{ "bcoid": "GLY_000429", "title": "SARS-CoV1 Gene Ontology (GO)", "description": "The SARS coronavirus (SARS-CoV-1) Gene Ontology (GO) dataset contains sarscov1 [taxid:694009] Gene Ontology ...", "filename": "sarscov1_protein_go_annotation.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-1)", "molecule": "Protein", "tags": "Gene Ontology (Go)", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P59596-1...", "M..." ], [ "P59596-1...", "M..." ] ], "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" } ], [ "P59596-1", "M", "GO_0019049", "mitigation of host antiviral defense response", "biological_process", "", "" ], [ "P59596-1", "M", "GO_0016020", "membrane", "cellular_component", "", "" ], [ "P59596-1", "M", "GO_0042802", "identical protein binding", "molecular_function", "", "" ], [ "P59596-1", "M", "GO_0019031", "viral envelope", "cellular_component", "", "" ], [ "P59596-1", "M", "GO_0055036", "virion membrane", "cellular_component", "", "" ], [ "P59596-1", "M", "GO_0039660", "structural constituent of virion", "molecular_function", "", "" ], [ "P59596-1", "M", "GO_0044178", "host cell Golgi membrane", "cellular_component", "", "" ], [ "P59594-1", "S", "GO_0016020", "membrane", "cellular_component", "", "" ], [ "P59594-1", "S", "GO_0042802", "identical protein binding", "molecular_function", "", "" ], [ "P59594-1", "S", "GO_0046598", "positive regulation of viral entry into host cell", "biological_process", "", "" ], [ "P59594-1", "S", "GO_0046718", "viral entry into host cell", "biological_process", "", "" ], [ "P59594-1", "S", "GO_0046813", "receptor-mediated virion attachment to host cell", "biological_process", "", "" ], [ "P59594-1", "S", "GO_0061025", "membrane fusion", "biological_process", "", "" ], [ "P59594-1", "S", "GO_0019031", "viral envelope", "cellular_component", "", "" ], [ "P59594-1", "S", "GO_0039502", "suppression by virus of host type I interferon-mediated signaling pathway", "biological_process", "", "" ], [ "P59594-1", "S", "GO_0019065", "receptor-mediated endocytosis of virus by host cell", "biological_process", "", "" ], [ "P59594-1", "S", "GO_0019064", "fusion of virus membrane with host plasma membrane", "biological_process", "", "" ], [ "P59594-1", "S", "GO_0046789", "host cell surface receptor binding", "molecular_function", "", "" ], [ "P59594-1", "S", "GO_0055036", "virion membrane", "cellular_component", "", "" ], [ "P59594-1", "S", "GO_0039587", "suppression by virus of host tetherin activity", "biological_process", "", "" ], [ "P59594-1", "S", "GO_0044173", "host cell endoplasmic reticulum-Golgi intermediate compartment membrane", "cellular_component", "", "" ], [ "P59594-1", "S", "GO_0075509", "endocytosis involved in viral entry into host cell", "biological_process", "", "" ], [ "P59594-1", "S", "GO_0020002", "host cell plasma membrane", "cellular_component", "", "" ], [ "P59594-1", "S", "GO_0039654", "fusion of virus membrane with host endosome membrane", "biological_process", "", "" ], [ "P59595-1", "N", "GO_0019074", "viral RNA genome packaging", "biological_process", "", "" ], [ "P59595-1", "N", "GO_0060090", "molecular adaptor activity", "molecular_function", "", "" ], [ "P59595-1", "N", "GO_0003677", "DNA binding", "molecular_function", "", "" ], [ "P59595-1", "N", "GO_0003723", "RNA binding", "molecular_function", "", "" ], [ "P59595-1", "N", "GO_0005886", "plasma membrane", "cellular_component", "", "" ], [ "P59595-1", "N", "GO_0042802", "identical protein binding", "molecular_function", "", "" ], [ "P59595-1", "N", "GO_0032688", "negative regulation of interferon-beta production", "biological_process", "", "" ], [ "P59595-1", "N", "GO_1990904", "ribonucleoprotein complex", "cellular_component", "", "" ], [ "P59595-1", "N", "GO_0019028", "viral capsid", "cellular_component", "", "" ], [ "P59595-1", "N", "GO_0019013", "viral nucleocapsid", "cellular_component", "", "" ], [ "P59595-1", "N", "GO_0044220", "host cell perinuclear region of cytoplasm", "cellular_component", "", "" ], [ "P59595-1", "N", "GO_0044172", "host cell endoplasmic reticulum-Golgi intermediate compartment", "cellular_component", "", "" ], [ "P59595-1", "N", "GO_0044177", "host cell Golgi apparatus", "cellular_component", "", "" ], [ "P0C6U8-1", "", "GO_0019082", "viral protein processing", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0003968", "RNA-dependent RNA polymerase activity", "molecular_function", "", "" ], [ "P0C6U8-1", "", "GO_0006508", "proteolysis", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0008242", "omega peptidase activity", "molecular_function", "", "" ], [ "P0C6U8-1", "", "GO_0008270", "zinc ion binding", "molecular_function", "", "" ], [ "P0C6U8-1", "", "GO_0016020", "membrane", "cellular_component", "", "" ], [ "P0C6U8-1", "", "GO_0019083", "viral transcription", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0042802", "identical protein binding", "molecular_function", "", "" ], [ "P0C6U8-1", "", "GO_0046983", "protein dimerization activity", "molecular_function", "", "" ], [ "P0C6U8-1", "", "GO_0070536", "protein K63-linked deubiquitination", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0003725", "double-stranded RNA binding", "molecular_function", "", "" ], [ "P0C6U8-1", "", "GO_0003727", "single-stranded RNA binding", "molecular_function", "", "" ], [ "P0C6U8-1", "", "GO_0004519", "endonuclease activity", "molecular_function", "", "" ], [ "P0C6U8-1", "", "GO_0002151", "G-quadruplex RNA binding", "molecular_function", "", "" ], [ "P0C6U8-1", "", "GO_0016540", "protein autoprocessing", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0019079", "viral genome replication", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0004197", "cysteine-type endopeptidase activity", "molecular_function", "", "" ], [ "P0C6U8-1", "", "GO_0016829", "lyase activity", "molecular_function", "", "" ], [ "P0C6U8-1", "", "GO_0039502", "suppression by virus of host type I interferon-mediated signaling pathway", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0004843", "cysteine-type deubiquitinase activity", "molecular_function", "", "" ], [ "P0C6U8-1", "", "GO_0071108", "protein K48-linked deubiquitination", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0039520", "induction by virus of host autophagy", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0039694", "viral RNA genome replication", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0044220", "host cell perinuclear region of cytoplasm", "cellular_component", "", "" ], [ "P0C6U8-1", "", "GO_0019785", "ISG15-specific peptidase activity", "molecular_function", "", "" ], [ "P0C6U8-1", "", "GO_0039657", "suppression by virus of host gene expression", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0039519", "modulation by virus of host autophagy", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0039548", "suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0039579", "suppression by virus of host ISG15-protein conjugation", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0039595", "induction by virus of catabolism of host mRNA", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0039604", "suppression by virus of host translation", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0039648", "modulation by virus of host protein ubiquitination", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0039690", "positive stranded viral RNA replication", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0030430", "host cell cytoplasm", "cellular_component", "", "" ], [ "P0C6U8-1", "", "GO_0039644", "suppression by virus of host NF-kappaB cascade", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0039714", "cytoplasmic viral factory", "cellular_component", "", "" ], [ "P0C6U8-1", "", "GO_0044165", "host cell endoplasmic reticulum", "cellular_component", "", "" ], [ "P0C6U8-1", "", "GO_0044177", "host cell Golgi apparatus", "cellular_component", "", "" ], [ "P0C6U8-1", "", "GO_0039501", "suppression by virus of host type I interferon production", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0039722", "suppression by virus of host toll-like receptor signaling pathway", "biological_process", "", "" ], [ "P0C6U8-1", "", "GO_0044174", "host cell endosome", "cellular_component", "", "" ], [ "P0C6U8-1", "", "GO_0062243", "double membrane vesicle viral factory outer membrane", "cellular_component", "", "" ], [ "P0C6U8-1", "", "GO_0039527", "suppression by virus of host TRAF-mediated signal transduction", "biological_process", "", "" ], [ "P59637-1", "E", "GO_0016020", "membrane", "cellular_component", "", "" ], [ "P59637-1", "E", "GO_0042802", "identical protein binding", "molecular_function", "", "" ], [ "P59637-1", "E", "GO_0055036", "virion membrane", "cellular_component", "", "" ], [ "P59637-1", "E", "GO_0044172", "host cell endoplasmic reticulum-Golgi intermediate compartment", "cellular_component", "", "" ] ] }, "readme": "Name\n - SARS-CoV1 Gene Ontology (GO)\n\nVersion\n - v-2.0.3\n\nCreated on\n - 2020-04-03T11:46:41.584409\n\nModified on\n - 2022-09-26T09:05:56.484478\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.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-1) Gene Ontology (GO) dataset contains sarscov1 [taxid:694009] 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 sequences.\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/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-coronavirus.nt\n URI: /data/shared/glyds/downloads/ebi/2022_05/uniprot-proteome-sars-coronavirus.nt\n Output Subdomain\n Name: sarscov1_protein_go_annotation.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/sarscov1_protein_go_annotation.csv\n Name: sarscov1_protein_go_annotation.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/sarscov1_protein_go_annotation.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"14\"\n Name: \"gene_symbol\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene names/symbols are approved by the HUGO Gene Nomenclature Committee (HGNC)\"\n Unique Values: \"6\"\n Name: \"go_term_id\"\n Description: \"The Gene Ontology (GO) term unique alphanumeric identifier\"\n Unique Values: \"120\"\n Name: \"go_term_label\"\n Description: \"The Gene Ontology (GO) name that is a word or string of words\"\n Unique Values: \"120\"\n Name: \"go_term_category\"\n Description: \"\"The Gene Ontology (GO) domain to which the term belongs. There are three ontology domain in GO - cellular component\"\n Unique Values: \"3\"\n Name: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"1\"\n Name: \"pmid\"\n Description: \"NCBI PubMed database Identifier\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.0.3/reviewed/sarscov1_protein_go_annotation.csv" }