{ "bcoid": "GLY_001407", "title": "SARS-CoV2 Proteoform Citations (Literature Mining)", "description": "The SARS coronavirus (SARS-CoV-2 or 2019-nCoV) Proteoform Citations [Automatic Literature Mining] dataset ...", "filename_list": "sarscov2_proteoform_citations_glycosylation_sites_literature_mining.csv", "filename": "sarscov2_proteoform_citations_glycosylation_sites_literature_mining.csv", "filetype": "csv", "categories": { "species": [ "Severe acute respiratory syndrome coronavirus 2" ], "molecule": [ "Proteoform" ], "tag": [ "Protein Citations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P0DTC2-1...", "The Impact o..." ], [ "P0DTC2-1...", "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" }, { "type": "string", "label": "isoform_mapping_notes" } ], [ "P0DTC2-1", "The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity.", "Cell", "2020 Sep 3", "Li Q, Wu J, Nie J, Zhang L, Hao H, Liu S, Zhao C, Zhang Q, Liu H, Nie L, Qin H, Wang M, Lu Q, Li X, Sun Q, Liu J, Zhang L, Li X, Huang W, Wang Y", "protein_xref_pubmed", "32730807", "protein_xref_pubmed", "32730807", "", "" ], [ "P0DTC2-1", "Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains.", "Frontiers in chemistry", "2021", "Tian Yuan, Parsons Lisa M, Jankowska Ewa, Cipollo John F", "protein_xref_pubmed", "34869209", "protein_xref_pubmed", "34869209", "", "" ] ] }, "readme": "Name\n - SARS-CoV2 Proteoform Citations (Literature Mining)\n\nVersion\n - v-2.11.1\n\nCreated on\n - 2025-04-15T14:35:14\n\nModified on\n - 2025-04-15T14:35:25.411Z\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 - \n\nChecksum\n - \n\nUsability Domain\n - The SARS coronavirus (SARS-CoV-2 or 2019-nCoV) Proteoform Citations [Automatic Literature Mining] dataset contains Severe acute respiratory syndrome coronavirus 2 [taxid:2697049] citation details of the publications present in the SARS-CoV2 Glycosylation Sites [Automatic Literature Mining] [Automatically verified] dataset (https://data.glygen.org/GLY_001399).\n\nDescription Domain\n Keywords\n - PMID\n - journal\n - citations\n - authors\n - Literature\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-2.11.1/compiled/all_blacklisted_pmids.csv\n Name: sarscov2_proteoform_citations_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.11.1/compiled/sarscov2_proteoform_citations_unicarbkb.csv\n Name: sarscov2_proteoform_glycosylation_sites_literature_mining.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.11.1/reviewed/sarscov2_proteoform_glycosylation_sites_literature_mining.csv\n Output Subdomain\n Name: sarscov2_proteoform_citations_glycosylation_sites_literature_mining.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.11.1/reviewed/sarscov2_proteoform_citations_glycosylation_sites_literature_mining.csv\n Name: sarscov2_proteoform_citations_glycosylation_sites_literature_mining.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.11.1/reviewed/sarscov2_proteoform_citations_glycosylation_sites_literature_mining.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"27\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"21\"\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: \"26\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"25\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"28\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"2\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"28\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"1\"\n Name: \"isoform_mapping_notes\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.11.1/reviewed/sarscov2_proteoform_citations_glycosylation_sites_literature_mining.csv" }