tooluniverse-comparative-genomics

Cross-species gene comparison and ortholog analysis. Integrates Ensembl Compara orthologs, NCBI Gene, UniProt, OLS, Monarch, and OpenTargets to identify orthologs, paralogs, sequence conservation, functional conservation across species, and lineage-specific gene gains/losses. Use for phylogenetic gene tracing, model-organism mapping, and evolutionary-genomics queries.

Quality

80%

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Quality

Content

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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 workflow skill with concrete tool calls, a clear six-phase sequence, and thoughtful fallback handling. Its main weakness is conciseness — portions of the reasoning framework re-explain evolutionary biology concepts Claude already knows.

Suggestions

Tighten the 'Conservation Reasoning Framework' by trimming definitions of basic concepts (purifying/positive/neutral selection, dN/dS interpretation) and keeping only the tool-specific guidance and thresholds Claude would not infer.

Add at least one fully runnable end-to-end example (e.g., a small Python snippet chaining ortholog discovery → CDS retrieval → dN/dS) to lift actionability from concrete-but-fragmented to copy-paste ready.

Introduce explicit validation checkpoints in the workflow (e.g., confirm ortholog homology type before downstream analysis; re-run with relaxed BLAST thresholds if no ortholog found) to formalize the existing fallbacks into feedback loops.

Dimension	Reasoning	Score
Conciseness	Mostly efficient and tool-focused, but the 'Conservation Reasoning Framework' explains biology Claude already knows (definitions of purifying/positive/neutral selection, dN/dS interpretation, PhastCons/GERP thresholds) that could be tightened without losing actionable value.	3 / 5
Actionability	Provides concrete tool calls with parameters (e.g., EnsemblCompara_get_orthologues with gene/species/target_species, Sequence_dn_ds(seq1=..., seq2=...), UniProt query syntax) across all six phases, with only minor gaps like the absence of a full end-to-end runnable example.	4 / 5
Workflow Clarity	A clearly sequenced six-phase workflow with an ASCII diagram, per-phase reasoning, and a dedicated Fallback Strategies section for error recovery; falls short of 5 because there are no explicit validate→fix→retry feedback loops or checklists.	4 / 5
Progressive Disclosure	Well-organized into clearly headed phases with one real, correctly-referenced bundle file (scripts/dnds.py) and a cross-link to a related skill; most content is appropriately inline for a workflow skill, though the file is a single ~175-line monolith with no separate reference files for detailed tool parameters.	4 / 5
	Total	15 / 20 Passed

Description

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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 names concrete capabilities and integrated data sources and provides an explicit 'Use for' trigger clause. It is third-person throughout with no first/second-person voice issues. The only minor gap is synonym coverage in trigger terms.

Dimension	Reasoning	Score
Specificity	Names the domain and multiple concrete actions — 'identify orthologs, paralogs, sequence conservation, functional conservation across species, and lineage-specific gene gains/losses' — alongside the specific integrated data sources, giving comprehensive coverage.	5 / 5
Completeness	Explicitly answers both 'what' (cross-species gene comparison and ortholog analysis integrating named databases) and 'when' via a concrete 'Use for phylogenetic gene tracing, model-organism mapping, and evolutionary-genomics queries' clause.	5 / 5
Trigger Term Quality	Includes natural user-facing terms ('ortholog', 'cross-species', 'conserved', 'gene tracing', 'model-organism mapping', 'evolutionary-genomics'), but misses some common synonyms (e.g., 'homolog', 'paralog analysis') that would push it to a 5.	4 / 5
Distinctiveness Conflict Risk	Occupies a clear comparative-genomics/ortholog niche with distinct triggers (ortholog discovery, conservation analysis, model-organism selection), giving minimal conflict risk with other skills.	5 / 5
	Total	19 / 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: plugin/skills/tooluniverse-comparative-genomics/SKILL.md
Commit: 1b02920

Reviewed: 1 day ago

Table of Contents

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