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musharna

plant-genomics-mcp

biological_context_synth

Resolves a UniProt accession and retrieves homologs, KEGG pathways, STRING-DB partners, and ATTED-II coexpression in parallel, then ranks consensus partners.

Instructions

Synthesis: one-call equivalent of the biological_context prompt. Resolves UniProt accession, then fans out to Gramene homologs, KEGG pathways, STRING-DB partners, and ATTED-II coexpression in parallel. Adds a consensus_partners ranking that merges STRING + ATTED scores.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYes
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxidarabidopsis_thaliana
top_nNo

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?

No annotations are provided, so the description carries the full burden. It discloses the main steps: resolving a UniProt accession, parallel fan-out to four sources, and building a consensus ranking. However, it does not cover failure conditions or rate limits, which are minor gaps for a read-only synthesis tool.

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 key phrase 'Synthesis: one-call equivalent'. Every sentence adds value, with no redundancy or unnecessary detail.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given that an output schema exists, the description does not need to cover return values. It explains the synthesis workflow adequately but leaves ambiguity about the input locus format. This is sufficient but not comprehensive, especially with low schema coverage.

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

Parameters2/5

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

Schema description coverage is only 33% (organism parameter has a description). The description does not elaborate on the 'locus' parameter format (e.g., if it must be a UniProt accession) or the 'top_n' parameter's meaning. It adds little value beyond the schema.

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 it is a 'one-call equivalent' that resolves a UniProt accession and fans out to multiple databases (Gramene, KEGG, STRING-DB, ATTED-II), differentiating it from sibling tools that target individual data sources.

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 as a convenience tool for combining multiple data sources, but does not explicitly state when to prefer this over individual tools or when not to use it. No alternatives or exclusions are mentioned.

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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