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musharna

plant-genomics-mcp

phytozome_lookup_locus

Fetches a gene record from Phytozome by locus name, returning genomic location and description. Supports many plant species via organism parameter.

Instructions

Fetch a gene record from Phytozome BioMart (phytozome-next.jgi.doe.gov). Defaults to arabidopsis_thaliana; pass organism= for other Phytozome proteomes (slug, scientific/common name, or NCBI taxid — e.g. glycine_max, sorghum_bicolor). Locus is the source-genome gene name (e.g. AT1G01010, Glyma.01G000100). Returns organism_name, gene_name, chromosome, gene_start, gene_end, strand, description.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYese.g. AT1G01010 (Arabidopsis), Glyma.01G000100 (soybean)
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxidarabidopsis_thaliana

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
organism_nameYes
gene_nameYes
chromosomeYes
gene_startYesString — BioMart TSV is untyped
gene_endYesString — BioMart TSV is untyped
strandYesString — typically "1" or "-1"
descriptionYes
Behavior3/5

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

No annotations are provided, so the description carries the burden. It discloses that the tool fetches a gene record and lists return fields, but does not mention rate limits, authentication, error handling, or other behavioral traits. Basic disclosure but not deep.

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?

Two concise sentences, front-loaded with the action and key details. Examples and return fields are included efficiently. No superfluous text.

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?

For a simple 2-parameter tool with an output schema, the description covers parameter default, accepted formats, and return fields. It lacks mention of error responses or pagination, but these are often covered by the output schema. Overall adequate.

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 description coverage is 100%, and the description adds valuable context: examples for locus (AT1G01010, Glyma.01G000100) and types for organism (slug, name, taxid). This enhances understanding beyond the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

Description clearly states the action ('Fetch a gene record') and the resource ('Phytozome BioMart'). It provides default organism and examples of locus and organism parameters. While it distinguishes from generic lookup tools by naming Phytozome, it does not explicitly differentiate from sibling tools like batch_phytozome_lookup_locus.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Description gives context on default organism and acceptable forms for the organism parameter, but does not specify when to use this tool vs alternatives (e.g., batch version for multiple loci). No exclusions or when-not guidance is provided.

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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