Jean — Molecular Biology & Genomics

lookup_ontology

Read-only

Resolve an ontology term, taxon, pathway or cell type: OLS ontologies, NCBI Taxonomy, QuickGO annotations, Reactome pathways, KEGG entries, Rfam RNA families, CellGuide/PanglaoDB cell types and markers, an antibody RRID, or an identifiers.org prefix and the pattern its ids follow.

Input Schema

Name	Required	Description
`limit`	No	maximum records (1–20).
`query`	Yes	a term, accession or command such as "get_go_annotations:P04637" or "map_reactome_pathways:TP53".
`_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: -[
-  "ols",
-  "quickgo",
-  "reactome",
-  "kegg",
-  "rfam",
-  "cellguide",
-  "panglaodb",
-  "antibodyregistry"
-]New value: +[
+  "ols",
+  "ncbi-taxonomy",
+  "quickgo",
+  "reactome",
+  "kegg",
+  "rfam",
+  "cellguide",
+  "panglaodb",
+  "antibodyregistry",
+  "identifiers-org"
+]

First observedOct 20, 2026

TDQS

A3.5/5.0

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 that it spans many authorities and mentions identifiers.org prefix patterns, but it does not state rate limits, authentication needs, or special behaviors for live external queries; with annotations present, this is an acceptable but not rich addition.

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?

The description is a single dense but front-loaded sentence that begins with the verb and then enumerates the domains. It has no filler, though the long authority list makes it slightly less scannable than an ideally structured definition.

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, complete annotations and 100% parameter description coverage, the description is sufficient for an agent to understand the resource breadth and invoke the tool. The main omission is sibling routing, which is more of a usage-guideline gap than a completeness gap for correct invocation.

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 baseline is 3. The description usefully maps the source concepts to authorities, but the source enum and query examples are already documented in the schema, so the description adds only marginal meaning beyond the structured fields.

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 uses a specific verb, 'Resolve', and enumerates the resource domains it covers: OLS ontologies, NCBI Taxonomy, QuickGO, Reactome, KEGG, Rfam, CellGuide/PanglaoDB, antibody RRIDs, and identifiers.org. That is far clearer than a tautology, but it does not distinguish this tool from sibling lookups such as lookup_gene, lookup_protein or lookup_variant.

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 list of supported authorities implies when the tool applies, but there is no explicit guidance on when to use lookup_ontology instead of lookup_gene, lookup_protein, lookup_variant, query_database or fetch_record. Usage is inferable rather than stated.

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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