{ "bcoid": "GLY_000242", "title": "Rat Gene Ontology (GO)", "description": "The Rat Gene Ontology (GO) dataset contains rat [taxid:10116] Gene Ontology Id and name, categories and ...", "filename": "rat_protein_go_annotation.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Protein", "tags": "Gene Ontology (Go)", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q5RJZ1-1...", "Rtel1..." ], [ "Q5RJZ1-1...", "Rtel1..." ] ], "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" } ], [ "Q5RJZ1-1", "Rtel1", "GO_0003677", "DNA binding", "molecular_function", "", "" ], [ "Q5RJZ1-1", "Rtel1", "GO_0005524", "ATP binding", "molecular_function", "", "" ], [ "Q5RJZ1-1", "Rtel1", "GO_0005634", "nucleus", "cellular_component", "", "" ], [ "Q5RJZ1-1", "Rtel1", "GO_0006281", "DNA repair", "biological_process", "", "" ], [ "Q5RJZ1-1", "Rtel1", "GO_0006310", "DNA recombination", "biological_process", "", "" ], [ "Q5RJZ1-1", "Rtel1", "GO_0046872", "metal ion binding", "molecular_function", "", "" ], [ "Q5RJZ1-1", "Rtel1", "GO_0051539", "4 iron, 4 sulfur cluster binding", "molecular_function", "", "" ], [ "Q5RJZ1-1", "Rtel1", "GO_0016887", "ATP hydrolysis activity", "molecular_function", "", "" ], [ "Q5RJZ1-1", "Rtel1", "GO_0000723", "telomere maintenance", "biological_process", "", "" ], [ "Q5RJZ1-1", "Rtel1", "GO_0006260", "DNA replication", "biological_process", "", "" ], [ "Q5RJZ1-1", "Rtel1", "GO_0003678", "DNA helicase activity", "molecular_function", "", "" ], [ "Q5RJZ1-1", "Rtel1", "GO_0010569", "regulation of double-strand break repair via homologous recombination", "biological_process", "", "" ], [ "A0A0G2K1R8-1", "Senp1", "GO_0016929", "deSUMOylase activity", "molecular_function", "", "" ], [ "A0A0G2K1R8-1", "Senp1", "GO_0010724", "regulation of definitive erythrocyte differentiation", "biological_process", "", "" ], [ "A0A0G2K1R8-1", "Senp1", "GO_0005634", "nucleus", "cellular_component", "", "" ], [ "A0A0G2K1R8-1", "Senp1", "GO_0045944", "positive regulation of transcription by RNA polymerase II", "biological_process", "", "" ], [ "A0A0G2K1R8-1", "Senp1", "GO_0097190", "apoptotic signaling pathway", "biological_process", "", "" ], [ "A0A0G2K1R8-1", "Senp1", "GO_0006919", "activation of cysteine-type endopeptidase activity involved in apoptotic process", "biological_process", "", "" ], [ "A0A0G2K1R8-1", "Senp1", "GO_0043161", "proteasome-mediated ubiquitin-dependent protein catabolic process", "biological_process", "", "" ], [ "A0A0G2K1R8-1", "Senp1", "GO_0032435", "negative regulation of proteasomal ubiquitin-dependent protein catabolic process", "biological_process", "", "" ], [ "A0A0G2K1R8-1", "Senp1", "GO_0070139", "SUMO-specific endopeptidase activity", "molecular_function", "", "" ], [ "A0A0G2K1R8-1", "Senp1", "GO_0016926", "protein desumoylation", "biological_process", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_1904385", "cellular response to angiotensin", "biological_process", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0000139", "Golgi membrane", "cellular_component", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0005524", "ATP binding", "molecular_function", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0005737", "cytoplasm", "cellular_component", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0005794", "Golgi apparatus", "cellular_component", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0030424", "axon", "cellular_component", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0045202", "synapse", "cellular_component", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0030659", "cytoplasmic vesicle membrane", "cellular_component", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0005770", "late endosome", "cellular_component", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0007568", "aging", "biological_process", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0004515", "nicotinate-nucleotide adenylyltransferase activity", "molecular_function", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0009435", "NAD biosynthetic process", "biological_process", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0005802", "trans-Golgi network", "cellular_component", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0000309", "nicotinamide-nucleotide adenylyltransferase activity", "molecular_function", "", "" ], [ "Q0HA29-1", "Nmnat2", "GO_0140768", "protein ADP-ribosyltransferase-substrate adaptor activity", "molecular_function", "", "" ], [ "Q9WVK3-1", "Pecr", "GO_0019166", "trans-2-enoyl-CoA reductase (NADPH) activity", "molecular_function", "", "" ], [ "Q9WVK3-1", "Pecr", "GO_0005102", "signaling receptor binding", "molecular_function", "", "" ], [ "Q9WVK3-1", "Pecr", "GO_0005777", "peroxisome", "cellular_component", "", "" ], [ "Q9WVK3-1", "Pecr", "GO_0033306", "phytol metabolic process", "biological_process", "", "" ], [ "A0A0G2JVG6-1", "Zfp59", "GO_0005634", "nucleus", "cellular_component", "", "" ], [ "A0A0G2JVG6-1", "Zfp59", "GO_0006357", "regulation of transcription by RNA polymerase II", "biological_process", "", "" ], [ "A0A0G2JVG6-1", "Zfp59", "GO_0046872", "metal ion binding", "molecular_function", "", "" ], [ "A0A0G2JVG6-1", "Zfp59", "GO_0000978", "RNA polymerase II cis-regulatory region sequence-specific DNA binding", "molecular_function", "", "" ], [ "A0A0G2JVG6-1", "Zfp59", "GO_0000981", "DNA-binding transcription factor activity, RNA polymerase II-specific", "molecular_function", "", "" ], [ "P30938-1", "Sstr5", "GO_0004994", "somatostatin receptor activity", "molecular_function", "", "" ], [ "P30938-1", "Sstr5", "GO_0004930", "G protein-coupled receptor activity", "molecular_function", "", "" ], [ "P30938-1", "Sstr5", "GO_0005737", "cytoplasm", "cellular_component", "", "" ], [ "P30938-1", "Sstr5", "GO_0005886", "plasma membrane", "cellular_component", "", "" ], [ "P30938-1", "Sstr5", "GO_0007193", "adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway", "biological_process", "", "" ], [ "P30938-1", "Sstr5", "GO_0007218", "neuropeptide signaling pathway", "biological_process", "", "" ], [ "P30938-1", "Sstr5", "GO_0042593", "glucose homeostasis", "biological_process", "", "" ], [ "P30938-1", "Sstr5", "GO_0043005", "neuron projection", "cellular_component", "", "" ], [ "P30938-1", "Sstr5", "GO_0050796", "regulation of insulin secretion", "biological_process", "", "" ], [ "P30938-1", "Sstr5", "GO_0042277", "peptide binding", "molecular_function", "", "" ], [ "P30938-1", "Sstr5", "GO_0071385", "cellular response to glucocorticoid stimulus", "biological_process", "", "" ], [ "P30938-1", "Sstr5", "GO_0032467", "positive regulation of cytokinesis", "biological_process", "", "" ], [ "P30938-1", "Sstr5", "GO_0042923", "neuropeptide binding", "molecular_function", "", "" ], [ "P32301-1", "Glp1r", "GO_0005886", "plasma membrane", "cellular_component", "", "" ], [ "P32301-1", "Glp1r", "GO_0007166", "cell surface receptor signaling pathway", "biological_process", "", "" ], [ "P32301-1", "Glp1r", "GO_0004967", "glucagon receptor activity", "molecular_function", "", "" ], [ "A0A8I5ZR95-1", "Osbp2", "GO_0005829", "cytosol", "cellular_component", "", "" ], [ "A0A8I5ZR95-1", "Osbp2", "GO_0005886", "plasma membrane", "cellular_component", "", "" ], [ "A0A8I5ZR95-1", "Osbp2", "GO_0016020", "membrane", "cellular_component", "", "" ], [ "A0A8I5ZR95-1", "Osbp2", "GO_0043231", "intracellular membrane-bounded organelle", "cellular_component", "", "" ], [ "A0A8I5ZR95-1", "Osbp2", "GO_0097038", "perinuclear endoplasmic reticulum", "cellular_component", "", "" ], [ "A0A8I5ZR95-1", "Osbp2", "GO_0007286", "spermatid development", "biological_process", "", "" ], [ "A0A8I5ZR95-1", "Osbp2", "GO_0015485", "cholesterol binding", "molecular_function", "", "" ], [ "A0A8I5ZR95-1", "Osbp2", "GO_0015248", "sterol transporter activity", "molecular_function", "", "" ], [ "A0A8I5ZR95-1", "Osbp2", "GO_0032934", "sterol binding", "molecular_function", "", "" ], [ "A0A8I5ZR95-1", "Osbp2", "GO_0097440", "apical dendrite", "cellular_component", "", "" ], [ "A0A0G2K069-1", "Col11a2", "GO_0005615", "extracellular space", "cellular_component", "", "" ], [ "A0A0G2K069-1", "Col11a2", "GO_0030198", "extracellular matrix organization", "biological_process", "", "" ], [ "A0A0G2K069-1", "Col11a2", "GO_0031012", "extracellular matrix", "cellular_component", "", "" ], [ "A0A0G2K069-1", "Col11a2", "GO_0001894", "tissue homeostasis", "biological_process", "", "" ], [ "A0A0G2K069-1", "Col11a2", "GO_0001501", "skeletal system development", "biological_process", "", "" ], [ "A0A0G2K069-1", "Col11a2", "GO_0030199", "collagen fibril organization", "biological_process", "", "" ], [ "A0A0G2K069-1", "Col11a2", "GO_0007605", "sensory perception of sound", "biological_process", "", "" ], [ "A0A0G2K069-1", "Col11a2", "GO_0048705", "skeletal system morphogenesis", "biological_process", "", "" ], [ "A0A0G2K069-1", "Col11a2", "GO_0060021", "roof of mouth development", "biological_process", "", "" ], [ "A0A0G2K069-1", "Col11a2", "GO_0001649", "osteoblast differentiation", "biological_process", "", "" ], [ "A0A0G2K069-1", "Col11a2", "GO_0002062", "chondrocyte differentiation", "biological_process", "", "" ], [ "A0A0G2K069-1", "Col11a2", "GO_0005581", "collagen trimer", "cellular_component", "", "" ] ] }, "readme": "Name\n - Rat Gene Ontology (GO)\n\nVersion\n - v-2.0.3\n\nCreated on\n - 2019-09-06T14:06:38.969307\n\nModified on\n - 2022-09-26T09:04:47.956734\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.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 Rat Gene Ontology (GO) dataset contains rat [taxid:10116] Gene Ontology Id and name, categories and evidence information for UniProtKB canonical accessions. The dataset is derived from 2019-09 UniProtKB 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-rattus-norvegicus.nt\n URI: /data/shared/glyds/downloads/ebi/2022_05/uniprot-proteome-rattus-norvegicus.nt\n Output Subdomain\n Name: rat_protein_go_annotation.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_protein_go_annotation.csv\n Name: rat_protein_go_annotation.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_protein_go_annotation.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"20748\"\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: \"21113\"\n Name: \"go_term_id\"\n Description: \"The Gene Ontology (GO) term unique alphanumeric identifier\"\n Unique Values: \"19184\"\n Name: \"go_term_label\"\n Description: \"The Gene Ontology (GO) name that is a word or string of words\"\n Unique Values: \"19184\"\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/rat_protein_go_annotation.csv" }