The reaction and metabolite IDs in BiGG Models are available in the following tab-separated text files. A universal COBRA model is also provided in JSON format with all reactions and metabolites from BiGG Models. (NOTE: All reactions in the universal model are irreversible).
Data available under the BiGG License. Database links provided by MetaNetX (CC BY 4.0).
BiGG Models can be accessed using a simple web API. Here we provide examples of the API reponses. All of the following are GET requests. Some general function that take advantage of this API will be collected in the BiGG Tools project.
Please be respectful when using this service and do not send more than 10 request per second. The API is very simple, but we hope to add features (including batch requests) over time.
If you experience any unexpected behavior with the API, you can submit an error report at the bottom of this page.
# Get the version and the date BiGG Models was last updated
curl 'http://bigg.ucsd.edu/api/v2/database_version'
{"bigg_models_version": "1.3.0",
"api_version": "v2",
"last_updated": "2018-02-24 08:16:33.924054"}
# Download a model in JSON format
curl 'http://bigg.ucsd.edu/api/v2/models/iND750/download'
# Returns the whole model as a JSON string
# Download models in other formats. These are not JSON responses, so the URLs look a little different. curl -O 'http://bigg.ucsd.edu/static/models/iMM904.xml.gz' curl -O 'http://bigg.ucsd.edu/static/models/iMM904.xml' curl -O 'http://bigg.ucsd.edu/static/models/iMM904.json' curl -O 'http://bigg.ucsd.edu/static/models/iMM904.mat'
# Saves the model to the current directory in the given format
# Get a list of models
curl 'http://bigg.ucsd.edu/api/v2/models'
{"results_count": 85,
"results": [{"bigg_id": "e_coli_core",
"metabolite_count": 72,
"organism": "Escherichia coli str. K-12 substr. MG1655",
"reaction_count": 95,
"gene_count": 137},
{"bigg_id": "iAB_RBC_283",
"metabolite_count": 342,
"organism": "Homo sapiens",
"reaction_count": 469,
"gene_count": 346},
...]
}
# Get model details
curl 'http://bigg.ucsd.edu/api/v2/models/iND750'
{"organism": "Saccharomyces cerevisiae S288c",
"genome": "PRJNA43747",
"metabolite_count": 1061,
"gene_count": 750,
"reaction_count": 1266,
"reference_type": "pmid",
"reference_id": "15197165"}
# Download a model in JSON format curl 'http://bigg.ucsd.edu/api/v2/models/iND750/download'
# Returns the whole model
# Download a model in another format curl 'http://bigg.ucsd.edu/static/models/iND750.xml' curl 'http://bigg.ucsd.edu/static/models/iND750.xml.gz' curl 'http://bigg.ucsd.edu/static/models/iND750.mat' curl 'http://bigg.ucsd.edu/static/models/iND750.json'
# Returns the whole model
# Get a list of model reactions
curl 'http://bigg.ucsd.edu/api/v2/models/iND750/reactions'
[{"bigg_id": "XPPT", "name": "Xanthine phosphoribosyltransferase", "organism": "Saccharomyces cerevisiae S288C", "model_bigg_id": "iND750"},
{"bigg_id": "XTSNt2", "name": "Xanthosine transport in via proton symport", "organism": "Saccharomyces cerevisiae S288C", "model_bigg_id": "iND750"},
...
]
curl 'http://bigg.ucsd.edu/api/v2/models/iND750/reactions/GAPD'
{"name": "glyceraldehyde-3-phosphate dehydrogenase",
"pseudoreaction": false,
"count": 1,
"model_bigg_id": "iND750"
"metabolites": [{"stoichiometry": -1,
"bigg_id": "pi",
"compartment_bigg_id": "c",
"name": "Phosphate"},
{"stoichiometry": 1,
"bigg_id": "nadh",
"compartment_bigg_id": "c",
"name": "Nicotinamide adenine dinucleotide - reduced"},
{"stoichiometry": -1,
"bigg_id": "nad",
"compartment_bigg_id": "c",
"name": "Nicotinamide adenine dinucleotide"},
{"stoichiometry": 1,
"bigg_id": "h",
"compartment_bigg_id": "c",
"name": "H+"},
{"stoichiometry": -1,
"bigg_id": "g3p",
"compartment_bigg_id": "c",
"name": "Glyceraldehyde 3-phosphate"
},
{"stoichiometry": 1,
"bigg_id": "13dpg",
"compartment_bigg_id": "c",
"name": "3-Phospho-D-glyceroyl phosphate"
}],
"database_links": {},
"escher_maps": [],
"other_models_with_reaction": ["iAPECO1_1312", "iSB619", ... ],
"count": 1,
"results": [
{"gene_reaction_rule": "(YJL052W) or (YGR192C) or (YJR009C)",
"lower_bound": -1000,
"upper_bound": 999999,
"objective_coefficient": 0,
"genes": [{"bigg_id": "YGR192C",
"name": "TDH3"},
{"bigg_id": "YJL052W",
"name": "YJL052W"},
{"bigg_id": "YJR009C",
"name": "YJR009C"}]}
]
}
curl 'http://bigg.ucsd.edu/api/v2/models/iND750/metabolites'
[{"bigg_id": "10fthf",
"model_bigg_id": "iND750",
"compartment_bigg_id": "c",
"name": "10-Formyltetrahydrofolate",
"organism": "Saccharomyces cerevisiae S288c"},
...
]
curl 'http://bigg.ucsd.edu/api/v2/models/iND750/metabolites/10fthf_c'
{"formula": "C20H21N7O7",
"bigg_id": "10fthf",
"compartment_bigg_id": "c",
"name": "10-Formyltetrahydrofolate",
"model_bigg_id": "iND750",
"old_identifiers": ["10fthf_c"],
"escher_maps": [],
"other_models_with_metabolite": [
{"bigg_id": "iAPECO1_1312",
"compartment_bigg_id": "c"}
...
],
"database_links": {
"KEGG": [{"link": "http://www.genome.jp/dbget-bin/www_bget?cpd:C00234",
"id": "C00234"}],
"MetaCyc": [{"link": "http://metacyc.org/META/NEW-IMAGE?type=COMPOUND&object=10-FORMYL-THF",
"id": "10-FORMYL-THF"}],
...
}
}
curl 'http://bigg.ucsd.edu/api/v2/models/iMM904/genes'
[{"bigg_id": "Q0045",
"organism": "Saccharomyces cerevisiae S288c",
"model_bigg_id": "iMM904",
"name": "Q0045"},
...
]
curl 'http://bigg.ucsd.edu/api/v2/models/iMM904/genes/Q0045'
{"bigg_id": "Q0045",
"name": "COX1",
"strand": "+",
"leftpos": 13818,
"genome_ref_string": "ncbi_assembly:GCF_000146045.2",
"database_links": {"Saccharomyces Genome Database": [{"link": "http://identifiers.org/sgd/S000007260", "id": "S000007260"}],
"NCBI Entrez Gene": [{"link": "http://identifiers.org/ncbigene/854598", "id": "854598"}]},
"rightpos": 26701,
"protein_sequence": " ",
"model_bigg_id": "iMM904",
"reactions": [{"bigg_id": "",
"name": "",
"gene_reaction_rule": ""}]
...
"old_identifiers": ["Q0045"],
"mapped_to_genbank": true,
"genome_name": "GCF_000146045.2",
"chromosome_ncbi_accession": "NC_001224.1"}
}
curl 'http://bigg.ucsd.edu/api/v2/universal/reactions'
[{"bigg_id": "12DGR120tipp", "model_bigg_id": "Universal", "name": "_1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C12:0)"},
{"bigg_id": "12DGR140tipp", "model_bigg_id": "Universal", "name": "_1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:0)"},
...
]
curl 'http://bigg.ucsd.edu/api/v2/universal/reactions/ADA'
{"bigg_id": "ADA",
"name": "Adenosine deaminase",
"database_links": {},
"pseudoreaction": false,
"models_containing_reaction": [
{"organism": "Escherichia coli APEC O1", "bigg_id": "iAPECO1_1312"},
...
],
"metabolites": [{"stoichiometry": -1.0, "bigg_id": "adn", "compartment_bigg_id": "c", "name": "Adenosine"},
{"stoichiometry": -1.0, "bigg_id": "h2o", "compartment_bigg_id": "c", "name": "H2O"},
{"stoichiometry": -1.0, "bigg_id": "h", "compartment_bigg_id": "c", "name": "H+"},
{"stoichiometry": 1.0, "bigg_id": "ins", "compartment_bigg_id": "c", "name": "Inosine"},
{"stoichiometry": 1.0, "bigg_id": "nh4", "compartment_bigg_id": "c", "name": "Ammonium"}],
}
curl 'http://bigg.ucsd.edu/api/v2/universal/metabolites'
[{"bigg_id": "10fthf", "model_bigg_id": "Universal", "name": "_10-Formyltetrahydrofolate"},
{"bigg_id": "12dgr120", "model_bigg_id": "Universal", "name": "_1,2-Diacyl-sn-glycerol (didodecanoyl, n-C12:0)"},
...
]
curl 'http://bigg.ucsd.edu/api/v2/universal/metabolites/g3p'
{"bigg_id": "g3p",
"name": "Glyceraldehyde 3-phosphate",
"formula": "C3H5O6P",
"old_identifiers": ["g3p"],
"database_links": {
"KEGG": [
{"link": "http://www.genome.jp/dbget-bin/www_bget?cpd:C00661",
"id": "C00661"},
{"link": "http://www.genome.jp/dbget-bin/www_bget?cpd:C00118",
"id": "C00118"}
],
"BRENDA": [
{"link": null,
"id": "BG17970"}
],
...
},
"compartments_in_models": [
{"model_bigg_id": "iAPECO1_1312",
"bigg_id": "c",
"organism": "escherichia coli apec o1"},
{"model_bigg_id": "iND750",
"bigg_id": "c",
"organism": "Saccharomyces cerevisiae S288c"},
...
]
}
curl 'http://bigg.ucsd.edu/api/v2/search?query=g3p&search_type=metabolites'
{"results_count": 10,
"results": [
{"model_bigg_id": "Universal", "bigg_id": "g3p", "name": "Glyceraldehyde 3-phosphate", "organism": ""},
{"model_bigg_id": "Universal", "bigg_id": "g3pc", "name": "sn-Glycero-3-phosphocholine", "organism": ""},
...
]
}
curl 'http://bigg.ucsd.edu/api/v2/search?query=gapA&search_type=genes'
{"results_count": 71,
"results": [
{"model_bigg_id": "iAF987", "bigg_id": "Gmet_1946", "name": "gapA", "organism": "Geobacter metallireducens GS-15"},
{"model_bigg_id": "iAF1260", "bigg_id": "b1779", "name": "gapA", "organism": "Escherichia coli str. K-12 substr. MG1655"},
...
]
}
curl 'http://bigg.ucsd.edu/api/v2/search?query=iJO1366&search_type=models'
{"results_count": 1,
"results": [{"bigg_id": "iJO1366",
"organism": "Escherichia coli str. K-12 substr. MG1655",
"metabolite_count": 1866,
"gene_count": 1367,
"reaction_count": 2644}]}
}