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jean — Molecular Biology & Genomics

lookup_omics

Read-only

Look up omics and regulation records: GEO and ArrayExpress experiments, PRIDE proteomics, MetaboLights, MGnify, ENCODE experiments and files, JASPAR motifs, or UniBind TF binding sites.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNomaximum records (1–20).
queryYesan accession or search term, or a command such as "geo_get_series:GSE12345" or "encode_get_file:ENCFF002JUR".
_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 profile is covered. The description adds useful scope detail by naming the external authorities queried, but it does not disclose rate limits, authentication needs, pagination, or other behavioral traits beyond the annotations.

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 with the purpose first and the source list second. Every element earns its place by scoping the tool's data coverage, with no filler or repetition.

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?

The tool has an output schema and 100% schema description coverage, so the description need not explain return values or parameter details. It adequately defines the domain and sources, but lacks explicit sibling-routing guidance, leaving a small completeness gap.

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 source, query, limit, _files, and _subject in detail. The description names the covered sources, which aligns with the source enum, but adds no syntax or format guidance beyond what the schema provides, making the baseline 3 appropriate.

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 ('omics and regulation records'), then enumerates concrete authorities including GEO, ArrayExpress, PRIDE, MetaboLights, MGnify, ENCODE, JASPAR, and UniBind. This gives an agent a precise domain and distinguishes it from other lookup_* siblings that retrieve genes, proteins, compounds, or variants.

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 listing the omics and regulation sources it covers, but it does not explicitly say when to choose this tool over alternatives such as lookup_gene or search_records. There is no when-not guidance or named sibling alternative, so usage is only inferred from the source scope.

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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