Orthodb Tools

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

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

Available Tools

OrthoDB_get_group_details (Type: OrthoDBTool)

Get detailed information about an OrthoDB orthologous group including functional annotations. Ret…

OrthoDB_get_group_details tool specification

Tool Information:

  • Name: OrthoDB_get_group_details

  • Type: OrthoDBTool

  • Description: Get detailed information about an OrthoDB orthologous group including functional annotations. Returns KEGG pathway associations, GO terms, and InterPro domain annotations for the group. Useful for understanding the evolutionary conservation and function of gene families. Example: group ‘727649at7742’ shows olfactory receptor group at Vertebrata level with associated KEGG pathways for signal transduction.

Parameters:

  • group_id (string) (required) OrthoDB group ID. Format: ‘numberATtaxid’. Examples: ‘727649at7742’ (Vertebrata level), ‘59506at9443’ (Primates level). Get IDs from OrthoDB_search_groups.

Example Usage:

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

OrthoDB_get_orthologs (Type: OrthoDBTool)

Get orthologous genes from an OrthoDB group, optionally filtered by species. Returns gene IDs, or…

OrthoDB_get_orthologs tool specification

Tool Information:

  • Name: OrthoDB_get_orthologs

  • Type: OrthoDBTool

  • Description: Get orthologous genes from an OrthoDB group, optionally filtered by species. Returns gene IDs, organism names, and descriptions for all members of an orthologous group. Useful for finding orthologs across species, evolutionary conservation analysis, and functional annotation transfer. Example: group ‘727649at7742’ with species=9606 returns human genes in that orthologous group.

Parameters:

  • group_id (string) (required) OrthoDB group ID. Format: ‘numberATtaxid’. Get IDs from OrthoDB_search_groups.

  • species ([‘string’, ‘null’]) (optional) Comma-separated NCBI taxonomy IDs to filter. Examples: ‘9606’ (human only), ‘9606,10090’ (human+mouse). Null for all species.

Example Usage:

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

OrthoDB_search_groups (Type: OrthoDBTool)

Search for orthologous groups by gene/protein name in OrthoDB v12. OrthoDB catalogs orthologous g…

OrthoDB_search_groups tool specification

Tool Information:

  • Name: OrthoDB_search_groups

  • Type: OrthoDBTool

  • Description: Search for orthologous groups by gene/protein name in OrthoDB v12. OrthoDB catalogs orthologous groups at different taxonomic levels (vertebrates, metazoa, eukaryotes, etc.), enabling evolutionary analysis of gene conservation. Returns group IDs that can be queried for details. Complements OMA and Ensembl Compara with group-level orthology at deep evolutionary scales. Example: searching ‘BRCA1’ with species=9606 returns orthologous groups containing BRCA1 at various taxonomic levels.

Parameters:

  • query (string) (required) Gene or protein name to search. Examples: ‘BRCA1’, ‘TP53’, ‘insulin’, ‘EGFR’.

  • species ([‘integer’, ‘null’]) (optional) NCBI taxonomy ID to filter by species. Examples: 9606 (human), 10090 (mouse), 7227 (fly). Null for all species.

  • level ([‘integer’, ‘null’]) (optional) Taxonomic level for group definition. Examples: 7742 (Vertebrata), 33208 (Metazoa), 2759 (Eukaryota). Null for all levels.

  • limit (integer) (optional) Maximum number of groups to return (1-50). Default: 10.

Example Usage:

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