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musharna

plant-genomics-mcp

locus_go_annotations

Retrieve Gene Ontology annotations for a plant locus by resolving it to a UniProt accession and querying QuickGO, returning annotations grouped by aspect.

Instructions

Fetch Gene Ontology annotations for a plant locus from QuickGO (EBI). Free, no API key. The locus is first resolved to a UniProt accession via the same logic as resolve_locus_to_uniprot, then QuickGO is queried by geneProductId. Returns annotations[] with goId/goName/goAspect/qualifier/evidence + a by_aspect rollup ({molecular_function: [{goId, goName}, ...], biological_process: [...], cellular_component: [...]}) deduped on goId so the high-level term set is one read away.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYese.g. AT1G01010 (Arabidopsis), Os01g0100100 (rice)
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxidarabidopsis_thaliana
limitNoMax annotations from QuickGO (1–100, default 50)

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYes
uniprot_accessionYesUniProt accession used to query QuickGO
numberOfHitsYesTotal annotations available upstream
returnedYesNumber of annotations in annotations[]
annotationsYes
by_aspectYesaspect → [{goId, goName}, ...], deduped on goId
Behavior3/5

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

With no annotations provided, the description carries full burden for behavioral disclosure. It explains the resolution to UniProt, the query to QuickGO, and the return format with deduped rollup. However, it does not address failure modes (e.g., unresolved locus, API errors) or rate limits, leaving some transparency gaps.

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 concise, front-loading the purpose and key details. It could be slightly more structured with bullet points or separate sentences for the workflow and output, but it remains efficient with no waste.

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?

Given the presence of an output schema, the description provides a thorough explanation of the return format and workflow. Minor omissions like error handling or timeouts keep it from a perfect 5, but it is largely complete for a query tool.

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 adds value by explaining the resolution workflow for 'locus' and the rollup structure, but it does not significantly enhance the schema descriptions for 'organism' and 'limit', which are already clear.

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?

The description clearly states it fetches GO annotations for a plant locus from QuickGO, including the resolution step to UniProt and the return structure (annotations array with by_aspect rollup). It distinguishes itself from sibling tools like batch_locus_go_annotations and resolve_locus_to_uniprot by focusing on single-locus query with a deduped rollup.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides clear context: it is for fetching GO annotations for a specific locus, free, no API key. It does not explicitly state when not to use it or compare to alternatives, but the single-locus vs batch distinction is implicit. The mention of using the same logic as resolve_locus_to_uniprot hints at dependencies.

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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