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plant-genomics-mcp

ensembl_plants_lookup_locus

Fetch gene metadata for a plant locus identifier from Ensembl Plants, supporting species like Arabidopsis, rice, and maize. Provide a TAIR-style locus and optional organism.

Instructions

Fetch metadata for a plant locus identifier from Ensembl Plants. Defaults to arabidopsis_thaliana; pass organism= for other plant species (oryza_sativa, zea_mays, ...). Locus is the TAIR-style identifier (e.g. AT1G01010 for Arabidopsis NAC001).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYese.g. AT1G01010 (Arabidopsis), Os01g0100100 (rice)
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxidarabidopsis_thaliana

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesLocus identifier, e.g. AT1G01010
organismYesPlant organism canonical slug, e.g. arabidopsis_thaliana
object_typeNoUsually "Gene"
biotypeNoprotein_coding, lncRNA, miRNA, ...
display_nameNoHuman-readable gene symbol
descriptionNo
seq_region_nameNoChromosome / contig name
startNo
endNo
strandNo1 forward, -1 reverse
assembly_nameNoe.g. TAIR10
db_typeNoUsually "core"
logic_nameNoSource annotation pipeline
sourceNo
canonical_transcriptNo
Behavior2/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure. It only states 'Fetch metadata', implying a read operation, but fails to mention any behavioral traits such as error handling, data freshness, required permissions, or whether the operation is safe. The lack of explicit read-only declaration reduces transparency.

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 two sentences long, front-loaded with the main purpose, and includes essential details (default organism, examples) without any fluff. Every sentence serves a purpose.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's simplicity (two parameters, one required) and the presence of an output schema (not shown but indicated as true), the description covers the necessary aspects: purpose, parameters, and usage examples. It does not need to explain return values. It is complete enough for an AI to decide when to use this tool.

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%, so baseline is 3. The description adds value by explaining the 'locus' parameter as a TAIR-style identifier with examples, and clarifying the 'organism' parameter's default value and accepted formats (canonical slug, scientific name, NCBI taxid). This goes beyond the schema descriptions.

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 metadata for a plant locus identifier from Ensembl Plants, with a specific verb ('Fetch'), resource ('metadata for a plant locus identifier'), and data source ('Ensembl Plants'). It also distinguishes from siblings by specifying the default organism and giving examples, making it clear what the tool does.

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 (to fetch plant locus metadata from Ensembl Plants) and how to use it (default organism is arabidopsis_thaliana, can be overridden). However, it does not explicitly exclude scenarios or compare to alternative sibling tools like tair_locus_info or phytozome_lookup_locus.

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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