190 56 0 http://edamontology.org/data_0872 Phylogenetic tree 'Phylogenetic tree' SubClassOf 'Data' 'Phylogenetic tree' SubClassOf 'Phylogenetic data' http://edamontology.org/data_1597 Codon usage table 'Codon usage table' SubClassOf 'Data' 'Codon usage table' SubClassOf 'Codon usage data' http://edamontology.org/operation_2990 Classification 'Classification' SubClassOf 'Analysis' 'Classification' SubClassOf 'Operation' http://edamontology.org/data_2337 Resource metadata 'Resource metadata' SubClassOf 'Data' 'Resource metadata' SubClassOf 'Report' http://edamontology.org/operation_2928 Alignment 'Alignment' SubClassOf 'Analysis' 'Alignment' SubClassOf 'Operation' 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 'Obsolete concept (EDAM)' http://edamontology.org/format_3604 svg 'svg' SubClassOf 'Binary format' 'svg' SubClassOf 'XML' http://edamontology.org/operation_3501 Enrichment 'Enrichment' SubClassOf 'Analysis' 'Enrichment' SubClassOf 'Operation' 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_1546 Protein distance matrix 'Protein distance matrix' SubClassOf 'Protein residue interactions' 'Protein distance matrix' SubClassOf 'Protein interaction report' 'Protein distance matrix' SubClassOf 'Distance matrix' 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_1542 Protein solvent accessibility 'Protein solvent accessibility' SubClassOf 'Protein residue interactions' 'Protein solvent accessibility' SubClassOf 'Protein structure report' http://edamontology.org/data_1540 Protein residue interactions 'Protein residue interactions' SubClassOf 'Protein property' 'Protein residue interactions' SubClassOf 'has topic' some 'Protein folding, stability and design' 'Protein residue interactions' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_3545 Mathematical modelling 'Mathematical modelling' SubClassOf 'Modelling and simulation' 'Mathematical modelling' SubClassOf 'Obsolete concept (EDAM)' 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 'Obsolete concept (EDAM)' http://edamontology.org/data_1483 Structure alignment (protein pair) 'Structure alignment (protein pair)' SubClassOf 'Structure alignment (protein)' 'Structure alignment (protein pair)' SubClassOf 'Structure alignment (pair)' 'Structure alignment (protein pair)' SubClassOf 'Obsolete concept (EDAM)' 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 'Obsolete concept (EDAM)' http://edamontology.org/operation_3435 Standardization and normalization 'Standardization and normalization' SubClassOf 'Analysis' 'Standardization and normalization' SubClassOf 'Operation' http://edamontology.org/operation_3434 Conversion 'Conversion' SubClassOf 'Utility operation' 'Conversion' SubClassOf 'Operation' 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://edamontology.org/operation_3438 Calculation 'Calculation' SubClassOf 'Analysis' 'Calculation' SubClassOf 'Operation' http://edamontology.org/operation_3433 Assembly 'Assembly' SubClassOf 'Analysis' 'Assembly' SubClassOf 'Operation' http://edamontology.org/operation_3432 Clustering 'Clustering' SubClassOf 'Analysis' 'Clustering' SubClassOf 'Operation' http://edamontology.org/operation_3440 Genome assembly 'Genome assembly' SubClassOf 'Sequence assembly' 'Genome assembly' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_3441 Plotting 'Plotting' SubClassOf 'Analysis' 'Plotting' SubClassOf 'Operation' http://edamontology.org/operation_3443 Image analysis 'Image analysis' SubClassOf 'Operation (typed)' 'Image analysis' SubClassOf 'Analysis' http://edamontology.org/operation_3465 Correlation 'Correlation' SubClassOf 'Analysis' 'Correlation' SubClassOf 'Operation' http://edamontology.org/operation_3429 Generation 'Generation' SubClassOf 'Analysis' 'Generation' SubClassOf 'Operation' http://edamontology.org/data_3546 Image metadata 'Image metadata' SubClassOf 'Data' 'Image metadata' SubClassOf 'Report' http://edamontology.org/format_1964 plain text format (unformatted) 'plain text format (unformatted)' SubClassOf 'Sequence record format (text)' 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 'Obsolete concept (EDAM)' http://edamontology.org/data_1387 Sequence alignment (protein pair) 'Sequence alignment (protein pair)' SubClassOf 'Sequence alignment (pair)' 'Sequence alignment (protein pair)' SubClassOf 'Sequence alignment (protein)' 'Sequence alignment (protein pair)' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/topic_0180 Protein fold recognition 'Protein fold recognition' SubClassOf 'Structure prediction' 'Protein fold recognition' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/topic_0199 Genetic variation 'Genetic variation' SubClassOf 'Genotype and phenotype' 'Genetic variation' SubClassOf 'Genetics' 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_0172 Protein structure prediction 'Protein structure prediction' SubClassOf 'Protein structure analysis' 'Protein structure prediction' SubClassOf 'Structure prediction' 'Protein structure prediction' SubClassOf 'Obsolete concept (EDAM)' 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 'Obsolete concept (EDAM)' http://edamontology.org/topic_0177 Molecular docking 'Molecular docking' SubClassOf 'Structure prediction' 'Molecular docking' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_0559 Immunogenicity prediction 'Immunogenicity prediction' SubClassOf 'has output' some 'Protein structure' 'Immunogenicity prediction' SubClassOf 'Peptide immunogenicity prediction' 'Immunogenicity prediction' SubClassOf 'has topic' some 'Protein folding, stability and design' 'Immunogenicity prediction' SubClassOf 'has topic' some 'Immunology' 'Immunogenicity prediction' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_3283 Anonymisation 'Anonymisation' SubClassOf 'Utility operation' 'Anonymisation' SubClassOf 'Operation' http://edamontology.org/topic_0159 Sequence comparison 'Sequence comparison' SubClassOf 'Sequence analysis' 'Sequence comparison' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_3351 Protein surface analysis 'Protein surface analysis' SubClassOf 'Protein property calculation (from structure)' 'Protein surface analysis' SubClassOf 'has topic' some 'Protein structural motifs and surfaces' 'Protein surface analysis' SubClassOf 'Structure analysis' 'Protein surface analysis' SubClassOf 'has topic' some 'Protein properties' http://edamontology.org/operation_0567 Phylogenetic tree visualisation 'Phylogenetic tree visualisation' SubClassOf 'Phylogenetic tree processing' 'Phylogenetic tree visualisation' SubClassOf 'Phylogenetic tree analysis' http://edamontology.org/operation_0566 Sequence cluster visualisation 'Sequence cluster visualisation' SubClassOf 'has topic' some 'Sequence comparison' http://edamontology.org/operation_0563 Codon usage table formatting 'Codon usage table formatting' SubClassOf '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 'has input' some 'Codon usage table' 'Codon usage table formatting' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_0562 Sequence alignment formatting 'Sequence alignment formatting' SubClassOf 'has input' some 'Sequence alignment' 'Sequence alignment formatting' SubClassOf 'has output' some 'Sequence alignment' 'Sequence alignment formatting' SubClassOf 'Formatting' 'Sequence alignment formatting' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_0561 Sequence formatting 'Sequence formatting' SubClassOf 'has input' some 'Sequence' 'Sequence formatting' SubClassOf 'Formatting' 'Sequence formatting' SubClassOf 'has output' some 'Sequence' 'Sequence formatting' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_0560 DNA vaccine design 'DNA vaccine design' SubClassOf 'Design' 'DNA vaccine design' SubClassOf 'has topic' some 'Nucleic acid structure prediction' http://edamontology.org/topic_3517 GWAS study 'GWAS study' SubClassOf 'Laboratory techniques' 'GWAS study' SubClassOf http://edamontology.org/topic_3678 http://edamontology.org/topic_3523 RNAi experiment 'RNAi experiment' SubClassOf 'Sequencing' 'RNAi experiment' SubClassOf 'Laboratory techniques' http://edamontology.org/operation_2233 Representative sequence identification 'Representative sequence identification' SubClassOf 'has topic' some 'Sequence comparison' 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/topic_1312 Promoters 'Promoters' SubClassOf 'Gene transcription features' 'Promoters' SubClassOf 'Transcription factors and regulatory sites' http://edamontology.org/data_1235 Sequence cluster 'Sequence cluster' SubClassOf 'has topic' some 'Sequence comparison' http://edamontology.org/data_1274 Map 'Map' SubClassOf 'Data' 'Map' SubClassOf 'Map data' http://edamontology.org/operation_3191 Trim to reference 'Trim to reference' SubClassOf 'Sequence trimming' 'Trim to reference' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_3190 Trim vector 'Trim vector' SubClassOf 'Sequence trimming' 'Trim vector' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/data_0971 Article 'Article' SubClassOf 'Data' 'Article' SubClassOf 'Article data' http://edamontology.org/data_0906 Protein interaction report 'Protein interaction report' SubClassOf 'Protein report' 'Protein interaction report' SubClassOf 'Protein structure report' http://edamontology.org/operation_3189 Trim ends 'Trim ends' SubClassOf 'Sequence trimming' 'Trim ends' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_3219 Read pre-processing 'Read pre-processing' SubClassOf 'Validation' 'Read pre-processing' SubClassOf 'Sequencing quality control' http://edamontology.org/operation_3214 Spectral analysis 'Spectral analysis' SubClassOf 'has topic' some 'Proteomics' http://edamontology.org/operation_3213 Genome indexing (suffix arrays) 'Genome indexing (suffix arrays)' SubClassOf 'Genome indexing' 'Genome indexing (suffix arrays)' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_3212 Genome indexing (Burrows-Wheeler) 'Genome indexing (Burrows-Wheeler)' SubClassOf 'Genome indexing' 'Genome indexing (Burrows-Wheeler)' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_3229 Exome analysis 'Exome analysis' SubClassOf 'Nucleic acid sequence analysis' 'Exome analysis' SubClassOf 'Sequence assembly' http://edamontology.org/operation_0303 Protein fold recognition 'Protein fold recognition' SubClassOf 'has topic' some 'Protein fold recognition' http://edamontology.org/data_2767 Identifier with metadata 'Identifier with metadata' SubClassOf 'Identifier' 'Identifier with metadata' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/data_2048 Report 'Report' SubClassOf 'Resource metadata' 'Report' SubClassOf 'Data' http://edamontology.org/topic_3298 Phenomics 'Phenomics' SubClassOf 'Omics' http://edamontology.org/data_1150 Disease ID 'Disease ID' SubClassOf 'is identifier of' some 'Disease report' 'Disease ID' SubClassOf 'Identifier (typed)' 'Disease ID' SubClassOf http://edamontology.org/data_3667 http://edamontology.org/operation_1832 Residue contact calculation (residue-nucleic acid) 'Residue contact calculation (residue-nucleic acid)' SubClassOf 'Protein-nucleic acid binding site analysis' 'Residue contact calculation (residue-nucleic acid)' SubClassOf 'Residue contact calculation' 'Residue contact calculation (residue-nucleic acid)' SubClassOf 'Protein structural motif recognition' 'Residue contact calculation (residue-nucleic acid)' SubClassOf 'Obsolete concept (EDAM)' 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_1835 Residue contact calculation (residue-negative ion) 'Residue contact calculation (residue-negative ion)' SubClassOf 'Residue contact calculation' 'Residue contact calculation (residue-negative ion)' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_1831 Metal-bound cysteine detection 'Metal-bound cysteine detection' SubClassOf 'Residue interaction calculation' http://edamontology.org/operation_1826 Full torsion angle calculation 'Full torsion angle calculation' SubClassOf 'Torsion angle calculation' 'Full torsion angle calculation' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_1825 Backbone torsion angle calculation 'Backbone torsion angle calculation' SubClassOf 'Torsion angle calculation' 'Backbone torsion angle calculation' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_1828 Tau angle calculation 'Tau angle calculation' SubClassOf 'Torsion angle calculation' 'Tau angle calculation' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_1827 Cysteine torsion angle calculation 'Cysteine torsion angle calculation' SubClassOf 'Torsion angle calculation' 'Cysteine torsion angle calculation' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_1846 HET group detection 'HET group detection' SubClassOf 'Residue contact calculation (residue-ligand)' 'HET group detection' SubClassOf 'Obsolete concept (EDAM)' 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_1841 Rotamer likelihood prediction 'Rotamer likelihood prediction' SubClassOf 'Protein modelling (side chains)' 'Rotamer likelihood prediction' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_1842 Proline mutation value calculation 'Proline mutation value calculation' SubClassOf 'Protein modelling (mutation)' 'Proline mutation value calculation' SubClassOf 'Obsolete concept (EDAM)' 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_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 'Obsolete concept (EDAM)' http://edamontology.org/operation_1837 Residue symmetry contact calculation 'Residue symmetry contact calculation' SubClassOf 'Residue contact calculation (residue-residue)' 'Residue symmetry contact calculation' SubClassOf 'Obsolete concept (EDAM)' 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_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 'Obsolete concept (EDAM)' 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 'Obsolete concept (EDAM)' http://edamontology.org/operation_1824 Protein surface calculation (accessible) 'Protein surface calculation (accessible)' SubClassOf 'Protein surface calculation' 'Protein surface calculation (accessible)' SubClassOf 'Obsolete concept (EDAM)' 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 'Obsolete concept (EDAM)' 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 'Obsolete concept (EDAM)' 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 'Obsolete concept (EDAM)' http://edamontology.org/operation_1816 Surface rendering 'Surface rendering' SubClassOf 'Protein surface calculation' 'Surface rendering' SubClassOf 'Protein surface analysis' 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 'Obsolete concept (EDAM)' 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 'Obsolete concept (EDAM)' http://edamontology.org/operation_2495 Gene expression data analysis 'Gene expression data analysis' SubClassOf 'Operation (typed)' 'Gene expression data analysis' SubClassOf 'Analysis' 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' 'Pathway or network analysis' SubClassOf 'has topic' some 'Molecular interactions, pathways and networks' 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 'Obsolete concept (EDAM)' 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 'Obsolete concept (EDAM)' http://edamontology.org/operation_2480 Structure analysis 'Structure analysis' SubClassOf 'Operation (typed)' 'Structure analysis' SubClassOf 'Analysis' http://edamontology.org/operation_3083 Pathway or network visualisation 'Pathway or network visualisation' SubClassOf 'Pathway or network processing' 'Pathway or network visualisation' SubClassOf 'Pathway or network analysis' http://edamontology.org/operation_3096 Editing 'Editing' SubClassOf 'Utility operation' 'Editing' SubClassOf 'Operation' http://edamontology.org/operation_1848 Structure formatting 'Structure formatting' SubClassOf 'Formatting' 'Structure formatting' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_2460 Protein atom surface calculation 'Protein atom surface calculation' SubClassOf 'Protein surface and interior calculation' 'Protein atom surface calculation' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_2461 Protein residue surface calculation 'Protein residue surface calculation' SubClassOf 'Protein surface and interior calculation' 'Protein residue surface calculation' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_2464 Protein-protein interaction prediction 'Protein-protein interaction prediction' SubClassOf 'Protein function prediction' http://edamontology.org/operation_2462 Protein surface calculation 'Protein surface calculation' SubClassOf 'Protein surface and interior calculation' 'Protein surface calculation' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_2451 Sequence comparison 'Sequence comparison' SubClassOf 'has topic' some 'Sequence comparison' 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 'Obsolete concept (EDAM)' 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 topic' some 'Protein properties' 'Protein solvent accessibility calculation' SubClassOf 'Protein surface analysis' 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 property calculation (from structure)' 'Protein hydropathy calculation (from structure)' SubClassOf 'Protein structure analysis' 'Protein hydropathy calculation (from structure)' SubClassOf 'Obsolete concept (EDAM)' 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 'Obsolete concept (EDAM)' http://edamontology.org/operation_0387 Protein surface and interior calculation 'Protein surface and interior calculation' SubClassOf 'has topic' some 'Protein structural motifs and surfaces' 'Protein surface and interior calculation' SubClassOf 'Protein solvent accessibility calculation' 'Protein surface and interior calculation' SubClassOf 'Protein surface analysis' http://edamontology.org/operation_0391 Protein distance matrix calculation 'Protein distance matrix calculation' SubClassOf 'Residue interaction calculation' 'Protein distance matrix calculation' SubClassOf 'Residue contact calculation' 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 'Obsolete concept (EDAM)' http://edamontology.org/operation_0393 Protein residue cluster calculation 'Protein residue cluster calculation' SubClassOf 'Residue contact calculation (residue-residue)' 'Protein residue cluster calculation' SubClassOf 'Residue contact calculation' http://edamontology.org/operation_0392 Protein contact map calculation 'Protein contact map calculation' SubClassOf 'Residue contact calculation (residue-residue)' 'Protein contact map calculation' SubClassOf 'Protein distance matrix calculation' 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 'Obsolete concept (EDAM)' http://edamontology.org/operation_2430 Design 'Design' SubClassOf 'Analysis' 'Design' SubClassOf 'Operation' http://edamontology.org/operation_2438 Pathway or network processing 'Pathway or network processing' SubClassOf 'has topic' some 'Molecular interactions, pathways and networks' 'Pathway or network processing' SubClassOf 'Operation (typed)' 'Pathway or network processing' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_2420 Operation (typed) 'Operation (typed)' SubClassOf 'Operation' 'Operation (typed)' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_2423 Prediction and recognition 'Prediction and recognition' SubClassOf 'Analysis' 'Prediction and recognition' SubClassOf 'Operation' http://edamontology.org/operation_2425 Optimisation and refinement 'Optimisation and refinement' SubClassOf 'Analysis' 'Optimisation and refinement' SubClassOf 'Operation' http://edamontology.org/operation_2424 Comparison 'Comparison' SubClassOf 'Analysis' 'Comparison' SubClassOf 'Operation' http://edamontology.org/operation_2426 Modelling and simulation 'Modelling and simulation' SubClassOf 'Analysis' 'Modelling and simulation' SubClassOf 'Operation' http://edamontology.org/operation_2429 Mapping 'Mapping' SubClassOf 'Analysis' 'Mapping' SubClassOf 'Operation' http://edamontology.org/operation_2428 Validation 'Validation' SubClassOf 'Analysis' 'Validation' SubClassOf 'Operation' http://edamontology.org/operation_2409 Utility operation 'Utility operation' SubClassOf 'Operation' 'Utility operation' SubClassOf 'Analysis' http://edamontology.org/operation_2403 Sequence analysis 'Sequence analysis' SubClassOf 'Operation (typed)' 'Sequence analysis' SubClassOf 'Analysis' 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 'Phylogenetic tree processing' 'Phylogenetic tree editing' SubClassOf 'Phylogenetic tree analysis' http://edamontology.org/operation_0323 Phylogenetic tree generation '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 'has output' some 'Phylogenetic data' 'Phylogenetic tree analysis' SubClassOf 'Phylogenetic tree processing' 'Phylogenetic tree analysis' SubClassOf 'has input' some 'Phylogenetic tree' 'Phylogenetic tree analysis' SubClassOf 'has topic' some 'Phylogeny' 'Phylogenetic tree analysis' SubClassOf 'Analysis' http://edamontology.org/operation_0321 Protein model validation 'Protein model validation' SubClassOf 'has topic' some 'Protein structure prediction' http://edamontology.org/operation_0336 Format validation 'Format validation' SubClassOf 'Utility operation' http://edamontology.org/operation_0338 Sequence database search 'Sequence database search' SubClassOf 'has topic' some 'Sequence comparison' http://edamontology.org/operation_0330 Protein SNP mapping 'Protein SNP mapping' SubClassOf 'Mapping' 'Protein SNP mapping' SubClassOf 'Protein modelling (mutation)' 'Protein SNP mapping' SubClassOf 'has topic' some 'SNP' 'Protein SNP mapping' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_0410 Protein crystallizability prediction 'Protein crystallizability prediction' SubClassOf 'Protein hydropathy calculation (from sequence)' 'Protein crystallizability prediction' SubClassOf 'Protein hydropathy calculation' http://edamontology.org/operation_0413 MHC peptide immunogenicity prediction 'MHC peptide immunogenicity prediction' SubClassOf 'Peptide immunogenicity prediction' 'MHC peptide immunogenicity prediction' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_0408 Protein globularity prediction '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 '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 '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 'Protein hydropathy calculation' http://edamontology.org/operation_0401 Protein hydropathy calculation (from sequence) 'Protein hydropathy calculation (from sequence)' SubClassOf 'Protein hydropathy calculation' 'Protein hydropathy calculation (from sequence)' SubClassOf 'Protein sequence analysis' 'Protein hydropathy calculation (from sequence)' SubClassOf 'Obsolete concept (EDAM)' 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_0438 Regulatory element prediction 'Regulatory element prediction' SubClassOf 'Gene component prediction' 'Regulatory element prediction' SubClassOf 'Gene prediction' 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 '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_0435 Operon prediction 'Operon prediction' SubClassOf 'Whole gene prediction' 'Operon prediction' SubClassOf 'Gene prediction' 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_0429 Quadruplex formation site detection 'Quadruplex formation site detection' SubClassOf 'has topic' some 'Nucleic acid structure prediction' http://edamontology.org/operation_0425 Whole gene prediction 'Whole gene prediction' SubClassOf 'Gene prediction' 'Whole gene prediction' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_0426 Gene component prediction 'Gene component prediction' SubClassOf 'Gene prediction' 'Gene component prediction' SubClassOf 'Obsolete concept (EDAM)' 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_3346 Sequence search 'Sequence search' SubClassOf 'Sequence analysis' 'Sequence search' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/topic_3344 Biomedical science 'Biomedical science' SubClassOf 'Biology' 'Biomedical science' SubClassOf 'Medicine' 'Biomedical science' SubClassOf 'Topic' http://edamontology.org/operation_0419 Protein binding site prediction (from sequence) 'Protein binding site prediction (from sequence)' SubClassOf 'Protein sequence feature detection' 'Protein binding site prediction (from sequence)' SubClassOf 'Protein binding site prediction' 'Protein binding site prediction (from sequence)' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/topic_3307 Computational biology 'Computational biology' SubClassOf 'Biology' 'Computational biology' SubClassOf 'Computer science' 'Computational biology' SubClassOf 'Topic' http://edamontology.org/topic_3391 Omics 'Omics' SubClassOf 'Biology' 'Omics' SubClassOf 'Topic' http://edamontology.org/topic_3379 Preclinical and clinical studies 'Preclinical and clinical studies' SubClassOf http://edamontology.org/topic_3678 http://edamontology.org/operation_0483 Structured RNA prediction and optimisation 'Structured RNA prediction and optimisation' SubClassOf 'has topic' some 'Nucleic acid structure prediction' http://edamontology.org/topic_0594 Sequence classification 'Sequence classification' SubClassOf 'Sequence analysis' 'Sequence classification' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_0464 tRNA gene prediction 'tRNA gene prediction' SubClassOf 'Whole gene prediction' 'tRNA gene prediction' SubClassOf 'Gene prediction' http://edamontology.org/operation_1913 Residue validation 'Residue validation' SubClassOf 'Protein model validation' 'Residue validation' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/operation_0474 Protein structure prediction 'Protein structure prediction' SubClassOf 'has topic' some 'Protein structure prediction' http://edamontology.org/operation_0475 Nucleic acid structure prediction 'Nucleic acid structure prediction' SubClassOf 'has topic' some 'Nucleic acid structure analysis' http://edamontology.org/operation_0478 Molecular docking 'Molecular docking' SubClassOf 'has topic' some 'Molecular docking' http://edamontology.org/topic_3123 Expression signals 'Expression signals' SubClassOf 'Gene structure' 'Expression signals' SubClassOf 'Gene expression' 'Expression signals' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/data_1646 Molecular weights standard fingerprint 'Molecular weights standard fingerprint' SubClassOf 'Peptide mass fingerprint' 'Molecular weights standard fingerprint' SubClassOf 'Obsolete concept (EDAM)' 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_0582 Ontology 'Ontology' SubClassOf 'Data' 'Ontology' SubClassOf 'Ontology data' http://edamontology.org/topic_3179 ChIP-on-chip 'ChIP-on-chip' SubClassOf http://edamontology.org/topic_3656 http://edamontology.org/topic_3170 RNA-Seq 'RNA-Seq' SubClassOf 'Obsolete concept (EDAM)' 'RNA-Seq' SubClassOf 'Sequencing' http://edamontology.org/topic_0749 Transcription factors and regulatory sites 'Transcription factors and regulatory sites' SubClassOf 'Promoters' 'Transcription factors and regulatory sites' SubClassOf 'Gene transcription features' http://edamontology.org/operation_0291 Sequence clustering 'Sequence clustering' SubClassOf 'has topic' some 'Sequence comparison' http://edamontology.org/operation_0299 3D profile-to-3D profile alignment '3D profile-to-3D profile alignment' SubClassOf 'Alignment' http://edamontology.org/topic_0769 Workflows 'Workflows' SubClassOf 'Obsolete concept (EDAM)' 'Workflows' SubClassOf 'Data management' http://edamontology.org/operation_2501 Nucleic acid analysis 'Nucleic acid analysis' SubClassOf 'Operation (typed)' 'Nucleic acid analysis' SubClassOf 'Analysis' http://edamontology.org/operation_2502 Protein analysis 'Protein analysis' SubClassOf 'has topic' some 'Proteins' 'Protein analysis' SubClassOf 'Operation (typed)' 'Protein analysis' SubClassOf 'has topic' some 'Proteomics' 'Protein analysis' SubClassOf 'Analysis' http://edamontology.org/operation_0226 Annotation 'Annotation' SubClassOf 'Analysis' 'Annotation' SubClassOf 'Operation' http://edamontology.org/operation_0227 Indexing 'Indexing' SubClassOf 'Utility operation' 'Indexing' SubClassOf 'Operation' http://edamontology.org/operation_0248 Residue interaction calculation 'Residue interaction calculation' SubClassOf 'has output' some 'Protein residue interactions' 'Residue interaction calculation' SubClassOf 'Residue interaction calculation' http://edamontology.org/operation_0250 Protein property calculation 'Protein property calculation' SubClassOf 'has output' some 'Protein property' 'Protein property calculation' SubClassOf 'has topic' some 'Protein properties' http://edamontology.org/operation_0267 Protein secondary structure prediction 'Protein secondary structure prediction' SubClassOf 'has topic' some 'Protein structure prediction' http://edamontology.org/operation_2575 Protein binding site prediction 'Protein binding site prediction' SubClassOf 'Protein feature detection' http://edamontology.org/operation_0278 RNA secondary structure prediction 'RNA secondary structure prediction' SubClassOf 'has topic' some 'Nucleic acid structure prediction' http://edamontology.org/operation_0279 Nucleic acid folding prediction 'Nucleic acid folding prediction' SubClassOf 'has topic' some 'Nucleic acid structure prediction' http://edamontology.org/operation_0274 Protein-protein interaction prediction (from protein sequence) 'Protein-protein interaction prediction (from protein sequence)' SubClassOf 'Protein function prediction' 'Protein-protein interaction prediction (from protein sequence)' SubClassOf 'Protein-protein interaction prediction' 'Protein-protein interaction prediction (from protein sequence)' SubClassOf 'Obsolete concept (EDAM)' 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 structure analysis' 'Protein-protein interaction prediction (from protein structure)' SubClassOf 'Protein feature detection' 'Protein-protein interaction prediction (from protein structure)' SubClassOf 'Obsolete concept (EDAM)' http://edamontology.org/format_3665 K-mer countgraph 'K-mer countgraph' SubClassOf 'Graph format' 'K-mer countgraph' SubClassOf 'Binary format' http://edamontology.org/format_3652 dta 'dta' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_3653 pkl 'pkl' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_3650 netCDF 'netCDF' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_3651 MGF 'MGF' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_3657 GPML 'GPML' SubClassOf 'Biological pathway or network format' 'GPML' SubClassOf 'XML' http://edamontology.org/format_3654 mzXML 'mzXML' SubClassOf 'Mass spectrometry data format' http://edamontology.org/format_3655 pepXML 'pepXML' SubClassOf 'Mass spectrometry data format' http://edamontology.org/topic_3656 Immunoprecipitation experiment 'Immunoprecipitation experiment' SubClassOf 'Laboratory techniques' http://edamontology.org/topic_3676 Exome sequencing 'Exome sequencing' SubClassOf 'Sequencing' http://edamontology.org/topic_3679 Animal study 'Animal study' SubClassOf 'Experimental design and studies' 'Animal study' SubClassOf 'Laboratory animal science' http://edamontology.org/topic_3678 Experimental design and studies 'Experimental design and studies' SubClassOf 'Topic' http://edamontology.org/topic_3673 Whole genome sequencing 'Whole genome sequencing' SubClassOf 'Sequencing' http://edamontology.org/topic_3674 Methylated DNA immunoprecipitation 'Methylated DNA immunoprecipitation' SubClassOf 'Immunoprecipitation experiment' http://edamontology.org/format_3626 MAT 'MAT' SubClassOf 'is format of' some '3D-1D scoring matrix' 'MAT' SubClassOf 'Matrix format' http://edamontology.org/data_3671 Text 'Text' SubClassOf 'Parameter' 'Text' SubClassOf 'Article data' http://edamontology.org/data_3670 Online course 'Online course' SubClassOf 'Training material' http://edamontology.org/data_3667 Disease identifier 'Disease identifier' SubClassOf 'is identifier of' some 'Disease report' 'Disease identifier' SubClassOf 'Accession' 'Disease identifier' SubClassOf 'Identifier (typed)' http://edamontology.org/data_3669 Training material 'Training material' SubClassOf 'Data' http://edamontology.org/data_3668 Disease name 'Disease name' SubClassOf 'Name' 'Disease name' SubClassOf 'Disease identifier' http://edamontology.org/topic_3557 Protein interaction experiment 'Protein interaction experiment' SubClassOf 'Laboratory techniques' 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/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 'Peptide database search' 'Validation of peptide-spectrum matches' SubClassOf 'Validation' http://edamontology.org/operation_3647 Blind peptide database search 'Blind peptide database search' SubClassOf 'Peptide database search' http://edamontology.org/operation_3629 Deisotoping 'Deisotoping' SubClassOf 'has input' some 'Mass spectrometry spectra' 'Deisotoping' SubClassOf 'Spectral analysis' http://edamontology.org/operation_3631 Peptide identification 'Peptide identification' SubClassOf 'has input' some 'Mass spectrometry spectra' 'Peptide identification' SubClassOf 'Spectral analysis' http://edamontology.org/operation_3630 Quantification 'Quantification' SubClassOf 'has input' some 'Mass spectrometry spectra' 'Quantification' SubClassOf 'Spectral analysis' http://edamontology.org/operation_3633 Retention times calculation 'Retention times calculation' SubClassOf 'Calculation' http://edamontology.org/operation_3632 Isotopic distributions calculation 'Isotopic distributions calculation' SubClassOf 'Calculation' 'Isotopic distributions calculation' SubClassOf 'has input' some 'Mass spectrometry spectra' 'Isotopic distributions calculation' SubClassOf 'has topic' some 'Proteomics' http://edamontology.org/operation_3635 Labeled quantification 'Labeled quantification' SubClassOf 'Quantification' http://edamontology.org/operation_3634 Label-free quantification 'Label-free quantification' SubClassOf 'Quantification' http://edamontology.org/operation_3637 Spectral counting 'Spectral counting' SubClassOf 'Label-free quantification' http://edamontology.org/operation_3636 MRM/SRM 'MRM/SRM' SubClassOf 'Quantification' http://edamontology.org/operation_3639 iTRAQ 'iTRAQ' SubClassOf 'Labeled quantification' http://edamontology.org/operation_3638 SILAC 'SILAC' SubClassOf 'Labeled quantification' 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/operation_3660 Metabolic network modelling 'Metabolic network modelling' SubClassOf 'Network simulation' 'Metabolic network modelling' SubClassOf 'has topic' some 'Systems biology' http://edamontology.org/operation_3666 Molecular surface comparison 'Molecular surface comparison' SubClassOf 'Molecular surface analysis' 'Molecular surface comparison' SubClassOf 'Structure comparison' 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/operation_3627 Mass spectra calibration 'Mass spectra calibration' SubClassOf 'Spectral analysis' 'Mass spectra calibration' SubClassOf 'has input' some 'Mass spectrometry spectra' http://edamontology.org/operation_3628 Chromatographic alignment 'Chromatographic alignment' SubClassOf 'Spectral analysis' 'Chromatographic alignment' SubClassOf 'has input' some 'Mass spectrometry spectra' http://edamontology.org/operation_3625 Relationship inference 'Relationship inference' SubClassOf 'has output' some 'Article data' 'Relationship inference' SubClassOf 'has input' some 'Article' 'Relationship inference' SubClassOf 'Text mining' 'Relationship inference' SubClassOf 'has topic' some 'Literature and reference' 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' 'Variant filtering' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/operation_3672 Gene functional annotation 'Gene functional annotation' SubClassOf 'Sequence annotation'