{ "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", "tags": "Protein Citations", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "D3ZB48-1...", "Quantitative..." ], [ "Q5M9G6-1...", "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", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "D3ZB48" ], [ "Q5M9G6-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "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", "Abumrad N.A., Besnard P., Clement L., Degrace P., Glatz J.F., Monnot M.C., Nassir F., Niot I., Pelsers M.M., Petit V., Poirier H., Tran T.T.", "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", "Febbraio M., Besnard P., Niot I., Laugerette F., Montmayeur J.P., Passilly-Degrace P., Patris B.", "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", "El-Maghrabi M.R., Lopez E., Abumrad N.A., Amri E.-Z., Grimaldi P.A.", "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 J., Crosara-Alberto D.P., Franchini K.G., Kobarg C.B., Theizen T.H.", "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", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "Q62949-1", "A cortical neuropeptide with neuronal depressant and sleep-modulating properties.", "Nature", "1996", "Danielson P.E., Sutcliffe J.G., de Lecea L., Henriksen S.J., Gautvik K.M., Criado J.R., Dunlop C.L.M., Prospero-Garcia O., Schweitzer P., Siggins G.R.", "protein_xref_pubmed", "8622767", "protein_xref_uniprotkb", "Q62949" ], [ "P01946-1", "Molecular cloning and characterization of two sets of alpha-theta genes in the rat alpha-like globin gene cluster.", "Gene", "1999", "Sato H., Okazaki T., Satoh H., Nagae Y., Inokuchi N.", "protein_xref_pubmed", "10196478", "protein_xref_uniprotkb", "P01946" ], [ "P01946-1", "The amino acid sequence of the alpha chain of the major haemoglobin of the rat (Rattus norvegicus).", "Biochem. 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Biochem.", "1997", "Pehrson J.R., Costanzi C., Dharia C.", "protein_xref_pubmed", "9138085", "protein_xref_uniprotkb", "Q02874" ], [ "Q05474-1", "The carboxyl extension of a ubiquitin-like protein is rat ribosomal protein S30.", "J. Biol. Chem.", "1993", "Olvera J., Wool I.G.", "protein_xref_pubmed", "8394356", "protein_xref_uniprotkb", "Q05474" ], [ "Q99JD4-1", "Clasps are CLIP-115 and -170 associating proteins involved in the regional regulation of microtubule dynamics in motile fibroblasts.", "Cell", "2001", "Akhmanova A., Hoogenraad C.C., Galjart N., Grosveld F., Stepanova T., Vermeulen W., Burgering B.M., Dortland B., Drabek K., Verkerk T., de Zeeuw C.I.", "protein_xref_pubmed", "11290329", "protein_xref_uniprotkb", "Q99JD4" ], [ "Q99JD4-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "Q99JD4" ], [ "Q99JD1-1", "Cross-species analysis of the mammalian beta-defensin gene family: presence of syntenic gene clusters and preferential expression in the male reproductive tract.", "Physiol. Genomics", "2005", "Cai Y., Zhang G., Sang Y., Patil A.A., Blecha F.", "protein_xref_pubmed", "16033865", "protein_xref_uniprotkb", "Q99JD1" ], [ "Q99JD1-1", "Cloning and characterization of a novel sperm-associated isoantigen (E-3) with defensin- and lectin-like motifs expressed in rat epididymis.", "Biol. Reprod.", "2003", "Herr J.C., Sherman N.E., Flickinger C.J., Wolkowicz M.J., Rao J., Bush L.A., Black M., Reddi P.P.", "protein_xref_pubmed", "12493725", "protein_xref_uniprotkb", "Q99JD1" ], [ "Q99JD3-1", "Identification of the human mitochondrial oxodicarboxylate carrier. Bacterial expression, reconstitution, functional characterization, tissue distribution and chromosomal location.", "J. Biol. Chem.", "2001", "Dolce V., Palmieri F., Ventura M., Runswick M.J., Walker J.E., Palmieri L., Fiermonte G.", "protein_xref_pubmed", "11083877", "protein_xref_uniprotkb", "Q99JD3" ], [ "Q02294-1", "Molecular cloning of the alpha-1 subunit of an omega-conotoxin-sensitive calcium channel.", "Proc. Natl. Acad. Sci. U.S.A.", "1992", "Catterall W.A., Snutch T.P., Hell J.W., Ahlijanian M.K., Dubel S.J., Enyeart J.J., Starr T.V.B.", "protein_xref_pubmed", "1317580", "protein_xref_uniprotkb", "Q02294" ], [ "Q02294-1", "Calcium channel beta-subunit binds to a conserved motif in the I-II cytoplasmic linker of the alpha 1-subunit.", "Nature", "1994", "Tanabe T., Mori Y., Campbell K.P., Snutch T.P., Pragnell M., de Waard M.", "protein_xref_pubmed", "7509046", "protein_xref_uniprotkb", "Q02294" ], [ "Q02294-1", "Differential phosphorylation of two size forms of the N-type calcium channel alpha 1 subunit which have different COOH termini.", "J. Biol. Chem.", "1994", "Catterall W.A., Warner C., Hell J.W., Appleyard S.M., Yokoyama C.T.", "protein_xref_pubmed", "8125957", "protein_xref_uniprotkb", "Q02294" ] ] }, "readme": "Name\n - Rat Protein Citations (UniProtKB)\n\nVersion\n - 1.7.10\n\nCreated on\n - 2019-09-06T14:06:38.980261\n\nModified on\n - 2020-04-10T12:01:50.512815\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]\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/ln2wwwdata/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/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-rattus-norvegicus.nt\n URI: https://data.glygen.org/ln2wwwdata/source/uniprot-proteome-rattus-norvegicus.nt\n Name: rat_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/rat_protein_masterlist.csv\n Name: rat_protein_blacklisted_pmids_uniprotkb.csv\n URI: https://data.glygen.org/ln2wwwdata/compiled/rat_protein_blacklisted_pmids_uniprotkb.csv\n Output Subdomain\n Name: rat_protein_citations_uniprotkb.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/rat_protein_citations_uniprotkb.csv\n Name: rat_protein_citations_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/rat_protein_citations_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"8902\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"12579\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"12571\"\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: \"8902\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"639\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"12264\"\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: \"55\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.7.10/reviewed/rat_protein_citations_uniprotkb.csv" }