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

82%

Does it follow best practices?

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Securityby

Passed

No findings from the security scan

Quality

Content

65%

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

A highly actionable, well-structured research skill with concrete tool calls and reference tables, but it loses points on conciseness (restated evidence grading, a duplicated KEGG ID), lacks explicit workflow validation checkpoints, and keeps large inline tables that could be progressively disclosed into a reference file.

Suggestions

Deduplicate the evidence-grading definition — state the T1–T4 tiers once (e.g. in Phase 4) and reference them from Key principles, and fix the repeated ath04712 (circadian rhythm should be a distinct KEGG ID).

Add an explicit validation checkpoint to the workflow (e.g. confirm species/organism codes via POWO or kegg_search_pathway before running pathway queries), since the Reasoning Strategy already warns against assuming KEGG codes.

Move the KEGG pathway-ID and organism-code tables into a one-level-deep reference file (e.g. references/plant_pathways.md) and link to it from SKILL.md to improve progressive disclosure.

Dimension	Reasoning	Score
Conciseness	Largely efficient and much of the reasoning prose is genuinely plant-specific (homeologs, evidence grading), but evidence grading is stated twice (Key principles #5 and Phase 4) and the KEGG pathway table repeats id ath04712, indicating slack that could be tightened.	2 / 3
Actionability	Provides copy-paste-ready, parameterized examples — ensembl_lookup_gene(species="arabidopsis_thaliana"), UniProt_search(query="...taxonomy_id:3702 AND reviewed:true"), KEGG_get_pathway_genes(pathway_id="ath00941") — plus concrete KEGG organism-code and pathway-ID tables.	3 / 3
Workflow Clarity	Phases 0–4 are clearly sequenced in the diagram, but there are no validation/verification checkpoints or feedback loops; the sequence is present yet checkpoints are only implicit.	2 / 3
Progressive Disclosure	A single well-organized file with no nested references, but at ~146 lines it keeps sizable reference tables (KEGG pathways, organism codes) inline that could be split into a one-level-deep reference file for easier navigation.	2 / 3
	Total	9 / 12 Passed

Description

100%

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, third-person description that names concrete data sources and actions, provides an explicit "Use for" trigger clause, and occupies a clearly distinct plant-genomics niche. It avoids fluff and over-claims while remaining concise.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete capabilities and data sources — "PlantReactome pathways, Ensembl Plants gene structure, POWO species taxonomy, UniProt annotation, KEGG plant pathways" and "Handles polyploidy (wheat hexaploidy etc.) and homeologous gene copies" — rather than vague language.	3 / 3
Completeness	Explicitly answers both what (the listed research areas and data sources) and when via the explicit "Use for crop-gene annotation, plant secondary metabolism queries, and plant-disease/stress-response biology" trigger clause.	3 / 3
Trigger Term Quality	Includes natural terms users would say — "plant genomics", "crop-gene annotation", "plant secondary metabolism", "plant-disease/stress-response biology" — alongside source names, giving good coverage.	3 / 3
Distinctiveness Conflict Risk	Carves a clear plant-genomics niche with distinct triggers and explicitly distinct from human/systems-biology and phylogenetics skills, making mis-triggering unlikely.	3 / 3
	Total	12 / 12 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: 089eb8e

Reviewed: about 8 hours ago

Table of Contents

Discovery Implementation Validation

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