Uniprot Taxonomy Tools#

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

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

Available Tools#

UniProtTaxonomy_get_taxon (Type: UniProtTaxonomyTool)#

Get detailed taxonomy information for a species by NCBI taxonomy ID from UniProt. Returns scienti…

UniProtTaxonomy_get_taxon tool specification

Tool Information:

  • Name: UniProtTaxonomy_get_taxon

  • Type: UniProtTaxonomyTool

  • Description: Get detailed taxonomy information for a species by NCBI taxonomy ID from UniProt. Returns scientific name, common name, taxonomic rank, mnemonic code, full lineage (up to 30 levels), and protein statistics (reviewed/unreviewed counts). Essential for cross-referencing species in protein databases and understanding taxonomic relationships. Example: taxon 9606 returns Homo sapiens (Human), rank=species, mnemonic=HUMAN, 20,432 reviewed proteins (Swiss-Prot), 184,812 unreviewed (TrEMBL), with lineage from cellular organisms through Eumetazoa to Primates. Obsolete identifiers are answered with the current record, not an error: UniProt redirects a merged (retired) taxon to the node it was merged into, so always compare ‘taxon_id’ in the response against ‘query_taxon_id’. When they differ the response also carries ‘merged_from’ and a metadata note – e.g. taxon 46170 (Staphylococcus aureus subsp. aureus, the subspecies node many older MRSA records are filed under) resolves to 1280 (Staphylococcus aureus), whose protein counts cover the whole species rather than the subspecies asked for.

Parameters:

  • taxon_id (integer) (required) NCBI taxonomy ID. Examples: 9606 (human), 10090 (mouse), 7227 (fruit fly), 6239 (C. elegans), 559292 (S. cerevisiae), 562 (E. coli).

Example Usage:

query = {
    "name": "UniProtTaxonomy_get_taxon",
    "arguments": {
        "taxon_id": 10
    }
}
result = tu.run(query)

UniProtTaxonomy_search (Type: UniProtTaxonomyTool)#

Search UniProt taxonomy entries with official cursor pagination. Returns taxa, ranks, and protein…

UniProtTaxonomy_search tool specification

Tool Information:

  • Name: UniProtTaxonomy_search

  • Type: UniProtTaxonomyTool

  • Description: Search UniProt taxonomy entries with official cursor pagination. Returns taxa, ranks, and protein statistics; metadata reports the true upstream total and next_cursor.

Parameters:

  • query (string) (required) Search query (species name, common name, or partial match). Examples: ‘homo sapiens’, ‘mouse’, ‘arabidopsis’, ‘escherichia’.

  • size (integer) (optional) Maximum number of results. Default 10, max 500.

  • cursor (string) (optional) Opaque cursor from metadata.next_cursor. Omit for the first page.

Example Usage:

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