Mibig Tools

Configuration File: mibig_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

MIBiG_get_stats (Type: BaseRESTTool)

Get summary statistics from the MIBiG biosynthetic gene cluster repository. Returns total BGC cou…

MIBiG_get_stats tool specification

Tool Information:

  • Name: MIBiG_get_stats

  • Type: BaseRESTTool

  • Description: Get summary statistics from the MIBiG biosynthetic gene cluster repository. Returns total BGC counts by status (active, retired, complete, partial, pending), counts by biosynthetic class (PKS, NRPS, Terpene, Saccharide, Ribosomal, Other), and counts by source organism phylum (Actinomycetota, Ascomycota, Pseudomonadota, etc.). Essential for understanding the landscape of characterized natural product biosynthesis across the tree of life.

Parameters:

No parameters required.

Example Usage:

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

MIBiG_list_clusters (Type: BaseRESTTool)

List biosynthetic gene clusters (BGCs) from the MIBiG repository. MIBiG (Minimum Information abou…

MIBiG_list_clusters tool specification

Tool Information:

  • Name: MIBiG_list_clusters

  • Type: BaseRESTTool

  • Description: List biosynthetic gene clusters (BGCs) from the MIBiG repository. MIBiG (Minimum Information about a Biosynthetic Gene Cluster) is the standard repository for experimentally characterized BGCs producing natural products like antibiotics, antifungals, and anticancer compounds. Returns all BGC entries with accession, products, biosynthetic class (PKS, NRPS, Terpene, etc.), organism, quality, and completeness. Contains 3,013 BGC entries from bacteria, fungi, and plants. Use search_term to filter results client-side by product name or organism.

Parameters:

  • search_term (string) (optional) Optional text to filter results by product name or organism. The API returns all entries; filtering is applied client-side. Examples: ‘erythromycin’, ‘vancomycin’, ‘Streptomyces’, ‘PKS’. Leave empty to get all 3,013 BGC entries.

Example Usage:

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