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jean — Molecular Biology & Genomics

search_literature

Read-only

Search the published literature: PubMed, Europe PMC (including open-access full-text sections), OpenAlex, Crossref, arXiv, bioRxiv/medRxiv preprints or DataCite datasets.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNomaximum records (1–20).
queryYessearch terms, or a command such as "pmid:35486828", "fulltext:PMC9046468" or "openalex_search_works:CRISPR".
_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

A3.6/5.0
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-network profile is covered. The description usefully adds that Europe PMC includes open-access full-text sections and that bioRxiv/medRxiv and DataCite return preprints and datasets rather than indexed articles, but it says nothing about rate limits, auth, or result volume beyond the schema's limit field.

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?

A single front-loaded sentence states the action first and then the source list, with no filler or repetition. It is dense but appropriately sized for the number of sources; it stops one step short of maximal efficiency only because the sentence is a long enumeration.

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 an output schema present, return values need not be described, and read-only/open-world annotations cover the safety profile. The source characterisations make the description largely self-sufficient for a tool with five parameters; the only real gap is guidance on selecting among the sources.

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 description coverage is 100%, so the baseline is 3, but the description adds genuine meaning beyond the enum by characterising what each source yields (full-text sections, preprints, datasets), which helps an agent map the `source` values to intent. It does not add anything for `query`, `limit`, or the nested `_subject`/`_files` parameters.

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 gives a specific verb and resource ("Search the published literature") and enumerates the eight source systems it reaches, so an agent knows exactly what domain this covers. It does not differentiate itself from neighbouring retrieval tools such as search_records or query_database, but the listed literature databases make the scope unambiguous enough.

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?

Usage is implied rather than stated: you call this tool when you want published literature. The enumerated sources loosely guide the required `source` choice, but there is no explicit when-to-use/when-not, no guidance on picking between PubMed, Europe PMC and OpenAlex, and no alternative tool is named.

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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