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ensembl-mcp-server

by io.github.cyanheads

Query Genomic Region

ensembl_query_region
Read-onlyIdempotent

Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory elements, or exons. Returns each feature with its stable ID, type, location, biotype, and name. Useful for "what's in this locus?" and for seeding follow-up lookups. Region format is chr:start-end (e.g. 13:32315086-32400268 for the BRCA2 locus). Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. The feature parameter defaults to gene only to prevent overwhelming returns — requesting variation in an 85 kb region returns 44,000+ entries. Explicitly include variation, regulatory, transcript, or exon only when needed. Exon rows carry the parent transcript ID, so the same exon appears once per transcript it belongs to.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
regionYesGenomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. For large regions (>100 kb), limit to gene feature type to avoid overwhelming results.
biotypeNoOptional biotype filter (e.g. protein_coding, lncRNA, SNV). Applied server-side by Ensembl. Not all feature types support biotype filtering.
featureNoFeature types to retrieve. Default is gene only. Requesting variation in a large region can return tens of thousands of features. Include variation only for targeted small regions (single gene loci or smaller).
speciesYesSpecies in Ensembl internal format (e.g. homo_sapiens, mus_musculus). Use ensembl_list_species to discover valid values.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent when the call failed. Absent on success.
noticeNoWarning or guidance about the result set.
regionNoThe region queried, as provided.
speciesNoThe species queried.
featuresNoGenomic features found in the requested region.
totalCountNoNumber of features returned. Note: very large regions may return truncated results.

TDQS

A4.4/5.0
Behavior5/5

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

It discloses highly relevant behavioral traits beyond the readOnlyHint annotation: Ensembl chromosome-name normalization, omission of the chr prefix in canonical output, the default feature broadening to gene to prevent overwhelming results, the scale of variation returns, and the rule that exon rows appear once per parent transcript. These are exactly the kind of behavioral details that affect invocation expectations.

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 verbose but each sentence earns its place by adding essential usage detail. It is front-loaded with the purpose and returns list, then addresses region format and parameter defaults. The text repeats some schema descriptions, which is a minor waste, but overall tightly structured.

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?

Given the four parameters, strong annotations, output-schema presence, and the provided schema descriptions, the description covers everything an agent needs to call correctly: the region format, normalization, the default feature type, the risk of large returns, and the per-transcript exon disambiguation. No critical calling context is missing.

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 input schema already documents all parameters comprehensively. The description adds some runtime behavior around the feature parameter (flooding risk, exon duplication semantics), but does not provide meaningful new meaning that is not already present in the schema. It hits the baseline for well-covered schemas.

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?

The description opens with a specific verb phrase, "Find genomic features overlapping a chromosomal region," listing the resource types and clearly distinguishing it from sibling tools like gene-centric ensembl_lookup_gene or sequence-focused ensembl_get_sequence. The introductory purpose is concrete and unambiguous.

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?

The description gives clear context for when to use this tool ("what's in this locus?") and for seeding follow-up lookups, and it warns about defaulting to gene-only to avoid huge returns. However, it does not explicitly list alternative tools for cases like single-gene lookup, leaving some usage routing to the agent's inference.

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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TDQS

A4.5/5.0
Disambiguation5/5

Each tool targets a distinct genomic resource: homology, sequence, xrefs, species metadata, gene lookup, variant prediction, and region query. There is no overlap in their purposes, and the descriptions clearly delineate when to use each.

Naming Consistency5/5

All tool names follow the consistent pattern 'ensembl_' plus an action verb (get, list, lookup, predict, query) and a noun. The naming style is uniformly snake_case and lowercase, making the tool set predictable and easy to navigate.

Tool Count5/5

With 7 tools, the server is well-scoped for its purpose. Each tool addresses a core Ensembl query need without redundancy or bloat, fitting comfortably in the ideal range for a domain-specific toolkit.

Completeness5/5

The tool set covers the primary lifecycle of genomic investigation: discovering species, resolving gene identifiers, fetching sequences, obtaining cross-references, querying regions, finding homologs, and predicting variant consequences. There are no critical gaps for typical use cases.

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