{ "bcoid": "GLY_000253", "title": "Rat Protein Citations (UniProtKB)", "description": "The Rat Protein Citations dataset contains publication information for rat [taxid:10116] UniProtKB accessions ...", "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": [ [ "D3ZB48-1...", "Quantitative..." ], [ "P11980-1...", "Quantitative..." ] ], "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" } ], [ "D3ZB48-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "D3ZB48" ], [ "P11980-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "A0A0G2JVG3" ], [ "Q5M9G6-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "Q5M9G6" ], [ "Q07969-1", "Luminal lipid regulates CD36 levels and downstream signaling to stimulate chylomicron synthesis.", "J. Biol. Chem.", "2011", "Tran TT, Poirier H, Clement L, Nassir F, Pelsers MM, Petit V, Degrace P, Monnot MC, Glatz JF, Abumrad NA, Besnard P, Niot I", "protein_xref_pubmed", "21610069", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "CD36 involvement in orosensory detection of dietary lipids, spontaneous fat preference, and digestive secretions.", "J. Clin. Invest.", "2005", "Laugerette F, Passilly-Degrace P, Patris B, Niot I, Febbraio M, Montmayeur JP, Besnard P", "protein_xref_pubmed", "16276419", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "FAT/CD36: a major regulator of neuronal fatty acid sensing and energy homeostasis in rats and mice.", "Diabetes", "2013", "Dunn-Meynell A., Le Foll C., Levin B.E., Magnan C., Musatov S.", "protein_xref_pubmed", "23557700", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Fatty acid translocase/CD36 mediates the uptake of palmitate by type II pneumocytes.", "Am. J. Physiol.", "1999", "Spener F., Haupt R., Guthmann F., Looman A.C., Ruestow B.", "protein_xref_pubmed", "10409247", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Purification of the major substrate for palmitoylation in rat adipocytes: N-terminal homology with CD36 and evidence for cell surface acylation.", "J. Lipid Res.", "1993", "Hays J., Jochen A.", "protein_xref_pubmed", "7504047", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Cloning of a rat adipocyte membrane protein implicated in binding or transport of long-chain fatty acids that is induced during preadipocyte differentiation. Homology with human CD36.", "J. Biol. Chem.", "1993", "Abumrad NA, el-Maghrabi MR, Amri EZ, Lopez E, Grimaldi PA", "protein_xref_pubmed", "7688729", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Binding of sulfosuccinimidyl fatty acids to adipocyte membrane proteins: isolation and amino-terminal sequence of an 88-kD protein implicated in transport of long-chain fatty acids.", "J. Membr. Biol.", "1993", "Abumrad N.A., Harmon C.M.", "protein_xref_pubmed", "8320718", "protein_xref_uniprotkb", "Q07969" ], [ "A0A096MJY4-1", "MEF2C DNA-binding activity is inhibited through its interaction with the regulatory protein Ki-1/57.", "FEBS Lett.", "2005", "Kobarg CB, Kobarg J, Crosara-Alberto DP, Theizen TH, Franchini KG", "protein_xref_pubmed", "15862299", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A0G2KA92-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "A0A096MJY0" ], [ "A0A8J8XIU8-1", "Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites.", "Proc. Natl. Acad. Sci. U.S.A.", "2006", "Hoffert JD, Pisitkun T, Wang G, Shen RF, Knepper MA", "protein_xref_pubmed", "16641100", "protein_xref_uniprotkb", "A0A8J8XIU8" ], [ "A0A8J8XIU8-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "A0A8J8XIU8" ], [ "A0A8J8XIU8-1", "Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites.", "Proc. Natl. Acad. Sci. U.S.A.", "2006", "Hoffert JD, Pisitkun T, Wang G, Shen RF, Knepper MA", "protein_xref_pubmed", "16641100", "protein_xref_uniprotkb", "A0A8J8XIU1" ], [ "A0A8J8XIU8-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "A0A8J8XIU1" ], [ "Q62949-1", "A cortical neuropeptide with neuronal depressant and sleep-modulating properties.", "Nature", "1996", "de Lecea L, Criado JR, Prospero-Garcia O, Gautvik KM, Schweitzer P, Danielson PE, Dunlop CL, Siggins GR, Henriksen SJ, Sutcliffe JG", "protein_xref_pubmed", "8622767", "protein_xref_uniprotkb", "Q62949" ], [ "P01946-1", "Novel natural peptide substrates for endopeptidase 24.15, neurolysin, and angiotensin-converting enzyme.", "J. Biol. 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Biochem.", "1990", "Pages G, Rouayrenc JF, Le Cam G, Mariller M, Le Cam A", "protein_xref_pubmed", "1694763", "protein_xref_uniprotkb", "P09006" ], [ "P09006-1", "Molecular cloning and characterization of rat contrapsin-like protease inhibitor and related proteins.", "J. Biochem.", "1991", "Ikehara Y., Misumi Y., Ogata S., Ohkubo K., Takami N.", "protein_xref_pubmed", "1864837", "protein_xref_uniprotkb", "P09006" ], [ "P09006-1", "Accelerated evolution in the reactive centre regions of serine protease inhibitors.", "Nature", "1987", "Hastie N.D., Hill R.E.", "protein_xref_pubmed", "3493437", "protein_xref_uniprotkb", "P09006" ], [ "P09006-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "P09006" ], [ "D4A781-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "M0RB74" ], [ "Q9JHY8-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "Q9JHY8" ] ] }, "readme": "Name\n - Rat Protein Citations (UniProtKB)\n\nVersion\n - v-2.2.1\n\nCreated on\n - 2019-09-06T14:06:38.980261\n\nModified on\n - 2022-09-26T09:04:47.895366\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@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 Protein Citations dataset contains publication information for rat [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 as per https://data.glygen.org/ln2data/releases/data/v-1.12.3/compiled/rat_protein_blacklisted_pmids_uniprotkb.csv. 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 - 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: rat_protein_blacklisted_pmids_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/compiled/rat_protein_blacklisted_pmids_uniprotkb.csv\n Name: uniprot-proteome-rattus-norvegicus.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2023_10_30/uniprot-proteome-rattus-norvegicus.nt\n Output Subdomain\n Name: rat_protein_citations_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/rat_protein_citations_uniprotkb.csv\n Name: rat_protein_citations_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/rat_protein_citations_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"8802\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"13249\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"666\"\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: \"60\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"13086\"\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: \"13259\"\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: \"11264\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/rat_protein_citations_uniprotkb.csv" }