{ "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": [ [ "Q0HA29-1...", "protein_xref..." ], [ "Q0HA29-1...", "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" } ], [ "Q0HA29-1", "protein_xref_reactome", "R-RNO-196807", "Nicotinate metabolism" ], [ "Q0HA29-1", "protein_xref_reactome", "R-RNO-196807", "Nicotinate metabolism" ], [ "A0A0G2JVG6-1", "protein_xref_reactome", "R-RNO-212436", "Generic Transcription Pathway" ], [ "P30938-1", "protein_xref_reactome", "R-RNO-375276", "Peptide ligand-binding receptors" ], [ "P30938-1", "protein_xref_reactome", "R-RNO-418594", "G alpha (i) signalling events" ], [ "A0A8I5Y4X4-1", "protein_xref_reactome", "R-RNO-8951664", "Neddylation" ], [ "A0A8I5Y4X4-1", "protein_xref_reactome", "R-RNO-8951664", "Neddylation" ], [ "P30937-1", "protein_xref_reactome", "R-RNO-375276", "Peptide ligand-binding receptors" ], [ "P30937-1", "protein_xref_reactome", "R-RNO-418594", "G alpha (i) signalling events" ], [ "O35152-1", "protein_xref_reactome", "R-RNO-6807878", "COPI-mediated anterograde transport" ], [ "O35152-1", "protein_xref_reactome", "R-RNO-6807878", "COPI-mediated anterograde transport" ], [ "O35152-1", "protein_xref_reactome", "R-RNO-6807878", "COPI-mediated anterograde transport" ], [ "O35152-1", "protein_xref_reactome", "R-RNO-6811438", "Intra-Golgi traffic" ], [ "O35152-1", "protein_xref_reactome", "R-RNO-6811438", "Intra-Golgi traffic" ], [ "O35152-1", "protein_xref_reactome", "R-RNO-6811438", "Intra-Golgi traffic" ], [ "P30936-1", "protein_xref_reactome", "R-RNO-375276", "Peptide ligand-binding receptors" ], [ "P30936-1", "protein_xref_reactome", "R-RNO-418594", "G alpha (i) signalling events" ], [ "P30936-1", "protein_xref_reactome", "R-RNO-5620922", "BBSome-mediated cargo-targeting to cilium" ], [ "P30936-1", "protein_xref_reactome", "R-RNO-5620922", "BBSome-mediated cargo-targeting to cilium" ], [ "O35158-1", "protein_xref_reactome", "R-RNO-525793", "Myogenesis" ], [ "O35158-1", "protein_xref_reactome", "R-RNO-525793", "Myogenesis" ], [ "O35158-1", "protein_xref_reactome", "R-RNO-525793", "Myogenesis" ], [ "O35158-1", "protein_xref_reactome", "R-RNO-5632681", "Ligand-receptor interactions" ], [ "O35158-1", "protein_xref_reactome", "R-RNO-5635838", "Activation of SMO" ], [ "P02764-1", "protein_xref_reactome", "R-RNO-114608", "Platelet degranulation " ], [ "P02764-1", "protein_xref_reactome", "R-RNO-6798695", "Neutrophil degranulation" ], [ "P02764-1", "protein_xref_reactome", "R-RNO-6798695", "Neutrophil degranulation" ], [ "P02764-1", "protein_xref_reactome", "R-RNO-6798695", "Neutrophil degranulation" ], [ "P02767-1", "protein_xref_reactome", "R-RNO-2453902", "The canonical retinoid cycle in rods (twilight vision)" ], [ "P02767-1", "protein_xref_reactome", "R-RNO-2453902", "The canonical retinoid cycle in rods (twilight vision)" ], [ "P02767-1", "protein_xref_reactome", "R-RNO-6798695", "Neutrophil degranulation" ], [ "P02767-1", "protein_xref_reactome", "R-RNO-975634", "Retinoid metabolism and transport" ], [ "D4A4W9-1", "protein_xref_reactome", "R-RNO-156827", "L13a-mediated translational silencing of Ceruloplasmin expression" ], [ "D4A4W9-1", "protein_xref_reactome", "R-RNO-1799339", "SRP-dependent cotranslational protein targeting to membrane" ], [ "D4A4W9-1", "protein_xref_reactome", "R-RNO-6791226", "Major pathway of rRNA processing in the nucleolus and cytosol" ], [ "D4A4W9-1", "protein_xref_reactome", "R-RNO-72689", "Formation of a pool of free 40S subunits" ], [ "D4A4W9-1", "protein_xref_reactome", "R-RNO-72706", "GTP hydrolysis and joining of the 60S ribosomal subunit" ], [ "D4A4W9-1", "protein_xref_reactome", "R-RNO-72706", "GTP hydrolysis and joining of the 60S ribosomal subunit" ], [ "D4A4W9-1", "protein_xref_reactome", "R-RNO-975956", "Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)" ], [ "D4A4W9-1", "protein_xref_reactome", "R-RNO-975957", "Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)" ], [ "D4A4W9-1", "protein_xref_reactome", "R-RNO-975957", "Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)" ], [ "D4A4W9-1", "protein_xref_reactome", "R-RNO-975957", "Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)" ], [ "F7EN52-1", "protein_xref_reactome", "R-RNO-193775", "Synthesis of bile acids and bile salts via 24-hydroxycholesterol" ], [ "F7EN52-1", "protein_xref_reactome", "R-RNO-211976", "Endogenous sterols" ], [ "D4A4W5-1", "protein_xref_reactome", "R-RNO-936837", "Ion transport by P-type ATPases" ], [ "D4A4W5-1", "protein_xref_reactome", "R-RNO-936837", "Ion transport by P-type ATPases" ], [ "P01237-1", "protein_xref_reactome", "R-RNO-1170546", "Prolactin receptor signaling" ], [ "P01237-1", "protein_xref_reactome", "R-RNO-1170546", "Prolactin receptor signaling" ], [ "P01237-1", "protein_xref_reactome", "R-RNO-1170546", "Prolactin receptor signaling" ], [ "P01237-1", "protein_xref_reactome", "R-RNO-1170546", "Prolactin receptor signaling" ], [ "P01237-1", "protein_xref_reactome", "R-RNO-1170546", "Prolactin receptor signaling" ], [ "P01237-1", "protein_xref_reactome", "R-RNO-1170546", "Prolactin receptor signaling" ], [ "P01237-1", "protein_xref_reactome", "R-RNO-1170546", "Prolactin receptor signaling" ], [ "P01237-1", "protein_xref_reactome", "R-RNO-982772", "Growth hormone receptor signaling" ], [ "P01230-1", "protein_xref_reactome", "R-RNO-8866910", "TFAP2 (AP-2) family regulates transcription of growth factors and their receptors" ], [ "P01230-1", "protein_xref_reactome", "R-RNO-975578", "Reactions specific to the complex N-glycan synthesis pathway" ], [ "P01230-1", "protein_xref_reactome", "R-RNO-193048", "Androgen biosynthesis" ], [ "P01230-1", "protein_xref_reactome", "R-RNO-193993", "Mineralocorticoid biosynthesis" ], [ "P01230-1", "protein_xref_reactome", "R-RNO-209822", "Glycoprotein hormones" ], [ "P01230-1", "protein_xref_reactome", "R-RNO-209822", "Glycoprotein hormones" ], [ "P01230-1", "protein_xref_reactome", "R-RNO-375281", "Hormone ligand-binding receptors" ], [ "Q9JHY1-1", "protein_xref_reactome", "R-RNO-202733", "Cell surface interactions at the vascular wall" ], [ "Q9JHY1-1", "protein_xref_reactome", "R-RNO-202733", "Cell surface interactions at the vascular wall" ], [ "Q9JHY1-1", "protein_xref_reactome", "R-RNO-216083", "Integrin cell surface interactions" ], [ "Q9JHY1-1", "protein_xref_reactome", "R-RNO-2173791", "TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition)" ], [ "Q9JHY1-1", "protein_xref_reactome", "R-RNO-2173791", "TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition)" ], [ "Q9JHY1-1", "protein_xref_reactome", "R-RNO-2173791", "TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition)" ], [ "Q9JHY1-1", "protein_xref_reactome", "R-RNO-420029", "Tight junction interactions" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-141430", "Inactivation of APC/C via direct inhibition of the APC/C complex" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-141444", "Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-141444", "Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-141444", "Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-141444", "Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-2467813", "Separation of Sister Chromatids" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-2467813", "Separation of Sister Chromatids" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-2500257", "Resolution of Sister Chromatid Cohesion" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-2500257", "Resolution of Sister Chromatid Cohesion" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-2500257", "Resolution of Sister Chromatid Cohesion" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-2500257", "Resolution of Sister Chromatid Cohesion" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-4615885", "SUMOylation of DNA replication proteins" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-5663220", "RHO GTPases Activate Formins" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-5663220", "RHO GTPases Activate Formins" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-68877", "Mitotic Prometaphase" ], [ "Q9JHY7-1", "protein_xref_reactome", "R-RNO-8951664", "Neddylation" ] ] }, "readme": "Name\n - Rat UniProtKB Xref Reactome\n\nVersion\n - v-2.0.3\n\nCreated on\n - 2019-09-06T14:06:38.987144\n\nModified on\n - 2022-09-26T09:04:47.987292\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], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@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/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/2022_05/uniprot-proteome-rattus-norvegicus.nt\n Output Subdomain\n Name: rat_protein_xref_reactome.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_protein_xref_reactome.csv\n Name: rat_protein_xref_reactome.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_protein_xref_reactome.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"8048\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"1346\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"1346\"", "downloadurl": "/ln2data/releases/data/v-2.0.3/reviewed/rat_protein_xref_reactome.csv" }