Orthodb Tools#

Configuration File: orthodb_tools.json Tool Type: Local Tools Count: 4

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 v12 orthologous group using the current group schema. R…

OrthoDB_get_group_details tool specification

Tool Information:

  • Name: OrthoDB_get_group_details

  • Type: OrthoDBTool

  • Description: Get detailed information about an OrthoDB v12 orthologous group using the current group schema. Returns all GO annotations across biological-process, cellular-component, molecular-function, and unclassified buckets; all InterPro domains and legacy KEGG annotations; plus EC numbers, functional categories, phyletic profile, evolutionary rate, and gene architecture. metadata.annotation_counts makes completeness explicit.

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_group_fasta (Type: OrthoDBTool)#

Retrieve a resumable structured page of member protein sequences for an OrthoDB orthologous group…

OrthoDB_get_group_fasta tool specification

Tool Information:

  • Name: OrthoDB_get_group_fasta

  • Type: OrthoDBTool

  • Description: Retrieve a resumable structured page of member protein sequences for an OrthoDB orthologous group, optionally restricted to a species. data.total_sequences is the exact number parsed from the downloaded FASTA; continue with next_offset while has_more is true. The legacy data.fasta field remains the complete raw FASTA and metadata.fasta_contains_all_sequences makes that scope explicit.

Parameters:

  • group_id (string) (required) OrthoDB orthologous group ID, e.g. ‘794361at2759’ (BRCA2 at Eukaryota level). Obtain from OrthoDB_search_groups.

  • species ([‘string’, ‘null’]) (optional) Optional NCBI taxon ID to restrict members to one species, e.g. ‘9606’ (human), ‘10090’ (mouse). Leave empty for all member species.

  • limit ([‘integer’, ‘null’]) (optional) Structured page size (default: 50, max: 500). The full raw FASTA is always returned in the ‘fasta’ field.

  • offset ([‘integer’, ‘null’]) (optional) Zero-based structured sequence offset. Continue with data.next_offset.

Example Usage:

query = {
    "name": "OrthoDB_get_group_fasta",
    "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, with local offset pa…

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, with local offset pagination over the API’s first 5,000 records. Continue with next_offset while has_more is true. metadata.total_is_lower_bound explicitly warns when the upstream 5,000-record window is exhausted.

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.

  • limit (integer) (optional) Maximum ortholog records per page (default 100, max 1000).

  • offset (integer) (optional) Zero-based offset in the fetched ortholog list. Continue with next_offset while has_more is true.

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 with server-backed offset pagin…

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 with server-backed offset pagination. OrthoDB catalogs orthologous groups at different taxonomic levels. metadata/data total_groups uses OrthoDB’s authoritative count (not the API’s fixed 100-record window); continue with next_offset while has_more is true. Every bare search ID is enriched through /tab; each record exposes enrichment_status, and metadata.group_enrichment reports any per-group failure instead of silently presenting a bare ID as complete.

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) Page size (1-50). Default: 10.

  • offset (integer) (optional) Zero-based result offset. Default 0; continue with data.next_offset.

Example Usage:

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