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Search polygenic scores

search_scores
Read-only

Find polygenic scores in the PGS Catalog by PGP or PubMed ID, trait ontology ID, or known score IDs; returns traits, citations, variant counts, ancestry, license, and FTP file URLs.

Instructions

Search the PGS Catalog for polygenic scores by publication (PGP ID or PubMed ID) or by trait ontology ID (EFO/HP/MONDO). Provide pgs_ids alone to fetch a known set of scores directly. Returns scores with traits, publication citation, variant counts, weight type, ancestry distribution, license, and the FTP scoring-file URL.

Input Schema

NameRequiredDescriptionDefault
fullNoReturn the complete upstream record including every field. Verbose; use only when the compact projection is not enough.
pmidNoPubMed ID of the publication that developed the score, without the 'PMID:' prefix.
limitNoResults per page. The PGS Catalog default is 50 and the maximum is 250.
fieldsNoOptional comma-separated list of fields to return (dotted paths allowed, e.g. 'id,trait_reported,publication.title'). Omit for the default compact projection.
offsetNoZero-based offset into the full result set, used to page through matches.
pgp_idNoPGS Catalog Publication ID (PGP), e.g. PGP000001.
pgs_idsNoIDs to fetch, as a comma-separated string or an array of IDs.
trait_idNoTrait ontology ID exactly as returned by search_traits or get_trait (e.g. MONDO_0004989 for breast carcinoma). IDs shown in upstream API docs may be outdated, so resolve them with search_traits first.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.4/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With readOnlyHint and openWorldHint already declared, the description adds real value by disclosing the returned payload (traits, citation, variant counts, weight type, ancestry, license, FTP scoring-file URL). It omits paging/limits behavior and any catalog rate-limit caveats, but the core read-only, remote-catalog profile is clear.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three sentences, front-loaded with the search modes, then the special pgs_ids case, then the return shape. No filler; every clause carries information an agent needs.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

No output schema exists, so the description correctly takes on the burden of describing returned fields, and it covers all query modes. It leaves open the behavior of an unfiltered call (full-catalog scan vs first page) and whether filters may be combined, which is a modest remaining gap for an 8-parameter tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so baseline is 3; the description earns an increment by adding a constraint absent from the schema — that pgs_ids should be supplied alone for direct fetch — and by framing pmid/pgp_id/trait_id as alternative query modes rather than separate filters.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource ('Search the PGS Catalog for polygenic scores') and enumerates the exact lookup keys (PGP ID, PubMed ID, EFO/HP/MONDO trait ID). The 'pgs_ids alone' batch-fetch mode also delineates it from the single-record get_score sibling.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Clear context for each mode: filter by publication or trait, or pass pgs_ids alone for direct batch retrieval. It does not explicitly route to siblings such as search_publications or get_score, nor state what happens when no filter is supplied, so it stops short of full when/when-not guidance.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.