{ "bcoid": "GLY_000139", "title": "Mouse Proteoform Citations (UniCarbKB)", "description": "The Mouse Proteoform Citations (UniCarbKB) contains Mus musculus [taxid:10090] publication information ...", "filename_list": "mouse_proteoform_citations_glycosylation_sites_unicarbkb.csv", "filename": "mouse_proteoform_citations_glycosylation_sites_unicarbkb.csv", "filetype": "csv", "categories": { "species": [ "Mus musculus" ], "molecule": [ "Proteoform" ], "file_type": [ "csv" ], "tag": [ "Protein Citations" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Q09163-1...", "Glycosylatio..." ], [ "P04925-1...", "Site-specifi..." ] ], "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" } ], [ "Q09163-1", "Glycosylation analysis and protein structure determination of murine fetal antigen 1 (mFA1)--the circulating gene product of the delta-like protein (dlk), preadipocyte factor 1 (Pref-1) and stromal-cell-derived protein 1 (SCP-1) cDNAs.", "European journal of biochemistry", "1997 Mar 1", "Krogh TN, Bachmann E, Teisner B, Skjodt K, Hojrup P", "protein_xref_pubmed", "9118998", "protein_xref_unicarbkb_ds", "GLY_000041", "G01614ZM" ], [ "P04925-1", "Site-specific characterization of the N-linked glycans of murine prion protein by high-performance liquid chromatography/electrospray mass spectrometry and exoglycosidase digestions.", "Biochemistry", "1999 Apr 13", "Stimson E, Hope J, Chong A, Burlingame AL", "protein_xref_pubmed", "10200178", "protein_xref_unicarbkb_ds", "GLY_000041", "" ] ] }, "readme": "Name\n - Mouse Proteoform Citations (UniCarbKB)\n\nVersion\n - v-2.9.1\n\nCreated on\n - 2019-04-16T16:44:35.331041\n\nModified on\n - 2024-12-10T17:31:31.661Z\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 Mouse Proteoform Citations (UniCarbKB) contains Mus musculus [taxid:10090] 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: all_blacklisted_pmids.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/compiled/all_blacklisted_pmids.csv\n Name: mouse_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/mouse_proteoform_glycosylation_sites_unicarbkb.csv\n Output Subdomain\n Name: mouse_proteoform_citations_glycosylation_sites_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/mouse_proteoform_citations_glycosylation_sites_unicarbkb.csv\n Name: mouse_proteoform_citations_glycosylation_sites_unicarbkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/mouse_proteoform_citations_glycosylation_sites_unicarbkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"21\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"8\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"6\"\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: \"8\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"8\"\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: \"8\"\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: \"72\"", "downloadurl": "/ln2data/releases/data/v-2.9.1/reviewed/mouse_proteoform_citations_glycosylation_sites_unicarbkb.csv" }