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musharna

plant-genomics-mcp

bar_aiv_interactions

Retrieve Arabidopsis gene regulatory network references or rice protein interaction predictions for a given locus. Input an AGI or MSU locus to get curated literature or co-expression-based partners.

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
locusYes
organismYes
kindYesDiscriminator: grn_papers (Arabidopsis) or ppi_predictions (rice)
countYesTotal rows returned (len of papers or partners)
papersNoGRN paper refs (populated when kind=grn_papers)
partnersNoPPI predictions (populated when kind=ppi_predictions)
source_urlYesBAR AIV endpoint URL for traceability
Behavior5/5

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

No annotations provided, so description covers all behavioral aspects: dispatch by organism changes response shape (grn_papers vs ppi_predictions), rice requires MSU format, unsupported organisms raise OrganismNotSupported. Discloses key behavioral differences without contradictions.

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?

Single well-structured paragraph with front-loaded purpose. Each sentence adds value: purpose, organism-specific details, format requirement, supported organisms. No waste.

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 presence of output schema, description sufficiently covers response fields for both organisms, error cases, and organism-specific behavior. Complete for the tool's complexity.

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%, but description adds value by clarifying locus format per organism, organism parameter flexibility (slug, scientific name, taxid), and how response shape relates to organism. Adds meaning beyond 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?

Clearly states it fetches BAR AIV interactions for Arabidopsis or rice locus. The verb 'Fetch' is specific, and the resource is well-defined. Distinguishes from siblings by being single-locus and organism-specific.

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?

Provides clear context on when to use: for Arabidopsis returns curated GRN paper refs; for rice returns predicted PPI partners. Specifies locus format constraints and organism support. However, does not explicitly contrast with other interaction tools like string_interactions or atted_coexpression.

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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