{ "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-680145..." ], [ "R-SCE-680132...", "R-ALL-680145..." ] ], "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": "xref_type" } ], [ "R-SCE-6801328", "R-ALL-6801458", "5,10-methenyl-THF [mitochondrial matrix]", "output", "57455", "ChEBI" ], [ "R-SCE-6801328", "R-ALL-6801458", "5,10-methenyl-THF [mitochondrial matrix]", "output", "HMDB0062623", "HMDB Metabolite" ], [ "R-SCE-6801328", "R-ALL-6801458", "5,10-methenyl-THF [mitochondrial matrix]", "output", "000004228270", "ZINC" ], [ "R-SCE-192160", "R-ALL-191980", "5beta-cholestan-7alpha-ol-3-one [cytosol]", "input", "000013543210", "ZINC" ], [ "R-SCE-192160", "R-ALL-191980", "5beta-cholestan-7alpha-ol-3-one [cytosol]", "input", "C05451", "COMPOUND" ], [ "R-SCE-192160", "R-ALL-191980", "5beta-cholestan-7alpha-ol-3-one [cytosol]", "input", "HMDB0006892", "HMDB Metabolite" ], [ "R-SCE-192160", "R-ALL-191980", "5beta-cholestan-7alpha-ol-3-one [cytosol]", "input", "2290", "ChEBI" ], [ "R-SCE-192160", "R-ALL-192030", "5beta-cholestan-3alpha,7alpha-diol [cytosol]", "output", "28047", "ChEBI" ], [ "R-SCE-192160", "R-ALL-192030", "5beta-cholestan-3alpha,7alpha-diol [cytosol]", "output", "C05452", "COMPOUND" ], [ "R-SCE-192160", "R-ALL-192030", "5beta-cholestan-3alpha,7alpha-diol [cytosol]", "output", "000013512028", "ZINC" ], [ "R-SCE-192160", "R-ALL-192030", "5beta-cholestan-3alpha,7alpha-diol [cytosol]", "output", "HMDB0006893", "HMDB Metabolite" ], [ "R-SCE-6790127", "R-SCE-6790193", "tRNA(Leu) containing U-20 [cytoplasm]", "input", "29169", "ChEBI" ], [ "R-SCE-6790127", "R-SCE-6790193", "tRNA(Leu) containing U-20 [cytoplasm]", "input", "73747", "ChEBI" ], [ "R-SCE-6790127", "R-SCE-6790164", "tRNA(Leu) containing dihydroU-20 [cytosol]", "output", "29169", "ChEBI" ], [ "R-SCE-6790127", "R-SCE-6790164", "tRNA(Leu) containing dihydroU-20 [cytosol]", "output", "74443", "ChEBI" ], [ "R-SCE-2046098", "R-ALL-2046044", "LINA [endoplasmic reticulum lumen]", "input", "000004474613", "ZINC" ], [ "R-SCE-2046098", "R-ALL-2046044", "LINA [endoplasmic reticulum lumen]", "input", "HMDB0000673", "HMDB Metabolite" ], [ "R-SCE-2046098", "R-ALL-2046044", "LINA [endoplasmic reticulum lumen]", "input", "17351", "ChEBI" ], [ "R-SCE-2046098", "R-ALL-2046044", "LINA [endoplasmic reticulum lumen]", "input", "C01595", "COMPOUND" ], [ "R-SCE-2046098", "R-ALL-2046044", "LINA [endoplasmic reticulum lumen]", "input", "1052", "Guide to Pharmacology - Ligands" ], [ "R-SCE-2046098", "R-ALL-2046063", "LA-CoA [endoplasmic reticulum lumen]", "output", "15530", "ChEBI" ], [ "R-SCE-2046098", "R-ALL-2046063", "LA-CoA [endoplasmic reticulum lumen]", "output", "HMDB0001064", "HMDB Metabolite" ], [ "R-SCE-2046098", "R-ALL-2046063", "LA-CoA [endoplasmic reticulum lumen]", "output", "C02050", "COMPOUND" ], [ "R-SCE-2046098", "R-ALL-2046063", "LA-CoA [endoplasmic reticulum lumen]", "output", "8143234", "PubChem Substance" ], [ "R-SCE-162857", "R-ALL-8855657", "N-acetylglucosaminyl-PI [integral component of cytoplasmic side of endoplasmic reticulum membrane]", "input", "57265", "ChEBI" ], [ "R-SCE-162857", "R-ALL-8855661", "glucosaminyl-PI [integral component of cytoplasmic side of endoplasmic reticulum membrane]", "output", "57997", "ChEBI" ], [ "R-SCE-2046085", "R-ALL-162743", "CoA-SH [endoplasmic reticulum lumen]", "input", "57287", "ChEBI" ], [ "R-SCE-2046085", "R-ALL-162743", "CoA-SH [endoplasmic reticulum lumen]", "input", "C00010", "COMPOUND" ], [ "R-SCE-2046085", "R-ALL-162743", "CoA-SH [endoplasmic reticulum lumen]", "input", "000008551087", "ZINC" ], [ "R-SCE-2046085", "R-ALL-2046056", "ALA [endoplasmic reticulum lumen]", "input", "HMDB0001388", "HMDB Metabolite" ], [ "R-SCE-2046085", "R-ALL-2046056", "ALA [endoplasmic reticulum lumen]", "input", "1049", "Guide to Pharmacology - Ligands" ], [ "R-SCE-2046085", "R-ALL-2046056", "ALA [endoplasmic reticulum lumen]", "input", "27432", "ChEBI" ], [ "R-SCE-2046085", "R-ALL-2046056", "ALA [endoplasmic reticulum lumen]", "input", "000003802189", "ZINC" ], [ "R-SCE-2046085", "R-ALL-2046056", "ALA [endoplasmic reticulum lumen]", "input", "C06427", "COMPOUND" ], [ "R-SCE-2046085", "R-ALL-2046049", "PPi [endoplasmic reticulum membrane]", "output", "C00013", "COMPOUND" ], [ "R-SCE-2046085", "R-ALL-2046049", "PPi [endoplasmic reticulum membrane]", "output", "33019", "ChEBI" ], [ "R-SCE-2046085", "R-ALL-2046049", "PPi [endoplasmic reticulum membrane]", "output", "2466-09-3", "CAS" ], [ "R-SCE-2046085", "R-ALL-2046049", "PPi [endoplasmic reticulum membrane]", "output", "PPI", "AraCyc" ], [ "R-SCE-2046085", "R-ALL-2046049", "PPi [endoplasmic reticulum membrane]", "output", "2466", "CAS" ], [ "R-SCE-2046085", "R-ALL-2046049", "PPi [endoplasmic reticulum membrane]", "output", "000006827695", "ZINC" ], [ "R-SCE-2046085", "R-ALL-2046049", "PPi [endoplasmic reticulum membrane]", "output", "1023", "PubChem Compound" ], [ "R-SCE-2046085", "R-ALL-2046049", "PPi [endoplasmic reticulum membrane]", "output", "4097574", "PubChem Compound" ], [ "R-SCE-2046085", "R-ALL-2046062", "ALA-CoA [endoplasmic reticulum lumen]", "output", "51985", "ChEBI" ], [ "R-SCE-2046085", "R-ALL-2046064", "adenosine 5'-monophosphate [endoplasmic reticulum membrane]", "output", "456215", "ChEBI" ], [ "R-SCE-2046085", "R-ALL-2046064", "adenosine 5'-monophosphate [endoplasmic reticulum membrane]", "output", "000003860156", "ZINC" ], [ "R-SCE-5661256", "R-ALL-5661264", "D-glucuronate [cytosol]", "input", "15748", "ChEBI" ], [ "R-SCE-5661256", "R-ALL-5661268", "L-gulonate [cytosol]", "output", "13115", "ChEBI" ], [ "R-SCE-5661256", "R-ALL-5661268", "L-gulonate [cytosol]", "output", "000003869787", "ZINC" ], [ "R-SCE-5661256", "R-ALL-5661268", "L-gulonate [cytosol]", "output", "C00800", "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", "C00038", "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-174401", "R-ALL-83909", "Ade-Rib [cytosol]", "output", "C00212", "COMPOUND" ], [ "R-SCE-174401", "R-ALL-83909", "Ade-Rib [cytosol]", "output", "16335", "ChEBI" ], [ "R-SCE-174401", "R-ALL-83909", "Ade-Rib [cytosol]", "output", "8143428", "PubChem Substance" ], [ "R-SCE-174401", "R-ALL-83909", "Ade-Rib [cytosol]", "output", "HMDB0000050", "HMDB Metabolite" ], [ "R-SCE-174401", "R-ALL-83909", "Ade-Rib [cytosol]", "output", "2844", "Guide to Pharmacology - Ligands" ], [ "R-SCE-174401", "R-ALL-83909", "Ade-Rib [cytosol]", "output", "000002169830", "ZINC" ], [ "R-SCE-3232162", "R-SCE-201592", "RTG3 [nucleoplasm]", "input", "NP_009447.1", "RefSeq" ], [ "R-SCE-3232162", "R-SCE-201592", "RTG3 [nucleoplasm]", "input", "P38165", "UniProt" ], [ "R-SCE-3232162", "R-SCE-201592", "RTG3 [nucleoplasm]", "input", "P38165", "PRO" ], [ "R-SCE-3232162", "R-SCE-3232153", "RTG3 [nucleoplasm]", "output", "P38165", "UniProt" ], [ "R-SCE-3232162", "R-SCE-3232153", "RTG3 [nucleoplasm]", "output", "NP_009447.1", "RefSeq" ], [ "R-SCE-3232162", "R-SCE-3232153", "RTG3 [nucleoplasm]", "output", "P38165", "PRO" ], [ "R-SCE-6790128", "R-SCE-6790143", "tRNA(Ala) containing A-37 [cytoplasm]", "input", "62885", "ChEBI" ], [ "R-SCE-6790128", "R-SCE-6790143", "tRNA(Ala) containing A-37 [cytoplasm]", "input", "29170", "ChEBI" ], [ "R-SCE-6790128", "R-ALL-1132163", "NH3 [cytoplasm]", "output", "16134", "ChEBI" ], [ "R-SCE-6790128", "R-ALL-1132163", "NH3 [cytoplasm]", "output", "8145696", "PubChem Substance" ], [ "R-SCE-6790128", "R-ALL-1132163", "NH3 [cytoplasm]", "output", "HMDB0000051", "HMDB Metabolite" ], [ "R-SCE-6790128", "R-ALL-1132163", "NH3 [cytoplasm]", "output", "C00014", "COMPOUND" ], [ "R-SCE-6790128", "R-ALL-1132163", "NH3 [cytoplasm]", "output", "HMDB0033934", "HMDB Metabolite" ], [ "R-SCE-6790128", "R-SCE-6790137", "tRNA(Ala) containing I-37 [cytoplasm]", "output", "29170", "ChEBI" ], [ "R-SCE-6790128", "R-SCE-6790137", "tRNA(Ala) containing I-37 [cytoplasm]", "output", "82852", "ChEBI" ], [ "R-SCE-5358592", "R-ALL-29358", "ATP [nucleoplasm]", "input", "30616", "ChEBI" ], [ "R-SCE-5358592", "R-ALL-29358", "ATP [nucleoplasm]", "input", "C00002", "COMPOUND" ], [ "R-SCE-5358592", "R-ALL-29358", "ATP [nucleoplasm]", "input", "000004261765", "ZINC" ], [ "R-SCE-5358592", "R-ALL-5358610", "DNA containing single strand nick (5' phosphate, 3' hydroxyl) [nucleoplasm]", "input", "4705", "ChEBI" ], [ "R-SCE-5358592", "R-ALL-109966", "Repaired double-stranded DNA [nucleoplasm]", "output", "4705", "ChEBI" ], [ "R-SCE-6814797", "R-ALL-2239407", "lysophosphatidylcholine [plasma membrane]", "input", "2508", "Guide to Pharmacology - Ligands" ], [ "R-SCE-6814797", "R-ALL-2239407", "lysophosphatidylcholine [plasma membrane]", "input", "60479", "ChEBI" ], [ "R-SCE-6814797", "R-ALL-6814794", "ChoP [extracellular region]", "output", "18132", "ChEBI" ] ] }, "readme": "Name\n - Yeast Reaction Participants (Reactome)\n\nVersion\n - v-2.3.1\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-2.3.1/reviewed/yeast_protein_participants_reactome.csv\n Name: yeast_protein_participants_reactome.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/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: \"1921\"\n Name: \"participant_name\"\n Description: \"\"\n Unique Values: \"1184\"\n Name: \"role\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"3449\"\n Name: \"xref_type\"\n Description: \"\"\n Unique Values: \"27\"", "downloadurl": "/ln2data/releases/data/v-2.3.1/reviewed/yeast_protein_participants_reactome.csv" }