55 47 24 http://edamontology.org/operation_0331 Protein modelling (mutation) 'Protein modelling (mutation)' SubClassOf 'Protein modelling' 'Protein modelling (mutation)' SubClassOf 'Prediction and recognition' http://edamontology.org/operation_0389 Protein-nucleic acid binding site analysis 'Protein-nucleic acid binding site analysis' SubClassOf 'Protein interaction analysis' 'Protein-nucleic acid binding site analysis' SubClassOf 'Protein function prediction' http://edamontology.org/operation_0397 Ramachandran plot validation 'Ramachandran plot validation' SubClassOf 'Protein geometry validation' 'Ramachandran plot validation' SubClassOf 'has input' some 'Ramachandran plot' 'Ramachandran plot validation' SubClassOf 'has output' some 'Protein structural quality report' 'Ramachandran plot validation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_0365 Nucleic acid restriction digest 'Nucleic acid restriction digest' SubClassOf 'Sequence generation (nucleic acid)' 'Nucleic acid restriction digest' SubClassOf 'Sequence generation' http://edamontology.org/operation_0366 Protein sequence cleavage 'Protein sequence cleavage' SubClassOf 'Sequence generation (protein)' 'Protein sequence cleavage' SubClassOf 'Sequence generation' http://edamontology.org/operation_0363 Nucleic acid sequence reverse and complement 'Nucleic acid sequence reverse and complement' SubClassOf 'Sequence generation (nucleic acid)' 'Nucleic acid sequence reverse and complement' SubClassOf 'Sequence generation' http://edamontology.org/data_2399 Gene transcriptional features report 'Gene transcriptional features report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2397 Gene features report (exon) 'Gene features report (exon)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2963 Codon usage bias plotting 'Codon usage bias plotting' SubClassOf 'Sequence visualisation' 'Codon usage bias plotting' SubClassOf 'has output' some 'Codon usage bias plot' 'Codon usage bias plotting' SubClassOf 'Codon usage bias calculation' 'Codon usage bias plotting' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2949 Protein interaction analysis 'Protein interaction analysis' SubClassOf 'Protein function analysis' 'Protein interaction analysis' SubClassOf 'Protein function prediction' http://edamontology.org/operation_0478 Molecular docking 'Molecular docking' SubClassOf 'Protein interaction prediction' 'Molecular docking' SubClassOf 'Protein function prediction' http://edamontology.org/operation_1778 Protein function comparison 'Protein function comparison' SubClassOf 'Protein function analysis' 'Protein function comparison' SubClassOf 'Protein function prediction' http://edamontology.org/operation_1777 Protein function prediction 'Protein function prediction' SubClassOf 'Protein function analysis' 'Protein function prediction' SubClassOf 'Analysis' http://edamontology.org/topic_2844 Structural clustering 'Structural clustering' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass 'Structural clustering' SubClassOf 'Clustering' http://edamontology.org/topic_0176 Molecular dynamics 'Molecular dynamics' SubClassOf http://edamontology.org/topic_3892 http://edamontology.org/operation_0418 Protein signal peptide detection 'Protein signal peptide detection' SubClassOf 'Protein subcellular localisation prediction' 'Protein signal peptide detection' SubClassOf 'Protein function prediction' http://edamontology.org/operation_3185 Base-calling 'Base-calling' SubClassOf 'Sequence generation (nucleic acid)' 'Base-calling' SubClassOf 'Sequence generation' http://edamontology.org/operation_0252 Peptide immunogenicity prediction 'Peptide immunogenicity prediction' SubClassOf 'Protein interaction prediction' 'Peptide immunogenicity prediction' SubClassOf 'Protein function prediction' http://edamontology.org/format_1475 PDB database entry format 'PDB database entry format' SubClassOf 'is format of' some http://edamontology.org/data_3870 http://edamontology.org/operation_3280 Named-entity and concept recognition 'Named-entity and concept recognition' SubClassOf 'Text mining' 'Named-entity and concept recognition' SubClassOf http://edamontology.org/operation_3907 http://edamontology.org/data_1456 Protein features report (membrane regions) 'Protein features report (membrane regions)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3590 hdf5 'hdf5' SubClassOf http://edamontology.org/format_3867 http://edamontology.org/operation_2513 Sequence generation (nucleic acid) 'Sequence generation (nucleic acid)' SubClassOf 'Sequence generation' 'Sequence generation (nucleic acid)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2514 Sequence generation (protein) 'Sequence generation (protein)' SubClassOf 'Sequence generation' 'Sequence generation (protein)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2575 Protein binding site prediction 'Protein binding site prediction' SubClassOf 'Protein interaction prediction' 'Protein binding site prediction' SubClassOf 'Protein function prediction' http://edamontology.org/data_3275 Phenotype name 'Phenotype name' SubClassOf 'Identifier (by type of data)' http://edamontology.org/data_0922 Nucleic acid features report (primers) 'Nucleic acid features report (primers)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2754 Gene features report (intron) 'Gene features report (intron)' 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 http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2867 Nucleic acid features report (VNTR) 'Nucleic acid features report (VNTR)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2868 Nucleic acid features report (microsatellite) 'Nucleic acid features report (microsatellite)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2885 Nucleic acid features report (polymorphism) 'Nucleic acid features report (polymorphism)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2533 Nucleic acid features report (mutation) 'Nucleic acid features report (mutation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_3644 de Novo sequencing 'de Novo sequencing' SubClassOf 'Sequence generation (protein)' 'de Novo sequencing' SubClassOf 'Sequence generation' http://edamontology.org/data_3022 NCBI genetic code ID 'NCBI genetic code ID' SubClassOf 'Identifier (by type of data)' 'NCBI genetic code ID' SubClassOf 'Genetic code identifier' http://edamontology.org/operation_2414 Protein function analysis 'Protein function analysis' SubClassOf 'Analysis' 'Protein function analysis' SubClassOf 'has output' some 'Protein report' 'Protein function analysis' SubClassOf 'has topic' some 'Proteins' 'Protein function analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2422 Data retrieval 'Data retrieval' SubClassOf http://edamontology.org/operation_3908 http://edamontology.org/format_3650 netCDF 'netCDF' SubClassOf http://edamontology.org/format_3867 'netCDF' SubClassOf 'Binary format' http://edamontology.org/operation_2499 Splicing model analysis 'Splicing model analysis' SubClassOf 'Sequence analysis' 'Splicing model analysis' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/data_3118 Protein features report (topological domains) 'Protein features report (topological domains)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2492 Protein interaction prediction 'Protein interaction prediction' SubClassOf 'Protein function prediction' http://edamontology.org/data_3125 Nucleic acid features report (binding) 'Nucleic acid features report (binding)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3126 Nucleic acid repeats (report) 'Nucleic acid repeats (report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3127 Nucleic acid features report (replication and recombination) 'Nucleic acid features report (replication and recombination)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/operation_2464 Protein-protein interaction prediction 'Protein-protein interaction prediction' SubClassOf 'Protein interaction prediction' 'Protein-protein interaction prediction' SubClassOf 'Protein binding site prediction' http://edamontology.org/data_3123 Nucleic acid features report (expression signal) 'Nucleic acid features report (expression signal)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3139 Nucleic acid features report (STS) 'Nucleic acid features report (STS)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3135 Nucleic acid features report (signal or transit peptide) 'Nucleic acid features report (signal or transit peptide)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1305 Nucleic acid features report (restriction sites) 'Nucleic acid features report (restriction sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1304 Nucleic acid features report (CpG island and isochore) 'Nucleic acid features report (CpG island and isochore)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1308 Nucleic acid features report (matrix/scaffold attachment sites) 'Nucleic acid features report (matrix/scaffold attachment sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1307 Nucleic acid features report (splice sites) 'Nucleic acid features report (splice sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1302 Nucleic acid features report (PolyA signal or site) 'Nucleic acid features report (PolyA signal or site)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1312 Nucleic acid features report (promoters) 'Nucleic acid features report (promoters)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1311 Gene features report (operon) 'Gene features report (operon)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/format_3909 BpForms 'BpForms' SubClassOf 'Raw sequence format' 'BpForms' SubClassOf 'is format of' some 'Sequence features' 'BpForms' SubClassOf 'Chemical formula format' 'BpForms' SubClassOf 'Textual format' http://edamontology.org/format_3906 NMReDATA 'NMReDATA' SubClassOf 'NMR data format' 'NMReDATA' SubClassOf 'Textual format' http://edamontology.org/format_3911 msh 'msh' SubClassOf 'Raw sequence format' 'msh' SubClassOf 'is format of' some 'Sequence checksum' 'msh' SubClassOf 'Binary format' http://edamontology.org/format_3910 trr 'trr' SubClassOf 'Textual format' 'trr' SubClassOf 'Tertiary structure format' 'trr' SubClassOf 'Trajectory format (text)' http://edamontology.org/format_3882 PSF 'PSF' SubClassOf 'Topology format' 'PSF' SubClassOf 'Tertiary structure format' 'PSF' SubClassOf 'Textual format' http://edamontology.org/format_3881 AMBER top 'AMBER top' SubClassOf 'Topology format' 'AMBER top' SubClassOf 'Tertiary structure format' 'AMBER top' SubClassOf 'Textual format' http://edamontology.org/format_3884 FF parameter format 'FF parameter format' SubClassOf 'is format of' some 'Topology data' 'FF parameter format' SubClassOf 'Format (by type of data)' http://edamontology.org/format_3883 GROMACS itp 'GROMACS itp' SubClassOf 'Tertiary structure format' 'GROMACS itp' SubClassOf 'Textual format' 'GROMACS itp' SubClassOf 'Topology format' 'GROMACS itp' SubClassOf 'FF parameter format' http://edamontology.org/format_3880 GROMACS top 'GROMACS top' SubClassOf 'Textual format' 'GROMACS top' SubClassOf 'Tertiary structure format' 'GROMACS top' SubClassOf 'Topology format' http://edamontology.org/format_3889 AMBER off 'AMBER off' SubClassOf 'Textual format' 'AMBER off' SubClassOf 'FF parameter format' http://edamontology.org/format_3886 RST 'RST' SubClassOf 'Textual format' 'RST' SubClassOf 'Tertiary structure format' 'RST' SubClassOf 'Trajectory format (text)' http://edamontology.org/format_3885 BinPos 'BinPos' SubClassOf 'Trajectory format (binary)' 'BinPos' SubClassOf 'Binary format' http://edamontology.org/format_3888 AMBER frcmod 'AMBER frcmod' SubClassOf 'FF parameter format' 'AMBER frcmod' SubClassOf 'Textual format' http://edamontology.org/format_3887 CHARMM rtf 'CHARMM rtf' SubClassOf 'Textual format' 'CHARMM rtf' SubClassOf 'Tertiary structure format' 'CHARMM rtf' SubClassOf 'Topology format' http://edamontology.org/format_3873 HDF 'HDF' SubClassOf 'Binary format' 'HDF' SubClassOf 'Trajectory format (binary)' http://edamontology.org/format_3879 Topology format 'Topology format' SubClassOf 'Format (by type of data)' 'Topology format' SubClassOf 'is format of' some 'Topology data' http://edamontology.org/format_3878 mdcrd 'mdcrd' SubClassOf 'Textual format' 'mdcrd' SubClassOf 'Tertiary structure format' 'mdcrd' SubClassOf 'Trajectory format (text)' http://edamontology.org/format_3875 XTC 'XTC' SubClassOf 'Binary format' 'XTC' SubClassOf 'Trajectory format (binary)' http://edamontology.org/format_3874 PCAzip 'PCAzip' SubClassOf 'Trajectory format (binary)' 'PCAzip' SubClassOf 'Binary format' http://edamontology.org/format_3877 XYZ 'XYZ' SubClassOf 'Tertiary structure format' 'XYZ' SubClassOf 'Textual format' 'XYZ' SubClassOf 'Trajectory format (text)' http://edamontology.org/format_3876 TNG 'TNG' SubClassOf 'Trajectory format (binary)' 'TNG' SubClassOf 'Binary format' http://edamontology.org/format_3868 Trajectory format (text) 'Trajectory format (text)' SubClassOf 'Trajectory format' http://edamontology.org/format_3867 Trajectory format (binary) 'Trajectory format (binary)' SubClassOf 'Trajectory format' http://edamontology.org/format_3866 Trajectory format 'Trajectory format' SubClassOf 'is format of' some 'Trajectory data' 'Trajectory format' SubClassOf 'Format (by type of data)' http://edamontology.org/topic_3912 Genetic engineering 'Genetic engineering' SubClassOf 'Genetics' 'Genetic engineering' SubClassOf 'Biotechnology' http://edamontology.org/topic_3895 Synthetic biology 'Synthetic biology' SubClassOf 'Biotechnology' 'Synthetic biology' SubClassOf 'Biology' http://edamontology.org/topic_3892 Biomolecular simulation 'Biomolecular simulation' SubClassOf 'Computational biology' http://edamontology.org/operation_3899 Protein-protein docking 'Protein-protein docking' SubClassOf 'has output' some 'Protein-ligand complex' 'Protein-protein docking' SubClassOf 'has topic' some 'Protein interactions' 'Protein-protein docking' SubClassOf 'Molecular docking' http://edamontology.org/operation_3898 Metal-binding site prediction 'Metal-binding site prediction' SubClassOf 'Binding site prediction' http://edamontology.org/operation_3897 Ligand-binding site prediction 'Ligand-binding site prediction' SubClassOf 'Binding site prediction' http://edamontology.org/operation_3896 Active site prediction 'Active site prediction' SubClassOf 'Binding site prediction' http://edamontology.org/operation_3891 Essential dynamics 'Essential dynamics' SubClassOf 'Simulation analysis' 'Essential dynamics' SubClassOf 'Nucleic acid structure analysis' http://edamontology.org/operation_3890 Trajectory visualization 'Trajectory visualization' SubClassOf 'Structure visualisation' 'Trajectory visualization' SubClassOf 'has output' some 'Helical wheel' http://edamontology.org/operation_3894 DNA profiling 'DNA profiling' SubClassOf 'Nucleic acid sequence analysis' http://edamontology.org/operation_3893 Forcefield parameterisation 'Forcefield parameterisation' SubClassOf 'Modelling and simulation' 'Forcefield parameterisation' SubClassOf 'has output' some 'DNA substitution model' 'Forcefield parameterisation' SubClassOf 'has topic' some 'Phylogeny' http://edamontology.org/operation_3903 DNA binding site prediction 'DNA binding site prediction' SubClassOf 'Nucleic acids-binding site prediction' http://edamontology.org/operation_3902 RNA binding site prediction 'RNA binding site prediction' SubClassOf 'Nucleic acids-binding site prediction' http://edamontology.org/operation_3901 RNA-binding protein prediction 'RNA-binding protein prediction' SubClassOf 'Protein-nucleic acid interaction analysis' 'RNA-binding protein prediction' SubClassOf 'has topic' some 'Protein interactions' 'RNA-binding protein prediction' SubClassOf 'has output' some 'Protein interaction data' http://edamontology.org/operation_3900 DNA-binding protein prediction 'DNA-binding protein prediction' SubClassOf 'Protein-nucleic acid interaction analysis' 'DNA-binding protein prediction' SubClassOf 'has topic' some 'Protein interactions' 'DNA-binding protein prediction' SubClassOf 'has output' some 'Protein interaction data' http://edamontology.org/operation_3907 Information extraction 'Information extraction' SubClassOf 'Text mining' http://edamontology.org/operation_3904 Protein disorder prediction 'Protein disorder prediction' SubClassOf 'has topic' some 'Microbiology' 'Protein disorder prediction' SubClassOf 'Prediction and recognition' 'Protein disorder prediction' SubClassOf 'Protein feature detection' http://edamontology.org/operation_3908 Information retrieval 'Information retrieval' SubClassOf 'Text mining' http://edamontology.org/data_3869 Simulation 'Simulation' SubClassOf 'Data' http://edamontology.org/data_3870 Trajectory data 'Trajectory data' SubClassOf 'Simulation' http://edamontology.org/data_3871 Forcefield parameters 'Forcefield parameters' SubClassOf 'Simulation' http://edamontology.org/data_3872 Topology data 'Topology data' SubClassOf 'Simulation' http://edamontology.org/data_3905 Histogram 'Histogram' SubClassOf 'Plot' http://edamontology.org/data_2399 Gene transcriptional features report 'Gene transcriptional features report' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2397 Gene features report (exon) 'Gene features report (exon)' 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 http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_0922 Nucleic acid features report (primers) 'Nucleic acid features report (primers)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2754 Gene features report (intron) 'Gene features report (intron)' 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 http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2867 Nucleic acid features report (VNTR) 'Nucleic acid features report (VNTR)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2868 Nucleic acid features report (microsatellite) 'Nucleic acid features report (microsatellite)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2885 Nucleic acid features report (polymorphism) 'Nucleic acid features report (polymorphism)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_2533 Nucleic acid features report (mutation) 'Nucleic acid features report (mutation)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3118 Protein features report (topological domains) 'Protein features report (topological domains)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3125 Nucleic acid features report (binding) 'Nucleic acid features report (binding)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3126 Nucleic acid repeats (report) 'Nucleic acid repeats (report)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3127 Nucleic acid features report (replication and recombination) 'Nucleic acid features report (replication and recombination)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3123 Nucleic acid features report (expression signal) 'Nucleic acid features report (expression signal)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3139 Nucleic acid features report (STS) 'Nucleic acid features report (STS)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_3135 Nucleic acid features report (signal or transit peptide) 'Nucleic acid features report (signal or transit peptide)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1305 Nucleic acid features report (restriction sites) 'Nucleic acid features report (restriction sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1304 Nucleic acid features report (CpG island and isochore) 'Nucleic acid features report (CpG island and isochore)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1308 Nucleic acid features report (matrix/scaffold attachment sites) 'Nucleic acid features report (matrix/scaffold attachment sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1307 Nucleic acid features report (splice sites) 'Nucleic acid features report (splice sites)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1302 Nucleic acid features report (PolyA signal or site) 'Nucleic acid features report (PolyA signal or site)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1312 Nucleic acid features report (promoters) 'Nucleic acid features report (promoters)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass http://edamontology.org/data_1311 Gene features report (operon) 'Gene features report (operon)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass