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musharna

plant-genomics-mcp

by musharna

BAR: Predicted Interactions

bar_aiv_interactions
Read-onlyIdempotent

Fetch Arabidopsis or rice locus interactions: curated gene regulatory network papers for Arabidopsis, or predicted protein-protein interaction partners for rice with co-expression scores.

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, comments, pipe-split tags); 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
Behavior4/5

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

Annotations already declare readOnlyHint, openWorldHint, idempotentHint. Description adds organism dispatch logic, response shape differences, and format requirements for rice. No contradictions, and adds significant behavioral context.

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?

Description is front-loaded with core purpose and is well-structured. Every sentence adds value, though it is somewhat lengthy due to necessary detail. No redundancy.

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 (organism-specific endpoints, response shapes, format requirements, error handling), the description covers all needed context. Output schema exists, so return values need not be detailed.

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?

Schema coverage is 100% with descriptions for both parameters. The description adds meaning by explaining locus format (AGI vs. MSU) and the effect of the organism parameter on the response shape, complementing 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 states it fetches BAR AIV interactions for Arabidopsis or rice locus, specifying endpoints and response shapes per organism. It clearly distinguishes from siblings by organism-specific behavior.

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?

Explicitly says when to use (Arabidopsis or rice locus) and when not to (other organisms raise OrganismNotSupported). Also notes rice requires MSU format, rejecting RAP-DB. Provides clear context and 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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