{ "bcoid": "GLY_000260", "title": "Rat UniProtKB Xref Reactome", "description": "The Rat UniProtKB Xref Reactome contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced ...", "filename": "rat_protein_xref_reactome.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Protein", "tags": "Reactome cross-references", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q5RJK9-1...", "protein_xref..." ], [ "Q5RJK9-1...", "protein_xref..." ] ], "headers": [ "uniprotkb_ca...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "xref_label" } ], [ "Q5RJK9-1", "protein_xref_reactome", "R-RNO-5250924", "B-WICH complex positively regulates rRNA expression" ], [ "Q5RJK9-1", "protein_xref_reactome", "R-RNO-5250924", "B-WICH complex positively regulates rRNA expression" ], [ "Q5RJK9-1", "protein_xref_reactome", "R-RNO-73762", "RNA Polymerase I Transcription Initiation" ], [ "Q5RJK9-1", "protein_xref_reactome", "R-RNO-73762", "RNA Polymerase I Transcription Initiation" ], [ "Q5RJK9-1", "protein_xref_reactome", "R-RNO-73772", "RNA Polymerase I Promoter Escape" ], [ "Q5RJK9-1", "protein_xref_reactome", "R-RNO-73772", "RNA Polymerase I Promoter Escape" ], [ "Q5RJK9-1", "protein_xref_reactome", "R-RNO-73863", "RNA Polymerase I Transcription Termination" ], [ "Q5RJK9-1", "protein_xref_reactome", "R-RNO-76061", "RNA Polymerase III Transcription Initiation From Type 1 Promoter" ], [ "Q5RJK9-1", "protein_xref_reactome", "R-RNO-76066", "RNA Polymerase III Transcription Initiation From Type 2 Promoter" ], [ "Q5RJK9-1", "protein_xref_reactome", "R-RNO-76071", "RNA Polymerase III Transcription Initiation From Type 3 Promoter" ], [ "Q5RJK8-1", "protein_xref_reactome", "R-RNO-77289", "Mitochondrial Fatty Acid Beta-Oxidation" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-1433557", "Signaling by SCF-KIT" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-202433", "Generation of second messenger molecules" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-202433", "Generation of second messenger molecules" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-202433", "Generation of second messenger molecules" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-202433", "Generation of second messenger molecules" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-202433", "Generation of second messenger molecules" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-202433", "Generation of second messenger molecules" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-202433", "Generation of second messenger molecules" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2424491", "DAP12 signaling" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2424491", "DAP12 signaling" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2871796", "FCERI mediated MAPK activation" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2424491", "DAP12 signaling" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2424491", "DAP12 signaling" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2424491", "DAP12 signaling" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2424491", "DAP12 signaling" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2424491", "DAP12 signaling" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2424491", "DAP12 signaling" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2424491", "DAP12 signaling" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2871796", "FCERI mediated MAPK activation" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2871796", "FCERI mediated MAPK activation" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2871796", "FCERI mediated MAPK activation" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2871796", "FCERI mediated MAPK activation" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2871796", "FCERI mediated MAPK activation" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2871796", "FCERI mediated MAPK activation" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2871796", "FCERI mediated MAPK activation" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2871809", "FCERI mediated Ca+2 mobilization" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2871809", "FCERI mediated Ca+2 mobilization" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-2871809", "FCERI mediated Ca+2 mobilization" ], [ "D3ZG10-1", "protein_xref_reactome", "R-RNO-389356", "CD28 co-stimulation" ], [ "D3ZB44-1", "protein_xref_reactome", "R-RNO-212436", "Generic Transcription Pathway" ], [ "D3ZZY2-1", "protein_xref_reactome", "R-RNO-6791226", "Major pathway of rRNA processing in the nucleolus and cytosol" ], [ "D3ZZY2-1", "protein_xref_reactome", "R-RNO-6791226", "Major pathway of rRNA processing in the nucleolus and cytosol" ], [ "D3ZZY2-1", "protein_xref_reactome", "R-RNO-6791226", "Major pathway of rRNA processing in the nucleolus and cytosol" ], [ "P30349-1", "protein_xref_reactome", "R-RNO-2142691", "Synthesis of Leukotrienes (LT) and Eoxins (EX)" ], [ "P30349-1", "protein_xref_reactome", "R-RNO-9018676", "Biosynthesis of D-series resolvins" ], [ "P30349-1", "protein_xref_reactome", "R-RNO-9018676", "Biosynthesis of D-series resolvins" ], [ "P30349-1", "protein_xref_reactome", "R-RNO-9018681", "Biosynthesis of protectins" ], [ "P30349-1", "protein_xref_reactome", "R-RNO-9018681", "Biosynthesis of protectins" ], [ "P30349-1", "protein_xref_reactome", "R-RNO-9018896", "Biosynthesis of E-series 18(S)-resolvins" ], [ "P30349-1", "protein_xref_reactome", "R-RNO-9020265", "Biosynthesis of aspirin-triggered D-series resolvins" ], [ "P30349-1", "protein_xref_reactome", "R-RNO-9020265", "Biosynthesis of aspirin-triggered D-series resolvins" ], [ "P30349-1", "protein_xref_reactome", "R-RNO-9023661", "Biosynthesis of E-series 18(R)-resolvins" ], [ "P30349-1", "protein_xref_reactome", "R-RNO-6798695", "Neutrophil degranulation" ], [ "P30349-1", "protein_xref_reactome", "R-RNO-6798695", "Neutrophil degranulation" ], [ "Q5RJK5-1", "protein_xref_reactome", "R-RNO-73772", "RNA Polymerase I Promoter Escape" ], [ "Q5RJK5-1", "protein_xref_reactome", "R-RNO-8953750", "Transcriptional Regulation by E2F6" ], [ "Q5RJK5-1", "protein_xref_reactome", "R-RNO-8953750", "Transcriptional Regulation by E2F6" ], [ "Q5RJK6-1", "protein_xref_reactome", "R-RNO-1855183", "Synthesis of IP2, IP, and Ins in the cytosol" ], [ "Q5RJK6-1", "protein_xref_reactome", "R-RNO-1855183", "Synthesis of IP2, IP, and Ins in the cytosol" ], [ "Q6MG56-1", "protein_xref_reactome", "R-RNO-114608", "Platelet degranulation " ], [ "A0A0G2K0H3-1", "protein_xref_reactome", "R-RNO-4641262", "Disassembly of the destruction complex and recruitment of AXIN to the membrane" ], [ "A0A0G2K0H3-1", "protein_xref_reactome", "R-RNO-4641262", "Disassembly of the destruction complex and recruitment of AXIN to the membrane" ], [ "A0A0G2K0H3-1", "protein_xref_reactome", "R-RNO-4641262", "Disassembly of the destruction complex and recruitment of AXIN to the membrane" ], [ "A0A0G2K0H3-1", "protein_xref_reactome", "R-RNO-3772470", "Negative regulation of TCF-dependent signaling by WNT ligand antagonists" ], [ "A0A0G2K0H3-1", "protein_xref_reactome", "R-RNO-3772470", "Negative regulation of TCF-dependent signaling by WNT ligand antagonists" ], [ "A0A0G2K0H3-1", "protein_xref_reactome", "R-RNO-4641263", "Regulation of FZD by ubiquitination" ], [ "A0A0G2K0H3-1", "protein_xref_reactome", "R-RNO-4641263", "Regulation of FZD by ubiquitination" ], [ "A0A0G2K0H3-1", "protein_xref_reactome", "R-RNO-4641263", "Regulation of FZD by ubiquitination" ], [ "A0A0G2K0H3-1", "protein_xref_reactome", "R-RNO-3772470", "Negative regulation of TCF-dependent signaling by WNT ligand antagonists" ], [ "A0A0G2K0H3-1", "protein_xref_reactome", "R-RNO-4641262", "Disassembly of the destruction complex and recruitment of AXIN to the membrane" ], [ "Q5XIH0-1", "protein_xref_reactome", "R-RNO-8943724", "Regulation of PTEN gene transcription" ], [ "Q5XIH0-1", "protein_xref_reactome", "R-RNO-8943724", "Regulation of PTEN gene transcription" ], [ "P20961-1", "protein_xref_reactome", "R-RNO-75205", "Dissolution of Fibrin Clot" ], [ "P20961-1", "protein_xref_reactome", "R-RNO-75205", "Dissolution of Fibrin Clot" ], [ "P20961-1", "protein_xref_reactome", "R-RNO-75205", "Dissolution of Fibrin Clot" ], [ "P20961-1", "protein_xref_reactome", "R-RNO-3000178", "ECM proteoglycans" ], [ "P20961-1", "protein_xref_reactome", "R-RNO-114608", "Platelet degranulation " ], [ "Q6MG59-1", "protein_xref_reactome", "R-RNO-114604", "GPVI-mediated activation cascade" ], [ "Q6MG59-1", "protein_xref_reactome", "R-RNO-114604", "GPVI-mediated activation cascade" ], [ "Q6MG59-1", "protein_xref_reactome", "R-RNO-114604", "GPVI-mediated activation cascade" ], [ "Q4KLP0-1", "protein_xref_reactome", "R-RNO-389661", "Glyoxylate metabolism and glycine degradation" ], [ "M0RAP5-1", "protein_xref_reactome", "R-RNO-1483248", "Synthesis of PIPs at the ER membrane" ], [ "M0RAP5-1", "protein_xref_reactome", "R-RNO-1483248", "Synthesis of PIPs at the ER membrane" ] ] }, "readme": "Name\n - Rat UniProtKB Xref Reactome\n\nVersion\n - 1.8.24\n\nCreated on\n - 2019-09-06T14:06:38.987144\n\nModified on\n - 2020-04-10T12:03:36.049296\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 UniProtKB Xref Reactome contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced to Reactome database accessions/identifiers. 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 - REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database.\n\nDescription Domain\n Keywords\n - pathways\n - reactions\n - REACTOME\n - cross-reference\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB canonical accessions that are cross-referenced to REACTOME 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-rattus-norvegicus.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.24/source/uniprot-proteome-rattus-norvegicus.nt\n Name: rat_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_protein_masterlist.csv\n Output Subdomain\n Name: rat_protein_xref_reactome.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_protein_xref_reactome.csv\n Name: rat_protein_xref_reactome.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_protein_xref_reactome.stat.csv\n\nFields\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"119\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"119\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"120\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"49\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"118\"\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: \"117\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"115\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.8.24/reviewed/rat_protein_xref_reactome.csv" }