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musharna

plant-genomics-mcp

phytozome_lookup_locus

Fetch plant gene records from Phytozome BioMart by locus and optional organism. Returns gene name, chromosome, genomic coordinates, strand, and description.

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 full burden. It discloses the return fields but does not explicitly state that the tool is read-only or safe, nor discuss side effects, rate limits, or authentication. The listed return values add some behavioral context.

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 sentences long, front-loaded with the action, and contains no unnecessary words. Every sentence adds value: action, defaults/examples, return fields.

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 (2 parameters, output schema exists), the description is largely complete. It covers purpose, parameters with examples, and return fields. It lacks error handling or limit information, but is sufficient 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?

Schema coverage is 100%, and the description adds significant meaning beyond the schema by providing example values and explaining that organism can be a slug, scientific/common name, or NCBI taxid. This helps the agent understand parameter formats.

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?

The description clearly states the tool fetches a gene record from Phytozome BioMart, with a specific verb and resource. It provides examples and explains defaults. However, 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?

The description explains when to use the tool (default Arabidopsis, pass organism for others) but does not provide explicit when-not-to-use or alternatives. Usage guidance is implied rather than explicit.

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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