{ "bcoid": "GLY_000253", "title": "Rat Protein Citations (UniProtKB)", "description": "The Rat Protein Citations dataset contains publication information for Rattus norvegicus [taxid:10116] ...", "filename_list": "rat_protein_citations_uniprotkb.csv", "filename": "rat_protein_citations_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Rattus norvegicus" ], "molecule": [ "Protein" ], "tag": [ "Protein Citations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P83858-1...", "A neuropepti..." ], [ "Q9WUD9-1...", "The N2-Src n..." ] ], "headers": [ "uniprotkb_ca...", "title..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "title" }, { "type": "string", "label": "journal_name" }, { "type": "string", "label": "publication_date" }, { "type": "string", "label": "authors" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" } ], [ "P83858-1", "A neuropeptide ligand of the G protein-coupled receptor GPR103 regulates feeding, behavioral arousal, and blood pressure in mice.", "Proceedings of the National Academy of Sciences of the United States of America", "2006 May 9", "Takayasu S, Sakurai T, Iwasaki S, Teranishi H, Yamanaka A, Williams SC, Iguchi H, Kawasawa YI, Ikeda Y, Sakakibara I, Ohno K, Ioka RX, Murakami S, Dohmae N, Xie J, Suda T, Motoike T, Ohuchi T, Yanagisawa M, Sakai J", "protein_xref_pubmed", "16648250", "protein_xref_uniprotkb", "P83858" ], [ "Q9WUD9-1", "The N2-Src neuronal splice variant of C-Src has altered SH3 domain ligand specificity and a higher constitutive activity than N1-Src.", "FEBS letters", "2015 Jul 8", "Keenan S, Lewis PA, Wetherill SJ, Dunning CJ, Evans GJ", "protein_xref_pubmed", "26026271", "protein_xref_uniprotkb", "Q9WUD9" ] ] }, "readme": "Name\n - Rat Protein Citations (UniProtKB)\n\nVersion\n - v-2.10.1\n\nCreated on\n - 2019-09-06T14:06:38.980261\n\nModified on\n - 2024-05-17T11:23:53.776Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@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 Protein Citations dataset contains publication information for Rattus norvegicus [taxid:10116] UniProtKB accessions that includes PMID, journal name, date and author and title. Publications of large scale studies, and high frequency publications pertaining to genome sequencing, cDNA, chromosomes have been filtered out. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen. \n\nDescription Domain\n Keywords\n - publications\n - PMID\n - journal\n - citations\n - authors\n - UniProtKB\n - PubMed\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB publication data from the triplestore containing triples from nt file to retrieve the publication information associated with the UniProtKB accession and maps it to the UniProtKB canonical accessions. The script also filters out publications of large scale studies, and high frequency publications pertaining to DNA sequencing, cDNA, chromosomes using blacklisted PMIDs file. \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: all_blacklisted_pmids.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/compiled/all_blacklisted_pmids.csv\n Name: rat_protein_blacklisted_pmids_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/compiled/rat_protein_blacklisted_pmids_uniprotkb.csv\n Name: rat_protein_function_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/rat_protein_function_uniprotkb.csv\n Name: rat_protein_ptm_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/rat_protein_ptm_annotation_uniprotkb.csv\n Name: rat_protein_site_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/rat_protein_site_annotation_uniprotkb.csv\n Name: uniprot-proteome-rattus-norvegicus.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2025_10_01/uniprot-proteome-rattus-norvegicus.nt\n Output Subdomain\n Name: rat_protein_citations_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/rat_protein_citations_uniprotkb.csv\n Name: rat_protein_citations_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/rat_protein_citations_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"8897\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"13735\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"965\"\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: \"3515\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"13531\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"13703\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"9129\"", "downloadurl": "/ln2data/releases/data/v-2.10.1/reviewed/rat_protein_citations_uniprotkb.csv" }