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musharna

plant-genomics-mcp

by musharna

GO Annotations

locus_go_annotations
Read-onlyIdempotent

Fetch Gene Ontology annotations for a plant locus from QuickGO, returning terms grouped by molecular function, biological process, and cellular component with evidence.

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

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYes
returnedYesNumber of annotations in annotations[]
by_aspectYesaspect → [{goId, goName}, ...], deduped on goId
annotationsYes
numberOfHitsYesTotal annotations available upstream
uniprot_accessionYesUniProt accession used to query QuickGO
Behavior5/5

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

Annotations already mark the tool as readOnly, openWorld, idempotent, and non-destructive. The description adds substantial context: the free access, the resolution step to UniProt, the query by geneProductId, and the exact return structure (annotations[] with specific fields plus a by_aspect rollup deduped on goId). No contradictions.

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?

The description is a single, well-structured paragraph of 4-5 sentences. It front-loads the core purpose and source, then efficiently covers the resolution logic, return format, and deduplication. Every sentence adds value without redundancy.

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 tool's complexity (dependency on another tool, structured return data) and the presence of an output schema (not shown), the description compensates by detailing the return fields and the rollup structure. It omits error handling or limitations, but coverage is high for a tool with many siblings.

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 coverage is 100% for the three parameters, each with a description. The description reiterates the locus resolution but does not add new semantic meaning beyond the schema. The baseline is 3, and the description does not elevate it further.

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 'Fetch Gene Ontology annotations for a plant locus from QuickGO (EBI).' It specifies the resource (QuickGO), the operation (fetch annotations), and the target (plant locus). It distinguishes from siblings like go_enrichment and locus_plant_ontology by mentioning the specific data source and the deduplication strategy.

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 notes 'Free, no API key,' indicating no authentication barrier. It also explains the dependency on resolve_locus_to_uniprot logic, linking to a sibling tool. However, it does not explicitly state when to use this tool over alternatives like go_enrichment, nor does it give negative guidance. The context is clear but lacks explicit exclusions.

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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