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jean — Molecular Biology & Genomics

lookup_compound

Read-only

Look up a chemical compound or drug: ChEMBL molecules, mechanisms of action and bioactivity, PubChem properties, ChEBI ontology, Rhea reactions, or purchasable ZINC compounds.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNomaximum records (1–20).
queryYesa compound name, SMILES or identifier, or a command such as "mechanism:CHEMBL941" or "admet:CHEMBL941".
_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

A4/5.0
Behavior3/5

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

Annotations already declare readOnlyHint, openWorldHint, and destructiveHint, covering the safety profile. The description adds no further behavioral context such as authentication needs, rate limits, or data freshness, though it does not contradict 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 sentence that front-loads the verb and resource before listing sources; every clause earns its place.

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 input schema, output schema, and annotations, the description need not document parameters or return values. It covers the main source categories but omits 'bindingdb' from the source enum and offers no guidance on the query command syntax (covered by schema), so a 4.

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%, establishing a baseline of 3. The description goes beyond the schema's generic source descriptions by mapping each enum value to specific content (e.g., ChEMBL molecules and mechanisms, ZINC purchasable compounds), which helps parameter selection.

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?

It names a specific verb ('Look up') and resource ('chemical compound or drug'), and enumerates source-specific content types (ChEMBL mechanisms, PubChem properties, etc.), which clearly distinguishes it from the many lookup_* siblings in genomics and proteins.

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 gives the domain context (chemical compounds/drugs) but does not explicitly state when to choose this over lookup_gene, lookup_protein, or other alternatives, nor any when-not conditions. Usage is implied by the source list, so a 3.

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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