{ "bcoid": "GLY_000516", "title": "Human Proteoform Citations (Literature Mining)", "description": "The dataset provides citation details corresponding to the PubMed ID (PMID) from file https://data.glygen.org/GLYDS000481. ...", "filename": "human_proteoform_citations_literature_mining.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Proteoform", "tags": "Protein Citations", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P02730-1...", "..." ], [ "Q9Y6Y9-1...", "..." ] ], "headers": [ "uniprotkb_ca...", "glytoucan_ac..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glytoucan_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" } ], [ "P02730-1", "", "Processing of N-linked oligosaccharide depends on its location in the anion exchanger, AE1, membrane glycoprotein.", "The Biochemical journal", "2000 Jul 1", "Li J, Quilty J, Popov M, Reithmeier RA", "protein_xref_automatic_literature_mining", "10861210", "protein_xref_glygen_ds", "GLYDS000481" ], [ "Q9Y6Y9-1", "", "N-linked glycosylations at Asn(26) and Asn(114) of human MD-2 are required for toll-like receptor 4-mediated activation of NF-kappaB by lipopolysaccharide.", "Journal of immunology (Baltimore, Md. : 1950)", "2001 Sep 15", "Ohnishi T, Muroi M, Tanamoto K", "protein_xref_automatic_literature_mining", "11544325", "protein_xref_glygen_ds", "GLYDS000481" ], [ "P34998-1", "", "N-glycosylation of CRF receptor type 1 is important for its ligand-specific interaction.", "American journal of physiology. Endocrinology and metabolism", "2001 Nov", "Assil IQ, Abou-Samra AB", "protein_xref_automatic_literature_mining", "11595658", "protein_xref_glygen_ds", "GLYDS000481" ], [ "P29965-1", "", "Determination of carbohydrate structures N-linked to soluble CD154 and characterization of the interactions of CD40 with CD154 expressed in Pichia pastoris and Chinese hamster ovary cells.", "Protein expression and purification", "2001 Nov", "Khandekar SS, Silverman C, Wells-Marani J, Bacon AM, Birrell H, Brigham-Burke M, DeMarini DJ, Jonak ZL, Camilleri P, Fishman-Lobell J", "protein_xref_automatic_literature_mining", "11676606", "protein_xref_glygen_ds", "GLYDS000481" ], [ "P01106-1", "", "Dynamic interplay between O-glycosylation and O-phosphorylation of nucleocytoplasmic proteins: alternative glycosylation/phosphorylation of THR-58, a known mutational hot spot of c-Myc in lymphomas, is regulated by mitogens.", "The Journal of biological chemistry", "2002 May 24", "Kamemura K, Hayes BK, Comer FI, Hart GW", "protein_xref_automatic_literature_mining", "11904304", "protein_xref_glygen_ds", "GLYDS000481" ], [ "P13497-1", "", "Post-translational modification of bone morphogenetic protein-1 is required for secretion and stability of the protein.", "The Journal of biological chemistry", "2002 Nov 8", "Garrigue-Antar L, Hartigan N, Kadler KE", "protein_xref_automatic_literature_mining", "12218058", "protein_xref_glygen_ds", "GLYDS000481" ], [ "P25103-1", "", "Functional consequences of alteration of N-linked glycosylation sites on the neurokinin 1 receptor.", "Proceedings of the National Academy of Sciences of the United States of America", "2007 Jun 19", "Tansky MF, Pothoulakis C, Leeman SE", "protein_xref_automatic_literature_mining", "17563389", "protein_xref_glygen_ds", "GLYDS000481" ], [ "Q04206-1", "", "NFkappaB activation is associated with its O-GlcNAcylation state under hyperglycemic conditions.", "Proceedings of the National Academy of Sciences of the United States of America", "2008 Nov 11", "Yang WH, Park SY, Nam HW, Kim DH, Kang JG, Kang ES, Kim YS, Lee HC, Kim KS, Cho JW", "protein_xref_automatic_literature_mining", "18988733", "protein_xref_glygen_ds", "GLYDS000481" ], [ "Q6PIU2-1", "", "Targeting of neutral cholesterol ester hydrolase to the endoplasmic reticulum via its N-terminal sequence.", "Journal of lipid research", "2010 Feb", "Igarashi M, Osuga J, Isshiki M, Sekiya M, Okazaki H, Takase S, Takanashi M, Ohta K, Kumagai M, Nishi M, Fujita T, Nagai R, Kadowaki T, Ishibashi S", "protein_xref_automatic_literature_mining", "19592704", "protein_xref_glygen_ds", "GLYDS000481" ], [ "Q8TAV3-1", "", "Colorectal cancer-specific cytochrome P450 2W1: intracellular localization, glycosylation, and catalytic activity.", "Molecular pharmacology", "2010 Dec", "Gomez A, Nekvindova J, Travica S, Lee MY, Johansson I, Edler D, Mkrtchian S, Ingelman-Sundberg M", "protein_xref_automatic_literature_mining", "20805301", "protein_xref_glygen_ds", "GLYDS000481" ], [ "P25116-1", "", "N-linked glycosylation regulates human proteinase-activated receptor-1 cell surface expression and disarming via neutrophil proteinases and thermolysin.", "The Journal of biological chemistry", "2011 Jul 1", "Xiao YP, Morice AH, Compton SJ, Sadofsky L", "protein_xref_automatic_literature_mining", "21550978", "protein_xref_glygen_ds", "GLYDS000481" ], [ "Q9Y4K0-1", "", "Post-translational modifications of recombinant human lysyl oxidase-like 2 (rhLOXL2) secreted from Drosophila S2 cells.", "The Journal of biological chemistry", "2013 Feb 22", "Xu L, Go EP, Finney J, Moon H, Lantz M, Rebecchi K, Desaire H, Mure M", "protein_xref_automatic_literature_mining", "23319596", "protein_xref_glygen_ds", "GLYDS000481" ], [ "P20827-1", "", "Biological and structural characterization of glycosylation on ephrin-A1, a preferred ligand for EphA2 receptor tyrosine kinase.", "The Journal of biological chemistry", "2013 Jun 21", "Ferluga S, Hantgan R, Goldgur Y, Himanen JP, Nikolov DB, Debinski W", "protein_xref_automatic_literature_mining", "23661698", "protein_xref_glygen_ds", "GLYDS000481" ], [ "Q15043-1", "", "An iron-regulated and glycosylation-dependent proteasomal degradation pathway for the plasma membrane metal transporter ZIP14.", "Proceedings of the National Academy of Sciences of the United States of America", "2014 Jun 24", "Zhao N, Zhang AS, Worthen C, Knutson MD, Enns CA", "protein_xref_automatic_literature_mining", "24927598", "protein_xref_glygen_ds", "GLYDS000481" ], [ "Q2MKA7-1", "", "N-Glycosylation of Human R-Spondin 1 Is Required for Efficient Secretion and Stability but Not for Its Heparin Binding Ability.", "International journal of molecular sciences", "2016 Jun 14", "Chang CF, Hsu LS, Weng CY, Chen CK, Wang SY, Chou YH, Liu YY, Yuan ZX, Huang WY, Lin H, Chen YH, Tsai JN", "protein_xref_automatic_literature_mining", "27314333", "protein_xref_glygen_ds", "GLYDS000481" ], [ "Q9ULZ9-1", "", "Expression and Characterization of Membrane-Type 4 Matrix Metalloproteinase (MT4-MMP) and its Different Forms in Melanoma.", "Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology", "2017", "Hieronimus B, Pfohl J, Busch C, Graeve L", "protein_xref_automatic_literature_mining", "28531887", "protein_xref_glygen_ds", "GLYDS000481" ], [ "Q96RD6-3", "", "N-Glycosylation Regulates Pannexin 2 Localization but Is Not Required for Interacting with Pannexin 1.", "International journal of molecular sciences", "2018 Jun 22", "Sanchez-Pupo RE, Johnston D, Penuela S", "protein_xref_automatic_literature_mining", "29932112", "protein_xref_glygen_ds", "GLYDS000481" ] ] }, "readme": "Name\n - Human Proteoform Citations (Literature Mining)\n\nVersion\n - 1.7.10\n\nCreated on\n - 2020-06-26T15:29:27.375356\n\nModified on\n - 2020-06-26T15:51:32.207997\n\nCreated by\n - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@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/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: human_proteoform_glycosylation_sites_literature_mining.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.7.10/reviewed/human_proteoform_glycosylation_sites_literature_mining.csv\n Output Subdomain\n Name: human_proteoform_citations_literature_mining.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.7.10/reviewed/human_proteoform_citations_literature_mining.csv\n Name: human_proteoform_citations_literature_mining.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.7.10/reviewed/human_proteoform_citations_literature_mining.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"17\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"17\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"17\"\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: \"1\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"10\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"17\"\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: \"16\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"1\"\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/human_proteoform_citations_literature_mining.csv" }