{ "bcoid": "GLY_000989", "title": "Chicken Protein Citations (UniProtKB)", "description": "The Chicken Protein Citations dataset contains publication information for Gallus gallus [taxid:9031] ...", "filename_list": "chicken_protein_citations_uniprotkb.csv", "filename": "chicken_protein_citations_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Gallus gallus" ], "molecule": [ "Protein" ], "tag": [ "Protein Citations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "F1NQJ3-1...", "MSH6- or PMS..." ], [ "P79987-1...", "Different ro..." ] ], "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" } ], [ "F1NQJ3-1", "MSH6- or PMS2-deficiency causes re-replication in DT40 B cells, but it has little effect on immunoglobulin gene conversion or on repair of AID-generated uracils.", "Nucleic acids research", "2013-03-01", "Campo Vanina A, Patenaude Anne-Marie, Kaden Svenja, Horb Lori, Firka Daniel, Jiricny Josef, Di Noia Javier M", "protein_xref_pubmed", "23314153", "protein_xref_uniprotkb", "F1NQJ3" ], [ "P79987-1", "Different roles of N-terminal and C-terminal halves of HIRA in transcription regulation of cell cycle-related genes that contribute to control of vertebrate cell growth.", "The Journal of biological chemistry", "2005-09-16", "Ahmad Ahyar, Kikuchi Hidehiko, Takami Yasunari, Nakayama Tatsuo", "protein_xref_pubmed", "16024922", "protein_xref_uniprotkb", "P79987" ] ] }, "readme": "Name\n - Chicken Protein Citations (UniProtKB)\n\nVersion\n - v-2.7.1\n\nModified on\n - 2024-05-17T11:24:20.996Z\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], 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 Chicken Protein Citations dataset contains publication information for Gallus gallus [taxid:9031] 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: chicken_protein_function_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/chicken_protein_function_uniprotkb.csv\n Name: chicken_protein_ptm_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/chicken_protein_ptm_annotation_uniprotkb.csv\n Name: chicken_protein_site_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/chicken_protein_site_annotation_uniprotkb.csv\n Name: uniprot-proteome-gallus-gallus.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2024_09_19/uniprot-proteome-gallus-gallus.nt\n Output Subdomain\n Name: chicken_protein_citations_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/chicken_protein_citations_uniprotkb.csv\n Name: chicken_protein_citations_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/chicken_protein_citations_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"2868\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"2809\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"382\"\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: \"660\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"2748\"\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: \"2807\"\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: \"2876\"", "downloadurl": "/ln2data/releases/data/v-2.7.1/reviewed/chicken_protein_citations_uniprotkb.csv" }