Bridgedb Tools

Configuration File: bridgedb_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

BridgeDb_attributes (Type: BridgeDbTool)

Get properties and attributes for a biological identifier from BridgeDb. Returns metadata such as…

BridgeDb_attributes tool specification

Tool Information:

  • Name: BridgeDb_attributes

  • Type: BridgeDbTool

  • Description: Get properties and attributes for a biological identifier from BridgeDb. Returns metadata such as molecular formula, molecular weight, InChI, InChIKey, synonyms, and other database-specific attributes. Especially useful for metabolites (HMDB, ChEBI, KEGG compound IDs) to get chemical properties, and for genes to get symbol and name information. System codes: Ch=HMDB, Ce=ChEBI, Ck=KEGG Compound, En=Ensembl, H=HGNC, S=UniProt.

Parameters:

  • operation (string) (required) Operation type (fixed: attributes)

  • identifier (string) (required) The identifier to look up (e.g., ‘HMDB0000122’ for glucose, ‘17234’ for ChEBI glucose)

  • source (string) (required) Source database name or system code. Common: Ch=HMDB, Ce=ChEBI, Ck=KEGG Compound, En=Ensembl, H=HGNC, S=UniProt

  • organism (string) (optional) Organism name (default: Human). Options: Human, Mouse, Rat, Yeast, etc.

Example Usage:

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

BridgeDb_search (Type: BridgeDbTool)

Search for biological identifiers by name using BridgeDb. Enter a gene name, metabolite name, or …

BridgeDb_search tool specification

Tool Information:

  • Name: BridgeDb_search

  • Type: BridgeDbTool

  • Description: Search for biological identifiers by name using BridgeDb. Enter a gene name, metabolite name, or protein name and get matching identifiers from supported databases. Useful for finding database-specific IDs when you only know the common name. Searches across all database sources available for the specified organism. Returns identifier-database pairs. For example, searching ‘glucose’ returns matches from MetaCyc, KEGG, and other databases.

Parameters:

  • operation (string) (required) Operation type (fixed: search)

  • query (string) (required) Name to search for (e.g., ‘glucose’, ‘TP53’, ‘ATP’)

  • organism (string) (optional) Organism name (default: Human). Options: Human, Mouse, Rat, Yeast, Worm, Fruit fly, Zebra fish, etc.

Example Usage:

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

BridgeDb_xrefs (Type: BridgeDbTool)

Map a biological identifier across databases using BridgeDb. Given an identifier from one databas…

BridgeDb_xrefs tool specification

Tool Information:

  • Name: BridgeDb_xrefs

  • Type: BridgeDbTool

  • Description: Map a biological identifier across databases using BridgeDb. Given an identifier from one database (e.g., HMDB0000122 from HMDB), returns equivalent identifiers in all other supported databases (ChEBI, KEGG, PubChem, Wikidata, CAS, etc.). Supports genes, proteins, metabolites, and other biological entities across 45+ databases and 30+ organisms. System codes: Ch=HMDB, Ce=ChEBI, Ck=KEGG Compound, En=Ensembl, H=HGNC, S=UniProt, L=NCBI Gene, Cpc=PubChem-compound, Ik=InChIKey. Use this when you need to convert between database identifiers for the same biological entity.

Parameters:

  • operation (string) (required) Operation type (fixed: xrefs)

  • identifier (string) (required) The identifier to look up (e.g., ‘HMDB0000122’ for glucose, ‘ENSG00000141510’ for TP53, ‘17234’ for ChEBI glucose)

  • source (string) (required) Source database name or system code. Common codes: Ch=HMDB, Ce=ChEBI, Ck=KEGG Compound, En=Ensembl, H=HGNC, S=UniProt, L=NCBI Gene, Cpc=PubChem-compound

  • organism (string) (optional) Organism name (default: Human). Options include: Human, Mouse, Rat, Yeast, Worm, Fruit fly, Zebra fish, Arabidopsis thaliana, and others.

  • target_source (string) (optional) Optional: filter results to a specific target database. Use database name or system code.

Example Usage:

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