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strchive-link

strchive-link

by berntpopp
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Hybrid

Get STRchive Locus

get_locus
Read-onlyIdempotent

Retrieve exact tandem-repeat disease locus data—benign, intermediate, and pathogenic repeat ranges, motifs, inheritance, and hg19/hg38/T2T coordinates—by locus ID, gene, or disease abbreviation.

Instructions

Get one STRchive tandem-repeat disease locus: benign/intermediate/pathogenic repeat-count ranges exactly as the source states them (closed [min,max] in repeat units; a range the source does not state is null with status not_stated_by_source), pathogenic/benign/unknown motifs and interruptions in gene and reference orientation (all alternative pathogenic motifs, e.g. RFC1), inheritance, evidence level, hg38/hg19/T2T coordinates (BED 0-based half-open; never lifted over), MONDO/OMIM ids and PMIDs. Signature: get_locus(locus, response_mode=).

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "locus": "<locus>"
    },
    "name": "get_locus"
  }
}

Input Schema

NameRequiredDescriptionDefault
locusYesSTRchive locus id (e.g. HD_HTT), gene symbol (e.g. HTT), or the source's disease abbreviation (e.g. SCA3). Case-insensitive. A gene with several loci (ARX, HOXA13) returns ambiguous_query with the locus ids to choose from.
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

A4/5.0
Behavior5/5

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

The description adds substantial behavioral detail beyond the read-only annotations: exact range semantics, null handling with not_stated_by_source, motif and interruption orientation, alternative pathogenic motifs, coordinate build conventions, and the fact that coordinates are never lifted over. These are precisely the interpretive rules an agent needs to use the returned data correctly.

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?

The description is front-loaded with the purpose and then enumerates returned data in a dense but coherent list. The signature adds little beyond what the schema already states and the single-sentence structure is less scannable, but there is no filler.

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

Completeness5/5

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 must carry return-value semantics; it does so thoroughly by describing ranges, motifs, orientation, inheritance, coordinates, identifiers, and status handling. Given the simple read-only lookup shape and rich schema annotations, it is complete enough to call the tool correctly.

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

Parameters3/5

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

Schema description coverage is 100%, so the parameter meanings are already well documented. The description mentions the locus and response_mode signature but does not add meaning beyond the schema, which is acceptable at baseline 3.

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

Purpose4/5

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

The description clearly states the specific operation and resource: retrieving one STRchive tandem-repeat disease locus with repeat-count ranges, motifs, inheritance, coordinates, and identifiers. It is not a tautology, but it does not explicitly differentiate this lookup from siblings such as search_loci or compare_repeat_length.

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

Usage Guidelines3/5

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

Usage is implied by the singular locus scope and the signature, and the schema handles ambiguity by returning locus ids when a gene maps to multiple loci. However, the description itself gives no explicit when-to-use or when-not-to-use guidance versus alternative tools.

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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