{ "bcoid": "GLY_000763", "title": "Yeast Reaction Participants (Reactome)", "description": "\"The Yeast Protein Reaction Participants (Reactome) dataset contains reactions participants information ...", "filename": "yeast_protein_participants_reactome.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Protein" ], "tag": [ "Reaction Participants (Reactome)" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "R-SCE-680132...", "R-ALL-569398..." ], [ "R-SCE-680132...", "R-ALL-569398..." ] ], "headers": [ "reaction_id...", "participant_..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "reaction_id" }, { "type": "string", "label": "participant_id" }, { "type": "string", "label": "participant_name" }, { "type": "string", "label": "role" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": 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"pristanate [peroxisomal matrix]", "output", "000005758688", "ZINC" ], [ "R-SCE-1482781", "R-ALL-1498773", "MLCL [mitochondrial inner membrane]", "input", "C18129", "COMPOUND" ], [ "R-SCE-1482781", "R-ALL-1498773", "MLCL [mitochondrial inner membrane]", "input", "60430", "ChEBI" ], [ "R-SCE-1482781", "R-ALL-1524072", "cardiolipin [mitochondrial inner membrane]", "output", "28494", "ChEBI" ], [ "R-SCE-1482781", "R-ALL-1524072", "cardiolipin [mitochondrial inner membrane]", "output", "C05980", "COMPOUND" ], [ "R-SCE-1482781", "R-ALL-1524079", "1-acyl LPC [mitochondrial inner membrane]", "output", "17504", "ChEBI" ], [ "R-SCE-1482781", "R-ALL-1524079", "1-acyl LPC [mitochondrial inner membrane]", "output", "C04230", "COMPOUND" ], [ "R-SCE-190141", "R-ALL-190173", "Pb2+ [cytosol]", "input", "27889", "ChEBI" ], [ "R-SCE-190141", "R-ALL-190173", "Pb2+ [cytosol]", "input", "C06696", "COMPOUND" ], [ "R-SCE-190141", "R-ALL-29426", "Zn2+ [cytosol]", "output", "29105", "ChEBI" ], [ "R-SCE-190141", "R-ALL-29426", "Zn2+ [cytosol]", "output", "HMDB0015532", "HMDB Metabolite" ], [ "R-SCE-190141", "R-ALL-29426", "Zn2+ [cytosol]", "output", "11533263", "PubChem Substance" ], [ "R-SCE-190141", "R-ALL-29426", "Zn2+ [cytosol]", "output", "C00038", "COMPOUND" ], [ "R-SCE-174401", "R-ALL-71285", "AdoHcy [cytosol]", "input", "C00021", "COMPOUND" ], [ "R-SCE-174401", "R-ALL-71285", "AdoHcy [cytosol]", "input", "57856", "ChEBI" ], [ "R-SCE-174401", "R-ALL-71285", "AdoHcy [cytosol]", "input", "000004228232", "ZINC" ], [ "R-SCE-174401", "R-ALL-83909", "Ade-Rib [cytosol]", "output", "16335", "ChEBI" ], [ "R-SCE-174401", "R-ALL-83909", "Ade-Rib [cytosol]", "output", "000002169830", "ZINC" ] ] }, "readme": "Name\n - Yeast Reaction Participants (Reactome)\n\nVersion\n - v-2.2.1\n\nCreated on\n - 2022-09-06T11:52:53.037427\n\nModified on\n - 2023-09-11T19:12:40\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 Protein Reaction Participants (Reactome) dataset contains reactions participants information for pathways for yeast [taxid:559292] UniProtKB accessions that includes reaction IDs, participant ID, participant name, role, xref ID etc from Reactome database. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB, Reactome and GlyGen\"\n\nDescription Domain\n Keywords\n - Reactome\n - Participant\n\n Pipeline Steps\n - Step-1: The script loads the Reactome participant data from the triplestore containing triples from nt file to retrieve the information extracts the dataset in the csv format.\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: database_accession.tsv\n URI: https:/data.glygen.org/ln2downloads/chebi/2023_10_11/database_accession.tsv\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_participants_reactome.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_participants_reactome.csv\n Name: yeast_protein_participants_reactome.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_participants_reactome.stat.csv\n\nFields\n Name: \"reaction_id\"\n Description: \"The identifier assigned to a reaction in Reactome database\"\n Unique Values: \"1366\"\n Name: \"participant_id\"\n Description: \"\"\n Unique Values: \"1914\"\n Name: \"participant_name\"\n Description: \"\"\n Unique Values: \"1182\"\n Name: \"role\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"3343\"\n Name: \"xref_type\"\n Description: \"\"\n Unique Values: \"26\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/yeast_protein_participants_reactome.csv" }