 'DEDS' ''DEDS'' SubClassOf 'is encoded in' some 'R language' ''DEDS'' SubClassOf 'is executed in' some 'differential expression analysis' ''DEDS'' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) ''DEDS'' SubClassOf 'implements' some ''FDR'' ''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 'is executed in' some 'descriptive statistical calculation' ''DEDS'' SubClassOf 'implements' some 'FC' ''DEDS'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000126 'DFP' ''DFP'' SubClassOf 'is executed in' some 'differential expression analysis' ''DFP'' SubClassOf 'is encoded in' some 'R language' ''DFP'' SubClassOf 'software' ''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')) ''DFP'' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some 'Textual format')) ''DFP'' SubClassOf 'R software' http://www.ebi.ac.uk/swo/license/SWO_9000080 lGPL 'lGPL' SubClassOf 'software license' 'lGPL' SubClassOf 'GNU Project Free Software License Type' 'lGPL' SubClassOf 'License without restrictions on derivatives' http://www.ebi.ac.uk/efo/swo/SWO_0000124 Cyber-T 'Cyber-T' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'UC Irvine')) http://edamontology.org/topic_3543 Protein sequence repeats 'Protein sequence repeats' SubClassOf 'Protein sites, features and motifs' 'Protein sequence repeats' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000121 CodeLink Expression Analysis Software 'CodeLink Expression Analysis Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Motorola Life Sciences')) http://www.ebi.ac.uk/swo/license/SWO_9000086 LPPL 'LPPL' SubClassOf 'has clause' some 'Distribution unrestricted' 'LPPL' SubClassOf 'has clause' some 'Source code available' 'LPPL' SubClassOf 'software license' 'LPPL' SubClassOf 'has clause' some 'No restrictions on derivatives' 'LPPL' SubClassOf 'GNU Project Free Software License Type' http://edamontology.org/format_1935 GCG 'GCG' SubClassOf 'Textual format' http://edamontology.org/topic_3542 Protein secondary structure 'Protein secondary structure' SubClassOf 'Protein sites, features and motifs' http://www.ebi.ac.uk/efo/swo/SWO_0000122 CodeLink Expression Scanning Software 'CodeLink Expression Scanning Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Motorola Life Sciences')) http://www.ebi.ac.uk/swo/license/SWO_9000087 OPL v1.0 'OPL v1.0' SubClassOf 'has clause' some 'derivative software allowed' 'OPL v1.0' SubClassOf 'software license' 'OPL v1.0' SubClassOf 'has clause' some 'Distribution restricted' 'OPL v1.0' SubClassOf 'has clause' some 'Source code available' 'OPL v1.0' SubClassOf 'Open source software license' http://edamontology.org/topic_3541 Protein post-translational modifications 'Protein post-translational modifications' SubClassOf 'Protein sites, features and motifs' 'Protein post-translational modifications' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/license/SWO_9000084 EPL v1 '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 'derivative code same license' 'EPL v1' SubClassOf 'GNU Project Free Software License Type' http://edamontology.org/topic_3540 Protein key folding sites 'Protein key folding sites' SubClassOf 'Protein folding, stability and design' 'Protein key folding sites' SubClassOf 'Protein sites, features and motifs' 'Protein key folding sites' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000120 'CoCiteStats' ''CoCiteStats'' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) ''CoCiteStats'' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some 'Textual format')) ''CoCiteStats'' SubClassOf 'is executed in' some 'descriptive statistical calculation' ''CoCiteStats'' SubClassOf 'implements' some 'Concordance' ''CoCiteStats'' SubClassOf 'is encoded in' some 'R language' ''CoCiteStats'' SubClassOf 'software' ''CoCiteStats'' SubClassOf 'implements' some 'Hubert’s gamma' ''CoCiteStats'' SubClassOf 'implements' some 'Jaccard’s index' ''CoCiteStats'' SubClassOf '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 clause' some 'Distribution with notices' 'Modified BSD' SubClassOf 'software license' 'Modified BSD' SubClassOf 'GNU Copyleft Software License Type' http://edamontology.org/topic_3544 Protein signal peptides 'Protein signal peptides' SubClassOf 'Protein sites, features and motifs' 'Protein signal peptides' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000134 'EBarrays' ''EBarrays'' SubClassOf 'software' ''EBarrays'' SubClassOf 'implements' some 'Lognormal Normal with Modied Variance Model' ''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 'is encoded in' some 'R language' ''EBarrays'' SubClassOf 'implements' some 'Gamma Gamma Model' ''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')) ''EBarrays'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000132 'DynDoc' ''DynDoc'' SubClassOf 'is encoded in' some 'R language' ''DynDoc'' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'Rnw')) ''DynDoc'' SubClassOf 'software' ''DynDoc'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000133 '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 'Textual format')) ''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')) ''EBImage'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000130 'DNAcopy' ''DNAcopy'' SubClassOf 'software' ''DNAcopy'' SubClassOf 'has specified data input' some ('data' 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://edamontology.org/format_1965 treecon sequence format 'treecon sequence format' SubClassOf 'Obsolete concept (EDAM)' '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 'Sequence record format (text)' http://edamontology.org/topic_2226 Structure determination 'Structure determination' SubClassOf 'Obsolete concept (EDAM)' 'Structure determination' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2225 Protein databases 'Protein databases' SubClassOf 'Obsolete concept (EDAM)' 'Protein databases' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000138 Expert 2100 'Expert 2100' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) 'Expert 2100' SubClassOf 'software' 'Expert 2100' SubClassOf 'Agilent Technologies Software' http://edamontology.org/topic_2230 Classification 'Classification' SubClassOf 'Obsolete concept (EDAM)' 'Classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000147 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 'is executed in' some 'feature extraction' 'Agilent Feature Extraction Software' SubClassOf 'Agilent Technologies Software' http://edamontology.org/topic_2232 Lipoproteins 'Lipoproteins' SubClassOf 'Obsolete concept (EDAM)' 'Lipoproteins' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1959 selex sequence format 'selex sequence format' SubClassOf 'Obsolete concept (EDAM)' 'selex sequence format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1956 phylipnon sequence format 'phylipnon sequence format' SubClassOf 'Obsolete concept (EDAM)' 'phylipnon sequence format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1955 phylip sequence format 'phylip sequence format' SubClassOf 'Obsolete concept (EDAM)' 'phylip sequence format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000158 GEOmetadb 'GEOmetadb' SubClassOf 'software' 'GEOmetadb' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'GEOmetadb' SubClassOf 'is encoded in' some 'R language' 'GEOmetadb' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000159 GEOquery 'GEOquery' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'GEOquery' SubClassOf 'software' 'GEOquery' SubClassOf 'is encoded in' some 'R language' 'GEOquery' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000154 GC-RMA Quantification 'GC-RMA Quantification' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) 'GC-RMA Quantification' SubClassOf 'software' 'GC-RMA Quantification' SubClassOf 'Agilent Technologies Software' http://www.ebi.ac.uk/efo/swo/SWO_0000155 GEMTools 2.4 'GEMTools 2.4' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Incyte Genomics')) http://www.ebi.ac.uk/efo/swo/SWO_0000152 GACK 'GACK' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Stanford University')) http://www.ebi.ac.uk/efo/swo/SWO_0000168 GOstats 'GOstats' SubClassOf 'implements' some 'Hypergeometric probability' 'GOstats' SubClassOf 'is encoded in' some 'R language' 'GOstats' SubClassOf 'software' 'GOstats' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) 'GOstats' SubClassOf 'implements' some ''t-test'' 'GOstats' SubClassOf 'has specified data input' some ('Gene list' and ('has format specification' some 'data format specification')) 'GOstats' SubClassOf 'is executed in' some 'differential expression analysis' 'GOstats' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) '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/efo/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')) http://www.ebi.ac.uk/efo/swo/SWO_0000163 GGtools 'GGtools' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'rda')) 'GGtools' SubClassOf 'is encoded in' some 'R language' 'GGtools' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some 'Textual format')) 'GGtools' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'GGtools' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'GGtools' SubClassOf 'software' 'GGtools' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000164 GLAD 'GLAD' SubClassOf 'implements' some 'Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)' '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 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'GLAD' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000161 GGBase 'GGBase' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'GGBase' SubClassOf 'has specified data output' some ('data' 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' and ('has format specification' some 'R data frame')) 'GGBase' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some 'Textual format')) 'GGBase' SubClassOf 'R software' http://edamontology.org/topic_2258 Cheminformatics 'Cheminformatics' SubClassOf 'Computer science' 'Cheminformatics' SubClassOf 'Chemistry' 'Cheminformatics' SubClassOf 'Informatics' http://edamontology.org/topic_2257 Phylogeny visualisation 'Phylogeny visualisation' SubClassOf 'Obsolete concept (EDAM)' 'Phylogeny visualisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1929 FASTA FASTA format 'FASTA format' SubClassOf 'Textual format' http://www.ebi.ac.uk/efo/swo/SWO_0000176 Gene Pix 'Gene Pix' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Molecular Devices')) http://edamontology.org/format_1924 clustal sequence format 'clustal sequence format' SubClassOf 'Obsolete concept (EDAM)' 'clustal sequence format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000175 GeneData Expressionist Analyst v4.0.5 'GeneData Expressionist Analyst v4.0.5' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Genedata')) http://www.ebi.ac.uk/efo/swo/SWO_0000170 GSEABase 'GSEABase' SubClassOf 'software' 'GSEABase' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) 'GSEABase' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'XML')) 'GSEABase' SubClassOf 'is encoded in' some 'R language' 'GSEABase' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'GSEABase' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000171 GSEAlm 'GSEAlm' SubClassOf 'software' 'GSEAlm' SubClassOf 'is executed in' some 'descriptive statistical calculation' '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' 'GSEAlm' SubClassOf 'R software' http://edamontology.org/format_1921 Alignment format 'Alignment format' SubClassOf 'is format of' some 'Sequence alignment' http://edamontology.org/format_1920 Sequence feature annotation format 'Sequence feature annotation format' SubClassOf 'is format of' some 'Sequence features' http://edamontology.org/format_1918 Atomic data format 'Atomic data format' SubClassOf 'Obsolete concept (EDAM)' 'Atomic data format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000189 GeneRegionScan 'GeneRegionScan' SubClassOf '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')) 'GeneRegionScan' SubClassOf 'R software' http://edamontology.org/format_1919 Sequence record format 'Sequence record format' SubClassOf 'is format of' some 'Sequence record' http://edamontology.org/topic_2271 Structure database search 'Structure database search' SubClassOf 'Obsolete concept (EDAM)' 'Structure database search' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2278 Transmembrane protein prediction 'Transmembrane protein prediction' SubClassOf 'Obsolete concept (EDAM)' 'Transmembrane protein prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_2277 SNP 'SNP' SubClassOf 'DNA polymorphism' 'SNP' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000188 GeneR 'GeneR' SubClassOf 'is encoded in' some 'R language' 'GeneR' SubClassOf 'software' 'GeneR' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'FASTA format')) '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' and ('has format specification' some 'R data frame')) 'GeneR' SubClassOf 'R software' http://edamontology.org/topic_2276 Protein function prediction 'Protein function prediction' SubClassOf 'Obsolete concept (EDAM)' 'Protein function prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1831 Metal-bound cysteine detection 'Metal-bound cysteine detection' SubClassOf 'Residue interaction calculation' http://edamontology.org/operation_0500 Secondary structure alignment generation 'Secondary structure alignment generation' SubClassOf 'Obsolete concept (EDAM)' 'Secondary structure alignment generation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1835 Residue contact calculation (residue-negative ion) 'Residue contact calculation (residue-negative ion)' SubClassOf 'Residue contact calculation' 'Residue contact calculation (residue-negative ion)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0504 Multiple structure alignment construction 'Multiple structure alignment construction' SubClassOf 'Obsolete concept (EDAM)' 'Multiple structure alignment construction' SubClassOf 'Structure alignment' http://edamontology.org/operation_1834 Residue contact calculation (residue-metal) 'Residue contact calculation (residue-metal)' SubClassOf 'Residue contact calculation' 'Residue contact calculation (residue-metal)' SubClassOf 'Protein binding site prediction (from structure)' 'Residue contact calculation (residue-metal)' SubClassOf 'Residue interaction calculation' http://edamontology.org/operation_0501 Protein secondary structure alignment generation 'Protein secondary structure alignment generation' SubClassOf 'has output' some 'Secondary structure alignment (protein)' http://www.ebi.ac.uk/efo/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://edamontology.org/operation_0502 RNA secondary structure alignment 'RNA secondary structure alignment' SubClassOf 'has input' some 'RNA secondary structure' 'RNA secondary structure alignment' SubClassOf 'has output' some 'Secondary structure alignment (RNA)' http://edamontology.org/operation_1832 Residue contact calculation (residue-nucleic acid) 'Residue contact calculation (residue-nucleic acid)' SubClassOf 'Protein structural motif recognition' 'Residue contact calculation (residue-nucleic acid)' SubClassOf 'Residue contact calculation' 'Residue contact calculation (residue-nucleic acid)' SubClassOf 'Protein-nucleic acid binding site analysis' 'Residue contact calculation (residue-nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000195 GeneTac Analyser 'GeneTac Analyser' SubClassOf 'output of' some ('software development process' and ('has participant' value 'Applied Biosystems')) http://www.ebi.ac.uk/efo/swo/SWO_0000192 GeneSelector 'GeneSelector' SubClassOf 'implements' some 'Wilcoxon' 'GeneSelector' SubClassOf 'implements' some 'Linear modelling' 'GeneSelector' SubClassOf 'implements' some 'WilcEbam' 'GeneSelector' SubClassOf 'implements' some 'BaldiLongT' 'GeneSelector' SubClassOf 'software' 'GeneSelector' SubClassOf 'implements' some ''t-test'' 'GeneSelector' SubClassOf 'implements' some 'Bayesian Model' 'GeneSelector' SubClassOf 'implements' some 'SAM' 'GeneSelector' SubClassOf 'is encoded in' some 'R language' 'GeneSelector' SubClassOf 'implements' some 'FoxDimmicT' 'GeneSelector' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000193 GeneSpring 'GeneSpring' SubClassOf 'has specified data output' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) '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 'output of' some ('software development process' and ('has participant' value 'Strand Life Sciences')) 'GeneSpring' SubClassOf 'is encoded in' some 'R language' 'GeneSpring' SubClassOf 'software' 'GeneSpring' SubClassOf 'Agilent Technologies Software' 'GeneSpring' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000190 GeneRfold 'GeneRfold' SubClassOf 'software' 'GeneRfold' SubClassOf 'is encoded in' some 'R language' 'GeneRfold' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'GeneRfold' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'PostScript')) 'GeneRfold' SubClassOf 'R software' http://edamontology.org/topic_2280 Nucleic acid structure comparison 'Nucleic acid structure comparison' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid structure comparison' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000191 GeneSelectMMD 'GeneSelectMMD' SubClassOf 'is executed in' some 'differential expression analysis' 'GeneSelectMMD' SubClassOf 'has specified data input' some ('Gene expression dataset' and ('has format specification' some 'data format specification')) '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 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) 'GeneSelectMMD' SubClassOf 'R software' http://edamontology.org/operation_1828 Tau angle calculation 'Tau angle calculation' SubClassOf 'Torsion 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 'Torsion angle calculation' 'Cysteine torsion angle calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1826 Full torsion angle calculation 'Full torsion angle calculation' SubClassOf 'Torsion angle calculation' 'Full torsion angle calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1825 Backbone torsion angle calculation 'Backbone torsion angle calculation' SubClassOf 'Torsion angle calculation' 'Backbone torsion angle calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1842 Proline mutation value calculation 'Proline mutation value calculation' SubClassOf 'Protein modelling (mutation)' 'Proline mutation value calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0511 Profile-to-profile alignment (pairwise) 'Profile-to-profile alignment (pairwise)' SubClassOf 'Profile-to-profile alignment' 'Profile-to-profile alignment (pairwise)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1841 Rotamer likelihood prediction 'Rotamer likelihood prediction' SubClassOf 'Protein modelling (side chains)' '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 'Obsolete concept (EDAM)' '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 'Residue contact calculation (residue-ligand)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'PDB file sequence retrieval' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0512 Sequence alignment generation (multiple profile) 'Sequence alignment generation (multiple profile)' SubClassOf 'Obsolete concept (EDAM)' '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 '3D profile-to-3D profile alignment' '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 'Residue non-canonical interaction detection' 'Residue packing validation' SubClassOf 'Protein model validation' http://edamontology.org/operation_0507 Pairwise structure alignment generation (local) 'Pairwise structure alignment generation (local)' SubClassOf 'Obsolete concept (EDAM)' '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 contact calculation (residue-residue)' 'Salt bridge calculation' SubClassOf 'Residue interaction calculation' http://edamontology.org/operation_0508 Pairwise structure alignment generation (global) 'Pairwise structure alignment generation (global)' SubClassOf 'Obsolete concept (EDAM)' '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 'Protein binding site prediction (from structure)' 'Residue contact calculation (residue-ligand)' SubClassOf 'Residue contact calculation' '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 'Obsolete concept (EDAM)' '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 'Residue contact calculation (residue-residue)' '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 'Obsolete concept (EDAM)' 'Structure alignment (RNA)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1836 Residue bump detection 'Residue bump detection' SubClassOf 'Residue non-canonical interaction detection' 'Residue bump detection' SubClassOf 'Protein model validation' http://edamontology.org/operation_1813 Sequence retrieval 'Sequence retrieval' SubClassOf 'Obsolete concept (EDAM)' 'Sequence retrieval' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1812 Loading 'Loading' SubClassOf 'has input' some 'Identifier' http://edamontology.org/operation_1820 Protein residue surface calculation (vacuum accessible) 'Protein residue surface calculation (vacuum accessible)' SubClassOf 'Protein residue surface calculation' '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 'Protein surface calculation' '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 'Protein surface calculation' '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 'Protein residue surface calculation' '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 'Protein residue surface calculation' '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 'Protein atom surface calculation' 'Protein atom surface calculation (accessible)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1816 Surface rendering 'Surface rendering' SubClassOf 'Protein surface calculation' 'Surface rendering' SubClassOf 'Protein surface analysis' http://edamontology.org/operation_1814 Structure retrieval 'Structure retrieval' SubClassOf 'Obsolete concept (EDAM)' '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 'Protein residue surface calculation' '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 'Protein atom surface calculation' '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 'has topic' some 'Genetic variation' http://edamontology.org/operation_0541 Phylogenetic tree generation (from continuous quantitative characters) 'Phylogenetic tree generation (from continuous quantitative characters)' SubClassOf 'has input' some 'Phylogenetic continuous quantitative data' http://edamontology.org/operation_0542 Phylogenetic tree generation (from gene frequencies) 'Phylogenetic tree generation (from gene frequencies)' SubClassOf 'has topic' some 'Gene expression' 'Phylogenetic tree generation (from gene frequencies)' SubClassOf 'has input' some 'Phylogenetic gene frequencies data' http://edamontology.org/format_1981 GenBank feature 'GenBank feature' SubClassOf 'Obsolete concept (EDAM)' 'GenBank feature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1980 EMBL feature 'EMBL feature' SubClassOf 'Obsolete concept (EDAM)' 'EMBL feature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0553 Phylogenetic tree analysis (gene family prediction) 'Phylogenetic tree analysis (gene family prediction)' SubClassOf 'has output' some 'Gene report' 'Phylogenetic tree analysis (gene family prediction)' SubClassOf 'has topic' some 'Phylogenomics' http://edamontology.org/operation_0559 Immunogenicity prediction 'Immunogenicity prediction' SubClassOf 'Peptide immunogenicity prediction' 'Immunogenicity prediction' SubClassOf 'has topic' some 'Immunology' 'Immunogenicity prediction' SubClassOf 'has topic' some 'Protein folding, stability and design' 'Immunogenicity prediction' SubClassOf 'has output' some 'Protein structure' 'Immunogenicity prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0557 Phylogenetic tree distances calculation 'Phylogenetic tree distances calculation' SubClassOf 'has output' some 'Phylogenetic tree distances' http://edamontology.org/operation_0550 DNA substitution modelling 'DNA substitution modelling' SubClassOf 'has output' some 'DNA substitution model' 'DNA substitution modelling' SubClassOf 'has topic' some 'Phylogeny' http://edamontology.org/format_1976 pir 'pir' SubClassOf 'Obsolete concept (EDAM)' 'pir' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1977 swiss feature 'swiss feature' SubClassOf 'Obsolete concept (EDAM)' 'swiss feature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1971 meganon sequence format 'meganon sequence format' SubClassOf 'Obsolete concept (EDAM)' 'meganon sequence format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0521 PCR primer design (based on gene structure) 'PCR primer design (based on gene structure)' SubClassOf 'PCR primer design' 'PCR primer design (based on gene structure)' SubClassOf 'has topic' some '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 'PCR primer design' '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 'PCR primer design' '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 'has topic' some 'Protein folding, stability and design' http://edamontology.org/operation_0518 PCR primer design (for genotyping polymorphisms) 'PCR primer design (for genotyping polymorphisms)' SubClassOf 'PCR primer design' 'PCR primer design (for genotyping polymorphisms)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0519 PCR primer design (for gene transcription profiling) 'PCR primer design (for gene transcription profiling)' SubClassOf 'has topic' some 'Gene expression' 'PCR primer design (for gene transcription profiling)' SubClassOf 'PCR primer design' '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 'Obsolete concept (EDAM)' 'Data retrieval (database metadata)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1848 Structure formatting 'Structure formatting' SubClassOf 'Formatting' 'Structure formatting' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/license/SWO_9000088 MPL 'MPL' SubClassOf 'software license' 'MPL' SubClassOf 'has clause' some 'Distribution with notices' 'MPL' SubClassOf 'has clause' some 'Source code available' 'MPL' SubClassOf 'Open source software license' http://edamontology.org/operation_0517 PCR primer design (for large scale sequencing) 'PCR primer design (for large scale sequencing)' SubClassOf 'has topic' some 'Sequencing' 'PCR primer design (for large scale sequencing)' SubClassOf 'PCR primer design' '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 'Obsolete concept (EDAM)' 'DSSP secondary structure assignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2528 Molecular data 'Molecular data' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Gene expression profile analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2529 Molecule report 'Molecule report' SubClassOf 'Obsolete concept (EDAM)' '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 'has output' some 'Pathway or network report' http://edamontology.org/operation_0530 SBS data processing 'SBS data processing' SubClassOf 'Obsolete concept (EDAM)' 'SBS data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0531 Heat map generation 'Heat map generation' SubClassOf 'has output' some 'Heatmap' http://edamontology.org/data_2524 Protein data 'Protein data' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Protein structure assignment (from NMR data)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2526 Article data 'Article data' SubClassOf 'data' 'Article data' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_2527 Parameter 'Parameter' SubClassOf 'data' 'Identifier' DisjointWith '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 'has input' some 'Protein circular dichroism (CD) spectroscopic data' http://edamontology.org/data_2522 Map data 'Map data' SubClassOf 'Obsolete concept (EDAM)' 'Map data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2523 Phylogenetic data 'Phylogenetic data' SubClassOf 'data' 'Phylogenetic data' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/operation_0529 MPSS data processing 'MPSS data processing' SubClassOf 'Obsolete concept (EDAM)' 'MPSS data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0527 Tag mapping 'Tag mapping' SubClassOf 'has output' some 'Sequence tag profile (with gene assignment)' http://edamontology.org/operation_0528 SAGE data processing 'SAGE data processing' SubClassOf 'Obsolete concept (EDAM)' 'SAGE data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1994 nexus alignment format 'nexus alignment format' SubClassOf 'Obsolete concept (EDAM)' 'nexus alignment format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1993 msf alignment format 'msf alignment format' SubClassOf 'Obsolete concept (EDAM)' 'msf alignment format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_1995 nexusnon alignment format 'nexusnon alignment format' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Operation (typed)' 'Sequence analysis' SubClassOf 'has topic' some 'Sequence analysis' 'Sequence analysis' SubClassOf 'Analysis' 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://edamontology.org/data_1327 Protein features (epitopes) 'Protein features (epitopes)' SubClassOf 'Obsolete concept (EDAM)' 'Protein features (epitopes)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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://edamontology.org/data_1326 Protein features report (binding sites) 'Protein features report (binding sites)' SubClassOf 'Obsolete concept (EDAM)' 'Protein features report (binding sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000079 Cytoscape 'Cytoscape' SubClassOf 'is executed in' some 'data visualization task' 'Cytoscape' SubClassOf 'has specified data input' only 'Interaction data' 'Cytoscape' SubClassOf 'has documentation' value "http://dx.doi.org/10.1101/gr.1239303" http://edamontology.org/data_1325 Protein features report (active sites) 'Protein features report (active sites)' SubClassOf 'Obsolete concept (EDAM)' 'Protein features report (active sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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://edamontology.org/operation_2407 Annotation processing 'Annotation processing' SubClassOf 'Obsolete concept (EDAM)' 'Annotation processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2406 Protein structure analysis 'Protein structure analysis' SubClassOf 'has topic' some 'Protein structure analysis' 'Protein structure analysis' SubClassOf 'has input' some 'Protein structure' http://edamontology.org/operation_2405 Protein interaction data processing 'Protein interaction data processing' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'MHC Class I epitopes report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2404 Sequence motif processing 'Sequence motif processing' SubClassOf 'Obsolete concept (EDAM)' 'Sequence motif processing' SubClassOf 'Sequence analysis' 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://edamontology.org/data_1324 Protein features (post-translation modifications) 'Protein features (post-translation modifications)' SubClassOf 'Obsolete concept (EDAM)' 'Protein features (post-translation modifications)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000073 Q 'Q' SubClassOf 'is executed in' some 'data processing task' 'Q' SubClassOf 'has interface' some 'graphical user interface' 'Q' SubClassOf 'is executed in' some 'data visualization task' http://edamontology.org/data_1323 Protein features report (cleavage sites) 'Protein features report (cleavage sites)' SubClassOf 'Obsolete concept (EDAM)' 'Protein features report (cleavage sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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')) 'CRG TCoffee 9.02.r1228' SubClassOf 'software with command line interface' http://edamontology.org/data_1322 Protein features report (signal peptides) 'Protein features report (signal peptides)' SubClassOf 'Obsolete concept (EDAM)' 'Protein features report (signal peptides)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000075 SPSS 'SPSS' SubClassOf 'is executed in' some 'data visualization task' 'SPSS' SubClassOf 'has interface' some 'graphical user interface' 'SPSS' SubClassOf 'is executed in' some 'data processing task' http://edamontology.org/data_1321 Protein features (sites) 'Protein features (sites)' SubClassOf 'Obsolete concept (EDAM)' 'Protein features (sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000074 Q 4.2 'Q 4.2' SubClassOf 'has documentation' value "http://www.q-researchsoftware.com" 'Q 4.2' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Numbers International Pty Ltd')) http://edamontology.org/format_2352 BioXSD 'BioXSD' SubClassOf 'is format of' some 'Sequence alignment' 'BioXSD' SubClassOf 'is format of' some 'Sequence' 'BioXSD' SubClassOf 'is format of' some 'Sequence features' http://edamontology.org/format_2350 Format (typed) 'Format (typed)' SubClassOf 'data format specification' 'Format (typed)' SubClassOf http://edamontology.org/format_1915 http://edamontology.org/data_1339 Sequence database hits alignments list 'Sequence database hits alignments list' SubClassOf 'Obsolete concept (EDAM)' '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 'has output' some 'Protein report' http://edamontology.org/data_0007 Tool 'Tool' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence profile processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2412 Data index processing 'Data index processing' SubClassOf 'Obsolete concept (EDAM)' 'Data index processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0005 Resource type 'Resource type' SubClassOf 'Obsolete concept (EDAM)' 'Resource type' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2411 Structural profile processing 'Structural profile processing' SubClassOf 'Obsolete concept (EDAM)' 'Structural profile processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2417 Physicochemical property data processing 'Physicochemical property data processing' SubClassOf 'Obsolete concept (EDAM)' 'Physicochemical property data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2416 Protein secondary structure analysis 'Protein secondary structure analysis' SubClassOf 'has output' some 'Protein secondary structure report' 'Protein secondary structure analysis' SubClassOf 'has topic' some 'Protein structure analysis' http://edamontology.org/operation_2415 Protein folding analysis 'Protein folding analysis' SubClassOf 'has output' some 'Protein structure report' 'Protein folding analysis' SubClassOf 'has topic' some 'Protein folding, stability and design' http://edamontology.org/data_1331 Protein features (PEST sites) 'Protein features (PEST sites)' SubClassOf 'Obsolete concept (EDAM)' 'Protein features (PEST sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2663 Carbohydrate identifier 'Carbohydrate identifier' SubClassOf 'is identifier of' some 'Carbohydrate structure' 'Carbohydrate identifier' SubClassOf 'is identifier of' some 'Carbohydrate report' 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 'PSI MI XML (MIF)' or 'SIF' or 'GML' or 'XGMML' or 'BioPAX RDF/XML format'))) http://edamontology.org/data_1330 MHC Class II epitopes report 'MHC Class II epitopes report' SubClassOf 'Obsolete concept (EDAM)' 'MHC Class II epitopes report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2410 Gene expression analysis 'Gene expression analysis' SubClassOf 'Obsolete concept (EDAM)' 'Gene expression analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2341 NCI-Nature pathway entry format 'NCI-Nature pathway entry format' SubClassOf 'Obsolete concept (EDAM)' 'NCI-Nature pathway entry format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2409 Utility operation 'Utility operation' SubClassOf 'information processing' 'Utility operation' SubClassOf 'has topic' some 'File management' 'Utility operation' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/operation_2408 Sequence feature analysis 'Sequence feature analysis' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'HMM emission and transition counts' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2678 Ensembl ID ('Dasypus novemcinctus') 'Ensembl ID ('Dasypus novemcinctus')' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Ensembl ID ('Echinops telfairi')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2674 Ensembl ID ('Cavia porcellus') 'Ensembl ID ('Cavia porcellus')' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Ensembl ID ('Ciona intestinalis')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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://edamontology.org/data_1340 Sequence database hits evaluation data 'Sequence database hits evaluation data' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'MEME motifs directive file' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1345 MEME background frequencies file 'MEME background frequencies file' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Ensembl ID ('Canis familiaris')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2376 RDF format 'RDF format' SubClassOf 'XML' 'RDF format' SubClassOf http://edamontology.org/format_3748 http://edamontology.org/data_1359 Prosite protein pattern 'Prosite protein pattern' SubClassOf 'Obsolete concept (EDAM)' 'Prosite protein pattern' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1358 Prosite nucleotide pattern 'Prosite nucleotide pattern' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Ensembl ID ('Myotis lucifugus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1353 Sequence motif 'Sequence motif' SubClassOf 'has topic' some 'Sequence sites, features and motifs' http://edamontology.org/data_2685 Ensembl ID ('Loxodonta africana') 'Ensembl ID ('Loxodonta africana')' SubClassOf 'Obsolete concept (EDAM)' 'Ensembl ID ('Loxodonta africana')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1352 Regular expression 'Regular expression' SubClassOf 'data' 'Regular expression' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_2686 Ensembl ID ('Macaca mulatta') 'Ensembl ID ('Macaca mulatta')' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Ensembl ID ('Gallus gallus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2683 Ensembl ID ('Gasterosteus aculeatus') 'Ensembl ID ('Gasterosteus aculeatus')' SubClassOf 'Obsolete concept (EDAM)' 'Ensembl ID ('Gasterosteus aculeatus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1354 Sequence profile 'Sequence profile' SubClassOf 'has topic' some 'Sequence sites, features and motifs' http://edamontology.org/data_2684 Ensembl ID ('Homo sapiens') 'Ensembl ID ('Homo sapiens')' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Ensembl ID ('Erinaceus europaeus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2447 Sequence processing (protein) 'Sequence processing (protein)' SubClassOf 'Obsolete concept (EDAM)' 'Sequence processing (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2446 Sequence processing 'Sequence processing' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Mathematical model' http://edamontology.org/data_2696 Ensembl ID ('Spermophilus tridecemlineatus') 'Ensembl ID ('Spermophilus tridecemlineatus')' SubClassOf 'Obsolete concept (EDAM)' 'Ensembl ID ('Spermophilus tridecemlineatus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2697 Ensembl ID ('Takifugu rubripes') 'Ensembl ID ('Takifugu rubripes')' SubClassOf 'Obsolete concept (EDAM)' 'Ensembl ID ('Takifugu rubripes')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2698 Ensembl ID ('Tupaia belangeri') 'Ensembl ID ('Tupaia belangeri')' SubClassOf 'Obsolete concept (EDAM)' 'Ensembl ID ('Tupaia belangeri')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2699 Ensembl ID ('Xenopus tropicalis') 'Ensembl ID ('Xenopus tropicalis')' SubClassOf 'Obsolete concept (EDAM)' 'Ensembl ID ('Xenopus tropicalis')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1368 Domainatrix signature 'Domainatrix signature' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'has topic' some 'Phylogeny' 'Phylogenetic tree processing' SubClassOf 'Operation (typed)' '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 'Obsolete concept (EDAM)' '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 'has output' some 'DNA structure' http://edamontology.org/data_2694 Ensembl ID ('Pan troglodytes') 'Ensembl ID ('Pan troglodytes')' SubClassOf 'Obsolete concept (EDAM)' '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 'has output' some 'RNA structure' 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 'Textual format')) 'Smultron' SubClassOf 'has version' value '3.5.1' 'Smultron' SubClassOf 'is executed in' some 'text editing' http://edamontology.org/data_2695 Ensembl ID ('Rattus norvegicus') 'Ensembl ID ('Rattus norvegicus')' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Structure processing (RNA)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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://edamontology.org/data_2690 Ensembl ID ("Ornithorhynchus anatinus") 'Ensembl ID ("Ornithorhynchus anatinus")' SubClassOf 'Obsolete concept (EDAM)' 'Ensembl ID ("Ornithorhynchus anatinus")' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2691 Ensembl ID ('Oryctolagus cuniculus') 'Ensembl ID ('Oryctolagus cuniculus')' SubClassOf 'Obsolete concept (EDAM)' 'Ensembl ID ('Oryctolagus cuniculus')' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000044 BLAST+ 2.2.26 '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 'GenBank format')) '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 '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 'software with command line interface' http://edamontology.org/operation_2457 GPCR coupling selectivity prediction 'GPCR coupling selectivity prediction' SubClassOf 'has output' some 'Protein report' http://edamontology.org/operation_2456 GPCR classification 'GPCR classification' SubClassOf 'has output' some 'Protein family report' 'GPCR classification' SubClassOf 'Sequence classification' 'GPCR classification' SubClassOf 'GPCR analysis' 'GPCR classification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2459 Structure processing (protein) 'Structure processing (protein)' SubClassOf 'Obsolete concept (EDAM)' 'Structure processing (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1375 Protein repeat signature 'Protein repeat signature' SubClassOf 'Obsolete concept (EDAM)' 'Protein repeat signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1374 Protein region signature 'Protein region signature' SubClassOf 'Obsolete concept (EDAM)' 'Protein region signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1373 Protein domain signature 'Protein domain signature' SubClassOf 'Obsolete concept (EDAM)' 'Protein domain signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1372 Protein family signature 'Protein family signature' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Protein binding site signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2454 Gene prediction 'Gene prediction' SubClassOf 'has topic' some 'Gene structure' 'Gene prediction' SubClassOf 'has output' some 'Gene report' http://edamontology.org/data_1378 Protein active site signature 'Protein active site signature' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence cluster processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1376 Protein site signature 'Protein site signature' SubClassOf 'Obsolete concept (EDAM)' 'Protein site signature' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2451 Sequence comparison 'Sequence comparison' SubClassOf 'has input' some 'Sequence' 'Sequence comparison' SubClassOf 'has output' some 'Sequence report' 'Sequence comparison' SubClassOf 'has topic' some 'Sequence comparison' http://edamontology.org/data_1371 HMMER NULL hidden Markov model 'HMMER NULL hidden Markov model' SubClassOf 'Obsolete concept (EDAM)' 'HMMER NULL hidden Markov model' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2303 STRING entry format (HTML) 'STRING entry format (HTML)' SubClassOf 'Obsolete concept (EDAM)' '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 'Analysis' 'Optimisation and refinement' SubClassOf http://edamontology.org/operation_0004 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://edamontology.org/operation_2424 Comparison 'Comparison' SubClassOf 'Analysis' 'Comparison' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/operation_2423 Prediction and recognition 'Prediction and recognition' SubClassOf 'Analysis' 'Prediction and recognition' SubClassOf http://edamontology.org/operation_0004 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://edamontology.org/operation_2422 Data retrieval 'Data retrieval' SubClassOf 'has input' some 'Identifier' 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://edamontology.org/operation_2429 Mapping 'Mapping' SubClassOf 'Analysis' 'Mapping' SubClassOf http://edamontology.org/operation_0004 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://edamontology.org/operation_2428 Validation 'Validation' SubClassOf 'Analysis' 'Validation' SubClassOf http://edamontology.org/operation_0004 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_2427 Data handling 'Data handling' SubClassOf 'Obsolete concept (EDAM)' 'Data handling' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2426 Modelling and simulation 'Modelling and simulation' SubClassOf 'has topic' some 'Molecular modelling' 'Modelling and simulation' SubClassOf 'Analysis' 'Modelling and simulation' SubClassOf http://edamontology.org/operation_0004 http://edamontology.org/data_1386 Sequence alignment (nucleic acid pair) 'Sequence alignment (nucleic acid pair)' SubClassOf 'Sequence alignment (pair)' 'Sequence alignment (nucleic acid pair)' SubClassOf 'Sequence alignment (nucleic acid)' 'Sequence alignment (nucleic acid pair)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2421 Database search 'Database search' SubClassOf 'has output' some 'Database search results' http://www.ebi.ac.uk/swo/SWO_0000051 Clustal 'Clustal' SubClassOf 'is executed in' some 'multiple sequence alignment' http://edamontology.org/data_1389 Multiple nucleotide sequence alignment 'Multiple nucleotide sequence alignment' SubClassOf 'Obsolete concept (EDAM)' 'Multiple nucleotide sequence alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2420 Operation (typed) 'Operation (typed)' SubClassOf 'information processing' '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 'Obsolete concept (EDAM)' '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 'Sequence alignment (protein)' 'Sequence alignment (protein pair)' SubClassOf 'Sequence alignment (pair)' 'Sequence alignment (protein pair)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2331 HTML 'HTML' SubClassOf 'data format specification' 'HTML' SubClassOf 'is format of' some 'Report' 'HTML' SubClassOf http://edamontology.org/format_1915 http://edamontology.org/format_2330 Textual format 'Textual format' SubClassOf http://edamontology.org/format_1915 http://edamontology.org/format_2333 Binary format binary format 'binary format' SubClassOf http://edamontology.org/format_1915 http://edamontology.org/format_2332 XML 'XML' SubClassOf http://edamontology.org/format_1915 http://edamontology.org/data_1382 Sequence alignment (multiple) 'Sequence alignment (multiple)' SubClassOf 'Obsolete concept (EDAM)' 'Sequence alignment (multiple)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1380 Protein post-translational modification signature 'Protein post-translational modification signature' SubClassOf 'Obsolete concept (EDAM)' '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 'has topic' some 'Sequence design' http://edamontology.org/format_2334 URI format 'URI format' SubClassOf 'Obsolete concept (EDAM)' 'URI format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2436 Functional enrichment 'Functional enrichment' SubClassOf 'Gene expression data analysis' 'Functional enrichment' SubClassOf 'has topic' some 'Function analysis' 'Functional enrichment' SubClassOf 'Gene set testing' 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://edamontology.org/operation_2435 Gene expression profile processing 'Gene expression profile processing' SubClassOf 'Obsolete concept (EDAM)' 'Gene expression profile processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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://edamontology.org/operation_2434 Data retrieval (codon usage table) 'Data retrieval (codon usage table)' SubClassOf 'Obsolete concept (EDAM)' 'Data retrieval (codon usage table)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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://edamontology.org/operation_2439 RNA secondary structure analysis 'RNA secondary structure analysis' SubClassOf 'has topic' some 'Nucleic acid structure analysis' 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://edamontology.org/operation_2438 Pathway or network processing 'Pathway or network processing' SubClassOf 'Operation (typed)' 'Pathway or network processing' SubClassOf 'has topic' some 'Molecular interactions, pathways and networks' '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 'has output' some 'Pathway or network report' 'Gene regulatory network prediction' SubClassOf 'has topic' some 'Gene regulatory networks' http://edamontology.org/data_1396 Aligned sequence order 'Aligned sequence order' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Score end gaps control' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000060 MUSCLE 'MUSCLE' SubClassOf 'is executed in' some 'multiple sequence alignment' http://edamontology.org/data_1394 Alignment score or penalty 'Alignment score or penalty' SubClassOf 'Parameter' 'Alignment score or penalty' SubClassOf 'Score' http://edamontology.org/operation_2432 Microarray data processing 'Microarray data processing' SubClassOf 'Obsolete concept (EDAM)' 'Microarray data processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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" 'MUSCLE 3.8.31' SubClassOf 'software with command line interface' 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://edamontology.org/operation_2430 Design 'Design' SubClassOf 'Analysis' 'Design' SubClassOf http://edamontology.org/operation_0004 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://edamontology.org/format_2322 BioCyc enzyme report format 'BioCyc enzyme report format' SubClassOf 'Obsolete concept (EDAM)' 'BioCyc enzyme report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1390 Multiple protein sequence alignment 'Multiple protein sequence alignment' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'GeneCards gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_2323 ENZYME enzyme report format 'ENZYME enzyme report format' SubClassOf 'Obsolete concept (EDAM)' 'ENZYME enzyme report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2489 Protein subcellular localization prediction 'Protein subcellular localization prediction' SubClassOf 'has topic' some 'Protein targeting and localization' 'Protein subcellular localization prediction' SubClassOf 'Prediction and recognition (protein)' http://edamontology.org/data_3107 Sequence feature name 'Sequence feature name' SubClassOf 'Name' 'Sequence feature name' SubClassOf 'Sequence feature identifier' 'Sequence feature name' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3108 Experimental measurement 'Experimental measurement' SubClassOf 'data' 'Experimental measurement' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/operation_2483 Structure comparison 'Structure comparison' SubClassOf 'has topic' some 'Structure comparison' http://edamontology.org/operation_2482 Secondary structure processing 'Secondary structure processing' SubClassOf 'Obsolete concept (EDAM)' 'Secondary structure processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3105 Geotemporal metadata 'Geotemporal metadata' SubClassOf 'Obsolete concept (EDAM)' '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 'has input' some 'Nucleic acid structure' 'Nucleic acid structure analysis' SubClassOf 'has topic' some 'Nucleic acid structure analysis' http://edamontology.org/operation_2480 Structure analysis 'Structure analysis' SubClassOf 'Operation (typed)' 'Structure analysis' SubClassOf 'has topic' some 'Structure analysis' 'Structure analysis' SubClassOf 'Analysis' http://edamontology.org/operation_2487 Protein structure comparison 'Protein structure comparison' SubClassOf 'has input' some 'Protein structure' http://edamontology.org/operation_2486 Topology diagram drawing 'Topology diagram drawing' SubClassOf 'has output' some 'Protein structure image' 'Topology diagram drawing' SubClassOf 'Protein secondary structure rendering' 'Topology diagram drawing' SubClassOf 'Structure visualisation' http://edamontology.org/data_3101 Protein domain classification node 'Protein domain classification node' SubClassOf 'Obsolete concept (EDAM)' '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 'has output' some 'Helical wheel' 'Helical wheel drawing' SubClassOf 'Protein secondary structure rendering' 'Helical wheel drawing' SubClassOf 'Structure visualisation' http://www.ebi.ac.uk/swo/license/SWO_1000061 free to use license 'free to use license' SubClassOf 'has clause' some 'Usage unrestricted' http://edamontology.org/operation_2499 Splicing model analysis 'Splicing model analysis' SubClassOf 'has topic' some 'Gene structure' http://www.ebi.ac.uk/swo/SWO_0000001 software 'software' SubClassOf 'is executed in' some 'information processing' http://edamontology.org/data_3118 Protein features report (topological domains) 'Protein features report (topological domains)' SubClassOf 'Obsolete concept (EDAM)' 'Protein features report (topological domains)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000004 Microsoft Excel 2007 'Microsoft Excel 2007' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'tab delimited file format')) '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 output' some ('data' and ('has format specification' some 'XML spreadsheet')) 'Microsoft Excel 2007' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'tab delimited file format')) 'Microsoft Excel 2007' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'XLS spreadsheet')) 'Microsoft Excel 2007' SubClassOf 'has specified data output' some ('data' 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/" http://edamontology.org/data_3119 Sequence features (compositionally-biased regions) 'Sequence features (compositionally-biased regions)' SubClassOf 'Obsolete concept (EDAM)' 'Sequence features (compositionally-biased regions)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000003 information processing 'data format specification' DisjointWith 'information processing' 'information processing' DisjointWith http://www.w3.org/2002/07/owl#DeprecatedClass 'data' DisjointWith 'information processing' 'Topic' DisjointWith 'information processing' 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 '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 'output of' some ('software development process' and ('has participant' value 'Stanford University')) 'Protege 4' SubClassOf 'has specified data input' some ('Ontology' and ('has format specification' some 'OWL-XML')) 'Protege 4' SubClassOf 'software' 'Protege 4' SubClassOf 'is executed in' some 'ontology engineering' 'Protege 4' SubClassOf 'has license' some 'MPL v1.1' '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')) 'Protege 4' SubClassOf 'ontology engineering software' http://www.ebi.ac.uk/swo/SWO_0000005 MATLAB 'MATLAB' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'MathWorks')) 'MATLAB' SubClassOf 'output of' some ('software development 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 license' some 'Proprietary commercial software license' 'MATLAB' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'Matlab .m file')) 'MATLAB' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'Matlab .m file')) http://edamontology.org/operation_2493 Codon usage data processing 'Codon usage data processing' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Microarray protocol annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2492 Protein interaction prediction 'Protein interaction prediction' SubClassOf 'has output' some 'Protein interaction report' 'Protein interaction prediction' SubClassOf 'has topic' some 'Protein interactions' http://edamontology.org/operation_2491 Hydrogen bond calculation (inter-residue) 'Hydrogen bond calculation (inter-residue)' SubClassOf 'Hydrogen bond calculation' 'Hydrogen bond calculation (inter-residue)' SubClassOf 'Residue contact calculation (residue-residue)' 'Hydrogen bond calculation (inter-residue)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2498 Sequencing-based expression profile data analysis 'Sequencing-based expression profile data analysis' SubClassOf 'Obsolete concept (EDAM)' '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 'has topic' some 'Gene expression' http://edamontology.org/operation_2497 Pathway or network analysis 'Pathway or network analysis' SubClassOf 'has input' some 'Pathway or network' 'Pathway or network analysis' SubClassOf 'Pathway or network processing' 'Pathway or network analysis' SubClassOf 'Analysis' http://edamontology.org/operation_2496 Gene regulatory network processing 'Gene regulatory network processing' SubClassOf 'Obsolete concept (EDAM)' 'Gene regulatory network processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2495 Gene expression data analysis 'Gene expression data analysis' SubClassOf 'Operation (typed)' 'Gene expression data analysis' SubClassOf 'has topic' some 'Gene expression' 'Gene expression data analysis' SubClassOf '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 GPL v3' 'Mozilla Public License Version 2.0' SubClassOf 'GNU Copyleft Software License Type' http://www.ebi.ac.uk/swo/license/SWO_1000057 Artistic License v2.0 'Artistic License v2.0' SubClassOf 'has clause' some 'Distribution with notices' 'Artistic License v2.0' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'Artistic License v2.0' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'Artistic License v2.0' SubClassOf 'has clause' some 'Source code available' 'Artistic License v2.0' SubClassOf 'GNU Copyleft Software License Type' http://edamontology.org/operation_2490 Residue contact calculation (residue-residue) 'Residue contact calculation (residue-residue)' SubClassOf 'Residue contact calculation' 'Residue contact calculation (residue-residue)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000008 Racket 'Racket' SubClassOf 'has license' some 'GNU GPL' 'Racket' SubClassOf 'output of' some ('software development process' and ('has participant' value 'PLT Scheme Inc')) http://www.ebi.ac.uk/swo/SWO_0000007 OmniOutliner 'OmniOutliner' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'OmniOutline format')) 'OmniOutliner' SubClassOf 'has license' some 'Proprietary commercial software license' '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 'is executed in' some 'document outlining' 'OmniOutliner' SubClassOf 'output of' some ('software development process' and ('has participant' value 'Omni')) http://www.ebi.ac.uk/swo/SWO_0000009 Kakadu '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' 'Kakadu' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'JPEG 2000')) 'Kakadu' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'image format')) 'Kakadu' SubClassOf 'software with image input' http://www.ebi.ac.uk/swo/license/SWO_1000050 CC BY 2.0 'CC BY 2.0' SubClassOf 'has clause' some 'derivative software allowed' 'CC BY 2.0' SubClassOf 'has clause' some 'Distribution unrestricted' 'CC BY 2.0' SubClassOf 'has clause' some 'Source code available' 'CC BY 2.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY 2.0' SubClassOf 'GNU Copyleft Software License Type' http://www.ebi.ac.uk/swo/license/SWO_1000052 CC BY-SA 2.0 'CC BY-SA 2.0' SubClassOf 'has clause' some 'Source code available' 'CC BY-SA 2.0' SubClassOf 'has clause' some 'Copyleft' 'CC BY-SA 2.0' SubClassOf 'has clause' some 'Distribution unrestricted' 'CC BY-SA 2.0' SubClassOf 'has clause' some 'Attribution required' 'CC BY-SA 2.0' SubClassOf 'GNU Project Free Software License Type' http://edamontology.org/operation_2469 Data retrieval (protein interaction annotation) 'Data retrieval (protein interaction annotation)' SubClassOf 'Obsolete concept (EDAM)' 'Data retrieval (protein interaction annotation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000011 IntelliJ IDEA 'IntelliJ IDEA' SubClassOf 'has license' some ('Proprietary commercial software license' or 'Apache license v2') 'IntelliJ IDEA' SubClassOf 'has specified data output' some ('data' 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 interface' some 'graphical user interface' 'IntelliJ IDEA' SubClassOf 'output of' some ('software development process' and ('has participant' value 'JetBrains')) 'IntelliJ IDEA' SubClassOf 'has specified data input' some ('data' and ('has format specification' some '.java file')) http://edamontology.org/operation_2468 Data retrieval (phylogenetic tree) 'Data retrieval (phylogenetic tree)' SubClassOf 'Obsolete concept (EDAM)' 'Data retrieval (phylogenetic tree)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000010 WordStar 'WordStar' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'WordStar format')) '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 input' some ('data' and ('has format specification' some 'WordStar format')) 'WordStar' SubClassOf 'is executed in' some 'word processing' http://edamontology.org/operation_2467 Data retrieval (protein annotation) 'Data retrieval (protein annotation)' SubClassOf 'Obsolete concept (EDAM)' 'Data retrieval (protein annotation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000013 COPASI 'COPASI' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'SBML')) 'COPASI' SubClassOf 'has website homepage' value "http://www.copasi.org" 'COPASI' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'CopasiML')) 'COPASI' SubClassOf 'is executed in' some 'simulation and analysis of biochemical networks' http://edamontology.org/operation_2466 Map annotation 'Map annotation' SubClassOf 'Obsolete concept (EDAM)' 'Map annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000012 Java 'Java' SubClassOf 'has website homepage' value "http://www.java.com" http://edamontology.org/data_3129 Protein features report (repeats) 'Protein features report (repeats)' SubClassOf 'Obsolete concept (EDAM)' 'Protein features report (repeats)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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' http://www.ebi.ac.uk/swo/SWO_0000014 Microsoft Excel 2003 'Microsoft Excel 2003' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'XML spreadsheet')) 'Microsoft Excel 2003' SubClassOf 'has version' value 'Microsoft 2003 version' 'Microsoft Excel 2003' SubClassOf 'software before Microsoft 2007' http://www.ebi.ac.uk/swo/SWO_0000017 MATLAB 6 'MATLAB 6' SubClassOf 'has version' value 'Matlab R12' http://edamontology.org/topic_1770 Structure comparison 'Structure comparison' SubClassOf 'Structure analysis' 'Structure comparison' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000016 MATLAB 7 'MATLAB 7' SubClassOf 'has version' value 'Matlab R14' http://edamontology.org/data_3125 Nucleic acid features report (binding) 'Nucleic acid features report (binding)' SubClassOf 'Obsolete concept (EDAM)' '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 'Protein surface and interior 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 'Obsolete concept (EDAM)' '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 'Protein surface and interior 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 'Obsolete concept (EDAM)' 'Nucleic acid features report (replication and recombination)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2465 Structure processing 'Structure processing' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'has output' some 'Protein interaction report' 'Protein-protein interaction prediction' SubClassOf 'has topic' some 'Protein interactions' 'Protein-protein interaction prediction' SubClassOf 'Protein function prediction' http://edamontology.org/data_3123 Nucleic acid features report (expression signal) 'Nucleic acid features report (expression signal)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence alignment processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2462 Protein surface calculation 'Protein surface calculation' SubClassOf 'Protein surface and interior calculation' 'Protein surface calculation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000019 STARLIMS 'STARLIMS' SubClassOf 'is executed in' some 'laboratory information management' 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/SWO_0000022 Linux 'Linux' SubClassOf 'has interface' some 'command-line interface' 'Linux' SubClassOf 'is executed in' some 'manage computer operations' 'Linux' SubClassOf 'software' 'Linux' SubClassOf 'software with command line interface' 'Linux' SubClassOf 'operating system' http://edamontology.org/operation_2479 Protein sequence analysis 'Protein sequence analysis' SubClassOf 'has input' some 'Protein sequence' http://www.ebi.ac.uk/swo/SWO_0000021 operating system 'operating system' EquivalentTo 'is executed in' some 'manage computer operations' http://edamontology.org/operation_2478 Nucleic acid sequence analysis 'Nucleic acid sequence analysis' SubClassOf 'has input' some 'Nucleic acid sequence' 'Nucleic acid sequence analysis' SubClassOf 'has topic' some 'Nucleic acids' http://www.ebi.ac.uk/swo/SWO_0000024 Adobe Illustrator 10 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'Microsoft Word doc')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'JPEG')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'DWG')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'PNG')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'AI')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'DXF')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'JPEG')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'BMP')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'SVG')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'TIFF')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'DXF')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'DWG')) 'Adobe Illustrator 10' SubClassOf 'software' 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'CGM')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'AI')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'SVG')) 'Adobe Illustrator 10' SubClassOf 'output of' some ('software development process' and ('has participant' value 'Adobe Systems')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'pdf')) 'Adobe Illustrator 10' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'BMP')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'pdf')) 'Adobe Illustrator 10' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'GIF')) 'Adobe Illustrator 10' SubClassOf 'has interface' some 'graphical user interface' 'Adobe Illustrator 10' SubClassOf 'software with image input' http://www.ebi.ac.uk/swo/SWO_0000026 software with image input 'software with image input' EquivalentTo 'has specified data input' some ('data' and ('has format specification' some 'image format')) http://www.ebi.ac.uk/swo/SWO_0000025 Microsoft Word 'Microsoft Word' SubClassOf 'is executed in' some 'word processing' 'Microsoft Word' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'Microsoft Word doc')) 'Microsoft Word' SubClassOf 'has interface' some 'graphical user interface' 'Microsoft Word' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'Microsoft Word doc')) 'Microsoft Word' SubClassOf 'output of' some ('software development process' and ('has participant' value 'Microsoft')) 'Microsoft Word' SubClassOf 'software' 'Microsoft Word' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Microsoft')) 'Microsoft Word' SubClassOf 'Microsoft developed software' 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 input' some ('Ontology' and ('has format specification' some 'OBO')) '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 output' some ('Ontology' and ('has format specification' some 'OBO')) 'OBO-Edit' SubClassOf 'ontology engineering software' http://edamontology.org/operation_2472 Data retrieval (gene annotation) 'Data retrieval (gene annotation)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'has output' some 'Structure' 'Molecular dynamics simulation' SubClassOf 'has topic' some 'Structure prediction' 'Molecular dynamics simulation' SubClassOf 'has topic' some 'Molecular dynamics' http://edamontology.org/data_3133 Nucleic acid features (stem loop) 'Nucleic acid features (stem loop)' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid features (stem loop)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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' 'Unix' SubClassOf 'operating system' 'Unix' SubClassOf 'software with command line interface' http://edamontology.org/data_3135 Nucleic acid features report (signal or transit peptide) 'Nucleic acid features report (signal or transit peptide)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Sequence motif matches (nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/SWO_0000029 Microsoft developed software 'Microsoft developed software' EquivalentTo 'output of' some ('software development process' and ('has participant' value 'Microsoft')) http://edamontology.org/data_3147 Mass spectrometry experiment 'Mass spectrometry experiment' SubClassOf 'Obsolete concept (EDAM)' 'Mass spectrometry experiment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3143 SCOP superfamily 'SCOP superfamily' SubClassOf 'Obsolete concept (EDAM)' 'SCOP superfamily' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3144 SCOP family 'SCOP family' SubClassOf 'Obsolete concept (EDAM)' 'SCOP family' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3145 SCOP protein 'SCOP protein' SubClassOf 'Obsolete concept (EDAM)' 'SCOP protein' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3146 SCOP species 'SCOP species' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'SCOP class' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3142 SCOP fold 'SCOP fold' SubClassOf 'Obsolete concept (EDAM)' 'SCOP fold' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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://edamontology.org/topic_3510 Protein sites, features and motifs 'Protein sites, features and motifs' SubClassOf 'Proteins' http://edamontology.org/data_3165 NGS experiment 'NGS experiment' SubClassOf 'Obsolete concept (EDAM)' 'NGS experiment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/license/SWO_1000044 GNU Copyleft Software License Type 'GNU Copyleft Software License Type' EquivalentTo 'GNU Project Free Software License Type' and ('has clause' some 'Copyleft') http://www.ebi.ac.uk/swo/license/SWO_1000049 CC0 'CC0' SubClassOf 'has clause' some 'Source code available' 'CC0' SubClassOf 'has clause' some 'No restrictions on derivatives' 'CC0' SubClassOf 'has clause' some 'Usage unrestricted' 'CC0' SubClassOf 'has clause' some 'Number of users unrestricted' 'CC0' SubClassOf 'has clause' some 'Number of installations unrestricted' 'CC0' SubClassOf 'has clause' some 'Time for use unrestricted' 'CC0' SubClassOf 'has clause' some 'Distribution unrestricted' 'CC0' SubClassOf 'GNU Copyleft Software License Type' 'CC0' SubClassOf 'License without restrictions on derivatives' http://edamontology.org/topic_3514 Protein-ligand interactions 'Protein-ligand interactions' SubClassOf 'Protein interactions' 'Protein-ligand interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3511 Nucleic acid sites, features and motifs 'Nucleic acid sites, features and motifs' SubClassOf 'Nucleic acids' http://edamontology.org/topic_3517 GWAS study 'GWAS study' SubClassOf 'Laboratory techniques' 'GWAS study' SubClassOf http://edamontology.org/topic_3678 http://edamontology.org/topic_3515 Protein-drug interactions 'Protein-drug interactions' SubClassOf 'Protein-ligand interactions' 'Protein-drug interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/license/SWO_1000043 GNU Project Free Software License Type 'GNU Project Free Software License Type' EquivalentTo 'software license' and ('has clause' some 'Source code available') and ('has clause' some ('Distribution unrestricted' or 'Distribution with notices')) 'GNU Project Free Software License Type' SubClassOf 'software license' 'GNU Project Free Software License Type' SubClassOf 'Open source software license' http://www.ebi.ac.uk/efo/swo/SWO_0000103 multiscan 'multiscan' SubClassOf 'has specified data output' some 'Graph plot' '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' 'multiscan' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000104 affy 'affy' SubClassOf 'implements' some ('RMA' and ''MAS5'') 'affy' SubClassOf 'is published by' value 'Bioconductor' 'affy' SubClassOf 'software' 'affy' SubClassOf 'has specified data input' some ('has format specification' some ('CDF binary format' or 'CEL binary format' or 'CDF ASCII format' or 'CEL ASCII format')) 'affy' SubClassOf 'has specified data output' some ('Image' and 'Text data set' and 'Graph plot') 'affy' SubClassOf 'is executed in' some ('background correction' and 'data normalization' and 'differential expression analysis') 'affy' SubClassOf 'is encoded in' some 'R language' 'affy' SubClassOf 'R software' 'affy' SubClassOf 'BioConductor Software' http://www.ebi.ac.uk/efo/swo/SWO_0000101 ChipSkipper 'ChipSkipper' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'EMBL')) http://edamontology.org/data_0903 Protein folding report 'Protein folding report' SubClassOf 'Obsolete concept (EDAM)' 'Protein folding report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3521 2D PAGE experiment '2D PAGE experiment' SubClassOf 'Proteomics 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 'Obsolete concept (EDAM)' 'Protein architecture report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000100 ChipReader 3.1 'ChipReader 3.1' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Bio-Rad Laboratories, Inc.')) http://edamontology.org/data_0901 Protein features report (domains) 'Protein features report (domains)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Protein interactions' 'Protein-nucleic acid interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3523 RNAi experiment 'RNAi experiment' SubClassOf 'Sequencing' 'RNAi experiment' SubClassOf 'Laboratory techniques' http://www.ebi.ac.uk/efo/swo/SWO_0000109 Annotation-Driven Clustering 'Annotation-Driven Clustering' SubClassOf 'implements' some 'k-means' 'Annotation-Driven Clustering' SubClassOf 'is encoded in' some 'R language' 'Annotation-Driven Clustering' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some 'Textual format')) 'Annotation-Driven Clustering' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) 'Annotation-Driven Clustering' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) 'Annotation-Driven Clustering' SubClassOf 'software' 'Annotation-Driven Clustering' SubClassOf 'implements' some ''FDR'' 'Annotation-Driven Clustering' SubClassOf 'R software' http://edamontology.org/topic_3522 Northern blot experiment 'Northern blot experiment' SubClassOf 'Proteomics 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 'Molecular interactions, pathways and networks' 'Environmental information processing pathways' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000107 Feature Extraction Software 'Feature Extraction Software' SubClassOf 'is executed in' some 'feature extraction' http://edamontology.org/topic_3528 Disease pathways 'Disease pathways' SubClassOf 'Molecular interactions, pathways and networks' 'Disease pathways' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3527 Cellular process pathways 'Cellular process pathways' SubClassOf 'Molecular interactions, pathways and networks' 'Cellular process pathways' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000105 affycomp 'affycomp' SubClassOf 'implements' some ('RMA' and ''MAS5'') 'affycomp' SubClassOf 'software' 'affycomp' SubClassOf 'is encoded in' some 'R language' 'affycomp' SubClassOf 'has specified data output' some ('Text data set' and 'Graph plot') 'affycomp' SubClassOf 'is executed in' some ('dataset comparison' and 'correction') 'affycomp' SubClassOf 'has specified data input' some 'CSV data set' 'affycomp' SubClassOf 'R software' http://edamontology.org/topic_3526 Protein-protein interactions 'Protein-protein interactions' SubClassOf 'Protein interactions' 'Protein-protein interactions' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/topic_3413 Infectious tropical disease 'Infectious tropical disease' SubClassOf 'Infectious disease' 'Infectious tropical disease' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000004 50-50 MANOVA '50-50 MANOVA' SubClassOf 'is encoded in' some 'MATLAB language' '50-50 MANOVA' SubClassOf 'is encoded in' some 'R language' '50-50 MANOVA' SubClassOf 'implements' some '50-50 MANOVA algorithm' '50-50 MANOVA' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Matforsk')) '50-50 MANOVA' SubClassOf 'software' '50-50 MANOVA' SubClassOf 'R software' '50-50 MANOVA' SubClassOf 'matlab software' http://www.ebi.ac.uk/efo/swo/SWO_0000005 ABarray 'ABarray' SubClassOf 'implements' some 'Local-pooled-error' 'ABarray' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) '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 'software' 'ABarray' SubClassOf 'implements' some ''FDR'' '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 ''t-test'' 'ABarray' SubClassOf 'has specified data input' some ('CSV data set' and ('has format specification' some 'data format specification')) 'ABarray' SubClassOf 'implements' some ''ANOVA'' 'ABarray' SubClassOf 'R software' http://edamontology.org/format_1810 ColiCard report format 'ColiCard report format' SubClassOf 'Obsolete concept (EDAM)' 'ColiCard report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000008 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 'output of' some ('software development process' and ('has participant' value 'Affymetrix')) 'Affymetrix Expression Console' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'CHP binary format')) http://www.ebi.ac.uk/efo/swo/SWO_0000009 AIDA 'AIDA' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Raytest')) http://www.ebi.ac.uk/efo/swo/SWO_0000007 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' 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 'is encoded in' some 'R language' 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'software' 'Algorithms for Calculating Microarray Enrichment' SubClassOf 'R software' http://edamontology.org/data_3085 Protein sequence composition 'Protein sequence composition' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Nucleic acid sequence composition (report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 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 'Distribution unrestricted' 'GNU GPL' SubClassOf 'software license' 'GNU GPL' SubClassOf 'has clause' some 'Number of users unrestricted' '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' 'GNU GPL' SubClassOf 'GNU Project Free Software License Type' http://www.ebi.ac.uk/swo/license/SWO_1000005 Apache license v2 'Apache license v2' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'Apache license v2' SubClassOf 'software license' 'Apache license v2' SubClassOf 'has clause' some 'Distribution with notices' 'Apache license v2' SubClassOf 'has clause' some 'No restrictions on derivatives' 'Apache license v2' SubClassOf 'has clause' some 'Source code available' 'Apache license v2' SubClassOf 'GNU Copyleft Software License Type' 'Apache license v2' SubClassOf 'License without restrictions on derivatives' http://www.ebi.ac.uk/swo/license/SWO_1000006 Academic Free License version 3 'Academic Free License version 3' SubClassOf 'has clause' some 'derivative software allowed' 'Academic Free License version 3' SubClassOf 'has clause' some 'Source code available' 'Academic Free License version 3' SubClassOf 'has clause' some 'Distribution unrestricted' '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' 'Academic Free License version 3' SubClassOf 'GNU Project Free Software License Type' http://www.ebi.ac.uk/swo/license/SWO_1000007 FreeBSD 'FreeBSD' SubClassOf 'is compatible license of' some 'GNU GPL v3' 'FreeBSD' SubClassOf 'is compatible license of' some 'GNU GPL v2' 'FreeBSD' SubClassOf 'has clause' some 'Source code available' 'FreeBSD' SubClassOf 'has clause' some 'derivative software allowed' 'FreeBSD' SubClassOf 'has clause' some 'Distribution with notices' 'FreeBSD' SubClassOf 'software license' 'FreeBSD' SubClassOf 'GNU Copyleft Software License Type' http://www.ebi.ac.uk/efo/swo/SWO_0000026 Affymetrix Software 'Affymetrix Software' EquivalentTo 'software' and ('is published by' value 'Affymetrix') http://www.ebi.ac.uk/efo/swo/SWO_0000027 Agi4x44PreProcess 'Agi4x44PreProcess' SubClassOf 'software' 'Agi4x44PreProcess' SubClassOf 'implements' some 'Loess algorithm' 'Agi4x44PreProcess' SubClassOf 'has specified data input' some ('Heatmap' and ('has format specification' some 'image format')) 'Agi4x44PreProcess' SubClassOf 'is executed in' some 'differential expression analysis' 'Agi4x44PreProcess' SubClassOf 'is executed in' some 'data normalization' '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 'has specified data input' some ('Text data set' and ('has format specification' some 'Textual format')) 'Agi4x44PreProcess' SubClassOf 'is executed in' some 'correction' '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 'software with image input' 'Agi4x44PreProcess' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000025 Affymetrix GeneChip Operating Software 'Affymetrix GeneChip Operating Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Affymetrix')) http://www.ebi.ac.uk/efo/swo/SWO_0000022 'AffyExpress' ''AffyExpress'' SubClassOf 'is executed in' some 'correction' ''AffyExpress'' SubClassOf 'implements' some ''ANOVA'' ''AffyExpress'' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some 'Textual format')) ''AffyExpress'' SubClassOf 'is executed in' some 'differential expression analysis' ''AffyExpress'' SubClassOf 'is executed in' some 'data normalization' ''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 'has specified data output' some ('Graph plot' and ('has format specification' some 'data format specification')) ''AffyExpress'' SubClassOf 'has specified data input' some ('Image' and ('has format specification' some 'CEL binary format')) ''AffyExpress'' SubClassOf 'software' ''AffyExpress'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000021 '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 'is encoded in' some 'R language' ''AffyCompatible'' SubClassOf 'is executed in' some 'parse' ''AffyCompatible'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000037 Applied Biosystems 1700 Expression Array System Software 'Applied Biosystems 1700 Expression Array System Software' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Applied Biosystems')) http://edamontology.org/data_0832 HGNC vocabulary 'HGNC vocabulary' SubClassOf 'Obsolete concept (EDAM)' 'HGNC vocabulary' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0831 MeSH vocabulary 'MeSH vocabulary' SubClassOf 'Obsolete concept (EDAM)' 'MeSH vocabulary' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000035 'AnnotationDbi' ''AnnotationDbi'' SubClassOf 'software' ''AnnotationDbi'' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some 'Textual format')) ''AnnotationDbi'' SubClassOf 'is encoded in' some 'R language' ''AnnotationDbi'' SubClassOf 'has specified data output' some ('Bitmap object' and ('has format specification' some 'data format specification')) ''AnnotationDbi'' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'sqlite')) ''AnnotationDbi'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000034 Agilent Technologies Software 'Agilent Technologies Software' EquivalentTo 'output of' some ('software publishing process' and ('has participant' value 'Agilent Technologies')) http://edamontology.org/data_0835 UMLS vocabulary 'UMLS vocabulary' SubClassOf 'Obsolete concept (EDAM)' 'UMLS vocabulary' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/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/efo/swo/SWO_0000039 ArrayGauge 'ArrayGauge' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Fujifilm')) http://www.ebi.ac.uk/efo/swo/SWO_0000048 BAC 'BAC' SubClassOf 'implements' some 'Bayesian Model' 'BAC' SubClassOf 'has specified data output' some ('has format specification' some 'BED format') 'BAC' SubClassOf 'software' 'BAC' SubClassOf 'is encoded in' some 'R language' 'BAC' SubClassOf 'is published by' value 'Bioconductor' 'BAC' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) 'BAC' SubClassOf 'BioConductor Software' 'BAC' SubClassOf 'R software' http://edamontology.org/data_0843 Database entry 'Database entry' SubClassOf 'Obsolete concept (EDAM)' 'Database entry' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0842 Identifier 'Identifier' DisjointWith 'Report' 'Identifier' SubClassOf 'data' 'Identifier' DisjointWith 'Parameter' 'Identifier' SubClassOf 'is identifier of' some 'data' 'Identifier' SubClassOf http://edamontology.org/data_0006 http://www.ebi.ac.uk/efo/swo/SWO_0000046 AtlasImage 'AtlasImage' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Clontech Laboratories, Inc')) http://www.ebi.ac.uk/efo/swo/SWO_0000042 ArrayVision 'ArrayVision' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'GE Healthcare Life Sciences')) http://www.ebi.ac.uk/efo/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')) http://www.ebi.ac.uk/efo/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 'implements' some 'RMA' ''ArrayTools'' SubClassOf 'is encoded in' some 'R language' ''ArrayTools'' SubClassOf 'software' ''ArrayTools'' SubClassOf 'is executed in' some 'differential expression analysis' ''ArrayTools'' SubClassOf 'R software' http://edamontology.org/operation_1914 Structure retrieval (water) 'Structure retrieval (water)' SubClassOf 'Obsolete concept (EDAM)' 'Structure retrieval (water)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_1913 Residue validation 'Residue validation' SubClassOf 'Protein model validation' 'Residue validation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0855 Sequence metadata 'Sequence metadata' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'GeneIlluminator gene report format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000059 'BSgenome' ''BSgenome'' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'FASTA format')) ''BSgenome'' SubClassOf 'software' ''BSgenome'' SubClassOf 'is encoded in' some 'R language' ''BSgenome'' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'dcf')) ''BSgenome'' SubClassOf 'R software' http://edamontology.org/data_0854 Sequence length specification 'Sequence length specification' SubClassOf 'Obsolete concept (EDAM)' 'Sequence length specification' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000057 BPMAP 'BPMAP' SubClassOf 'is published by' value 'Affymetrix' http://edamontology.org/data_0852 Sequence mask type 'Sequence mask type' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'BacMap gene card format' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000058 BRB-ArrayTools 'BRB-ArrayTools' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Biometric Research Branch')) http://edamontology.org/data_0859 Sequence signature model 'Sequence signature model' SubClassOf 'Obsolete concept (EDAM)' 'Sequence signature model' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000053 '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 'is executed in' some 'differential expression analysis' ''BGmix'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000054 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 'has specified data input' some ('biological sequence data' and ('has format specification' some 'FASTA format')) 'BLAST' SubClassOf 'output of' some ('software development process' and ('has participant' value 'NIH')) 'BLAST' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'NIH')) 'BLAST' SubClassOf 'is executed in' some 'multiple sequence alignment' http://www.ebi.ac.uk/efo/swo/SWO_0000050 'BCRANK' ''BCRANK'' SubClassOf 'has specified data input' some ('data' 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'' ''BCRANK'' SubClassOf 'R software' http://edamontology.org/data_0851 Sequence mask character 'Sequence mask character' SubClassOf 'Obsolete concept (EDAM)' 'Sequence mask character' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0850 Sequence set 'Sequence set' SubClassOf 'data' 'Sequence set' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_0866 Sequence alignment metadata 'Sequence alignment metadata' SubClassOf 'Obsolete concept (EDAM)' 'Sequence alignment metadata' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0864 Sequence alignment parameter 'Sequence alignment parameter' SubClassOf 'Obsolete concept (EDAM)' 'Sequence alignment parameter' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000068 'BioMVCClass' ''BioMVCClass'' SubClassOf 'is encoded in' some 'R language' ''BioMVCClass'' SubClassOf 'software' ''BioMVCClass'' SubClassOf 'R software' http://edamontology.org/data_0863 Sequence alignment 'Sequence alignment' SubClassOf 'has topic' some 'Sequence comparison' http://www.ebi.ac.uk/efo/swo/SWO_0000066 'BicARE' ''BicARE'' SubClassOf 'is encoded in' some 'R language' ''BicARE'' SubClassOf 'software' ''BicARE'' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) ''BicARE'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000065 Beadstudio 'Beadstudio' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Illumina')) http://www.ebi.ac.uk/efo/swo/SWO_0000063 BasReader 3.01 'BasReader 3.01' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Raytest')) http://www.ebi.ac.uk/efo/swo/SWO_0000060 BZScan 'BZScan' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Technological Advances for Genomics and Clinics, France')) http://edamontology.org/data_0861 Sequence alignment (words) 'Sequence alignment (words)' SubClassOf 'Obsolete concept (EDAM)' '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' 'Sequence signature data' SubClassOf 'has topic' some 'Sequence sites, features and motifs' 'Sequence signature data' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_0877 Protein features report (super-secondary) 'Protein features report (super-secondary)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Protein features report (secondary structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0875 Protein topology 'Protein topology' SubClassOf 'Obsolete concept (EDAM)' 'Protein topology' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000079 'CALIB' ''CALIB'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'image format')) ''CALIB'' SubClassOf 'has specified data input' some ('Text data set' and ('has format specification' some 'Textual format')) ''CALIB'' SubClassOf 'is executed in' some 'differential expression analysis' ''CALIB'' SubClassOf 'is encoded in' some 'R language' ''CALIB'' SubClassOf 'software' ''CALIB'' SubClassOf 'is executed in' some 'data normalization' ''CALIB'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000077 'BufferedMatrix' ''BufferedMatrix'' SubClassOf 'has specified data output' some ('Text data set' and ('has format specification' some 'Textual format')) ''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 input' some ('Text data set' and ('has format specification' some 'Textual format')) ''BufferedMatrix'' SubClassOf 'software' ''BufferedMatrix'' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'pdf')) ''BufferedMatrix'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000078 'BufferedMatrixMethods' ''BufferedMatrixMethods'' SubClassOf 'has specified data input' some ('Gene expression data' and ('has format specification' some 'CEL binary format')) ''BufferedMatrixMethods'' SubClassOf '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')) ''BufferedMatrixMethods'' SubClassOf 'R software' http://edamontology.org/data_0879 Secondary structure alignment metadata (protein) 'Secondary structure alignment metadata (protein)' SubClassOf 'Obsolete concept (EDAM)' 'Secondary structure alignment metadata (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000075 'Biostrings' ''Biostrings'' SubClassOf 'implements' some ''Needleman-Wunsch'' ''Biostrings'' SubClassOf 'is encoded in' some 'R language' ''Biostrings'' SubClassOf 'software' ''Biostrings'' SubClassOf 'implements' some ''Smith-Waterman'' ''Biostrings'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000076 BlueFuse 'BlueFuse' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Cambridge Bluegnome')) http://www.ebi.ac.uk/efo/swo/SWO_0000071 'BiocCaseStudies' ''BiocCaseStudies'' SubClassOf 'software' ''BiocCaseStudies'' SubClassOf 'is encoded in' some 'R language' ''BiocCaseStudies'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000072 BioConductor Software 'BioConductor Software' SubClassOf 'is executed in' some 'biological data processing' 'BioConductor Software' EquivalentTo 'software' and ('is published by' value 'Bioconductor') http://edamontology.org/data_0872 Phylogenetic tree 'Phylogenetic tree' SubClassOf 'has topic' some 'Phylogeny' 'Phylogenetic tree' SubClassOf 'data' 'Phylogenetic tree' SubClassOf 'Phylogenetic data' http://www.ebi.ac.uk/efo/swo/SWO_0000070 'Biobase' ''Biobase'' SubClassOf 'is encoded in' some 'R language' ''Biobase'' SubClassOf 'software' ''Biobase'' SubClassOf 'R software' http://edamontology.org/data_0886 Structure alignment 'Structure alignment' SubClassOf 'has topic' some 'Structure comparison' http://edamontology.org/data_0885 Structure database search results 'Structure database search results' SubClassOf 'Obsolete concept (EDAM)' 'Structure database search results' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000088 CHP binary format 'CHP binary format' SubClassOf 'is published by' value 'Affymetrix' http://www.ebi.ac.uk/efo/swo/SWO_0000086 'CGHcall' ''CGHcall'' SubClassOf 'software' ''CGHcall'' SubClassOf 'implements' some 'CBS algorithm' ''CGHcall'' SubClassOf 'has specified data output' some ('Graph plot' and ('has format specification' some 'R data frame')) ''CGHcall'' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) ''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' ''CGHcall'' SubClassOf 'R software' http://edamontology.org/data_0889 Structural profile 'Structural profile' SubClassOf 'has topic' some 'Structure comparison' 'Structural profile' SubClassOf 'data' 'Structural profile' SubClassOf http://edamontology.org/data_0006 http://www.ebi.ac.uk/efo/swo/SWO_0000087 'CGHregions' ''CGHregions'' SubClassOf 'implements' some 'CBS algorithm' ''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' ''CGHregions'' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'R data frame')) ''CGHregions'' SubClassOf 'R software' http://edamontology.org/data_0880 RNA secondary structure 'RNA secondary structure' SubClassOf 'has topic' some 'Nucleic acid structure analysis' http://www.ebi.ac.uk/efo/swo/SWO_0000084 CEL binary format 'CEL binary format' SubClassOf 'is published by' value 'Affymetrix' http://www.ebi.ac.uk/efo/swo/SWO_0000085 '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' 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/efo/swo/SWO_0000083 CDF binary format 'CDF binary format' SubClassOf 'is published by' value 'Affymetrix' http://edamontology.org/data_0884 Tertiary structure record 'Tertiary structure record' SubClassOf 'Obsolete concept (EDAM)' 'Tertiary structure record' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000080 'CAMERA' ''CAMERA'' SubClassOf 'has specified data output' some ('CSV data set' and ('has format specification' some 'Textual format')) ''CAMERA'' SubClassOf 'is encoded in' some 'R language' ''CAMERA'' SubClassOf 'has specified data input' some ('LC-MS data' and ('has format specification' some 'data format specification')) ''CAMERA'' SubClassOf 'is executed in' some 'data annotation' ''CAMERA'' SubClassOf 'software' ''CAMERA'' SubClassOf 'R software' http://edamontology.org/data_0883 Structure 'Structure' SubClassOf 'data' 'Structure' SubClassOf 'has topic' some 'Structure analysis' 'Structure' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_0882 Secondary structure alignment metadata (RNA) 'Secondary structure alignment metadata (RNA)' SubClassOf 'Obsolete concept (EDAM)' 'Secondary structure alignment metadata (RNA)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0899 Protein structural motifs and surfaces 'Protein structural motifs and surfaces' SubClassOf 'Obsolete concept (EDAM)' 'Protein structural motifs and surfaces' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000099 'ChemmineR' ''ChemmineR'' SubClassOf 'has specified data input' some ('data' and ('has format specification' some 'SDF format')) ''ChemmineR'' SubClassOf 'is encoded in' some 'R language' ''ChemmineR'' SubClassOf 'is executed in' some 'distance calculation' ''ChemmineR'' SubClassOf 'has specified data output' some ('Image' and ('has format specification' some 'image format')) ''ChemmineR'' SubClassOf 'software' ''ChemmineR'' SubClassOf 'implements' some 'Binning clustering method' ''ChemmineR'' SubClassOf 'has specified data output' some ('HTML report' and ('has format specification' some 'HTML')) ''ChemmineR'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000098 Category 'Category' SubClassOf 'has specified data output' some ('Heatmap' and ('has format specification' some 'image format')) 'Category' SubClassOf 'has specified data output' some 'Graph plot' 'Category' SubClassOf 'is encoded in' some 'R language' 'Category' SubClassOf 'software' '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' 'Category' SubClassOf 'R software' 'Category' SubClassOf 'BioConductor Software' http://edamontology.org/data_0891 Sequence-3D profile alignment 'Sequence-3D profile alignment' SubClassOf 'Obsolete concept (EDAM)' 'Sequence-3D profile alignment' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000096 CARMAweb 'CARMAweb' SubClassOf 'output of' some ('software publishing process' and ('has participant' value 'Institute for Genomics and Bioinformatics Graz University of Technology')) http://edamontology.org/data_0895 Peptide annotation 'Peptide annotation' SubClassOf 'Obsolete concept (EDAM)' 'Peptide annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0894 Amino acid annotation 'Amino acid annotation' SubClassOf 'Obsolete concept (EDAM)' 'Amino acid annotation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/efo/swo/SWO_0000092 'CORREP' ''CORREP'' SubClassOf 'is executed in' some 'descriptive statistical calculation' ''CORREP'' SubClassOf 'has specified data output' some ('data' and ('has format specification' some 'R data frame')) ''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 'software' ''CORREP'' SubClassOf 'R software' http://www.ebi.ac.uk/efo/swo/SWO_0000090 'CMA' ''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' ''CMA'' SubClassOf 'R software' http://edamontology.org/data_2601 Small molecule data 'Small molecule data' SubClassOf 'Obsolete concept (EDAM)' 'Small molecule data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2602 Genotype and phenotype data 'Genotype and phenotype data' SubClassOf 'Obsolete concept (EDAM)' 'Genotype and phenotype data' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2603 Microarray data Gene expression data 'Gene expression data' SubClassOf 'has topic' some 'Gene expression' 'Gene expression data' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_2600 Pathway or network 'Pathway or network' SubClassOf 'data' 'Pathway or network' SubClassOf 'has topic' some 'Molecular interactions, pathways and networks' 'Pathway or network' SubClassOf http://edamontology.org/data_0006 http://edamontology.org/data_2611 ICD identifier 'ICD identifier' SubClassOf 'is identifier of' some 'Disease report' http://edamontology.org/data_2627 Molecular interaction ID 'Molecular interaction ID' SubClassOf 'Obsolete concept (EDAM)' 'Molecular interaction ID' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2621 TAIR accession (protein) 'TAIR accession (protein)' SubClassOf 'is identifier of' some 'Sequence record' http://edamontology.org/data_1306 Nucleosome exclusion sequences 'Nucleosome exclusion sequences' SubClassOf 'Obsolete concept (EDAM)' 'Nucleosome exclusion sequences' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1305 Nucleic acid features report (restriction sites) 'Nucleic acid features report (restriction sites)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Nucleic acid features (quadruplexes)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1309 Gene features (exonic splicing enhancer) 'Gene features (exonic splicing enhancer)' SubClassOf 'Obsolete concept (EDAM)' 'Gene features (exonic splicing enhancer)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1308 Nucleic acid features report (matrix/scaffold attachment sites) 'Nucleic acid features report (matrix/scaffold attachment sites)' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid features report (matrix/scaffold attachment sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1307 Nucleic acid features report (splice sites) 'Nucleic acid features report (splice sites)' SubClassOf 'Obsolete concept (EDAM)' 'Nucleic acid features report (splice sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1302 Nucleic acid features report (PolyA signal or site) 'Nucleic acid features report (PolyA signal or site)' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Gene and transcript structure (report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1315 Transcription factor binding sites 'Transcription factor binding sites' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Gene features (SECIS element)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1313 Coding region 'Coding region' SubClassOf 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' '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 'Obsolete concept (EDAM)' 'Nucleic acid features (microRNA)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://www.ebi.ac.uk/swo/data/SWO_3000085 .sql '.sql' SubClassOf 'Textual format' http://www.ebi.ac.uk/swo/data/SWO_3000084 .mysql '.mysql' SubClassOf 'Textual format' http://www.ebi.ac.uk/swo/data/SWO_3000083 .mgf '.mgf' SubClassOf 'Textual format' http://www.ebi.ac.uk/swo/data/SWO_3000082 .csv '.csv' SubClassOf 'Textual format' http://www.ebi.ac.uk/swo/data/SWO_3000081 .bw '.bw' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/data/SWO_3000080 RIFF 'RIFF' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/data/SWO_3000079 audio format 'audio format' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/data/SWO_3000078 .zip '.zip' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/data/SWO_3000077 .gz '.gz' SubClassOf 'data format specification' http://www.ebi.ac.uk/swo/SWO_0000154 COBRA 'COBRA' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000153 VCell 'VCell' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000156 COBRA Toolbox 'COBRA Toolbox' SubClassOf 'COBRA' http://www.ebi.ac.uk/swo/SWO_0000155 COBRApy 'COBRApy' SubClassOf 'COBRA' http://edamontology.org/data_3668 Disease name 'Disease name' SubClassOf 'Name' 'Disease name' SubClassOf 'Disease identifier' http://www.ebi.ac.uk/swo/SWO_0000158 libSBML 'libSBML' SubClassOf 'R software' http://edamontology.org/data_3669 Training material 'Training material' SubClassOf 'Data' http://www.ebi.ac.uk/swo/SWO_0000159 GNU Octave 'GNU Octave' SubClassOf 'programming language' http://edamontology.org/data_3667 Disease identifier 'Disease identifier' SubClassOf 'Identifier (typed)' 'Disease identifier' SubClassOf 'Accession' http://www.ebi.ac.uk/swo/SWO_0000152 iBioSim 'iBioSim' SubClassOf 'software' http://www.ebi.ac.uk/swo/SWO_0000151 OS X 'OS X' SubClassOf 'Mac OS' http://edamontology.org/data_3671 Text 'Text' SubClassOf 'Text data' http://www.ebi.ac.uk/swo/SWO_0000161 S language 'S language' SubClassOf 'programming language' http://www.ebi.ac.uk/swo/SWO_0000160 GWT 'GWT' SubClassOf 'programming language' http://www.ebi.ac.uk/swo/SWO_0000162 Excel 'Excel' SubClassOf 'programming language' http://edamontology.org/data_3670 Online course 'Online course' SubClassOf 'Training material' http://edamontology.org/operation_3465 Correlation 'Correlation' SubClassOf 'Operation' http://www.ebi.ac.uk/swo/SWO_0000149 Mac OS 'Mac OS' SubClassOf 'operating system' http://www.ebi.ac.uk/swo/algorithm/SWO_4000006 ODE Algorithm 'ODE Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/algorithm/SWO_4000009 DAE Algorithm 'DAE Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/algorithm/SWO_4000008 Monte Carlo 'Monte Carlo' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/algorithm/SWO_4000007 Gillespie's Stochastic Simulation Algorithm 'Gillespie's Stochastic Simulation Algorithm' SubClassOf 'algorithm' http://www.ebi.ac.uk/swo/algorithm/SWO_4000010 PDE Algorithm 'PDE Algorithm' SubClassOf 'algorithm' http://edamontology.org/data_3743 Ordination plot 'Ordination plot' SubClassOf 'Protein property' 'Ordination plot' SubClassOf 'Plot' 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/data_3759 ProteomeXchange ID 'ProteomeXchange ID' SubClassOf 'Experiment annotation ID' http://edamontology.org/data_3753 Over-representation report 'Over-representation report' SubClassOf 'Report' http://edamontology.org/data_3754 GO-term enrichment report 'GO-term enrichment report' SubClassOf 'Over-representation report' http://edamontology.org/data_3768 Clustered gene expression profiles 'Clustered gene expression profiles' SubClassOf 'Gene expression data' http://edamontology.org/data_3769 BRENDA ontology concept ID 'BRENDA ontology concept ID' SubClassOf 'Ontology concept ID' http://edamontology.org/data_3779 Annotated text 'Annotated text' SubClassOf 'Text' http://edamontology.org/data_3786 Query script 'Query script' SubClassOf 'Data' http://edamontology.org/operation_3557 Imputation 'Imputation' SubClassOf 'Statistical calculation' http://edamontology.org/operation_3559 Ontology visualisation 'Ontology visualisation' SubClassOf 'Visualisation' 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/operation_3566 Simulated gene expression data generation 'Simulated gene expression data generation' SubClassOf 'Modelling and simulation' 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_3565 RNA-seq time series data analysis 'RNA-seq time series data analysis' SubClassOf 'RNA-Seq analysis' 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_3707 Biodiversity report 'Biodiversity report' SubClassOf 'Ecological data' 'Biodiversity report' SubClassOf 'Report' http://edamontology.org/data_3716 Biosafety report 'Biosafety report' SubClassOf 'Report' http://edamontology.org/data_3717 Isolation report 'Isolation report' SubClassOf 'Report' http://edamontology.org/data_3718 Pathogenicity report 'Pathogenicity report' SubClassOf 'Biosafety report' http://edamontology.org/data_3719 Biosafety classification 'Biosafety classification' SubClassOf 'Biosafety report' http://edamontology.org/data_3723 Morphology parameter 'Morphology parameter' SubClassOf 'Experimental measurement' http://edamontology.org/data_3724 Cultivation parameter 'Cultivation parameter' SubClassOf 'Experimental measurement' 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/data_3739 Gamma diversity data 'Gamma diversity data' SubClassOf 'Biodiversity report' http://edamontology.org/data_3734 Lane identifier 'Lane identifier' SubClassOf 'Sequencing metadata name' http://edamontology.org/data_3735 Run number 'Run number' SubClassOf 'Sequencing metadata name' http://edamontology.org/data_3736 Ecological data 'Ecological data' SubClassOf 'Data' http://edamontology.org/data_3737 Alpha diversity data 'Alpha diversity data' SubClassOf 'Biodiversity report' http://edamontology.org/data_3732 Sequencing metadata name 'Sequencing metadata name' SubClassOf 'Name' http://edamontology.org/data_3733 Flow cell identifier 'Flow cell identifier' SubClassOf 'Sequencing metadata name' http://edamontology.org/data_3546 Image metadata 'Image metadata' SubClassOf 'Report' http://edamontology.org/data_3558 Clinical trial report 'Clinical trial report' SubClassOf 'Report' 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/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/format_3590 hdf5 'hdf5' SubClassOf 'binary format' 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/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/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/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/format_3547 Image format 'Image format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_3596 ppm 'ppm' SubClassOf 'binary format' 'ppm' SubClassOf 'Image format' http://edamontology.org/format_3595 pcx 'pcx' SubClassOf 'binary format' 'pcx' SubClassOf 'Image format' http://edamontology.org/format_3598 xbm 'xbm' SubClassOf 'Image format' 'xbm' SubClassOf 'binary format' 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/format_3593 im 'im' SubClassOf 'Image format' 'im' SubClassOf 'binary format' http://edamontology.org/format_3599 xpm 'xpm' SubClassOf 'binary format' 'xpm' SubClassOf 'Image format' http://edamontology.org/operation_0004 Operation http://edamontology.org/topic_3656 Immunoprecipitation experiment 'Immunoprecipitation experiment' SubClassOf 'Laboratory techniques' http://edamontology.org/topic_3674 Methylated DNA immunoprecipitation 'Methylated DNA immunoprecipitation' SubClassOf 'Immunoprecipitation experiment' http://edamontology.org/topic_3673 Whole genome sequencing 'Whole genome sequencing' SubClassOf 'Sequencing' 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/topic_3676 Exome sequencing 'Exome sequencing' SubClassOf 'Sequencing' http://edamontology.org/topic_3697 Microbial ecology 'Microbial ecology' SubClassOf 'Microbiology' 'Microbial ecology' SubClassOf 'Ecology' 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://edamontology.org/format_3790 SPARQL 'SPARQL' SubClassOf 'Textual format' 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/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/operation_3660 Metabolic network modelling 'Metabolic network modelling' SubClassOf 'Network simulation' http://edamontology.org/operation_3664 Statistical modelling 'Statistical modelling' SubClassOf 'Statistical calculation' http://edamontology.org/operation_3663 Homology-based gene prediction 'Homology-based gene prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_3662 Ab-initio gene prediction 'Ab-initio gene prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_3661 SNP annotation 'SNP annotation' SubClassOf 'Sequence annotation' http://edamontology.org/format_3750 YAML 'YAML' SubClassOf 'Format' http://edamontology.org/format_3752 CSV 'CSV' SubClassOf 'DSV' http://edamontology.org/format_3751 DSV 'DSV' SubClassOf 'Textual format' 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/operation_3631 Peptide identification 'Peptide identification' SubClassOf 'Spectral analysis' http://edamontology.org/operation_3630 Protein quantification 'Protein quantification' SubClassOf 'Spectral analysis' http://edamontology.org/format_3783 PubTator format 'PubTator format' SubClassOf 'Textual format' 'PubTator format' SubClassOf 'Annotated text format' http://edamontology.org/format_3782 BioC 'BioC' SubClassOf 'XML' 'BioC' SubClassOf 'Annotated text format' 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/format_3784 Open Annotation format 'Open Annotation format' SubClassOf 'Annotated text format' 'Open Annotation format' SubClassOf 'JSON-LD' 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/operation_3642 Dimethyl 'Dimethyl' SubClassOf 'Labeled quantification' http://edamontology.org/operation_3641 TMT-tag 'TMT-tag' SubClassOf 'Labeled quantification' http://edamontology.org/operation_3640 18O labeling '18O labeling' SubClassOf 'Labeled quantification' 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/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/operation_3695 Filtering 'Filtering' SubClassOf 'Data handling' http://edamontology.org/operation_3694 Mass spectrum visualisation 'Mass spectrum visualisation' SubClassOf 'Visualisation' 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/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://www.ebi.ac.uk/swo/license/SWO_1000143 Permission required for commercial use 'Permission required for commercial use' SubClassOf 'Commercial use only' http://www.ebi.ac.uk/swo/license/SWO_1000144 Permission required for derivative work 'Permission required for derivative work' SubClassOf 'Restrictions on derivative software' http://www.ebi.ac.uk/swo/license/SWO_1000145 Xenbase Academic Conditions of Use 'Xenbase Academic Conditions of Use' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000146 RIKEN Copyright 'RIKEN Copyright' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000147 Design Science License 'Design Science License' SubClassOf 'GNU Project Free License Type' http://www.ebi.ac.uk/swo/license/SWO_1000148 University of Concordia Terms of Use 'University of Concordia Terms of Use' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000149 OME Software Conditons of Use 'OME Software Conditons of Use' SubClassOf 'Vendor-specific License' 'OME Software Conditons of Use' SubClassOf 'GNU Project Free License Type' http://www.ebi.ac.uk/swo/license/SWO_1000140 Non-Commercial No-Fee License 'Non-Commercial No-Fee License' SubClassOf 'license' http://www.ebi.ac.uk/swo/license/SWO_1000141 DrugBank Academic License 'DrugBank Academic License' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000142 UCSC Genome Browser Commercial Software License 'UCSC Genome Browser Commercial Software License' SubClassOf 'Fee-Based Commercial License' 'UCSC Genome Browser Commercial Software License' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000129 RegenBase Terms of Use 'RegenBase Terms of Use' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000132 UCUM Terms of Use 'UCUM Terms of Use' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000133 UMLS Metathesaurus License 'UMLS Metathesaurus License' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000134 MHAS Data Policy 'MHAS Data Policy' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000135 ALFRED Copyright 'ALFRED Copyright' SubClassOf 'Vendor-specific License' 'ALFRED Copyright' SubClassOf 'License without restrictions on derivatives' 'ALFRED Copyright' SubClassOf 'GNU Project Free License Type' http://www.ebi.ac.uk/swo/license/SWO_1000136 Commercial use only 'Commercial use only' SubClassOf 'Usage restricted' http://www.ebi.ac.uk/swo/license/SWO_1000137 Fee-Based Commercial License 'Fee-Based Commercial License' SubClassOf 'license' http://www.ebi.ac.uk/swo/license/SWO_1000138 BRENDA License 'BRENDA License' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000139 TCGA Data Use Certification 'TCGA Data Use Certification' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000130 SABIO-RK Non-Commercial Purpose License 'SABIO-RK Non-Commercial Purpose License' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000131 Terms of Use for EMBL-EBI Services 'Terms of Use for EMBL-EBI Services' SubClassOf 'License without restrictions on derivatives' 'Terms of Use for EMBL-EBI Services' SubClassOf 'GNU Project Free License Type' 'Terms of Use for EMBL-EBI Services' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000150 ImmPort Conditions of Use 'ImmPort Conditions of Use' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000100 ODC-By v1.0 'ODC-By v1.0' SubClassOf 'Open Data Commons' 'ODC-By v1.0' SubClassOf 'GNU Project Free License Type' http://www.ebi.ac.uk/swo/license/SWO_1000101 PDDL v1.0 'PDDL v1.0' SubClassOf 'GNU GPL Compatible License Type' 'PDDL v1.0' SubClassOf 'Open Data Commons' 'PDDL v1.0' SubClassOf 'License without restrictions on derivatives' http://www.ebi.ac.uk/swo/license/SWO_1000102 obsolete_Modified BSD License 'obsolete_Modified BSD License' SubClassOf 'Obsolete concept (EDAM)' http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License 'Vendor-specific License' SubClassOf 'license' http://www.ebi.ac.uk/swo/license/SWO_1000104 NIDA NIH Data Access Policy 'NIDA NIH Data Access Policy' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000105 Addgene Terms of Use 'Addgene Terms of Use' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000106 CAS Information Use Policy 'CAS Information Use Policy' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000118 LOINC RELMA Terms of Use 'LOINC RELMA Terms of Use' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000119 MIACA Full Copyright 'MIACA Full Copyright' SubClassOf 'Open source software license' 'MIACA Full Copyright' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000121 NIH Genomic Data Sharing Policy 'NIH Genomic Data Sharing Policy' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000122 Facebase Data Access Policy 'Facebase Data Access Policy' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000123 ORCID Terms of Use 'ORCID Terms of Use' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000124 PPDB Academic License 'PPDB Academic License' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000125 SciCrunch Terms and Conditions 'SciCrunch Terms and Conditions' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000126 ProDom Commercial License 'ProDom Commercial License' SubClassOf 'Vendor-specific License' 'ProDom Commercial License' SubClassOf 'Fee-Based Commercial License' http://www.ebi.ac.uk/swo/license/SWO_1000127 SBGN Open License with Attribution 'SBGN Open License with Attribution' SubClassOf 'Vendor-specific License' 'SBGN Open License with Attribution' SubClassOf 'License without restrictions on derivatives' 'SBGN Open License with Attribution' SubClassOf 'GNU Project Free License Type' http://www.ebi.ac.uk/swo/license/SWO_1000128 NLM Open License with Attribution 'NLM Open License with Attribution' SubClassOf 'GNU Project Free License Type' 'NLM Open License with Attribution' SubClassOf 'License without restrictions on derivatives' 'NLM Open License with Attribution' SubClassOf 'Vendor-specific License' http://edamontology.org/topic_3557 Protein interaction experiment 'Protein interaction experiment' SubClassOf 'Laboratory techniques' http://www.ebi.ac.uk/swo/license/SWO_1000120 ORCID MIT-Style License (MIT) 'ORCID MIT-Style License (MIT)' SubClassOf 'Vendor-specific License' 'ORCID MIT-Style License (MIT)' SubClassOf 'GNU GPL Compatible License Type' http://www.ebi.ac.uk/swo/license/SWO_1000107 CellFinder Copyright 'CellFinder Copyright' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000108 LINCS Data Policy 'LINCS Data Policy' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000109 GeneNetwork Conditions of Use 'GeneNetwork Conditions of Use' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000110 GMD Academic License 'GMD Academic License' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000111 GeneProf Academic License 'GeneProf Academic License' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000112 European Medicines Agency Copyright 'European Medicines Agency Copyright' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000113 miRTaBase Data License 'miRTaBase Data License' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000114 GBIF Data Sharing Agreement 'GBIF Data Sharing Agreement' SubClassOf 'Vendor-specific License' 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 'GNU Project Free License Type' 'IUPAC/InChI-Trust InChI Licence No. 1.0' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000116 Labome Copyright 'Labome Copyright' SubClassOf 'Vendor-specific License' 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 'Vendor-specific License' http://edamontology.org/topic_3569 Applied mathematics 'Applied mathematics' SubClassOf 'Mathematics' 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/format_1915 Format http://edamontology.org/format_3729 dbGaP format 'dbGaP format' SubClassOf 'Textual format' http://edamontology.org/format_3728 LocARNA PP 'LocARNA PP' SubClassOf 'Textual format' http://edamontology.org/format_3725 SBOL 'SBOL' SubClassOf 'XML' http://edamontology.org/format_3727 OME-TIFF 'OME-TIFF' SubClassOf 'Image format' 'OME-TIFF' SubClassOf 'binary format' http://edamontology.org/format_3726 PMML 'PMML' SubClassOf 'XML' 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/format_3713 Mascot .dat file 'Mascot .dat file' SubClassOf 'Mass spectrometry data format' 'Mascot .dat file' SubClassOf 'Textual format' 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/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/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/format_3706 Biodiversity data format 'Biodiversity data format' SubClassOf 'Format (by type of data)' 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/format_3708 ABCD format 'ABCD format' SubClassOf 'Biodiversity data format' http://edamontology.org/format_3702 MSF 'MSF' SubClassOf 'Mass spectrometry data format' 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/operation_3731 Sample comparison 'Sample comparison' SubClassOf 'Comparison' http://edamontology.org/operation_3730 Cross-assembly 'Cross-assembly' SubClassOf 'Sequence assembly' 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_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_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/operation_3745 Ancestral reconstruction 'Ancestral reconstruction' SubClassOf 'Phylogenetic tree analysis' http://edamontology.org/operation_3744 Multiple sample visualisation 'Multiple sample visualisation' SubClassOf 'Visualisation' http://edamontology.org/data_0006 Data http://edamontology.org/operation_3742 Differential gene expression analysis 'Differential gene expression analysis' SubClassOf 'Comparison' 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/operation_3715 Metabolic labeling 'Metabolic labeling' SubClassOf 'Labeled quantification' 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_3778 Text annotation 'Text annotation' SubClassOf 'Annotation' 'Text annotation' SubClassOf 'Analysis' http://www.ebi.ac.uk/swo/license/SWO_1000090 CC BY-NC-SA 4.0 'CC BY-NC-SA 4.0' SubClassOf 'Creative Commons' 'CC BY-NC-SA 4.0' SubClassOf 'Non-Commercial No-Fee License' http://www.ebi.ac.uk/swo/license/SWO_1000099 FlowRepository Open Access Terms of Use 'FlowRepository Open Access Terms of Use' SubClassOf 'GNU Project Free License Type' 'FlowRepository Open Access Terms of Use' SubClassOf 'License without restrictions on derivatives' 'FlowRepository Open Access Terms of Use' SubClassOf 'Vendor-specific License' http://www.ebi.ac.uk/swo/license/SWO_1000091 CC BY-SA 2.1 JP 'CC BY-SA 2.1 JP' SubClassOf 'GNU Project Free License Type' 'CC BY-SA 2.1 JP' SubClassOf 'Creative Commons' http://www.ebi.ac.uk/swo/license/SWO_1000092 CC BY-SA 3.0 'CC BY-SA 3.0' SubClassOf 'Creative Commons' 'CC BY-SA 3.0' SubClassOf 'GNU Project Free License Type' http://www.ebi.ac.uk/swo/license/SWO_1000093 CC BY-SA 3.0 US 'CC BY-SA 3.0 US' SubClassOf 'Creative Commons' 'CC BY-SA 3.0 US' SubClassOf 'GNU Project Free License Type' http://www.ebi.ac.uk/swo/license/SWO_1000094 CC BY-SA 4.0 'CC BY-SA 4.0' SubClassOf 'Creative Commons' 'CC BY-SA 4.0' SubClassOf 'GNU Project Free License Type' http://www.ebi.ac.uk/swo/license/SWO_1000095 Open Data Commons 'Open Data Commons' SubClassOf 'license' http://www.ebi.ac.uk/swo/license/SWO_1000096 ODbL v1.0 'ODbL v1.0' SubClassOf 'GNU Project Free License Type' 'ODbL v1.0' SubClassOf 'Open Data Commons' http://www.ebi.ac.uk/swo/license/SWO_1000097 DbCL v1.0 'DbCL v1.0' SubClassOf 'Open Data Commons' 'DbCL v1.0' SubClassOf 'GNU Project Free License Type' http://www.ebi.ac.uk/swo/license/SWO_1000098 EMBLEM ELM Academic License 'EMBLEM ELM Academic License' SubClassOf 'Vendor-specific License' http://edamontology.org/operation_3755 PTM localisation 'PTM localisation' SubClassOf 'PTM identification' http://edamontology.org/format_3665 K-mer countgraph 'K-mer countgraph' SubClassOf 'Graph format' 'K-mer countgraph' SubClassOf 'binary format' http://edamontology.org/operation_3767 Protein identification 'Protein identification' SubClassOf 'Protein analysis' 'Protein identification' SubClassOf 'Spectral analysis' http://edamontology.org/operation_3766 Weighted correlation network analysis 'Weighted correlation network analysis' SubClassOf 'Pathway or network analysis' 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/operation_3761 Service discovery 'Service discovery' SubClassOf 'Service management' 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_3653 pkl 'pkl' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_3652 dta 'dta' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_3655 pepXML 'pepXML' SubClassOf 'Mass spectrometry data format' 'pepXML' SubClassOf 'XML' http://edamontology.org/format_3654 mzXML 'mzXML' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_3657 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