{ "bcoid": "GLY_000574", "title": "Rat Proteoform Citations (Literature Mining)", "description": "The dataset provides citation details corresponding to the PubMed ID (PMID) from file https://data.glygen.org/GLYDS000481. ...", "filename": "rat_proteoform_citations_glycosylation_sites_literature_mining.csv", "filetype": "csv", "categories": { "species": [ "Rattus norvegicus" ], "molecule": [ "Proteoform" ], "tag": [ "Protein Citations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P29975-1...", "A point muta..." ], [ "P47824-1...", "Roles of ind..." ] ], "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" }, { "type": "string", "label": "glytoucan_ac" } ], [ "P29975-1", "A point mutation at cysteine 189 blocks the water permeability of rat kidney water channel CHIP28k.", "Biochemistry", "1993 Mar 30", "Zhang R, van Hoek AN, Biwersi J, Verkman AS", "protein_xref_pubmed", "8457558", "protein_xref_automatic_literature_mining", "8457558", "" ], [ "P47824-1", "Roles of individual N-glycans for ATP potency and expression of the rat P2X1 receptor.", "The Journal of biological chemistry", "2000 Oct 27", "Rettinger J, Aschrafi A, Schmalzing G", "protein_xref_pubmed", "10942758", "protein_xref_automatic_literature_mining", "10942758", "" ], [ "P48199-1", "Derivation of the amino acid sequence of rat C-reactive protein from cDNA cloning with additional studies on the nature of its dimeric component.", "The Journal of biological chemistry", "1992 Feb 15", "Rassouli M, Sambasivam H, Azadi P, Dell A, Morris HR, Nagpurkar A, Mookerjea S, Murray RK", "protein_xref_pubmed", "1737750", "protein_xref_automatic_literature_mining", "1737750", "" ], [ "P09951-1", "Glycosylation sites flank phosphorylation sites on synapsin I: O-linked N-acetylglucosamine residues are localized within domains mediating synapsin I interactions.", "Journal of neurochemistry", "1999 Jul", "Cole RN, Hart GW", "protein_xref_pubmed", "10386995", "protein_xref_automatic_literature_mining", "10386995", "" ], [ "P33535-1", "The role of N53Q mutation on the rat mu-opioid receptor function.", "Journal of biomolecular techniques : JBT", "2010 Jul", "Rostami A, Rabbani M, Mir-Mohammad-Sadeghi M", "protein_xref_pubmed", "20592872", "protein_xref_automatic_literature_mining", "20592872", "" ], [ "O35433-1", "Characterization of rat transient receptor potential vanilloid 1 receptors lacking the N-glycosylation site N604.", "Neuroreport", "2005 Jun 21", "Wirkner K, Hognestad H, Jahnel R, Hucho F, Illes P", "protein_xref_pubmed", "15931076", "protein_xref_automatic_literature_mining", "15931076", "" ], [ "P16235-1", "Functional glycosylation sites of the rat luteinizing hormone receptor required for ligand binding.", "The Journal of biological chemistry", "1995-09-15", "Zhang R, Cai H, Fatima N, Buczko E, Dufau M L", "protein_xref_pubmed", "7665591", "protein_xref_automatic_literature_mining", "7665591", "" ], [ "Q05140-1", "A novel post-translational modification in nerve terminals: O-linked N-acetylglucosamine phosphorylation.", "Journal of proteome research", "2011 Jun 3", "Graham ME, Thaysen-Andersen M, Bache N, Craft GE, Larsen MR, Packer NH, Robinson PJ", "protein_xref_pubmed", "21500857", "protein_xref_automatic_literature_mining", "21500857", "" ], [ "P19493-1", "Characterization of the functional role of the N-glycans in the AMPA receptor ligand-binding domain.", "Journal of neurochemistry", "2003 Mar", "Pasternack A, Coleman SK, Fethiere J, Madden DR, LeCaer JP, Rossier J, Pasternack M, Keinanen K", "protein_xref_pubmed", "12603841", "protein_xref_automatic_literature_mining", "12603841", "" ], [ "P97639-1", "Functional role of N-linked glycosylation on the rat melanin-concentrating hormone receptor 1.", "FEBS letters", "2003 Jan 2", "Saito Y, Tetsuka M, Yue L, Kawamura Y, Maruyama K", "protein_xref_pubmed", "12505154", "protein_xref_automatic_literature_mining", "12505154", "" ], [ "P49653-1", "Role of the domain encompassing Arg304-Ile328 in rat P2X2 receptor conformation revealed by alterations in complex glycosylation at Asn298.", "The Biochemical journal", "2008 Nov 15", "Young MT, Zhang YH, Cao L, Broomhead H, Jiang LH", "protein_xref_pubmed", "18616429", "protein_xref_automatic_literature_mining", "18616429", "" ], [ "P18090-1", "Molecular cloning and expression of the rat beta 1-adrenergic receptor gene.", "The Journal of biological chemistry", "1990 Aug 5", "Machida CA, Bunzow JR, Searles RP, Van Tol H, Tester B, Neve KA, Teal P, Nipper V, Civelli O", "protein_xref_pubmed", "1695899", "protein_xref_automatic_literature_mining", "1695899", "" ], [ "P31000-1", "Vimentin is important in the neural differentiation of PC12 cells promoted by sialylation.", "Glycoconjugate journal", "2017 Feb", "Wu LH, Shao XT, Guo JX, Sun H, Chen Q, Pan J, Cai QQ, Dong YW, Chen ZY, Yan XM, Peng M, Zhong N, Wu XZ", "protein_xref_pubmed", "27726058", "protein_xref_automatic_literature_mining", "27726058", "" ], [ "P24942-1", "Localization of N-glycosylation sites and functional role of the carbohydrate units of GLAST-1, a cloned rat brain L-glutamate/L-aspartate transporter.", "European journal of biochemistry", "1995 May 1", "Conradt M, Storck T, Stoffel W", "protein_xref_pubmed", "7758463", "protein_xref_automatic_literature_mining", "7758463", "" ], [ "P14925-1", "Topological switching of the COOH-terminal domain of peptidylglycine alpha-amidating monooxygenase by alternative RNA splicing.", "Archives of biochemistry and biophysics", "1993 Feb 15", "Yun HY, Johnson RC, Mains RE, Eipper BA", "protein_xref_pubmed", "7680192", "protein_xref_automatic_literature_mining", "7680192", "" ], [ "P55018-1", "N-Glycosylation at two sites critically alters thiazide binding and activity of the rat thiazide-sensitive Na(+):Cl(-) cotransporter.", "Journal of the American Society of Nephrology : JASN", "2003 Feb", "Hoover RS, Poch E, Monroy A, Vazquez N, Nishio T, Gamba G, Hebert SC", "protein_xref_pubmed", "12538726", "protein_xref_automatic_literature_mining", "12538726", "" ], [ "P09951-1", "O-linked beta-N-acetylglucosamine (O-GlcNAc) site thr-87 regulates synapsin I localization to synapses and size of the reserve pool of synaptic vesicles.", "The Journal of biological chemistry", "2014 Feb 7", "Skorobogatko Y, Landicho A, Chalkley RJ, Kossenkov AV, Gallo G, Vosseller K", "protein_xref_pubmed", "24280219", "protein_xref_automatic_literature_mining", "24280219", "" ], [ "P14740-1", "Domain-specific N-glycosylation of the membrane glycoprotein dipeptidylpeptidase IV (CD26) influences its subcellular trafficking, biological stability, enzyme activity and protein folding.", "European journal of biochemistry", "1997 May 15", "Fan H, Meng W, Kilian C, Grams S, Reutter W", "protein_xref_pubmed", "9210490", "protein_xref_automatic_literature_mining", "9210490", "" ], [ "P19357-1", "Characterization of a mutant GLUT4 lacking the N-glycosylation site: studies in transfected rat adipose cells.", "Biochemical and biophysical research communications", "1996 Jan 5", "Ing BL, Chen H, Robinson KA, Buse MG, Quon MJ", "protein_xref_pubmed", "8573180", "protein_xref_automatic_literature_mining", "8573180", "" ] ] }, "readme": "Name\n - Rat Proteoform Citations (Literature Mining)\n\nVersion\n - v-2.4.1\n\nCreated on\n - 2021-06-04T10:25:25.298469\n\nModified on\n - 2023-03-14T17:00:46.458Z\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], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The dataset provides citation details corresponding to the PubMed ID (PMID) from file https://data.glygen.org/GLYDS000481. The script accesses the NCBI ENTREZ infrastructure to retrieve the publication information of the given PMID.\n\nDescription Domain\n Keywords\n - PMID\n - journal\n - citations\n - authors\n - Literature\n - PubMed\n\n Pipeline Steps\n - Step-1: The script parses the input file for PMIDs and accesses the NCBI Entrez infrastructure to download the publication information of the corresponding PMIDs.\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-proteoform-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_proteoform_glycosylation_sites_literature_mining.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/rat_proteoform_glycosylation_sites_literature_mining.csv\n Output Subdomain\n Name: rat_proteoform_citations_glycosylation_sites_literature_mining.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/rat_proteoform_citations_glycosylation_sites_literature_mining.csv\n Name: rat_proteoform_citations_glycosylation_sites_literature_mining.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/rat_proteoform_citations_glycosylation_sites_literature_mining.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"18\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"19\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"13\"\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: \"19\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"19\"\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: \"19\"\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: \"19\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/rat_proteoform_citations_glycosylation_sites_literature_mining.csv" }