{ "bcoid": "GLY_000276", "title": "Rat UniProtKB Xref RefSeq", "description": "The Rat [taxid:10116] UniprotKB Xref RefSeq contains rat UniProtKB canonical accessions cross-referenced ...", "filename": "rat_protein_xref_refseq.csv", "filetype": "csv", "categories": { "species": "Rattus Norvegicus", "molecule": "Protein", "tags": "Refseq cross-references", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q5RJK9-1...", "NP_001008331..." ], [ "Q5RJK8-1...", "NP_001011906..." ] ], "headers": [ "uniprotkb_ca...", "database_id..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "database_id" }, { "type": "string", "label": "database_label" } ], [ "Q5RJK9-1", "NP_001008331.1", "" ], [ "Q5RJK8-1", "NP_001011906.1", "" ], [ "D3ZB48-1", "NP_001101416.1", "" ], [ "Q6MG55-1", "NP_997696.1", "" ], [ "Q6MG56-1", "NP_001003691.1", "" ], [ "A0A0G2K0H3-1", "XP_017448147.1", "" ], [ "Q5XIH0-1", "NP_001014107.1", "" ], [ "Q6MG51-1", "NP_001003975.1", "" ], [ "F1M2W7-1", "NP_001100387.1", "" ], [ "Q6MG53-1", "NP_001001934.1", "" ], [ "D4AAV0-1", "NP_001102329.1", "" ], [ "P20961-1", "NP_036752.1", "" ], [ "Q6MG59-1", "NP_001003976.1", "" ], [ "Q4KLP0-1", "NP_001020891.1", "" ], [ "M0RAP5-1", "NP_001258102.1", "" ], [ "A0A0G2JVG8-1", "NP_001000969.1", "" ], [ "F1M1W4-1", "NP_001101860.2", "" ], [ "P34997-1", "NP_445755.1", "" ], [ "Q8R553-1", "NP_599203.1", "" ], [ "Q9QX69-1", "NP_446175.1", "" ], [ "P30348-1", "NP_446099.1", "" ], [ "A0A0G2JUK9-1", "NP_001000297.1", "" ], [ "D3ZLV0-1", "NP_001000397.1", "" ], [ "Q8VHI8-1", "NP_543173.1", "" ], [ "D3ZLV9-1", "NP_001127976.1", "" ], [ "O88181-1", "NP_075245.1", "" ], [ "Q2KMM2-1", "NP_001034467.1", "" ], [ "D3ZKU2-1", "NP_001000156.1", "" ], [ "O55043-1", "NP_001106994.1", "" ], [ "D4A831-1", "NP_001100368.1", "" ], [ "O54783-1", "NP_058873.1", "" ], [ "Q6QI33-1", "NP_001041443.1", "" ], [ "M0RCZ1-1", "NP_001000461.1", "" ], [ "P56571-1", "NP_001004225.1", "" ], [ "P56574-1", "NP_001014183.1", "" ], [ "P48965-1", "NP_598255.1", "" ], [ "M0R7U6-1", "NP_001102834.1", "" ], [ "P48966-1", "NP_598256.1", "" ], [ "P48961-1", "NP_036898.1", "" ], [ "O35158-1", "NP_059054.1", "" ], [ "M0R7U1-1", "NP_001102421.1", "" ], [ "Q6P7Q4-1", "NP_997477.1", "" ], [ "F1M4Y5-1", "NP_001178649.1", "" ], [ "Q14U74-1", "NP_001040579.1", "" ], [ "Q5M807-1", "NP_001102495.1", "" ], [ "P02764-1", "NP_445740.1", "" ], [ "D3ZNX2-1", "NP_001164065.1", "" ], [ "D4A4W8-1", "NP_001099679.1", "" ], [ "Q6AYD2-1", "NP_001011943.1", "" ], [ "D4A4W0-1", "NP_001000252.1", "" ], [ "D4A4W4-1", "NP_001102458.1", "" ], [ "D4A4W6-1", "NP_001102977.1", "" ], [ "D4A4W7-1", "NP_001103026.1", "" ], [ "G3V6I3-1", "NP_001101765.1", "" ], [ "G3V6I6-1", "XP_006249914.1", "" ], [ "D4ABH8-1", "NP_001000924.1", "" ], [ "G3V6I4-1", "NP_001094281.1", "" ], [ "Q6MG58-1", "NP_001001970.1", "" ], [ "Q561K4-1", "NP_001019416.1", "" ], [ "P63076-1", "NP_062071.1", "" ], [ "D3ZDS6-1", "NP_001030179.1", "" ], [ "D3ZDS4-1", "NP_001101358.2", "" ], [ "Q8CF82-1", "NP_775429.1", "" ], [ "D3ZVN9-1", "NP_001101743.1", "" ], [ "D3ZDS9-1", "NP_001099363.2", "" ], [ "P39020-1", "NP_058845.1", "" ], [ "Q2VWP9-1", "NP_001032740.1", "" ], [ "Q6AY34-1", "NP_001012118.1", "" ], [ "D4AEG2-1", "NP_001102372.1", "" ], [ "D4A2R5-1", "NP_001100847.1", "" ], [ "M0RBX0-1", "NP_001000323.1", "" ], [ "A0A0G2K0T8-1", "NP_001128321.1", "" ], [ "A0A0G2JZ70-1", "XP_006239129.1", "" ], [ "P83858-1", "NP_937842.1", "" ], [ "P20814-1", "NP_612523.1", "" ], [ "Q5I2P1-1", "NP_001009964.1", "" ], [ "Q562C9-1", "NP_954528.1", "" ], [ "P24135-1", "NP_058864.1", "" ], [ "D3ZZL9-1", "NP_001101103.1", "" ], [ "D3ZLN7-1", "NP_001102973.1", "" ], [ "O88457-1", "NP_062138.1", "" ], [ "P61227-1", "NP_596901.1", "" ], [ "Q08290-1", "NP_113935.1", "" ], [ "Q9QZH2-1", "NP_072144.1", "" ] ] }, "readme": "Name\n - Rat UniProtKB Xref RefSeq\n\nVersion\n - 1.4.5\n\nCreated on\n - 2019-09-06T14:06:39.002473\n\nModified on\n - \n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@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 [taxid:10116] UniprotKB Xref RefSeq contains rat UniProtKB canonical accessions cross-referenced to RefSeq database accessions/identifiers. The script extracts one-to-one UniProtKB isofrom ac to RefSeq ac and also UniProt ac to RefSeq ac where there is no UniProtKB isoforms other than the canonical ac. NCBI RefSeq is a comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein. The dataset is derived from 2019-05 UniProt release. 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 - protein accessions\n - RefSeq\n - cross-reference\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB canonical accessions that are cross-referenced to NCBI RefSeq database accessions/identifiers from the triplestore containing triples from nt file and extracts the data as a csv dataset\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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-10116-rattus-norvegicus-2019-05.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.4.5/source/uniprot-proteome-10116-rattus-norvegicus-2019-05.nt\n Name: rat_protein_idmapping.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/rat_protein_idmapping.csv\n Output Subdomain\n Name: rat_protein_xref_refseq.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/rat_protein_xref_refseq.csv\n Name: rat_protein_xref_refseq.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/rat_protein_xref_refseq.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"11047\"\n Name: \"database_label\"\n Description: \"Label or name assigned to the corresponding identifier in the source database\"\n Unique Values: \"1\"\n Name: \"database_id\"\n Description: \"Identifier in the database\"\n Unique Values: \"11046\"", "downloadurl": "/ln2data/releases/data/v-1.4.5/reviewed/rat_protein_xref_refseq.csv" }