Bioregistry Tools

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

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

Available Tools

Bioregistry_get_registry (Type: BioregistryTool)

Get metadata for a biological database/ontology by its Bioregistry prefix. Returns name, descript…

Bioregistry_get_registry tool specification

Tool Information:

  • Name: Bioregistry_get_registry

  • Type: BioregistryTool

  • Description: Get metadata for a biological database/ontology by its Bioregistry prefix. Returns name, description, homepage, ID pattern, URI format, example IDs, and synonyms. Covers 2600+ resources including UniProt, ChEBI, GO, PDB, Ensembl, HGNC, and many more.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_registry)

  • prefix (string) (required) Bioregistry prefix (e.g., ‘uniprot’, ‘chebi’, ‘go’, ‘pdb’, ‘ensembl’, ‘hgnc’, ‘pubmed’)

Example Usage:

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

Bioregistry_resolve_reference (Type: BioregistryTool)

Resolve a compact identifier (prefix:id) to provider URLs across 2600+ biological databases. Give…

Bioregistry_resolve_reference tool specification

Tool Information:

  • Name: Bioregistry_resolve_reference

  • Type: BioregistryTool

  • Description: Resolve a compact identifier (prefix:id) to provider URLs across 2600+ biological databases. Given a database prefix (e.g., ‘uniprot’, ‘chebi’, ‘go’, ‘pubmed’) and an identifier, returns URLs from all known providers. Useful for cross-database linking and identifier resolution.

Parameters:

  • operation (string) (optional) Operation type (fixed: resolve_reference)

  • prefix (string) (required) Database prefix (e.g., ‘uniprot’, ‘chebi’, ‘go’, ‘pubmed’, ‘ensembl’, ‘hgnc’)

  • identifier (string) (required) Database identifier (e.g., ‘P04637’ for UniProt, ‘17234’ for ChEBI, ‘0006915’ for GO)

Example Usage:

query = {
    "name": "Bioregistry_resolve_reference",
    "arguments": {
        "prefix": "example_value",
        "identifier": "example_value"
    }
}
result = tu.run(query)

Bioregistry_search_registries (Type: BioregistryTool)

Search the Bioregistry for databases, ontologies, and resources by keyword. Use to find the corre…

Bioregistry_search_registries tool specification

Tool Information:

  • Name: Bioregistry_search_registries

  • Type: BioregistryTool

  • Description: Search the Bioregistry for databases, ontologies, and resources by keyword. Use to find the correct prefix for identifier resolution, or to discover databases related to a topic (e.g., ‘protein’, ‘gene ontology’, ‘metabolite’).

Parameters:

  • operation (string) (optional) Operation type (fixed: search_registries)

  • query (string) (required) Search term (e.g., ‘protein’, ‘gene expression’, ‘metabolite’)

  • limit (integer) (optional) Maximum results to return (default: 10)

Example Usage:

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