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plant-genomics-mcp

by musharna

Ensembl Plants: Locus Metadata

ensembl_plants_lookup_locus
Read-onlyIdempotent

Fetch metadata for any plant locus identifier from Ensembl Plants. Supports Arabidopsis, rice, and more with optional organism parameter.

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
endNo
startNo
sourceNo
strandNo1 forward, -1 reverse
biotypeNoprotein_coding, lncRNA, miRNA, ...
db_typeNoUsually "core"
organismYesPlant organism canonical slug, e.g. arabidopsis_thaliana
logic_nameNoSource annotation pipeline
descriptionNo
object_typeNoUsually "Gene"
display_nameNoHuman-readable gene symbol
assembly_nameNoe.g. TAIR10
seq_region_nameNoChromosome / contig name
canonical_transcriptNo
Behavior3/5

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

Annotations already declare readOnlyHint=true, idempotentHint=true, destructiveHint=false, and openWorldHint=true. The description adds no contradictory information and provides minimal behavioral context beyond the annotations, resulting in an adequate but not enhanced score.

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?

Extremely concise at two sentences. Front-loaded with the core action, immediately followed by essential usage details and examples. No wasted words.

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 simple parameters, full schema coverage, rich annotations, and presence of an output schema, the description is sufficiently complete. Could optionally mention pagination or result limits, but it's not necessary for basic usage.

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?

Both parameters are fully described in the schema (100% coverage). The description adds value by providing real-world examples (e.g., AT1G01010 for Arabidopsis) and explaining the organism parameter's flexibility (canonical slug, name, taxid), which goes beyond the schema's basic 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 explicitly states 'Fetch metadata for a plant locus identifier from Ensembl Plants,' with a specific verb and resource. It distinguishes from sibling tools like phytozome_lookup_locus by specifying the Ensembl Plants origin and providing locus examples.

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 usage context: defaults to arabidopsis_thaliana, lists example organisms, and explains the locus identifier format. Does not explicitly mention when not to use, but the context is sufficiently clear.

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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