{ "bcoid": "GLY_001056", "title": "Arabidopsis Protein Citations (UniProtKB)", "description": "The Arabidopsis Protein Citations dataset contains publication information for Arabidopsis thaliana [taxid:3702] ...", "filename_list": "arabidopsis_protein_citations_uniprotkb.csv", "filename": "arabidopsis_protein_citations_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Arabidopsis thaliana" ], "molecule": [ "Protein" ], "tag": [ "Protein Citations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "A8MQY1-1...", "A membrane-b..." ], [ "Q42539-1...", "Protein repa..." ] ], "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" } ], [ "A8MQY1-1", "A membrane-bound NAC transcription factor regulates cell division in Arabidopsis.", "The Plant cell", "2006-11", "Kim Youn-Sung, Kim Sang-Gyu, Park Jung-Eun, Park Hye-Young, Lim Mi-Hye, Chua Nam-Hai, Park Chung-Mo", "protein_xref_pubmed", "17098812", "protein_xref_uniprotkb", "A8MQY1" ], [ "Q42539-1", "Protein repair L-isoaspartyl methyltransferase 1 is involved in both seed longevity and germination vigor in Arabidopsis.", "The Plant cell", "2008-11", "Og\u00e9 Laurent, Bourdais Gildas, Bove J\u00e9r\u00f4me, Collet Boris, Godin B\u00e9atrice, Granier Fabienne, Boutin Jean-Pierre, Job Dominique, Jullien Marc, Grappin Philippe", "protein_xref_pubmed", "19011119", "protein_xref_uniprotkb", "Q42539" ] ] }, "readme": "Name\n - Arabidopsis Protein Citations (UniProtKB)\n\nVersion\n - v-2.10.1\n\nCreated on\n - 2024-07-08T14:35:03\n\nModified on\n - 2024-07-08T14:39:43.781Z\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 Arabidopsis Protein Citations dataset contains publication information for Arabidopsis thaliana [taxid:3702] 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: arabidopsis_protein_function_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/arabidopsis_protein_function_uniprotkb.csv\n Name: arabidopsis_protein_ptm_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/arabidopsis_protein_ptm_annotation_uniprotkb.csv\n Name: arabidopsis_protein_site_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/arabidopsis_protein_site_annotation_uniprotkb.csv\n Name: uniprot-proteome-arabidopsis-thaliana.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2025_10_01/uniprot-proteome-arabidopsis-thaliana.nt\n Output Subdomain\n Name: arabidopsis_protein_citations_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/arabidopsis_protein_citations_uniprotkb.csv\n Name: arabidopsis_protein_citations_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/arabidopsis_protein_citations_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"27448\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"14677\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"551\"\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: \"2665\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"14188\"\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: \"14426\"\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: \"30824\"", "downloadurl": "/ln2data/releases/data/v-2.10.1/reviewed/arabidopsis_protein_citations_uniprotkb.csv" }