{ "bcoid": "GLY_000138", "title": "Human Proteoform Citations (UniCarbKB)", "description": "The Human Proteoform Citations (UniCarbKB) contains Homo sapiens [taxid:9606] publication information ...", "filename_list": "human_proteoform_citations_glycosylation_sites_unicarbkb.csv", "filename": "human_proteoform_citations_glycosylation_sites_unicarbkb.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Proteoform" ], "tag": [ "Protein Citations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "O00391-1...", "Precision ma..." ], [ "O00391-1...", "Precision ma..." ] ], "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" } ], [ "O00391-1", "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology.", "The EMBO journal", "2013 May 15", "Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Bennett EP, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H", "protein_xref_pubmed", "23584533", "protein_xref_unicarbkb_ds", "GLY_000040", "G57321FI" ], [ "O00391-1", "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology", "EMBO J", "2013", "Steentoft C., Vakhrushev S.Y., Joshi H.J., Kong Y., Vester-Christensen M.B., Schjoldager K.T., Lavrsen K., Dabelsteen S., Pedersen N.B., Marcos-Silva L., Gupta R., Bennett E.P., Mandel U., Brunak S., Wandall H.H., Levery S.B., Clausen H.", "protein_xref_doi", "10.1038/emboj.2013.79", "protein_xref_unicarbkb_ds", "GLY_000040", "G57321FI" ] ] }, "readme": "Name\n - Human Proteoform Citations (UniCarbKB)\n\nVersion\n - v-2.7.1\n\nCreated on\n - 2019-04-16T16:31:37.511217\n\nModified on\n - 2024-12-10T16:59:53.015Z\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 Human Proteoform Citations (UniCarbKB) contains Homo sapiens [taxid:9606] publication information of glycoproteins from UniCarbKB. The script accesses the NCBI ENTREZ infrastructure to retrieve the publication information of the given PMID from UniCarbKB. The dataset is contributed by UniCarbKB and processed by GlyGen. If you use this dataset please provide proper attribution to UniCarbKB and GlyGen [UniCarbKB - https://academic.oup.com/nar/article/42/D1/D215/1052197 ,https://doi.org/10.1093/nar/gkt1128]. \n\nDescription Domain\n Keywords\n - PMID\n - journal\n - citations\n - authors\n - UniCarbKB\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: doi_citations.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/compiled/doi_citations.csv\n Name: human_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/human_proteoform_glycosylation_sites_unicarbkb.csv\n Output Subdomain\n Name: human_proteoform_citations_glycosylation_sites_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/human_proteoform_citations_glycosylation_sites_unicarbkb.csv\n Name: human_proteoform_citations_glycosylation_sites_unicarbkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/human_proteoform_citations_glycosylation_sites_unicarbkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"1490\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"173\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"48\"\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: \"161\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"171\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"173\"\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: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"836\"", "downloadurl": "/ln2data/releases/data/v-2.7.1/reviewed/human_proteoform_citations_glycosylation_sites_unicarbkb.csv" }