Pgs Catalog Tools

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

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

Available Tools

PGSCatalog_get_score (Type: PGSCatalogTool)

Retrieve the full metadata for a specific polygenic score from the PGS Catalog by its PGS id (e.g…

PGSCatalog_get_score tool specification

Tool Information:

  • Name: PGSCatalog_get_score

  • Type: PGSCatalogTool

  • Description: Retrieve the full metadata for a specific polygenic score from the PGS Catalog by its PGS id (e.g. ‘PGS000001’): reported and EFO/MONDO traits, number of variants, development method, genome build, weight type, publication, training samples, ancestry distribution, and the downloadable scoring-file URL. Find PGS ids with PGSCatalog_get_scores_by_trait. No API key.

Parameters:

  • pgs_id (string) (required) PGS Catalog score id, e.g. ‘PGS000001’.

Example Usage:

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

PGSCatalog_get_scores_by_trait (Type: PGSCatalogTool)

List the published polygenic scores (PGS) for a trait in the PGS Catalog, given its EFO/MONDO tra…

PGSCatalog_get_scores_by_trait tool specification

Tool Information:

  • Name: PGSCatalog_get_scores_by_trait

  • Type: PGSCatalogTool

  • Description: List the published polygenic scores (PGS) for a trait in the PGS Catalog, given its EFO/MONDO trait id (find one with PGSCatalog_search_traits). Each score summary includes the PGS id, name, reported trait, number of variants, development method, genome build, and publication (author/journal/year/PMID/DOI) plus the scoring-file URL. Use PGSCatalog_get_score for the full record of one score. No API key.

Parameters:

  • trait_id (string) (required) EFO or MONDO trait id, e.g. ‘MONDO_0004989’ (breast carcinoma) or ‘EFO_0001645’ (coronary artery disease).

Example Usage:

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

PGSCatalog_search_traits (Type: PGSCatalogTool)

Search the PGS Catalog (pgscatalog.org, EMBL-EBI — the open database of published polygenic score…

PGSCatalog_search_traits tool specification

Tool Information:

  • Name: PGSCatalog_search_traits

  • Type: PGSCatalogTool

  • Description: Search the PGS Catalog (pgscatalog.org, EMBL-EBI — the open database of published polygenic scores) for traits/phenotypes matching a term. Returns each matching trait’s id (EFO/MONDO, e.g. ‘MONDO_0004989’), label, description, and the number of polygenic scores published for it. Use this first to find the trait_id, then PGSCatalog_get_scores_by_trait to list its scores. No API key.

Parameters:

  • query (string) (required) Trait or phenotype term, e.g. ‘coronary artery disease’, ‘type 2 diabetes’, ‘breast cancer’.

Example Usage:

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