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musharna

plant-genomics-mcp

bar_aiv_interactions

Retrieve gene interactions from BAR AIV: curated literature references for Arabidopsis or predicted protein-protein partners with co-expression evidence for rice 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, 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
Behavior4/5

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

No annotations provided, so the description carries full burden. It discloses that rice requires MSU format, the 'kind' field discriminates response shape, and unsupported organisms raise an error. It does not mention side effects, but as a fetch tool, none are expected.

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 front-loaded with purpose and packs substantial detail into three sentences. It could be slightly more concise, but the information density is justified given the tool's complexity.

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 presence of an output schema and the tool's complexity (dual response shapes, organism-specific constraints), the description is comprehensive. It covers dispatch logic, input constraints, and response discrimination, making it complete for effective tool 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?

Schema coverage is 100%, but the description adds significant value by explaining the flexible organism input (slug, name, taxid) and the locus format requirements. It also clarifies the response structure based on the 'kind' field.

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 clearly states the tool fetches BAR AIV interactions for Arabidopsis or rice loci, with distinct response types for each organism. It distinguishes itself from sibling tools by specifying the data source and supported organisms.

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 loci) and what input format is required (MSU for rice). It implicitly excludes other organisms by stating only two are supported, but does not explicitly mention alternatives or when not to use.

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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