tooluniverse-plant-genomics

Plant genomics and biology research — PlantReactome pathways, Ensembl Plants gene structure, POWO species taxonomy, UniProt annotation, KEGG plant pathways. Handles polyploidy (wheat hexaploidy etc.) and homeologous gene copies. Use for crop-gene annotation, plant secondary metabolism queries, and plant-disease/stress-response biology.

Quality

72%

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Quality

Content

61%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A well-structured, actionable plant-genomics skill with concrete tool calls and dense reference tables. The main weaknesses are explanatory padding of concepts Claude already knows, a duplicated KEGG pathway ID, and missing explicit validation checkpoints in the batch-lookup workflow.

Suggestions

Tighten the Reasoning Strategy by dropping general plant-biology background (polyploidy, gene-family expansion, Arabidopsis as model) that Claude already knows, keeping only ToolUniverse-specific guidance.

Fix the KEGG table: ath04712 is listed for both Brassinosteroid signaling and Circadian rhythm; correct the circadian entry to its actual pathway ID.

Add explicit validation checkpoints to the workflow (e.g. 'confirm the KEGG organism code exists via kegg_search_pathway before querying', 'verify a pathway ID returns genes before interpreting'), since the lookups are batch cross-reference operations.

Dimension	Reasoning	Score
Conciseness	Mostly efficient with dense, useful reference tables, but the Reasoning Strategy explains plant-genome biology (polyploidy, gene-family expansion, Arabidopsis as model) that Claude largely already knows, and KEGG ID ath04712 is duplicated across two pathway rows.	3 / 5
Actionability	Provides concrete, parameterized tool calls (e.g. ensembl_lookup_gene with species, UniProt_search with taxonomy_id:3702 AND reviewed:true, KEGG_get_pathway_genes with ath00941) plus specific organism-code and pathway-ID tables, with only minor gaps in Phase 0/2/3/4 which are ASCII diagrams rather than code.	4 / 5
Workflow Clarity	A clear 5-phase sequenced pipeline is present, but the workflow involves batch cross-reference lookups with no explicit validation/verification checkpoints beyond the 'LOOK UP DON'T GUESS' directive, capping this score per the batch-operations guidance.	3 / 5
Progressive Disclosure	Well-organized into clear sections (Reasoning Strategy, When to Use, Core Tools, Workflow, Limitations) with no nested references, though the two large KEGG/organism lookup tables are inline reference data that could be split into separate files.	4 / 5
	Total	14 / 20 Passed

Description

83%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A strong, specific description that clearly delineates a plant-genomics niche with named tools and an explicit 'Use for' clause. The main weakness is trigger phrasing that leans technical rather than mirroring natural user questions.

Suggestions

Add concrete user-style trigger phrases to the 'Use for' clause, e.g. 'Use when the user asks what pathway a plant gene belongs to, or asks to compare a gene across Arabidopsis and rice'.

Surface a couple of natural synonyms (e.g. 'crop genes', 'plant gene families') to broaden trigger matching.

Dimension	Reasoning	Score
Specificity	Names multiple concrete capabilities with their specific tools (PlantReactome pathways, Ensembl Plants gene structure, POWO taxonomy, UniProt annotation, KEGG plant pathways) plus polyploidy/homeolog handling, giving comprehensive coverage.	5 / 5
Completeness	Both 'what' (named tools and capabilities) and explicit 'when' ('Use for crop-gene annotation, plant secondary metabolism queries, and plant-disease/stress-response biology') are present, though the trigger guidance could be more explicit in the 'Use when the user mentions X' form.	4 / 5
Trigger Term Quality	Good keyword coverage including 'crop-gene annotation', 'plant secondary metabolism queries', and 'plant-disease/stress-response biology', but some natural user phrasings (e.g. 'what pathway is this gene in', 'is this gene the same in rice') are not surfaced as triggers.	4 / 5
Distinctiveness Conflict Risk	A clearly defined plant-genomics niche with distinct tools (PlantReactome, POWO) and domain-specific triggers, with explicit sibling-skill boundaries noted in the body, giving minimal conflict risk.	5 / 5
	Total	18 / 20 Passed

Validation

100%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: mims-harvard/ToolUniverse
Path: plugins/tooluniverse/skills/tooluniverse-plant-genomics/SKILL.md
Commit: 1b02920

Reviewed: 1 day ago

Table of Contents

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