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yeyuan98

BioMCP

by yeyuan98
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TypeScript
Remote

ensembl_region

Read-only

Query genes, transcripts, and known variants within a genomic interval on GRCh38 to triage loci and GWAS hit regions; variation is capped to a 50 kb window for spans over 50 kb.

Instructions

Query what lives in a genomic interval on the current assembly (GRCh38 for human): genes/transcripts (stable IDs, symbols, biotypes) and known variants (rsIDs, alleles, consequence terms, clinical significance).

Ideal for locus triage — "what genes and known variants sit in this GWAS hit interval?". Genes/transcripts are always fetched for the FULL requested span, but variation density can reach ~100k variants in dense loci (which times out upstream), so when the span exceeds 50 kb variation is queried only for a 50 kb window centered on the region midpoint — the result echoes effective_variation_window (the coordinates actually queried for variation) and variation_truncated (names the dropped span) when this cap applies. To sweep variation across a large interval, issue adjacent region calls. Keep spans modest (<1 Mb recommended); output is capped at limit with a truncated marker. For sequence text use genbank_get; for entity-level annotation chain IDs into gene_get / variant_get.

Input Schema

NameRequiredDescriptionDefault
limitNoMaximum features returned
regionYesGenomic region chr:start-end (1-based, GRCh38 for human) — e.g. 7:140450000-140480000
speciesNoSpecies — 'human' (default), 'mouse', …human
featuresNoFeature types to include

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.6.0-alpha.10
    • removedInput schema / additionalProperties
      Removed value: -false
  2. Changed1 schema field changedv1.6.0-alpha.7
    • addedInput schema / properties / region / minLength
      Added value: +1
  3. Addedv0.7.1

TDQS

A4.8/5.0
Behavior5/5

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

Annotations already declare readOnly/openWorld, and the description goes further: it discloses the 50 kb variation window cap centered on midpoint, the echo fields effective_variation_window and variation_truncated, upstream timeout risk, and an output limit with truncation marker. This is unusually rich disclosure of behavior beyond 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 core purpose, then a clear layered structure (use case, cap behavior, limits, alternatives). Dense but every sentence carries information; the parenthetical field names are somewhat packed but earn their place. Slightly long for the tool's size.

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?

No output schema exists, yet the description explains the notable return fields (effective_variation_window, variation_truncated, truncated marker), so an agent understands what it gets back. Combined with the cap and limit behavior, nothing essential for correct invocation is missing.

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, but the description adds real semantics — the 50 kb cap applies to variation over the region span, and limit caps returned features with a truncated marker. It clarifies the region/cap interaction not spelled out in the schema.

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 ('query what lives in') and resource (genomic interval) and enumerates the entities returned (genes/transcripts with IDs, symbols, biotypes; variants with rsIDs, alleles, consequence, clinical significance). It is immediately distinguishable from entity-level siblings like gene_get and variant_get, which it names.

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

Usage Guidelines5/5

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

Gives an explicit use case ('ideal for locus triage — what genes and known variants sit in this GWAS hit interval?'), explicit routing away to alternatives ('for sequence text use genbank_get; for entity-level annotation chain IDs into gene_get / variant_get'), and the alternative approach for large sweeps ('issue adjacent region calls').

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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