{ "bcoid": "GLY_000770", "title": "Yeast Reactions Rhea", "description": "The Yeast Protein Reactions (Rhea) dataset contains reactions information for pathways for yeast [taxid:559292] ...", "filename": "yeast_protein_reactions_rhea.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Protein" ], "tag": [ "Reactions Rhea" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "10040...", "..." ], [ "10100...", "..." ] ], "headers": [ "reaction_id...", "reaction_nam..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "reaction_id" }, { "type": "string", "label": "reaction_name" }, { "type": "string", "label": "cellular_location" }, { "type": "string", "label": "pmid" }, { "type": "string", "label": "pathway_id" }, { "type": "string", "label": "equation" }, { "type": "string", "label": "reaction_summary" } ], [ "10040", "", "", "", "", "adenosine 3',5'-bisphosphate + H2O = AMP + phosphate", "" ], [ "10100", "", "", "", "", "a sterol ester + H2O = a fatty acid + a sterol + H(+)", "" ], [ "10112", "", "", "", "", "L-homocysteine + L-serine = H2O + L,L-cystathionine", "" ], [ "10116", "", "", "", "", "6-phospho-D-gluconate + NADP(+) = CO2 + D-ribulose 5-phosphate + NADPH", "" ], [ "10164", "", "", "", "", "(2R)-2-phosphoglycerate = H2O + phosphoenolpyruvate", "" ], [ "10188", "", "", "", "", "acetoacetyl-CoA + acetyl-CoA + H2O = (3S)-hydroxy-3-methylglutaryl-CoA + CoA + H(+)", "" ], [ "10208", "", "", "", "", "an N-terminal L-alpha-aminoacyl-[protein] + L-arginyl-tRNA(Arg) = H(+) + N-terminal L-arginyl-L-amino acid-[protein] + tRNA(Arg)", "" ], [ "10216", "", "", "", "", "[DNA-directed RNA polymerase] + ATP = ADP + H(+) + phospho-[DNA-directed RNA polymerase]", "" ], [ "10217", "", "", "", "", "[DNA-directed RNA polymerase] + ATP => ADP + H(+) + phospho-[DNA-directed RNA polymerase]", "" ], [ "10220", "", "", "", "", "ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr)", "" ], [ "10224", "", "", "", "", "ATP + pyridoxal = ADP + H(+) + pyridoxal 5'-phosphate", "" ], [ "10248", "", "", "", "", "dUTP + H2O = diphosphate + dUMP + H(+)", "" ], [ "10264", "", "", "", "", "alpha-D-glucose = beta-D-glucose", "" ], [ "10276", "", "", "", "", "5-diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate + ATP + H(+) = 1,5-bis(diphospho)-1D-myo-inositol 2,3,4,6-tetrakisphosphate + ADP", "" ], [ "10292", "", "", "", "", "acetyl-CoA + D-glucosamine 6-phosphate = CoA + H(+) + N-acetyl-D-glucosamine 6-phosphate", "" ], [ "10300", "", "", "", "", "D-glyceraldehyde 3-phosphate + NAD(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADH", "" ], [ "10336", "", "", "", "", "citrate = D-threo-isocitrate", "" ], [ "10348", "", "", "", "", "5-oxo-L-proline + ATP + 2 H2O = ADP + H(+) + L-glutamate + phosphate", "" ], [ "10380", "", "", "", "", "diphosphate + orotidine 5'-phosphate = 5-phospho-alpha-D-ribose 1-diphosphate + orotate", "" ], [ "10412", "", "", "", "", "ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate + 2 H(+)", "" ], [ "10488", "", "", "", "", "(6S)-5-formyl-5,6,7,8-tetrahydrofolate + ATP = (6R)-5,10-methenyltetrahydrofolate + ADP + phosphate", "" ], [ "10508", "", "", "", "", "D-glyceraldehyde 3-phosphate + D-sedoheptulose 7-phosphate = aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate", "" ], [ "10580", "", "", "", "", "(6S)-5,6,7,8-tetrahydrofolyl-(gamma-L-Glu)(n) + ATP + L-glutamate = (6S)-5,6,7,8-tetrahydrofolyl-(gamma-L-Glu)(n+1) + ADP + H(+) + phosphate", "" ], [ "10596", "", "", "", "", "ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein]", "" ], [ "10684", "", "", "", "", "H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate", "" ], [ "10704", "", "", "", "", "ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val)", "" ], [ "10716", "", "", "", "", "D-glucose 6-phosphate = 1D-myo-inositol 3-phosphate", "" ], [ "10736", "", "", "", "", "a primary alcohol + NAD(+) = an aldehyde + H(+) + NADH", "" ], [ "10740", "", "", "", "", "a secondary alcohol + NAD(+) = a ketone + H(+) + NADH", "" ], [ "10748", "", "", "", "", "H(+) + hydrogencarbonate = CO2 + H2O", "" ], [ "10792", "", "", "", "", "5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + H(+) = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + CO2", "" ], [ "10868", "", "", "", "", "a 1,2-diacyl-sn-glycerol + an acyl-CoA = a triacyl-sn-glycerol + CoA", "" ], [ "10932", "", "", "", "", "ATP + L-aspartate + L-citrulline = 2-(N(omega)-L-arginino)succinate + AMP + diphosphate + H(+)", "" ], [ "10944", "", "", "", "", "H2O + psi-UMP = phosphate + pseudouridine", "" ], [ "10964", "", "", "", "", "ATP + D-xylulose = ADP + D-xylulose 5-phosphate + H(+)", "" ], [ "10992", "", "", "", "", "glycolate + NADP(+) = glyoxylate + H(+) + NADPH", "" ], [ "11016", "", "", "", "", "allantoate + H2O = (S)-ureidoglycolate + urea", "" ], [ "11020", "", "", "", "", "1D-myo-inositol 1,4,5-trisphosphate + ATP = 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ADP + H(+)", "" ], [ "11060", "", "", "", "", "ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile)", "" ], [ "11064", "", "", "", "", "beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate", "" ], [ "11092", "", "", "", "", "NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH", "" ], [ "11140", "", "", "", "", "alpha-D-mannose 1-phosphate = D-mannose 6-phosphate", "" ], [ "11148", "", "", "", "", "4 Fe(2+) + 4 H(+) + O2 = 4 Fe(3+) + 2 H2O", "" ], [ "11164", "", "", "", "", "a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + S-adenosyl-L-methionine = 1,2-diacyl-sn-glycero-3-phospho-N-methylethanolamine + H(+) + S-adenosyl-L-homocysteine", "" ], [ "11180", "", "", "", "", "ATP + L-asparagine + tRNA(Asn) = AMP + diphosphate + H(+) + L-asparaginyl-tRNA(Asn)", "" ], [ "11204", "", "", "", "", "apo-[propionyl-CoA:carbon-dioxide ligase (ADP-forming)] + ATP + biotin = AMP + diphosphate + H(+) + holo-[propionyl-CoA:carbon-dioxide ligase (ADP-forming)]", "" ], [ "11308", "", "", "", "", "acetyl-CoA + ATP + hydrogencarbonate = ADP + H(+) + malonyl-CoA + phosphate", "" ], [ "11332", "", "", "", "", "ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide", "" ], [ "11436", "", "", "", "", "4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O", "" ], [ "11484", "", "", "", "", "a quinol + 2 Fe(III)-[cytochrome c](out) = a quinone + 2 Fe(II)-[cytochrome c](out) + 2 H(+)(out)", "" ], [ "11576", "", "", "", "", "ATP + thiamine = AMP + H(+) + thiamine diphosphate", "" ], [ "11580", "", "", "", "", "a CDP-1,2-diacyl-sn-glycerol + myo-inositol = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + CMP + H(+)", "" ], [ "11596", "", "", "", "", "H(+) + orotidine 5'-phosphate = CO2 + UMP", "" ], [ "11612", "", "", "", "", "H2O + L-glutamate + NADP(+) = 2-oxoglutarate + H(+) + NADPH + NH4(+)", "" ], [ "11660", "", "", "", "", "a 6-(N-acetyl-alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol + H2O = acetate + an alpha-D-GlcN-(1->6)-(1,2-diacyl-sn-glycero-3-phospho)-1D-myo-inositol", "" ], [ "11680", "", "", "", "", "ATP + H2O + L-glutamine + XMP = AMP + diphosphate + GMP + 2 H(+) + L-glutamate", "" ], [ "11688", "", "", "", "", "ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)", "" ], [ "11708", "", "", "", "", "H2O + IMP + NAD(+) = H(+) + NADH + XMP", "" ], [ "11716", "", "", "", "", "a monoamide of a dicarboxylate + H2O = a dicarboxylate + NH4(+)", "" ], [ "11740", "", "", "", "", "2 glutathione + NADP(+) = glutathione disulfide + H(+) + NADPH", "" ], [ "11756", "", "", "", "", "ATP + biotin + L-lysyl-[protein] = AMP + diphosphate + H(+) + N(6)-biotinyl-L-lysyl-[protein]", "" ], [ "11800", "", "", "", "", "H2O + NAD(+) = AMP + beta-nicotinamide D-ribonucleotide + 2 H(+)", "" ], [ "11816", "", "", "", "", "alpha-D-glucose 6-phosphate = beta-D-fructose 6-phosphate", "" ], [ "11852", "", "", "", "", "phosphate + S-methyl-5'-thioadenosine = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate", "" ], [ "11920", "", "", "", "", "(4aS,6R)-4a-hydroxy-L-erythro-5,6,7,8-tetrahydrobiopterin = (6R)-L-erythro-6,7-dihydrobiopterin + H2O", "" ], [ "12044", "", "", "", "", "a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+)", "" ], [ "12045", "", "", "", "", "a triacylglycerol + H2O => a diacylglycerol + a fatty acid + H(+)", "" ], [ "12068", "", "", "", "", "apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP]", "" ], [ "12104", "", "", "", "", "(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + dUMP = 7,8-dihydrofolate + dTMP", "" ], [ "12168", "", "", "", "", "allyl alcohol + NADP(+) = acrolein + H(+) + NADPH", "" ], [ "12188", "", "", "", "", "2-oxoglutarate + H(+) + N(6)-[(R)-lipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] = CO2 + N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase]", "" ], [ "12228", "", "", "", "", "ATP + H2O + L-aspartate + L-glutamine = AMP + diphosphate + H(+) + L-asparagine + L-glutamate", "" ], [ "12292", "", "", "", "", "ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-seryl-tRNA(Ser)", "" ], [ "12304", "", "", "", "", "(S)-2-amino-6-oxohexanoate + H2O + NADP(+) = 2 H(+) + L-2-aminoadipate + NADPH", "" ], [ "12308", "", "", "", "", "(S)-2-amino-6-oxohexanoate + H2O + NAD(+) = 2 H(+) + L-2-aminoadipate + NADH", "" ], [ "12316", "", "", "", "", "a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate) + H2O = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + phosphate", "" ], [ "12356", "", "", "", "", "D-mannose 6-phosphate = D-fructose 6-phosphate", "" ], [ "12460", "", "", "", "", "(S)-malate = fumarate + H2O", "" ], [ "12461", "", "", "", "", "(S)-malate => fumarate + H2O", "" ], [ "12462", "", "", "", "", "fumarate + H2O => (S)-malate", "" ], [ "12540", "", "", "", "", "ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala)", "" ], [ "12556", "", "", "", "", "6-phospho-D-glucono-1,5-lactone + H2O = 6-phospho-D-gluconate + H(+)", "" ], [ "12593", "", "", "", "", "a CDP-1,2-diacyl-sn-glycerol + sn-glycerol 3-phosphate = 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycero-3'-phosphate) + CMP + H(+)", "" ], [ "12601", "", "", "", "", "2-oxoglutarate + L-2-aminoadipate = 2-oxoadipate + L-glutamate", "" ] ] }, "readme": "Name\n - Yeast Reactions Rhea\n\nVersion\n - v-2.4.1\n\nCreated on\n - 2022-09-06T11:37:59.766468\n\nModified on\n - 2023-09-11T19:20:48\n\nCreated by\n - [jeetvora@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Yeast Protein Reactions (Rhea) dataset contains reactions information for pathways for yeast [taxid:559292] UniProtKB accessions that includes reaction participants ID, reaction ID, pathway ID, summary etc from Rhea database. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB, Rhea and GlyGen\"\n\nDescription Domain\n Keywords\n - Rhea\n - Reactions\n - Participants\n - Enzymes\n\n Pipeline Steps\n - Step-1: The script loads the Rhea reaction data from the triplestore containing triples from nt file to retrieve the information associated with the Rhea reaction IDs and maps it to the UniProtKB canonical accessions and 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: uniprot-proteome-saccharomyces-cerevisiae.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2024_02_13/uniprot-proteome-saccharomyces-cerevisiae.nt\n Output Subdomain\n Name: yeast_protein_reactions_rhea.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_protein_reactions_rhea.csv\n Name: yeast_protein_reactions_rhea.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_protein_reactions_rhea.stat.csv\n\nFields\n Name: \"reaction_id\"\n Description: \"The identifier assigned to a reaction in Reactome database\"\n Unique Values: \"1668\"\n Name: \"reaction_name\"\n Description: \"The name assigned to a reaction in Reactome database\"\n Unique Values: \"1\"\n Name: \"cellular_location\"\n Description: \"The loaction in the cell where reaction occurs\"\n Unique Values: \"1\"\n Name: \"pmid\"\n Description: \"NCBI PubMed database Identifier\"\n Unique Values: \"1\"\n Name: \"pathway_id\"\n Description: \"Pathway Identifier\"\n Unique Values: \"1\"\n Name: \"equation\"\n Description: \"\"\n Unique Values: \"1668\"\n Name: \"reaction_summary\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/yeast_protein_reactions_rhea.csv" }