{ "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...", "A glycan gat..." ], [ "P0DTC2-1...", "Synthetic Ho..." ] ], "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" } ], [ "P0DTC2-1", "A glycan gate controls opening of the SARS-CoV-2 spike protein.", "bioRxiv : the preprint server for biology", "2021-05-17", "Sztain Terra, Ahn Surl-Hee, Bogetti Anthony T, Casalino Lorenzo, Goldsmith Jory A, Seitz Evan, McCool Ryan S, Kearns Fiona L, Acosta-Reyes Francisco, Maji Suvrajit, Mashayekhi Ghoncheh, McCammon J Andrew, Ourmazd Abbas, Frank Joachim, McLellan Jason S, Chong Lillian T, Amaro Rommie E", "protein_xref_pubmed", "33619492", "protein_xref_glygen_ds", "GLY_001399", "" ], [ "P0DTC2-1", "Synthetic Homogeneous Glycoforms of the SARS-CoV-2 Spike Receptor-Binding Domain Reveals Different Binding Profiles of Monoclonal Antibodies.", "Angewandte Chemie (International ed. in English)", "2021-06-01", "Ye Farong, Zhao Jie, Xu Peng, Liu Xinliang, Yu Jing, Shangguan Wei, Liu Jiazhi, Luo Xiaosheng, Li Cheng, Ying Tianlei, Wang Jing, Yu Biao, Wang Ping", "protein_xref_pubmed", "33709491", "protein_xref_glygen_ds", "GLY_001399", "" ] ] }, "readme": "Name\n - SARS-CoV2 Proteoform Citations (Literature Mining)\n\nVersion\n - v-2.9.1\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-2.9.1/compiled/all_blacklisted_pmids.csv\n Name: sarscov2_proteoform_citations_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/compiled/sarscov2_proteoform_citations_unicarbkb.csv\n Name: sarscov2_proteoform_glycosylation_sites_literature_mining.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/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-2.9.1/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-2.9.1/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: \"29\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"23\"\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: \"27\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"27\"\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: \"30\"\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: \"2\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.9.1/reviewed/sarscov2_proteoform_citations_glycosylation_sites_literature_mining.csv" }