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jean — Molecular Biology & Genomics

lookup_clinical

Read-only

Look up clinical and translational evidence: ClinicalTrials.gov trials, FDA labels and adverse events, Open Targets associations, CIViC cancer variant evidence, ClinGen curation, cBioPortal cohorts, or DepMap dependencies.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNomaximum records (1–20).
queryYesa drug, gene, disease or trial id, or a command such as "clingen_gene_validity:BRCA2".
_filesNoThe 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.
sourceYeswhich authority to ask.
_subjectNoThe 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

TableJSON Schema
NameRequiredDescriptionDefault
countYeshow many records came back, which is a result even when it is zero
recordsYesthe records the authority returned, in its own field names — wire them into a tool that takes ids, or read them in the transcript
envelopeYesthe authority's whole answer: paging, totals and the query it actually ran
provenanceYesthe 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.

  1. First observed

TDQS

A3.8/5.0
Behavior3/5

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 and external-query profile is covered structurally. The description adds useful context about which external authorities are queried (useful given openWorldHint), but says nothing about rate limits, per-source behavior differences, or result freshness. Adequate but not rich, which is fair against the annotation coverage.

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?

A single front-loaded sentence that names the verb and resource first, then the evidence sources. No filler or repetition of the title.

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?

With a full-coverage schema, an output schema (so return values need not be explained), and annotations covering the safety profile, the description is nearly self-sufficient for calling the tool. The only real gap is routing guidance against the many sibling lookup_* tools, which keeps it short of a 5.

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 source, query, and limit are already documented at baseline; the schema even supplies command syntax examples like "clingen_gene_validity:BRCA2". The description's source list reinforces the enum semantics but adds no query grammar or per-source syntax detail beyond the schema, so baseline 3 applies.

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 ('Look up') and resource ('clinical and translational evidence'), then enumerates the eight authority sources (ClinicalTrials.gov, FDA, Open Targets, CIViC, ClinGen, cBioPortal, DepMap) which map directly onto the source enum. This clearly distinguishes it from the other lookup_* siblings (lookup_gene, lookup_variant, lookup_omics), which target different evidence domains.

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 by naming the evidence domains, so an agent can infer this is the clinical/translational lookup, but it never states when to prefer this over lookup_variant, lookup_gene, or search_literature, nor any prerequisites or exclusions. Usage is implied rather than guided.

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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