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musharna

plant-genomics-mcp

plantcyc_locus_info

Checks subscription access for a PlantCyc locus and suggests free alternative backends when PlantCyc data is unavailable due to paid restrictions.

Instructions

Returns subscription-access info and alternatives for a PlantCyc locus. Does NOT fetch annotation or pathway data — PlantCyc requires paid SRI/Phoenix subscription. Use ensembl_plants_lookup_locus or phytozome_lookup_locus for canonical gene annotation; PlantCyc's pathway-membership value-add is not currently substituted. Returns structured redirect with rationale and probed_at date.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYesTAIR-canonical locus, e.g. AT1G01010

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYes
statusYesAlways "subscription_required" — upstream REST is paid-only.
probed_atYesISO date of the last live access probe (YYYY-MM-DD)
rationaleYesWhy this backend is gated
alternativesYesTool names users should call instead
alternatives_noteYesWhat the alternatives do and do NOT cover
plantcyc_web_urlYesBrowser URL for the PlantCyc gene page
Behavior5/5

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

With no annotations, the description carries full burden. It discloses that the tool does not fetch annotation or pathway data, requires a paid subscription, and returns a structured redirect with rationale and probed_at date, providing clear behavioral traits beyond the input schema.

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 three concise sentences: first sentence states the main purpose, second clarifies limitations and alternatives, third describes output structure. No extraneous information, each sentence earns its place.

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 single parameter, existing output schema, and presence of sibling tools, the description fully covers the tool's purpose, usage guidance, behavioral constraints, and output nature. It is complete for decision-making.

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

Parameters3/5

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

The input schema has 100% coverage for one parameter with a description of 'TAIR-canonical locus, e.g. AT1G01010'. The description adds no new semantic detail about the parameter beyond restating 'PlantCyc locus', so baseline 3 is appropriate.

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 returns subscription-access info and alternatives for a PlantCyc locus, and explicitly distinguishes from sibling tools by noting it does NOT fetch annotation or pathway data. The verb 'returns' is specific to the resource.

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 explicitly provides alternatives: 'Use ensembl_plants_lookup_locus or phytozome_lookup_locus for canonical gene annotation' and notes that the pathway-membership value-add is not currently substituted, guiding when to use this tool versus others.

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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