plant-genomics-mcp

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Family / Domain Members

entry_members

Read-onlyIdempotent

List every protein in a plant organism that carries a given InterPro, Pfam, or PANTHER entry, including the gene locus for each. Reverse lookup from protein domain to associated genes.

Instructions

List every protein in one organism that carries an InterPro, Pfam or PANTHER entry, with the gene locus each maps to — the reverse of interpro_domains / panther_family (entry -> genes, not gene -> entries). One UniProt query (rest.uniprot.org; free, no key). Each member gives accession, symbol and locus; locus is the id the locus-keyed tools accept, or null when UniProt links the protein to no gene (e.g. an old cDNA submission). reviewed_only=true (default) keeps Swiss-Prot entries: complete for Arabidopsis and rice, empty for most other crops, so pass reviewed_only=false there. total is UniProt's count across all pages; when truncated=true, pass next_cursor back as cursor= for the next page. An entry absent from the organism is ok with total 0. Defaults to arabidopsis_thaliana.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`entry`	Yes	InterPro (IPR010525), Pfam (PF06507) or PANTHER family (PTHR31384)
`cursor`	No	next_cursor from the previous page; omit for the first
`organism`	No	Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid	arabidopsis_thaliana
`page_size`	No
`reviewed_only`	No	Only Swiss-Prot (curated) proteins

Output Schema

TableJSON Schema

Name	Required	Description
`entry`	Yes	The entry asked about, e.g. IPR010525
`query`	Yes	The UniProt query that produced this answer
`taxid`	Yes
`total`	Yes	How many proteins matching the UniProt query exist upstream for this query, all pages (pre-cap) (#123)
`members`	Yes
`organism`	Yes
`returned`	Yes	Rows in this payload (#123)
`truncated`	Yes	True when more members follow next_cursor
`next_cursor`	No	Pass back as cursor= for the next page; null on the last
`reviewed_only`	Yes
`entry_database`	Yes
`upstream_version`	No	UniProt release that produced THIS response, as stated by its X-UniProt-Release header (e.g. '2026_02'). null means UniProt did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered.

Schema Changelog

Changes observed during successful MCP inspections.

Addedv1.22.0Sep 24, 2026

TDQS

A4.9/5.0

Behavior5/5

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

Even though annotations already mark the tool as read-only, open-world, and idempotent, the description adds substantial behavioral context: it reveals the underlying UniProt query, that it is free and keyless, what each member contains, the meaning of null locus, and the total/truncated/cursor pagination contract. This goes well beyond the annotation signals.

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 long but every sentence carries useful information, and the core purpose is front-loaded before the edge-case details. It reads as a compact reference that avoids filler while covering the important quirks.

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 tool's complexity, the description is complete: it explains the direction, required input, data source, output fields, null behavior, pagination, reviewed_only caveats, and default organism. With an output schema also present, nothing essential is missing for an agent to select and invoke the tool correctly.

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

Parameters4/5

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

The schema already covers 80% of parameter meaning, and the description adds extra value by explaining reviewed_only's organism-dependent behavior and how cursor interacts with the truncated field. The description also clarifies entry types through the entry format, building on the schema examples.

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 a specific action and resource: list every protein in an organism carrying an InterPro, Pfam, or PANTHER entry along with its gene locus. It also explicitly distinguishes itself from interpro_domains and panther_family by describing it as the reverse direction (entry -> genes).

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 clearly positions the tool against sibling tools by naming interpro_domains and panther_family and explaining the reverse relationship. It also gives concrete guidance on when to adjust reviewed_only, such as passing false for most crops because reviewed-only results are empty there.

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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