Bigg Models Tools

Configuration File: bigg_models_tools.json Tool Type: Local Tools Count: 7

This page contains all tools defined in the bigg_models_tools.json configuration file.

Available Tools

BiGG_get_database_version (Type: BiGGModelsTool)

Get BiGG Models database version and last update date. Returns BiGG version number, API version, …

BiGG_get_database_version tool specification

Tool Information:

  • Name: BiGG_get_database_version

  • Type: BiGGModelsTool

  • Description: Get BiGG Models database version and last update date. Returns BiGG version number, API version, and timestamp of last database update. Use for: checking data currency, version control, documentation, reproducibility. Check this to ensure using latest metabolic models data.

Parameters:

  • operation (string) (required) Operation type

Example Usage:

query = {
    "name": "BiGG_get_database_version",
    "arguments": {
        "operation": "example_value"
    }
}
result = tu.run(query)

BiGG_get_metabolite (Type: BiGGModelsTool)

Get detailed metabolite information including formula, compartments, and database cross-reference…

BiGG_get_metabolite tool specification

Tool Information:

  • Name: BiGG_get_metabolite

  • Type: BiGGModelsTool

  • Description: Get detailed metabolite information including formula, compartments, and database cross-references. Query from specific model or universal database. Returns metabolite names, formulas, compartment locations, and links to KEGG, MetaCyc, HMDB, ChEBI. Shows which models contain this metabolite. Use for: compound identification, formula lookup, database integration, metabolite annotation. Essential for understanding metabolic networks.

Parameters:

  • operation (string) (required) Operation type

  • metabolite_id (string) (required) Required: BiGG metabolite ID (e.g., ‘g3p_c’ with compartment, or ‘g3p’ without)

  • model_id (string) (optional) Model ID or ‘universal’ for universal metabolite database

Example Usage:

query = {
    "name": "BiGG_get_metabolite",
    "arguments": {
        "operation": "example_value",
        "metabolite_id": "example_value"
    }
}
result = tu.run(query)

BiGG_get_model (Type: BiGGModelsTool)

Get detailed information for a specific metabolic model. Returns organism, genome accession, reac…

BiGG_get_model tool specification

Tool Information:

  • Name: BiGG_get_model

  • Type: BiGGModelsTool

  • Description: Get detailed information for a specific metabolic model. Returns organism, genome accession, reaction/metabolite/gene counts, and publication reference (PMID). Use for: understanding model scope, checking model currency, finding publications, model selection. Essential metadata before downloading or analyzing a model. Example model IDs: iJO1366 (E. coli), iMM904 (S. cerevisiae), Recon3D (human).

Parameters:

  • operation (string) (required) Operation type

  • model_id (string) (required) Required: BiGG model ID (e.g., ‘iJO1366’, ‘iMM904’, ‘Recon3D’)

Example Usage:

query = {
    "name": "BiGG_get_model",
    "arguments": {
        "operation": "example_value",
        "model_id": "example_value"
    }
}
result = tu.run(query)

BiGG_get_model_reactions (Type: BiGGModelsTool)

Get all reactions in a metabolic model. Returns reaction IDs, names, and organisms for all bioche…

BiGG_get_model_reactions tool specification

Tool Information:

  • Name: BiGG_get_model_reactions

  • Type: BiGGModelsTool

  • Description: Get all reactions in a metabolic model. Returns reaction IDs, names, and organisms for all biochemical reactions in the model. Use for: analyzing metabolic capabilities, finding specific pathways, reaction enumeration, model comparison. Follow with BiGG_get_reaction for detailed reaction information including stoichiometry and gene-reaction rules.

Parameters:

  • operation (string) (required) Operation type

  • model_id (string) (required) Required: BiGG model ID

Example Usage:

query = {
    "name": "BiGG_get_model_reactions",
    "arguments": {
        "operation": "example_value",
        "model_id": "example_value"
    }
}
result = tu.run(query)

BiGG_get_reaction (Type: BiGGModelsTool)

Get detailed reaction information including stoichiometry, metabolites, gene-reaction rules, and …

BiGG_get_reaction tool specification

Tool Information:

  • Name: BiGG_get_reaction

  • Type: BiGGModelsTool

  • Description: Get detailed reaction information including stoichiometry, metabolites, gene-reaction rules, and database links. Query from specific model or universal database. Returns reaction equation, participating metabolites with coefficients, GPR (gene-protein-reaction) associations, bounds, and cross-references (KEGG, MetaCyc, BRENDA). Use for: understanding reaction mechanisms, gene associations, flux constraints, pathway analysis. Essential for metabolic modeling.

Parameters:

  • operation (string) (required) Operation type

  • reaction_id (string) (required) Required: BiGG reaction ID (e.g., ‘GAPD’, ‘PGI’)

  • model_id (string) (optional) Model ID or ‘universal’ for universal reaction database

Example Usage:

query = {
    "name": "BiGG_get_reaction",
    "arguments": {
        "operation": "example_value",
        "reaction_id": "example_value"
    }
}
result = tu.run(query)

BiGG_list_models (Type: BiGGModelsTool)

Get list of all genome-scale metabolic models in BiGG database (85+ models). Returns model IDs, o…

BiGG_list_models tool specification

Tool Information:

  • Name: BiGG_list_models

  • Type: BiGGModelsTool

  • Description: Get list of all genome-scale metabolic models in BiGG database (85+ models). Returns model IDs, organisms, reaction counts, metabolite counts, and gene counts for bacteria, archaea, and eukaryotes. Models cover E. coli, yeast, human, and other organisms. Use for: discovering available models, finding organism-specific models, comparing model sizes, metabolic modeling projects. Essential first step for flux balance analysis.

Parameters:

  • operation (string) (required) Operation type

Example Usage:

query = {
    "name": "BiGG_list_models",
    "arguments": {
        "operation": "example_value"
    }
}
result = tu.run(query)

BiGG_search (Type: BiGGModelsTool)

Search BiGG database for models, reactions, metabolites, or genes. Returns matching entries with …

BiGG_search tool specification

Tool Information:

  • Name: BiGG_search

  • Type: BiGGModelsTool

  • Description: Search BiGG database for models, reactions, metabolites, or genes. Returns matching entries with IDs, names, and organism info. Search types: models (find organisms), reactions (find biochemical reactions), metabolites (find compounds), genes (find gene names/IDs). Use for: discovery, finding specific entities, cross-model searches, identifying pathways. Flexible search across entire database.

Parameters:

  • operation (string) (required) Operation type

  • query (string) (required) Required: Search term (e.g., ‘glucose’, ‘gapA’, ‘E. coli’)

  • search_type (string) (optional) What to search for

Example Usage:

query = {
    "name": "BiGG_search",
    "arguments": {
        "operation": "example_value",
        "query": "example_value"
    }
}
result = tu.run(query)