{ "bcoid": "GLY_000554", "title": "SARS-CoV2 Protein Information (NCBI RefSeq)", "description": "The SARS coronavirus (SARS-CoV-2 or 2019-nCov) UniProtKB Xref NCBI Gene dataset contains sarscov2 [taxid:2697049] ...", "filename": "sarscov2_protein_info_refseq.csv", "filetype": "csv", "categories": { "species": [ "Severe acute respiratory syndrome coronavirus 2" ], "molecule": [ "Protein" ], "tag": [ "Protein Information" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Robel...", " mapped YP_0..." ], [ "Robel...", " feat YP_009..." ] ], "headers": [ "uniprotkb_ca...", "p_refseq_ac_..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "p_refseq_ac_best_match" }, { "type": "string", "label": "refseq_protein_name" }, { "type": "string", "label": "refseq_protein_length" }, { "type": "string", "label": "refseq_protein_summary" } ], [ "Robel", " mapped YP_009724389" ], [ "Robel", " feat YP_009724389" ], [ "P0DTD1-1", "YP_009724389", "ORF1ab polyprotein", "7096", "" ], [ "Robel", " mapped YP_009724390" ], [ "Robel", " feat YP_009724390" ], [ "P0DTC2-1", "YP_009724390", "surface glycoprotein", "1273", "" ], [ "Robel", " mapped YP_009724391" ], [ "Robel", " feat YP_009724391" ], [ "P0DTC3-1", "YP_009724391", "ORF3a protein", "275", "" ], [ "Robel", " mapped YP_009724392" ], [ "Robel", " feat YP_009724392" ], [ "P0DTC4-1", "YP_009724392", "envelope protein", "75", "" ], [ "Robel", " mapped YP_009724393" ], [ "Robel", " feat YP_009724393" ], [ "P0DTC5-1", "YP_009724393", "membrane glycoprotein", "222", "" ], [ "Robel", " mapped YP_009724394" ], [ "Robel", " feat YP_009724394" ], [ "P0DTC6-1", "YP_009724394", "ORF6 protein", "61", "" ], [ "Robel", " mapped YP_009724395" ], [ "Robel", " feat YP_009724395" ], [ "P0DTC7-1", "YP_009724395", "ORF7a protein", "121", "" ], [ "Robel", " mapped YP_009724396" ], [ "Robel", " feat YP_009724396" ], [ "P0DTC8-1", "YP_009724396", "ORF8 protein", "121", "" ], [ "Robel", " mapped YP_009724397" ], [ "Robel", " feat YP_009724397" ], [ "P0DTC9-1", "YP_009724397", "nucleocapsid phosphoprotein", "419", "" ], [ "Robel", " mapped YP_009725255" ], [ "Robel", " feat YP_009725255" ], [ "A0A663DJA2-1", "YP_009725255", "ORF10 protein", "38", "" ], [ "Robel", " mapped YP_009725295" ], [ "Robel", " feat YP_009725295" ], [ "P0DTC1-1", "YP_009725295", "ORF1a polyprotein", "4405", "" ], [ "Robel", " mapped YP_009725318" ], [ "Robel", " feat YP_009725318" ], [ "P0DTD8-1", "YP_009725318", "ORF7b", "43", "" ] ] }, "readme": "Name\n - SARS-CoV2 Protein Information (NCBI RefSeq)\n\nVersion\n - v-2.4.1\n\nCreated on\n - 2021-03-01T11:27:34.342151\n\nModified on\n - 2022-09-26T09:08:12.700740\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]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The SARS coronavirus (SARS-CoV-2 or 2019-nCov) UniProtKB Xref NCBI Gene dataset contains sarscov2 [taxid:2697049] protein information such as protein accession, name, length and protein function summary from NCBI RefSeq database. The dataset is derived from NCBI RefSeq Release 96, September 9, 2019. If you use this dataset please provide proper attribution to NCBI RefSeq and GlyGen\n\nDescription Domain\n Keywords\n - protein information\n - protein length\n - NCBI RefSeq\n - protein summary\n\n Pipeline Steps\n - Step-1: The script parses the NCBI RefSeq gpff files to extract the accession, length, protein summary and then maps the NCBI RefSeq accesion to the UniProtKB Canonical accessions\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: sarscov2_protein_xref_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/sarscov2_protein_xref_refseq.csv\n Name: refseq_protein_all_viral.gpff\n URI: https:/data.glygen.org/ln2downloads/ncbi/refseq/2024_02_18/refseq_protein_all_viral.gpff\n Output Subdomain\n Name: sarscov2_protein_info_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/sarscov2_protein_info_refseq.csv\n Name: sarscov2_protein_info_refseq.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/sarscov2_protein_info_refseq.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"13\"\n Name: \"p_refseq_ac_best_match\"\n Description: \"Best match NCBI RefSeq protein accession to UniProtKB canonical accession\"\n Unique Values: \"36\"\n Name: \"refseq_protein_name\"\n Description: \"Name of the protein in NCBI RefSeq database\"\n Unique Values: \"12\"\n Name: \"refseq_protein_length\"\n Description: \"Length of the protein in NCBI RefSeq database\"\n Unique Values: \"11\"\n Name: \"refseq_protein_summary\"\n Description: \"Function of the protein in NCBI RefSeq database\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/sarscov2_protein_info_refseq.csv" }