Ebi Taxonomy Tools

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

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

Available Tools

EBITaxonomy_get_by_id (Type: EBITaxonomyTool)

Get taxonomy classification by NCBI Taxonomy ID from the EBI Taxonomy service. Returns scientific…

EBITaxonomy_get_by_id tool specification

Tool Information:

  • Name: EBITaxonomy_get_by_id

  • Type: EBITaxonomyTool

  • Description: Get taxonomy classification by NCBI Taxonomy ID from the EBI Taxonomy service. Returns scientific name, common name, rank, division, full lineage string, genetic codes, authority citation, and alternative names. Example: tax_id 9606 returns Homo sapiens with lineage from Eukaryota to Homo.

Parameters:

  • tax_id (string) (required) NCBI Taxonomy ID (numeric). Examples: ‘9606’ (human), ‘10090’ (mouse), ‘562’ (E. coli), ‘3702’ (Arabidopsis thaliana).

Example Usage:

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

EBITaxonomy_get_by_scientific_name (Type: EBITaxonomyTool)

Look up taxonomy by scientific (Latin) name using the EBI Taxonomy service. Returns taxonomy ID, …

EBITaxonomy_get_by_scientific_name tool specification

Tool Information:

  • Name: EBITaxonomy_get_by_scientific_name

  • Type: EBITaxonomyTool

  • Description: Look up taxonomy by scientific (Latin) name using the EBI Taxonomy service. Returns taxonomy ID, lineage, rank, division, and genetic codes. Handles subspecies and strain names. Example: ‘Escherichia coli’ returns taxId 562 with full bacterial lineage.

Parameters:

  • scientific_name (string) (required) Scientific name of the organism. Examples: ‘Homo sapiens’, ‘Escherichia coli’, ‘Drosophila melanogaster’, ‘Arabidopsis thaliana’.

Example Usage:

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

EBITaxonomy_search_by_name (Type: EBITaxonomyTool)

Search for organisms by any name (scientific, common, or synonym) in EBI Taxonomy. Unlike scienti…

EBITaxonomy_search_by_name tool specification

Tool Information:

  • Name: EBITaxonomy_search_by_name

  • Type: EBITaxonomyTool

  • Description: Search for organisms by any name (scientific, common, or synonym) in EBI Taxonomy. Unlike scientific name lookup, this accepts common names like ‘mouse’, ‘fruit fly’, or ‘baker’s yeast’. Returns matching taxa with their IDs, scientific names, and lineage. Example: ‘mouse’ returns Mus musculus (10090) and Mus (10088).

Parameters:

  • name (string) (required) Any organism name (common name, scientific name, or synonym). Examples: ‘mouse’, ‘fruit fly’, ‘yeast’, ‘zebrafish’, ‘E. coli’.

Example Usage:

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

EBITaxonomy_suggest (Type: EBITaxonomyTool)

Get taxonomy name suggestions matching a partial query from EBI Taxonomy. Type-ahead style search…

EBITaxonomy_suggest tool specification

Tool Information:

  • Name: EBITaxonomy_suggest

  • Type: EBITaxonomyTool

  • Description: Get taxonomy name suggestions matching a partial query from EBI Taxonomy. Type-ahead style search that returns matching organism names and taxonomy IDs. Useful for finding the correct taxonomy ID when you only know part of the organism name. Example: ‘human’ suggests Homo sapiens (9606), human metagenome (646099), etc.

Parameters:

  • query (string) (required) Partial organism name to get suggestions for. Examples: ‘human’, ‘streptococc’, ‘salmo’, ‘candida’.

Example Usage:

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