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strchive-link

strchive-link

by berntpopp
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Hybrid

Search STRchive Loci

search_loci
Read-onlyIdempotent

Search the STRchive catalog of tandem-repeat disease loci by gene, locus ID, MONDO/OMIM/ORPHA ID, repeat motif, or disease term; omit the query to list all loci.

Instructions

Search the STRchive catalog of tandem-repeat (STR) disease loci. query matches, in rank order: an exact locus id / gene symbol / disease abbreviation; a MONDO:/OMIM:/ORPHA: id; a repeat motif in either orientation (e.g. CAG, AAGGG); words in the disease name, then in source tags (e.g. 'ataxia'), then in the locus HPO phenotype labels. Each row's matched_on says which. Omit query to list every locus. Returns results with total/truncated/next_offset. Signature: search_loci(query=, limit=, offset=, response_mode=).

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "search_loci"
  }
}

Input Schema

NameRequiredDescriptionDefault
limitNoPage size (1-100, default 20).
queryNoGene, locus id, MONDO/OMIM/Orphanet id, motif, or disease words. Omit to list all loci.
offsetNoRows to skip (default 0).
response_modeNoVerbosity: minimal (ids + ranges) | compact (default; + motifs, coordinates, ids, references) | standard (+ fenced source prose, HPO ids) | full (+ cross-references, additional literature).compact

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.1

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already declare readOnly, idempotent, non-destructive, and openWorld, so the safety profile is covered. Beyond that, the description discloses non-obvious behavior: the tiered rank order of query resolution and the presence of a matched_on field that records which tier fired, plus pagination fields total/truncated/next_offset. No contradiction with annotations.

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

Conciseness4/5

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

Front-loaded with the resource and the matching hierarchy, then the omit-query rule and the return envelope, all in tight prose. The trailing 'Signature:' line is largely redundant with the tool name and schema and is the one element that does not earn its place.

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?

There is no output schema, so the description correctly supplies the return envelope (total/truncated/next_offset, matched_on) and the response_mode verbosity ladder is documented in the schema. It stops short of describing row fields such as locus ranges or references, but response_mode's enum documentation covers that adequately for an agent to call the tool correctly.

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 would be 3, but the description adds real meaning for query that the schema's one-line summary does not: the priority ordering among gene/locus id/ontology id/motif/disease words/source tags/HPO labels, and how ties are surfaced. The limit/offset/response_mode semantics are left entirely to the schema, which is acceptable given the coverage.

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 STRchive catalog of tandem-repeat disease loci. The description goes further, enumerating exactly what the query matches and in what rank order, so an agent can tell this apart from the single-record sibling get_locus without opening either schema.

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?

Gives a clear conditional: pass a query to filter, omit it to list every locus, and explains which query forms are resolved first (exact id/symbol/abbreviation, then ontology ids, then motif, then disease words and tags). It does not explicitly route the agent away from get_locus or compare_repeat_length, but the search-versus-fetch distinction is clear from context.

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

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