{ "bcoid": "GLY_000470", "title": "SARS-CoV2 Protein Citations (UniProtKB)", "description": "The SARS coronavirus (SARS-CoV-2 or 2019-nCoV) Protein Citations dataset contains publication information ...", "filename_list": "sarscov2_protein_citations_uniprotkb.csv", "filename": "sarscov2_protein_citations_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Severe acute respiratory syndrome coronavirus 2" ], "molecule": [ "Protein" ], "tag": [ "Protein Citations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P0DTC7-1...", "SARS-CoV-2 a..." ], [ "P0DTC7-1...", "Functional l..." ] ], "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" } ], [ "P0DTC7-1", "SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to down-regulate MHC-I surface expression.", "Proceedings of the National Academy of Sciences of the United States of America", "2023-01-03", "Arshad Najla, Laurent-Rolle Maudry, Ahmed Wesam S, Hsu Jack Chun-Chieh, Mitchell Susan M, Pawlak Joanna, Sengupta Debrup, Biswas Kabir H, Cresswell Peter", "protein_xref_pubmed", "36574644", "protein_xref_uniprotkb", "P0DTC7" ], [ "P0DTC7-1", "Functional landscape of SARS-CoV-2 cellular restriction.", "Molecular cell", "2021 Jun 17", "Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Becker ME, Pratt D, Churas C, Rosenthal SB, Liu S, Weston S, De Jesus PD, O'Neill AM, Gounder AP, Nguyen C, Pu Y, Curry HM, Oom AL, Miorin L, Rodriguez-Frandsen A, Zheng F, Wu C, Xiong Y, Urbanowski M, Shaw ML, Chang MW, Benner C, Hope TJ, Frieman MB, Garcia-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK", "protein_xref_pubmed", "33930332", "protein_xref_uniprotkb", "P0DTC7" ] ] }, "readme": "Name\n - SARS-CoV2 Protein Citations (UniProtKB)\n\nVersion\n - v-2.9.1\n\nCreated on\n - 2020-04-19T11:32:35.963024\n\nModified on\n - 2024-06-03T21:21:42.530Z\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 SARS coronavirus (SARS-CoV-2 or 2019-nCoV) Protein Citations dataset contains publication information for Severe acute respiratory syndrome coronavirus 2 [taxid:2697049] UniProtKB accessions that includes PMID, journal name, date and author and title. 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-2.9.1/compiled/all_blacklisted_pmids.csv\n Name: sarscov2_protein_function_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/sarscov2_protein_function_uniprotkb.csv\n Name: sarscov2_protein_ptm_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/sarscov2_protein_ptm_annotation_uniprotkb.csv\n Name: sarscov2_protein_site_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/sarscov2_protein_site_annotation_uniprotkb.csv\n Name: uniprot-proteome-sars-cov-2.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2025_05_20/uniprot-proteome-sars-cov-2.nt\n Output Subdomain\n Name: sarscov2_protein_citations_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/sarscov2_protein_citations_uniprotkb.csv\n Name: sarscov2_protein_citations_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/sarscov2_protein_citations_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"17\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"170\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"82\"\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: \"93\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"169\"\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: \"169\"\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: \"17\"", "downloadurl": "/ln2data/releases/data/v-2.9.1/reviewed/sarscov2_protein_citations_uniprotkb.csv" }