{ "bcoid": "GLY_000035", "title": "Human Protein Citations (UniProtKB)", "description": "The Human Protein Citations dataset contains publication information for Homo sapiens [taxid:9606] UniProtKB ...", "filename_list": "human_protein_citations_uniprotkb.csv", "filename": "human_protein_citations_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Protein" ], "tag": [ "Protein Citations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P30613-1...", "Structure an..." ], [ "P23919-1...", "Structures o..." ] ], "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" } ], [ "P30613-1", "Structure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia.", "The Journal of biological chemistry", "2002 Jun 28", "Valentini G, Chiarelli LR, Fortin R, Dolzan M, Galizzi A, Abraham DJ, Wang C, Bianchi P, Zanella A, Mattevi A", "protein_xref_pubmed", "11960989", "protein_xref_uniprotkb", "P30613" ], [ "P23919-1", "Structures of human thymidylate kinase in complex with prodrugs: implications for the structure-based design of novel compounds.", "Biochemistry", "2003-03-11", "Ostermann Nils, Segura-Pe\u00f1a Dario, Meier Chris, Veit Thomas, Monnerjahn Christian, Konrad Manfred, Lavie Arnon", "protein_xref_pubmed", "12614151", "protein_xref_uniprotkb", "P23919" ] ] }, "readme": "Name\n - Human Protein Citations (UniProtKB)\n\nVersion\n - v-2.10.1\n\nCreated on\n - 2019-01-23T17:21:05.902655\n\nModified on\n - 2024-05-17T11:23:49.977Z\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 Protein Citations dataset contains publication information for Homo sapiens [taxid:9606] 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. 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/glygener/glygen-backend-integration/blob/master/dataset-maker/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: all_blacklisted_pmids.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/compiled/all_blacklisted_pmids.csv\n Name: human_protein_blacklisted_pmids_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/compiled/human_protein_blacklisted_pmids_uniprotkb.csv\n Name: human_protein_function_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/human_protein_function_uniprotkb.csv\n Name: human_protein_ptm_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/human_protein_ptm_annotation_uniprotkb.csv\n Name: human_protein_site_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/human_protein_site_annotation_uniprotkb.csv\n Name: uniprot-proteome-homo-sapiens.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2025_10_01/uniprot-proteome-homo-sapiens.nt\n Output Subdomain\n Name: human_protein_citations_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/human_protein_citations_uniprotkb.csv\n Name: human_protein_citations_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/human_protein_citations_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"19087\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"89365\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"2819\"\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: \"11940\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"88209\"\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: \"88863\"\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: \"31699\"", "downloadurl": "/ln2data/releases/data/v-2.10.1/reviewed/human_protein_citations_uniprotkb.csv" }