{ "bcoid": "GLY_000430", "title": "SARS-CoV2 Gene Ontology (GO)", "description": "The SARS coronavirus (SARS-CoV-2 or 2019-nCov) Gene Ontology (GO) dataset contains sarscov2 [taxid:2697049] ...", "filename": "sarscov2_protein_go_annotation.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-2 or 2019-nCoV)", "molecule": "Protein", "tags": "Gene Ontology (Go)", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P0DTD2-1...", "..." ], [ "P0DTD2-1...", "..." ] ], "headers": [ "uniprotkb_ca...", "gene_symbol..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "gene_symbol" }, { "type": "string", "label": "go_term_id" }, { "type": "string", "label": "go_term_label" }, { "type": "string", "label": "go_term_category" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "pmid" } ], [ "P0DTD2-1", "", "GO_0042025", "host cell nucleus", "cellular_component", "", "" ], [ "P0DTD2-1", "", "GO_0016020", "membrane", "cellular_component", "", "" ], [ "P0DTD2-1", "", "GO_0019012", "virion", "cellular_component", "", "" ], [ "P0DTD2-1", "", "GO_0033650", "host cell mitochondrion", "cellular_component", "", "" ], [ "P0DTD2-1", "", "GO_0044162", "host cell cytoplasmic vesicle membrane", "cellular_component", "", "" ], [ "P0DTD2-1", "", "GO_0039545", "suppression by virus of host MAVS activity", "biological_process", "", "" ], [ "P0DTD2-1", "", "GO_0044165", "host cell endoplasmic reticulum", "cellular_component", "", "" ], [ "P0DTD1-1", "rep", "GO_0042802", "identical protein binding", "molecular_function", "ECO_0000353", "32198291" ], [ "P0DTD1-1", "rep", "GO_0042802", "identical protein binding", "molecular_function", "ECO_0000353", "32745548" ], [ "P0DTD1-1", "rep", "GO_0042802", "identical protein binding", "molecular_function", "ECO_0000353", "32592996" ], [ "P0DTD1-1", "rep", "GO_0042803", "protein homodimerization activity", "molecular_function", "ECO_0000314", "32198291" ], [ "P0DTD1-1", "rep", "GO_0008234", "cysteine-type peptidase activity", "molecular_function", "ECO_0000314", "32198291" ], [ "P0DTD1-1", "rep", "GO_0004483", "mRNA (nucleoside-2'-O-)-methyltransferase activity", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0080009", "mRNA methylation", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0019082", "viral protein processing", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0003968", "RNA-directed 5'-3' RNA polymerase activity", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0005524", "ATP binding", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0006351", "transcription, DNA-templated", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0008270", "zinc ion binding", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0016021", "integral component of membrane", "cellular_component", "", "" ], [ "P0DTD1-1", "rep", "GO_0019083", "viral transcription", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0046983", "protein dimerization activity", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0070536", "protein K63-linked deubiquitination", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0003727", "single-stranded RNA binding", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0004519", "endonuclease activity", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0008168", "methyltransferase activity", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0004527", "exonuclease activity", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0016540", "protein autoprocessing", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0019079", "viral genome replication", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0004386", "helicase activity", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0004197", "cysteine-type endopeptidase activity", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0032259", "methylation", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0003678", "DNA helicase activity", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0000175", "3'-5'-exoribonuclease activity", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0090503", "RNA phosphodiester bond hydrolysis, exonucleolytic", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0039502", "suppression by virus of host type I interferon-mediated signaling pathway", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0004843", "thiol-dependent ubiquitin-specific protease activity", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0071108", "protein K48-linked deubiquitination", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0039520", "induction by virus of host autophagy", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0039694", "viral RNA genome replication", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0003724", "RNA helicase activity", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0044220", "host cell perinuclear region of cytoplasm", "cellular_component", "", "" ], [ "P0DTD1-1", "rep", "GO_0001172", "transcription, RNA-templated", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0019785", "ISG15-specific protease activity", "molecular_function", "", "" ], [ "P0DTD1-1", "rep", "GO_0039519", "modulation by virus of host autophagy", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0039548", "suppression by virus of host IRF3 activity", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0039579", "suppression by virus of host ISG15 activity", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0039595", "induction by virus of catabolism of host mRNA", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0039604", "suppression by virus of host translation", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0039648", "modulation by virus of host protein ubiquitination", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0039690", "positive stranded viral RNA replication", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0044172", "host cell endoplasmic reticulum-Golgi intermediate compartment", "cellular_component", "", "" ], [ "P0DTD1-1", "rep", "GO_0030430", "host cell cytoplasm", "cellular_component", "", "" ], [ "P0DTD1-1", "rep", "GO_0033644", "host cell membrane", "cellular_component", "", "" ], [ "P0DTD1-1", "rep", "GO_0039547", "suppression by virus of host TRAF activity", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0039644", "suppression by virus of host NF-kappaB transcription factor activity", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0039714", "cytoplasmic viral factory", "cellular_component", "", "" ], [ "P0DTD1-1", "rep", "GO_0039501", "suppression by virus of host type I interferon production", "biological_process", "", "" ], [ "P0DTD1-1", "rep", "GO_0039722", "suppression by virus of host toll-like receptor signaling pathway", "biological_process", "", "" ], [ "P0DTD3-1", "", "GO_0016021", "integral component of membrane", "cellular_component", "", "" ], [ "P0DTC7-1", "", "GO_0016021", "integral component of membrane", "cellular_component", "", "" ], [ "P0DTC7-1", "", "GO_0039502", "suppression by virus of host type I interferon-mediated signaling pathway", "biological_process", "", "" ], [ "P0DTC7-1", "", "GO_0019012", "virion", "cellular_component", "", "" ], [ "P0DTC7-1", "", "GO_0039587", "suppression by virus of host tetherin activity", "biological_process", "", "" ], [ "P0DTC7-1", "", "GO_0039646", "modulation by virus of host G0/G1 transition checkpoint", "biological_process", "", "" ], [ "P0DTC7-1", "", "GO_0044173", "host cell endoplasmic reticulum-Golgi intermediate compartment membrane", "cellular_component", "", "" ], [ "P0DTC7-1", "", "GO_0044178", "host cell Golgi membrane", "cellular_component", "", "" ], [ "P0DTC7-1", "", "GO_0044167", "host cell endoplasmic reticulum membrane", "cellular_component", "", "" ], [ "P0DTC6-1", "", "GO_0016020", "membrane", "cellular_component", "", "" ], [ "P0DTC6-1", "", "GO_0009405", "pathogenesis", "biological_process", "", "" ], [ "P0DTC6-1", "", "GO_0044178", "host cell Golgi membrane", "cellular_component", "", "" ], [ "P0DTC6-1", "", "GO_0044167", "host cell endoplasmic reticulum membrane", "cellular_component", "", "" ], [ "P0DTC5-1", "", "GO_0030683", "mitigation of host immune response by virus", "biological_process", "", "" ], [ "P0DTC5-1", "", "GO_0016021", "integral component of membrane", "cellular_component", "", "" ], [ "P0DTC5-1", "", "GO_0019031", "viral envelope", "cellular_component", "", "" ], [ "P0DTC5-1", "", "GO_0055036", "virion membrane", "cellular_component", "", "" ], [ "P0DTC5-1", "", "GO_0039660", "structural constituent of virion", "molecular_function", "", "" ], [ "P0DTC5-1", "", "GO_0044178", "host cell Golgi membrane", "cellular_component", "", "" ], [ "P0DTC4-1", "E", "GO_0016021", "integral component of membrane", "cellular_component", "", "" ], [ "P0DTC4-1", "E", "GO_0044178", "host cell Golgi membrane", "cellular_component", "", "" ], [ "P0DTC4-1", "E", "GO_0046760", "viral budding from Golgi membrane", "biological_process", "", "" ], [ "P0DTC4-1", "E", "GO_0039707", "pore formation by virus in membrane of host cell", "biological_process", "", "" ], [ "P0DTC3-1", "", "GO_0005216", "ion channel activity", "molecular_function", "", "" ], [ "P0DTC3-1", "", "GO_0005576", "extracellular region", "cellular_component", "", "" ] ] }, "readme": "Name\n - SARS-CoV2 Gene Ontology (GO)\n\nVersion\n - 1.8.24\n\nCreated on\n - 2020-04-03T11:46:41.584409\n\nModified on\n - 2020-04-10T12:26:18.336828\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The SARS coronavirus (SARS-CoV-2 or 2019-nCov) Gene Ontology (GO) dataset contains sarscov2 [taxid:2697049] Gene Ontology Id and name, categories and evidence information for UniProtKB canonical accessions. The dataset is derived from 2020-01 UniProt release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - go id\n - go name\n - molecular function\n - biological process\n - cellular component\n - Gene Ontology (GO)\n\n Pipeline Steps\n - Step-1: The script extracts the GO Id, name, category and evidence from the triplestore of NT file and maps it to the UniProtKB canonical sequnces\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: uniprot-proteome-sars-cov-2.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.24/source/uniprot-proteome-sars-cov-2.nt\n Name: sarscov2_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/sarscov2_protein_masterlist.csv\n Output Subdomain\n Name: sarscov2_protein_go_annotation.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/sarscov2_protein_go_annotation.csv\n Name: sarscov2_protein_go_annotation.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/sarscov2_protein_go_annotation.stat.csv\n\nFields\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"119\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"119\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"120\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"49\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"118\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"117\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"115\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.8.24/reviewed/sarscov2_protein_go_annotation.csv" }