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BioMCP

BioMCP

by yeyuan98
OverviewSchemaSourceRelated ServersDiscussionsAdmin
TypeScript
Remote

ensembl_homology

Read-only

Find orthologues or paralogues of a gene across species to map cross-species gene relationships, check conservation, and retrieve target IDs, symbols, species, and percent identity.

Instructions

Find orthologues or paralogues of a gene across species (Ensembl Compara) — the cross-species gene mapping source in biomcp.

Returns target stable IDs, gene symbols (when the assembly provides them, e.g. ARAF/RAF1 for BRAF paralogs), species, taxonomy level, and percent identity, sorted by identity. Accepts an HGNC symbol or Ensembl gene ID; scope to one species with target_species ('mouse') or target_taxon (10090). Use it for conservation questions ('is this gene conserved?', 'what is the mouse orthologue of BRAF?').

Input Schema

NameRequiredDescriptionDefault
geneYesGene symbol (BRAF) or Ensembl gene ID (ENSG00000157764)
typeNoHomology type to fetchorthologues
limitNoMaximum homologies to return (sorted by percent identity)
speciesNoSource species — 'human' (default), 'mouse', …human
target_taxonNoRestrict results to a taxon ID, e.g. 10090 (Mus musculus)
target_speciesNoRestrict results to one species, e.g. 'mouse'

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed3 schema fields changedv1.6.0-alpha.10
    • removedInput schema / additionalProperties
      Removed value: -false
    • addedInput schema / properties / target_taxon / maximum
      Added value: +9007199254740991
    • addedInput schema / properties / target_taxon / minimum
      Added value: +-9007199254740991
  2. Changed1 schema field changedv1.6.0-alpha.7
    • addedInput schema / properties / gene / minLength
      Added value: +1
  3. Addedv0.7.1

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already declare readOnly and openWorld, so the description adds real value with return semantics: stable IDs, gene symbols when available, species, taxonomy level, percent identity, sorted by identity. It also notes the input form (HGNC symbol or Ensembl ID). No output schema exists, so this return-shape disclosure is the main behavioral signal, though pagination/truncation behavior at the limit cap isn't discussed.

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-loads purpose and the key differentiator before the return-field list and usage examples. Each sentence carries content, though the example parentheticals (ARAF/RAF1 for BRAF) are slightly verbose.

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?

For a read-only, six-parameter lookup with no output schema, the description covers purpose, input forms, scoping, and return fields, which is enough to call it correctly. It does not mention what happens on empty results or invalid species names, a minor gap.

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?

With 100% schema coverage the baseline is 3, and the description still adds meaning beyond the schema: it explains the gene parameter accepts symbols or Ensembl IDs, demonstrates target_species ('mouse') and target_taxon (10090), and notes results are sorted by identity — clarifying how limit interacts with ordering.

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 ('Find orthologues or paralogues of a gene across species') and grounds it in the Ensembl Compara source, which separates it from the sibling ensembl_lookup/consequence/region tools that operate on a single gene or region. An agent can tell immediately what this returns: cross-species mappings.

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 concrete trigger questions ('is this gene conserved?', 'what is the mouse orthologue of BRAF?') and explains how to narrow scope via target_species or target_taxon with an example value. It implies positioning ('the cross-species gene mapping source') without explicitly naming a sibling to use instead for within-species lookups.

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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