Jean by Melad Labs

lookup_gene

Read-only

Look up a gene or genomic region: NCBI Gene records, HGNC nomenclature, Ensembl records, cross-references, MyGene identifiers, UCSC assembly data, GTEx expression, or BioMart tables.

Input Schema

Name	Required	Description
`limit`	No	maximum records (1–20).
`query`	Yes	a gene symbol or identifier (e.g. "BRCA2"), or a command such as "ensembl_lookup:BRCA2" or "ensembl_xrefs:ENSG00000139618".
`_files`	No	The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
`source`	Yes	which authority to ask.
`_subject`	No	The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

Output Schema

Name	Required	Description
`count`	Yes	how many records came back, which is a result even when it is zero
`records`	Yes	the records the authority returned, in its own field names — wire them into a tool that takes ids, or read them in the transcript
`envelope`	Yes	the authority's whole answer: paging, totals and the query it actually ran
`provenance`	Yes	the authority, the exact endpoints called and when — what makes an answer re-checkable without re-running it

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedOct 23, 2026

changedInput schema / properties / source / enum

Previous value: -[
-  "ensembl",
-  "mygene",
-  "ucsc",
-  "gtex",
-  "biomart"
-]New value: +[
+  "ncbi-gene",
+  "hgnc",
+  "ensembl",
+  "mygene",
+  "ucsc",
+  "gtex",
+  "biomart"
+]

First observedOct 20, 2026

TDQS

B3.2/5.0

Behavior2/5

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

Annotations already declare readOnlyHint=true, openWorldHint=true, and destructiveHint=false, so the safety profile is covered structurally. The description adds little behavioral context beyond naming the authorities; it does not mention external-service behavior, command-style query handling, or any practical constraints beyond what the schema provides.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The definition is a single front-loaded sentence that states the action and enumerates supported authorities without filler. The list is dense but appropriate for a multi-source lookup tool.

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?

The presence of an output schema and full schema coverage reduces the description's burden, and the source list helps orient the agent. However, the description omits sibling differentiation and does not explain when to choose among the many gene-related lookup or browsing tools, leaving a notable usage 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?

Schema coverage is 100%, so the baseline is 3, but the description adds useful semantic meaning to the source enum by associating values with record types like GTEx expression, UCSC assembly data, and BioMart tables. It still does not clarify the query command syntax or the nested _subject/_files parameters, but it meaningfully enriches source interpretation.

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 states a specific verb and resource: look up a gene or genomic region across named authorities such as NCBI Gene, HGNC, Ensembl, MyGene, UCSC, GTEx, and BioMart. It is clear what the tool does, but it does not explicitly distinguish itself from nearby siblings like lookup_variant, lookup_omics, or browse_region.

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

Usage Guidelines2/5

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

The description lists supported sources but gives no guidance on when to use this tool versus alternatives such as lookup_variant, lookup_omics, fetch_record, or browse_region. There are no exclusions, prerequisites, or decision rules for choosing among the source values.

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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