Data Access


Download reaction and metabolite namespaces


The reaction and metabolite IDs in BiGG Models are available in the following tab-separated text files. The column names are the same as those used in COBRApy and in the Web API (below).


Programmatic access with the BiGG Models API


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.


Database version

# Get the version and the date BiGG Models was last updated
curl 'http://bigg.ucsd.edu/api/v2/database_version'
{"bigg_models_version": "1.1.0",
 "api_version": "v2",
 "last_updated": "2016-03-21 17:24:11.138365"}

Download models

# 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

Models, reactions, metabolites, and genes

# Get a list of models
curl 'http://bigg.ucsd.edu/api/v2/models'
{"results_count": 76,
 "results": [{"bigg_id": "iAPECO1_1312",
              "organism": "Escherichia coli APEC O1",
              "metabolite_count": 1944,
              "gene_count": 1313,
              "reaction_count": 2737},

             {"bigg_id": "iND750",
              "organism": "Saccharomyces cerevisiae S288c",
              "metabolite_count": 1061,
              "gene_count": 750,
              "reaction_count": 1266},

             ... ]
}
# 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": "EX_4abut_e", "name": "4-Aminobutanoate exchange", "organism": "Saccharomyces cerevisiae S288c"},
 {"bigg_id": "EX_ac_e", "name": "Acetate exchange", "organism": "Saccharomyces cerevisiae S288c"},

...
]
curl 'http://bigg.ucsd.edu/api/v2/models/iND750/reactions/GAPD'
{"bigg_id": "GAPD",
 "name": "glyceraldehyde-3-phosphate dehydrogenase",
 "pseudoreaction": false,
 "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",
 "escher_maps": [],
 "reactions": [
   {"model_bigg_id": "iND750",
     "bigg_id": "AICART",
     "name": "phosphoribosylaminoimidazolecarboxamide formyltransferase"},
   {"model_bigg_id": "iND750",
     "bigg_id": "MTHFC",
     "name": "methenyltetrahydrofolate cyclohydrolase"},

   ...
   ],
 "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"}],
   ...
   },
 "other_models_with_metabolite": [
   {"bigg_id": "iAPECO1_1312",
    "compartment_bigg_id": "c"}

   ...
 ]
}
  
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": "",
 "leftpos": ,
 "rightpos": ,
 "model_bigg_id": "iMM904",
 "reactions": [{"bigg_id": "",
		        "name": "",
		        "gene_reaction_rule": ""}]
}
curl 'http://bigg.ucsd.edu/api/v2/universal/reactions'
[{"bigg_id": "12DGR120tipp", "name": "_1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C12:0)"},
 {"bigg_id": "12DGR140tipp", "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", "name": "_10-Formyltetrahydrofolate"},
 {"bigg_id": "12dgr120", "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",
 "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"},

   ...
 ]
}

Search

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": 55,
 "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}]}
}