plant-genomics-mcp

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GeneRIF Functional Statements

locus_gene_rifs

Read-onlyIdempotent

Retrieve manually curated, PubMed-linked GeneRIF statements for an Arabidopsis gene locus to get citable one-sentence functional evidence, complementing GO annotations and abstracts.

Instructions

Fetch curated GeneRIF functional statements for an Arabidopsis locus from ThaleMine (free, no key). A GeneRIF is a one-sentence, manually curated statement of what the gene does, each anchored to the PubMed ID of the publication that demonstrated it — dense, directly citable functional context that GO terms (locus_go_annotations) and raw abstracts (locus_literature) do not provide. Well-studied genes have many: HY5 (AT5G11260) has 114. Upstream order is preserved because ThaleMine supplies no meaningful ranking, so truncated means later statements were cut, not that they were less relevant. found=false means the gene exists but has no GeneRIF; an unknown locus raises a typed NotFoundError. Arabidopsis only.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`locus`	Yes	AGI locus, e.g. AT5G11260 (HY5)
`organism`	No	Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid. ThaleMine supports Arabidopsis only.	arabidopsis_thaliana

Output Schema

TableJSON Schema

Name	Required	Description
`found`	Yes	True if the gene has at least one GeneRIF
`locus`	Yes
`total`	Yes	How many GeneRIFs exist upstream for this query, all pages (pre-cap) (#123)
`organism`	Yes	Canonical organism slug (Arabidopsis only)
`returned`	Yes	Rows in this payload (#123)
`gene_rifs`	No	Curated statements in upstream order
`rif_count`	Yes	Total GeneRIFs (pre-cap)
`truncated`	Yes	True if the GeneRIF list was capped
`source_url`	Yes	ThaleMine gene report page — a link for the client to open or fetch; no tool on this server dereferences it
`gene_symbol`	No	Gene symbol from ThaleMine

Schema Changelog

Changes observed during successful MCP inspections.

Changed4 schema fields changedv1.22.0Sep 24, 2026

addedOutput schema / properties / returned

Added value: +{
+  "description": "Rows in this payload (#123)",
+  "title": "Returned",
+  "type": "integer"
+}

changedOutput schema / properties / source_url / description

Previous value: -"ThaleMine gene report page"New value: +"ThaleMine gene report page — a link for the client to open or fetch; no tool on this server dereferences it"

addedOutput schema / properties / total

Added value: +{
+  "description": "How many GeneRIFs exist upstream for this query, all pages (pre-cap) (#123)",
+  "title": "Total",
+  "type": "integer"
+}

changedOutput schema / required

Previous value: -[
-  "locus",
-  "organism",
-  "found",
-  "rif_count",
-  "truncated",
-  "source_url"
-]New value: +[
+  "total",
+  "returned",
+  "locus",
+  "organism",
+  "found",
+  "rif_count",
+  "truncated",
+  "source_url"
+]

Addedv1.18.2Jul 24, 2026

TDQS

A4.6/5.0

Behavior5/5

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

With readOnly/idempotent annotations already present, the description goes well beyond them: it discloses no API key required, ThaleMine provenance, preserved upstream order, the meaning of 'truncated,' the found=false semantics, and the typed NotFoundError for unknown loci. This directly informs how the agent should interpret results, and nothing contradicts the annotations.

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 front-loaded with the core action, and most sentences earn their place by explaining ranking, truncation, and NotFoundError behavior. It is slightly longer than strictly necessary, with minor redundancy between the opening 'Arabidopsis locus' and closing 'Arabidopsis only,' but the detail is justified by the tool's output semantics.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a tool with an output schema that documents the return shape, the description covers everything an agent needs to call it correctly: source, auth, organism restriction, ordering, truncation semantics, empty-result semantics, and error behavior. No significant call-time context is missing.

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?

The input schema already documents both parameters thoroughly (100% coverage), including the AT5G11260 locus example and the Arabidopsis-only organism constraint, so the baseline is 3. The description adds useful context such as 'well-studied genes have many' and output edge-case semantics, but it does not materially enrich the meaning of the parameters beyond the schema.

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 opens with a specific verb and resource: 'Fetch curated GeneRIF functional statements for an Arabidopsis locus from ThaleMine.' It also distinguishes itself from nearby siblings by explaining that GeneRIFs provide citable functional context that locus_go_annotations and locus_literature do not provide.

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

Usage Guidelines5/5

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

It explicitly frames when this tool is valuable—when dense, directly citable functional statements are needed—and names the alternatives (GO terms, raw abstracts) that fail to supply that. It also states the exclusion 'Arabidopsis only,' giving an agent a clear boundary versus multi-organism siblings.

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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