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musharna

plant-genomics-mcp

analyze_locus_synth

Resolves a plant gene locus across Ensembl Plants, UniProt, Europe PMC, and QuickGO, then synthesizes results with cross-source discrepancy alerts.

Instructions

Synthesis: one-call equivalent of the analyze_locus prompt. Resolves a locus through Ensembl Plants, then fans out to xrefs, UniProt, Europe PMC, and QuickGO in parallel. Returns a SynthesisEnvelope with per-step status and a reconciled summary flagging cross-source name/accession disagreements.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYesLocus name, e.g. AT1G01010
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxidarabidopsis_thaliana

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
toolYesSynthesis tool name, e.g. analyze_locus_synth
inputYesEchoed input arguments
started_atYesISO 8601 UTC timestamp
elapsed_sYesTotal orchestrator wall time
stepsYesPer-backend execution rows
resultNoComposed cross-source result; None if root step failed
Behavior4/5

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

With no annotations provided, the description carries the full burden. It discloses parallel fan-out behavior, the SynthesisEnvelope return type with per-step status, and reconciliation flagging cross-source disagreements. This is good behavioral context beyond a simple read operation.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is two sentences, efficiently summarizing purpose and behavior. It is front-loaded with the purpose. Slightly more structure could improve readability, but it is appropriately sized.

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's complexity (synthesis with multiple steps) and the presence of an output schema, the description adequately explains the process and output structure. It covers the key steps and what the returned envelope contains.

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 elaborating on the 'organism' parameter, specifying acceptable formats (canonical slug, scientific/common name, NCBI taxid), which goes beyond the schema's brief description.

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's action: it is the one-call equivalent of the analyze_locus prompt, resolving a locus and fanning out to multiple sources. It identifies the specific verb and resource, and distinguishes from sibling tools by being a synthesis tool that combines Ensembl Plants, xrefs, UniProt, Europe PMC, and QuickGO.

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 implies use for a comprehensive locus analysis but does not explicitly state when to use this tool versus alternatives like ensembl_plants_lookup_locus or batch tools. No when-not or alternative 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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