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musharna

plant-genomics-mcp

get_gene_xrefs

Fetch cross-database references for a plant locus from Ensembl Plants. Returns identifiers from UniProt, NCBI Gene, TAIR, and more, grouped by database for easy lookup.

Instructions

Fetch cross-database references (UniProt, NCBI Gene, TAIR, ArrayExpress, …) for a plant locus from Ensembl Plants. Defaults to arabidopsis_thaliana; pass organism= for other Ensembl Plants species. Returns count + raw xref list + a by_db rollup keyed on Ensembl's dbname (e.g. 'Uniprot_gn', 'EntrezGene') for fast lookup of a single foreign identifier.

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
locusYes
organismYes
countYesNumber of xref records returned
xrefsYesRaw Ensembl xref records
by_dbYesdbname → primary_ids[]; e.g. {'Uniprot_gn': ['Q0WV96']}
Behavior5/5

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

With no annotations provided, the description carries full burden for behavioral disclosure. It details the return structure: 'count + raw xref list + a by_db rollup', including example dbname keys. It also mentions the default organism and parameter flexibility. No contradictions are present.

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 with no fluff. The first sentence states purpose and default; the second details output format. Every sentence adds essential information, making it highly efficient.

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 tool has 2 parameters (1 required), an output schema exists, and no nested objects, the description provides sufficient context. It explains the return structure (count, list, by_db rollup) and highlights a use case (fast lookup of a single foreign identifier). The breadth of siblings is not addressed but not necessary for completeness.

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

Parameters5/5

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

Schema coverage is 100%, but the description adds significant value beyond the schema. For the 'locus' parameter, it provides concrete examples (e.g., AT1G01010). For 'organism', it enumerates accepted formats (canonical slug, scientific/common name, NCBI taxid) and states the default. This enriches the schema's minimal 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 verb 'Fetch' and the resource 'cross-database references for a plant locus from Ensembl Plants'. It specifies the default organism and how to change it, making the tool's purpose unambiguous. Sibling tools like batch_get_gene_xrefs are distinguished by implication (batch vs single), and other tools have different purposes.

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 guidance on the default organism and how to specify other species via the 'organism' parameter. While it does not explicitly state when not to use this tool or compare with siblings, the context implies its usage for single-locus xref retrieval. More explicit exclusions or alternatives would improve this dimension.

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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