{ "bcoid": "GLY_000244", "title": "Rat Proteome Masterlist (UniProtKB)", "description": "The Rat Proteome Master list dataset contains rat [taxid:10116] UniProtKB canonical accessions mapped ...", "filename": "rat_protein_masterlist.csv", "filetype": "csv", "categories": { "species": [ "Rattus norvegicus" ], "molecule": [ "Protein" ], "tags": [ "Protein Canonical Accessions" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "D3ZB44-1...", "unreviewed..." ], [ "D3ZB44-1...", "unreviewed..." ] ], "headers": [ "uniprotkb_ca...", "status..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "status" }, { "type": "string", "label": "gene_name" }, { "type": "string", "label": "reviewed_isoforms" }, { "type": "string", "label": "unreviewed_isoforms" } ], [ "D3ZB44-1", "unreviewed", "Zfp324", "", "D3ZB44-1" ], [ "D3ZB44-1", "unreviewed", "Zfp324", "", "A0A8I6GKG8-1" ], [ "D3ZB41-1", "unreviewed", "Zfp78", "", "D3ZB41-1" ], [ "D3ZB41-1", "unreviewed", "Zfp78", "", "D3ZXJ3-1" ], [ "D3ZB41-1", "unreviewed", "Zfp78", "", "D3ZVD4-1" ], [ "D3ZB41-1", "unreviewed", "Zfp78", "", "A0A8I6ASG2-1" ], [ "D3ZB49-1", "unreviewed", "Osgin2", "", "D3ZB49-1" ], [ "D3ZB49-1", "unreviewed", "Osgin2", "", "A0A8I6ASB1-1" ], [ "D3ZB49-1", "unreviewed", "Osgin2", "", "A0A8I6GKD4-1" ], [ "D3ZB48-1", "unreviewed", "Hook1", "", "D3ZB48-1" ], [ "D3ZB48-1", "unreviewed", "Hook1", "", "A0A8I6AX65-1" ], [ "A0A0G2JVG5-1", "unreviewed", "LOC102552378", "", "A0A0G2JVG5-1" ], [ "A0A0G2JVG6-1", "unreviewed", "Zfp59", "", "A0A0G2JVG6-1" ], [ "P30938-1", "reviewed", "Sstr5", "P30938-1", "G3V8G3-1" ], [ "A0A8I6A2G6-1", "unreviewed", "LOC102551431", "", "A0A8I6A2G6-1" ], [ "Q07969-1", "reviewed", "Cd36", "Q07969-1", "A0A096MJ39-1" ], [ "Q07969-1", "reviewed", "Cd36", "", "Q6IMX5-1" ], [ "Q07969-1", "reviewed", "Cd36", "", "F7F5B5-1" ], [ "Q07969-1", "reviewed", "Cd36", "", "A0A096MJX7-1" ], [ "Q07969-1", "reviewed", "Cd36", "", "A0A0G2JUY0-1" ], [ "Q07969-1", "reviewed", "Cd36", "", "A0A0G2K8B4-1" ], [ "Q07969-1", "reviewed", "Cd36", "", "A0A8J8YQ28-1" ], [ "Q07969-1", "reviewed", "Cd36", "", "F7F6C5-1" ], [ "A0A096MJY4-1", "reviewed", "Mef2c", "A0A096MJY4-1", "A0A096MJ29-1" ], [ "A0A096MJY4-1", "reviewed", "Mef2c", "", "A0A096MJ09-1" ], [ "A0A096MJY4-1", "reviewed", "Mef2c", "", "A0A096MJ23-1" ], [ "A0A096MJY4-1", "reviewed", "Mef2c", "", "A0A096MJD9-1" ], [ "A0A096MJY4-1", "reviewed", "Mef2c", "", "A0A096MKI4-1" ], [ "A0A096MJY7-1", "unreviewed", "Lsm14a", "", "A0A096MJY7-1" ], [ "A0A096MJY7-1", "unreviewed", "Lsm14a", "", "A0A0G2JUK2-1" ], [ "A0A096MJY7-1", "unreviewed", "Lsm14a", "", "B2GV58-1" ], [ "A0A096MJY1-1", "unreviewed", "Gpc6", "", "A0A096MJY1-1" ], [ "A0A096MJY1-1", "unreviewed", "Gpc6", "", "A0A8I6A609-1" ], [ "A0A096MJY2-1", "unreviewed", "Stoml3", "", "A0A096MJY2-1" ], [ "A0A096MJY2-1", "unreviewed", "Stoml3", "", "D4A100-1" ], [ "A0A8J8XIU8-1", "unreviewed", "Rbm39", "", "A0A8I6A8P3-1" ], [ "A0A8J8XIU8-1", "unreviewed", "Rbm39", "", "A0A8I6A9I1-1" ], [ "A0A8J8XIU8-1", "unreviewed", "Rbm39", "", "A0A8I6B1G7-1" ], [ "A0A8J8XIU8-1", "unreviewed", "Rbm39", "", "A0A8J8XIU1-1" ], [ "A0A8J8XIU8-1", "unreviewed", "Rbm39", "", "A0A8J8XIU8-1" ], [ "A0A8I5Y817-1", "unreviewed", "ENSRNOG00000069868", "", "A0A8I5Y817-1" ], [ "P01946-1", "reviewed", "Hba1", "P01946-1", "Q63910-1" ], [ "P01946-1", "reviewed", "Hba1", "", "A0A0A0MP82-1" ], [ "P01946-1", "reviewed", "Hba1", "", "A0A8I5ZYH2-1" ], [ "P01946-1", "reviewed", "Hba1", "", "A0A8I6AI13-1" ], [ "P01946-1", "reviewed", "Hba1", "", "A0A8I6AWV0-1" ], [ "P01946-1", "reviewed", "Hba1", "", "A0A8I6GMB4-1" ], [ "P01946-1", "reviewed", "Hba1", "", "A0A8L2QLW7-1" ], [ "P30937-1", "reviewed", "Sstr4", "P30937-1", "" ], [ "O35152-1", "reviewed", "Bet1l", "O35152-1", "A0A0G2JSM4-1" ], [ "O35152-1", "reviewed", "Bet1l", "", "A0A8I6A3U1-1" ], [ "P30936-1", "reviewed", "Sstr3", "P30936-1", "" ], [ "O35158-1", "reviewed", "Cdon", "O35158-1", "G3V7K7-1" ], [ "O35158-1", "reviewed", "Cdon", "O35158-2", "A0A8I6A2E2-1" ], [ "F7FI04-1", "unreviewed", "Snx10", "", "A0A8I6APC8-1" ], [ "F7FI04-1", "unreviewed", "Snx10", "", "F7FI04-1" ], [ "P02761-1", "reviewed", "", "P02761-1", "A0A096MK41-1" ], [ "P02761-1", "reviewed", "", "", "A0A096MJW3-1" ], [ "P02761-1", "reviewed", "", "", "F1LQM1-1" ], [ "P02761-1", "reviewed", "", "", "A0A096MIX6-1" ], [ "P02761-1", "reviewed", "", "", "Q9JJH9-1" ], [ "P02761-1", "reviewed", "", "", "Q9JJI3-1" ], [ "P02761-1", "reviewed", "", "", "F7ET54-1" ], [ "P02761-1", "reviewed", "", "", "M0RBS2-1" ], [ "P02761-1", "reviewed", "", "", "A0A0G2JTN2-1" ], [ "P02761-1", "reviewed", "", "", "A0A8I5Y2J8-1" ], [ "P02761-1", "reviewed", "", "", "A0A8I5YBU2-1" ], [ "P02761-1", "reviewed", "", "", "A0A8I5ZYK0-1" ], [ "P02761-1", "reviewed", "", "", "A0A8I6A5C6-1" ], [ "P02761-1", "reviewed", "", "", "A0A8I6A7F8-1" ], [ "P02761-1", "reviewed", "", "", "A0A8I6ABS4-1" ], [ "P02761-1", "reviewed", "", "", "A0A8I6AJN1-1" ], [ "P02761-1", "reviewed", "", "", "A0A8I6AMI2-1" ], [ "Q9QYH1-1", "reviewed", "Mpp4", "Q9QYH1-1", "A0A8I5ZZC2-1" ], [ "Q9QYH1-1", "reviewed", "Mpp4", "Q9QYH1-2", "A0A8I6ASJ9-1" ], [ "Q9QYH1-1", "reviewed", "Mpp4", "Q9QYH1-3", "D3ZUC7-1" ], [ "Q9QYH1-1", "reviewed", "Mpp4", "", "F1MA44-1" ], [ "P02764-1", "reviewed", "Orm1", "P02764-1", "A0A0H2UHF8-1" ], [ "P02764-1", "reviewed", "Orm1", "", "A0A8I5ZRW3-1" ], [ "P02764-1", "reviewed", "Orm1", "", "A0A8I5ZVI6-1" ], [ "P02767-1", "reviewed", "Ttr", "P02767-1", "A0A8L2QBL5-1" ], [ "D4A4W8-1", "unreviewed", "Tbxt", "", "D4A4W8-1" ], [ "D4A4W8-1", "unreviewed", "Tbxt", "", "A0A8I6AEA5-1" ], [ "D4A4W9-1", "unreviewed", "Rpl34-ps1", "", "D4A4W9-1" ] ] }, "readme": "Name\n - Rat Proteome Masterlist (UniProtKB)\n\nVersion\n - v-2.1.1\n\nCreated on\n - 2019-09-06T14:06:38.971023\n\nModified on\n - 2022-09-26T09:04:47.899178\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.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 Rat Proteome Master list dataset contains rat [taxid:10116] UniProtKB canonical accessions mapped to the reviewed (SwissProt) and unreviewed (TrEMBL) UniProtKB isoforms via gene grouping. The dataset is derived from 2019-09 UniProtKB release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen. \n\nDescription Domain\n Keywords\n - canonical accessions\n - gene name\n - protein isoforms\n - complete proteome\n - UniProtKB\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB proteome data from the triplestore containing triples from nt file to map UniProtKB canonical accessions to reviewed and unreviewed isoforms via gene grouping. \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: uniprot-proteome-rattus-norvegicus.nt\n URI: /data/shared/glyds/downloads/ebi/2023_02/uniprot-proteome-rattus-norvegicus.nt\n Output Subdomain\n Name: rat_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/rat_protein_masterlist.csv\n Name: rat_protein_masterlist.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/rat_protein_masterlist.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"22866\"\n Name: \"status\"\n Description: \"Status of the protein record in UniProtKB database that can be reviewed for UniProtKB/Swiss-Prot entry or unreviewed for UniProtKB/TrEMBL entry\"\n Unique Values: \"2\"\n Name: \"gene_name\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\"\n Unique Values: \"22702\"\n Name: \"reviewed_isoforms\"\n Description: \"\"Protein records from UniProtKB/SwissProt database that have been manually curated and annotated based on experimental results\"\n Unique Values: \"9817\"\n Name: \"unreviewed_isoforms\"\n Description: \"Protein records from UniProtKB/TrEMBL database that have been computationally annotated\"\n Unique Values: \"39665\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/rat_protein_masterlist.csv" }