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plant-genomics-mcp

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Python
Remote

BAR: Predicted Interactions

bar_aiv_interactions
Read-onlyIdempotent

Fetch Arabidopsis or rice gene interaction evidence from BAR AIV: curated GRN paper references for Arabidopsis loci, or predicted protein-protein interactions with co-expression scores for rice MSU loci.

Instructions

Fetch BAR AIV (Arabidopsis Interactions Viewer) interactions for an Arabidopsis or rice locus. Dispatches by organism: Arabidopsis returns curated GRN paper refs from /interactions/get_paper_by_agi/{locus} (PubMed ID, title, image URL, comments, pipe-split tags; the image is a link for the client to fetch, no tool on this server retrieves it); rice returns predicted PPI partners from /interactions/rice/{locus} with Pearson co-expression r (pcc), evidence hits, and quality score. The kind field discriminates the response shape (grn_papers vs ppi_predictions). Rice requires the MSU LOC_Os* locus format — RAP-DB Osg is rejected upstream. Only Arabidopsis and rice are supported by AIV; other organisms raise OrganismNotSupported.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYesAGI locus (AT1G01010) for Arabidopsis or MSU locus (LOC_Os01g01080) for rice
organismNoarabidopsis_thaliana or oryza_sativa — slug, scientific/common name, or NCBI taxidarabidopsis_thaliana

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
kindYesDiscriminator: grn_papers (Arabidopsis) or ppi_predictions (rice)
countYesTotal rows returned (len of papers or partners)
locusYes
papersNoGRN paper refs (populated when kind=grn_papers)
organismYes
partnersNoPPI predictions (populated when kind=ppi_predictions)
source_urlYesBAR AIV endpoint URL for traceability — a link for the client to open or fetch; no tool on this server dereferences it

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.22.0
    • changedOutput schema / $defs / BarAIVPaper / properties / image_url / description
      Previous value: -"BAR-hosted thumbnail of the GRN network diagram"New value: +"BAR-hosted thumbnail of the GRN network diagram — a link for the client to open or fetch; no tool on this server dereferences it"
    • changedOutput schema / properties / source_url / description
      Previous value: -"BAR AIV endpoint URL for traceability"New value: +"BAR AIV endpoint URL for traceability — a link for the client to open or fetch; no tool on this server dereferences it"
  2. First observedv1.8.0

TDQS

A4.8/5.0
Behavior5/5

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

Beyond the readOnlyHint and idempotentHint annotations, the description discloses substantive behavior: the response shape is discriminated by the `kind` field, the image URL is only a link and no tool on this server retrieves it, rice rejects RAP-DB Os*g* format upstream, and unsupported organisms raise OrganismNotSupported. This is rich, accurate behavioral context that goes well beyond 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.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is dense but every sentence earns its place. It front-loads the core purpose, then efficiently covers endpoint routing, response fields, organism-specific caveats, and failure behavior. There is no redundancy or filler.

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 this tool has an output schema and complete parameter schema coverage, the description adds the remaining context an agent needs: supported organisms, endpoint dispatch, response shape discrimination, the MSU locus requirement, and error behavior. Nothing critical is missing for correct invocation.

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?

Although the schema already documents both parameters well (100% coverage), the description adds essential semantics beyond it: the exact locus formats expected for each organism, the rejection of RAP-DB identifiers for rice, and how the `kind` field in the response relates to the organism-specific behavior. These details materially help an agent select correct parameter values.

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 BAR AIV (Arabidopsis Interactions Viewer) interactions for an Arabidopsis or rice locus.' It clearly defines the tool's scope, distinguishes it from generic interaction tools by naming AIV and the unique endpoints, and calls out the supported organisms. The purpose is unambiguous and not a tautology.

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 on when to use the tool: for Arabidopsis or rice AIV interactions, and explicitly says other organisms raise OrganismNotSupported. It also gives decisive routing guidance (curated GRN papers for Arabidopsis, predicted PPI partners for rice) and locus-format requirements. However, it does not explicitly name alternative tools or state when a sibling should be preferred, so it falls just short of full usage guidance.

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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