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musharna

plant-genomics-mcp

by musharna

GeneRIF Functional Statements

locus_gene_rifs
Read-onlyIdempotent

Fetch manually curated gene function statements (GeneRIFs) for an Arabidopsis locus, each linked to a PubMed ID, enabling precise, citable functional annotation.

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
NameRequiredDescriptionDefault
locusYesAGI locus, e.g. AT5G11260 (HY5)
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid. ThaleMine supports Arabidopsis only.arabidopsis_thaliana

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
foundYesTrue if the gene has at least one GeneRIF
locusYes
organismYesCanonical organism slug (Arabidopsis only)
gene_rifsNoCurated statements in upstream order
rif_countYesTotal GeneRIFs (pre-cap)
truncatedYesTrue if the GeneRIF list was capped
source_urlYesThaleMine gene report page
gene_symbolNoGene symbol from ThaleMine
Behavior5/5

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

The annotations already declare readOnlyHint=true, idempotentHint=true, destructiveHint=false. The description adds important behavioral context: upstream order is preserved, 'truncated' means later statements cut, and an unknown locus raises a 'typed NotFoundError'. No contradictions with 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 detailed and front-loaded with the main action, but some sentences (e.g., the example HY5 count) are slightly verbose. However, every sentence adds useful information, and the structure is logical. Could be slightly trimmed without losing value.

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?

Given the complexity (curated statements, ordering, truncation, errors, organism restriction) and the presence of an output schema (so return values need not be described), the description covers all necessary behavioral and contextual details. It differentiates well from many sibling tools and handles edge cases (found=false, unknown locus).

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, but the description adds value beyond schema: it gives an example value for 'locus' (AT5G11260), explains what 'organism' accepts (slug, scientific name, common name, or NCBI taxid), and clarifies the default and limitation (Arabidopsis only). This enriches parameter understanding.

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 states it fetches 'curated GeneRIF functional statements for an Arabidopsis locus from ThaleMine', clearly specifying verb, resource, and source. It distinguishes from siblings 'locus_go_annotations' and 'locus_literature' by explaining that GeneRIFs provide 'dense, directly citable functional context' that those do not.

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?

The description explicitly tells when to use this tool: when needing 'directly citable functional context' that GO terms and abstracts lack. It provides an example (HY5 with 114 statements) and explains the meaning of 'found=false' and error behavior for unknown loci. It also notes 'ThaleMine supports Arabidopsis only', setting clear scope and restrictions.

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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