Skip to main content
Glama

ensembl_lookup

Look up genes, transcripts, and variants by ID or symbol in the Ensembl database. Retrieve cross-references and translate identifiers across genomic databases.

Instructions

Look up genes, transcripts, variants by ID or symbol. Get cross-references and perform ID translation. Covers /lookup/* and /xrefs/* endpoints plus variant_recoder.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
identifierYesID or symbol to look up (gene, transcript, variant, etc.) (e.g., 'ENSG00000141510', 'BRCA1', 'rs699', 'ENST00000288602')
lookup_typeNoType of lookup to performid
speciesNoSpecies name (e.g., 'homo_sapiens', 'mus_musculus')homo_sapiens
expandNoAdditional data to include (e.g., ['Transcript', 'Exon'], ['Translation'], ['UTR'])
external_dbNoExternal database name for xrefs lookup (e.g., 'HGNC', 'UniProtKB/Swiss-Prot', 'RefSeq_mRNA')
Behavior2/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure. It mentions the tool 'covers' specific endpoints but doesn't describe response formats, error conditions, rate limits, authentication needs, or whether it's read-only versus mutative. For a tool with 5 parameters and no annotation coverage, this leaves significant behavioral gaps.

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 appropriately sized with two sentences that efficiently convey scope and endpoint coverage. It's front-loaded with the core purpose and avoids unnecessary elaboration, though the second sentence could be slightly more polished.

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

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a tool with 5 parameters, no annotations, and no output schema, the description provides adequate purpose and scope but lacks behavioral context and output expectations. It's complete enough to understand what the tool does but insufficient for an agent to fully predict how to use it effectively without trial and error.

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 schema already documents all 5 parameters thoroughly with examples and defaults. The description adds minimal value beyond the schema by mentioning endpoint coverage, but doesn't provide additional parameter semantics, syntax details, or usage patterns beyond what's in the structured fields.

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 clearly states the tool's purpose with specific verbs ('look up', 'get cross-references', 'perform ID translation') and resources ('genes, transcripts, variants'), distinguishing it from siblings by mentioning specific endpoints (/lookup/*, /xrefs/*, variant_recoder) that other tools likely don't cover.

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?

The description implies usage through endpoint references but doesn't explicitly state when to use this tool versus alternatives like ensembl_mapping or ensembl_variation. It provides context about what the tool covers but lacks explicit guidance on tool selection among siblings.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/effieklimi/ensembl-mcp-server'

If you have feedback or need assistance with the MCP directory API, please join our Discord server