{ "bcoid": "GLY_000760", "title": "Yeast Proteome Masterlist (UniProtKB)", "description": "The Yeast Proteome Masterlist dataset contains yeast [taxid:559292] UniProtKB canonical accessions mapped ...", "filename": "yeast_protein_masterlist.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Protein" ], "tag": [ "Protein Canonical Accessions" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P30619-1...", "reviewed..." ], [ "P39972-1...", "reviewed..." ] ], "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" } ], [ "P30619-1", "reviewed", "SEC1", "P30619-1", "" ], [ "P39972-1", "reviewed", "", "P39972-1", "" ], [ "P39970-1", "reviewed", "ACA1", "P39970-1", "" ], [ "P39971-1", "reviewed", "", "P39971-1", "" ], [ "P39976-1", "reviewed", "DLD3", "P39976-1", "" ], [ "P39977-1", "reviewed", "", "P39977-1", "" ], [ "P39974-1", "reviewed", "", "P39974-1", "" ], [ "P39975-1", "reviewed", "RMD6", "P39975-1", "" ], [ "P39978-1", "reviewed", "", "P39978-1", "" ], [ "P39979-1", "reviewed", "HPA3", "P39979-1", "" ], [ "P25379-1", "reviewed", "CHA1", "P25379-1", "" ], [ "P25378-1", "reviewed", "RHB1", "P25378-1", "" ], [ "P17121-1", "reviewed", "SAC7", "P17121-1", "" ], [ "P25374-1", "reviewed", "NFS1", "P25374-1", "" ], [ "P17123-1", "reviewed", "SPO12", "P17123-1", "" ], [ "P17122-1", "reviewed", "SPO16", "P17122-1", "" ], [ "P25371-1", "reviewed", "ADP1", "P25371-1", "" ], [ "P25370-1", "reviewed", "GFD2", "P25370-1", "" ], [ "P25373-1", "reviewed", "GRX1", "P25373-1", "" ], [ "P25372-1", "reviewed", "TRX3", "P25372-1", "" ], [ "Q03048-1", "reviewed", "COF1", "Q03048-1", "" ], [ "Q03049-1", "reviewed", "", "Q03049-1", "" ], [ "Q06567-1", "reviewed", "MCP2", "Q06567-1", "" ], [ "Q06563-1", "reviewed", "SYM1", "Q06563-1", "" ], [ "Q00539-1", "reviewed", "NAM8", "Q00539-1", "" ], [ "Q07748-1", "reviewed", "THI13", "Q07748-1", "" ], [ "Q07963-1", "reviewed", "UBR2", "Q07963-1", "" ], [ "Q07746-1", "reviewed", "", "Q07746-1", "" ], [ "Q07967-1", "reviewed", "", "Q07967-1", "" ], [ "Q00246-1", "reviewed", "RHO4", "Q00246-1", "" ], [ "Q00245-1", "reviewed", "RHO3", "Q00245-1", "" ], [ "P40422-1", "reviewed", "RPC10", "P40422-1", "" ], [ "P48566-1", "reviewed", "MSB3", "P48566-1", "" ], [ "P18494-1", "reviewed", "GLN3", "P18494-1", "" ], [ "P18496-1", "reviewed", "ATP10", "P18496-1", "" ], [ "P48568-1", "reviewed", "", "P48568-1", "" ], [ "Q08748-1", "reviewed", "", "Q08748-1", "" ], [ "Q08749-1", "reviewed", "TIM18", "Q08749-1", "" ], [ "Q08746-1", "reviewed", "RRS1", "Q08746-1", "" ], [ "Q08747-1", "reviewed", "UAF30", "Q08747-1", "" ], [ "Q08745-1", "reviewed", "RPS10A", "Q08745-1", "" ], [ "Q08742-1", "reviewed", "RDL2", "Q08742-1", "" ], [ "Q08743-1", "reviewed", "", "Q08743-1", "" ], [ "P32915-1", "reviewed", "SEC61", "P32915-1", "" ], [ "P32914-1", "reviewed", "SPT4", "P32914-1", "" ], [ "P32917-1", "reviewed", "STE5", "P32917-1", "" ], [ "P32916-1", "reviewed", "SRP101", "P32916-1", "" ], [ "P32911-1", "reviewed", "SUI1", "P32911-1", "" ], [ "P32910-1", "reviewed", "RPC34", "P32910-1", "" ], [ "P32913-1", "reviewed", "VPS17", "P32913-1", "" ], [ "P32912-1", "reviewed", "VAM7", "P32912-1", "" ], [ "Q04438-1", "reviewed", "SPG4", "Q04438-1", "" ], [ "Q04439-1", "reviewed", "MYO5", "Q04439-1", "" ], [ "Q04430-1", "reviewed", "CAB1", "Q04430-1", "" ], [ "Q04431-1", "reviewed", "KRE28", "Q04431-1", "" ], [ "Q04432-1", "reviewed", "HSP31", "Q04432-1", "" ], [ "Q04433-1", "reviewed", "FIT1", "Q04433-1", "" ], [ "Q04436-1", "reviewed", "", "Q04436-1", "" ], [ "Q04437-1", "reviewed", "YKU80", "Q04437-1", "" ], [ "P00546-1", "reviewed", "CDC28", "P00546-1", "" ], [ "P04385-1", "reviewed", "GAL1", "P04385-1", "" ], [ "P04387-1", "reviewed", "GAL80", "P04387-1", "" ], [ "P04386-1", "reviewed", "GAL4", "P04386-1", "" ], [ "Q08299-1", "reviewed", "ENB1", "Q08299-1", "" ], [ "Q08562-1", "reviewed", "ULS1", "Q08562-1", "" ], [ "Q08560-1", "reviewed", "", "Q08560-1", "" ], [ "Q08561-1", "reviewed", "IES4", "Q08561-1", "" ], [ "P25377-1", "reviewed", "ADH7", "P25377-1", "" ], [ "P25376-1", "reviewed", "AGP1", "P25376-1", "" ], [ "P09007-1", "reviewed", "SRD1", "P09007-1", "" ], [ "P04037-1", "reviewed", "COX4", "P04037-1", "" ], [ "P04039-1", "reviewed", "COX8", "P04039-1", "" ], [ "Q05779-1", "reviewed", "COQ9", "Q05779-1", "" ], [ "P00724-1", "reviewed", "SUC2", "P00724-1", "" ], [ "P00724-1", "reviewed", "SUC2", "P00724-2", "" ], [ "P00729-1", "reviewed", "PRC1", "P00729-1", "" ], [ "Q06568-1", "reviewed", "NDL1", "Q06568-1", "" ], [ "Q04689-1", "reviewed", "AIM32", "Q04689-1", "" ], [ "Q02872-1", "reviewed", "", "Q02872-1", "" ], [ "P36094-1", "reviewed", "SPC42", "P36094-1", "" ], [ "Q02875-1", "reviewed", "SYH1", "Q02875-1", "" ], [ "P23542-1", "reviewed", "AAT2", "P23542-1", "" ], [ "Q05473-1", "reviewed", "MRX8", "Q05473-1", "" ], [ "Q05471-1", "reviewed", "SWR1", "Q05471-1", "" ] ] }, "readme": "Name\n - Yeast Proteome Masterlist (UniProtKB)\n\nVersion\n - v-2.2.1\n\nCreated on\n - 2022-08-30T16:22:11.325302\n\nModified on\n - 2023-09-11T19:10:05\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], 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 Yeast Proteome Masterlist dataset contains yeast [taxid:559292] UniProtKB canonical accessions mapped to the reviewed (SwissProt) and unreviewed (TrEMBL) UniProtKB isoforms via gene grouping. The dataset is contributed by EMBL-EBI-UniProtKB and processed by GlyGen. 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-saccharomyces-cerevisiae.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2023_10_30/uniprot-proteome-saccharomyces-cerevisiae.nt\n Output Subdomain\n Name: yeast_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_masterlist.csv\n Name: yeast_protein_masterlist.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_masterlist.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"6060\"\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: \"1\"\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: \"5200\"\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: \"6090\"\n Name: \"unreviewed_isoforms\"\n Description: \"Protein records from UniProtKB/TrEMBL database that have been computationally annotated\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/yeast_protein_masterlist.csv" }