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tooluniverse-bioinformatics-resource-discovery

Discover which bioinformatics software tool, biomedical REST API, R/Bioconductor package, CRAN package, or training material exists for a task, before writing analysis code or building a pipeline. Covers ELIXIR bio.tools (30,000+ software tools/databases by keyword, EDAM topic, or EDAM operation), SmartAPI (biomedical API registry, incl. NCATS Translator components), ELIXIR TeSS (bioinformatics training materials/events), Bioconductor (R packages for computational biology), and CRAN (general R packages). Use when someone asks 'is there an existing tool/package for X', 'what software does [analysis]', 'find an API for Y', or 'is there a tutorial on Z'.

Quality

90%

Does it follow best practices?

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

75%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.

Highly actionable content with exact parameters, verified example calls, and good error-interpretation guidance, organized as a clean navigable catalog. The main weakness is conciseness: verification narrative, some pitfalls repeated across sections, and inline version/date facts could be trimmed or split out.

Suggestions

Trim the testing-methodology narrative from the 'Verified live' notes (e.g. the TeSS 'confirmed by re-running with a broader query and an empty-query call' clause) — keep the operational takeaway (empty list = nothing listed, retry broader) and cut the rest.

De-duplicate Common Pitfalls against the in-section notes: either state each pitfall once in Common Pitfalls and remove the inline digressions, or keep them inline and drop the redundant pitfall bullets.

Remove or quarantine time-sensitive specifics (DESeq2 '1.53.3', ggplot2 '4.0.3', the '2026-09-21' event) — they add tokens and will go stale; the record-shape demonstration works with the tool name alone.

DimensionReasoningScore

Conciseness

The tool tables are token-efficient, but several 'Verified live' passages pad with testing-process narrative rather than instructions — e.g. "confirmed by re-running with a broader query and an empty-query call, both of which returned real, different, non-empty result sets" — and the Common Pitfalls section restates points already made in Sections 1 and 3. Inline time-sensitive facts ("Version: '1.53.3'", "2026-09-21" event) also fall outside a deprecated/old-patterns section.

3 / 5

Actionability

Gives exact tool names, exact parameter names with case-sensitivity warnings ("biotoolsID", "toolType", "package_name" ... "not `package`"), copy-paste-ready example calls with real outputs ("BioTools_search {\"q\": \"RNA-seq\", \"size\": 3}\" -> 6,081 total matches"), and per-question-type entry points ("start with BioTools_search"). This matches the fully-executable 5 anchor.

5 / 5

Workflow Clarity

The dispatch workflow is clear — the 'When to Use' section maps question types to resources, each section names which tool to start with, and 'Choosing Among the Five' gives an explicit fallback order ("try Bioconductor first ... fall back to CRAN"), with error-recovery loops like checking `count` and paging further, and retrying a broader TeSS query. It falls short of a 5 because the overall lookup sequence is never laid out as explicit ordered steps with validation checkpoints; the guidance is distributed across sections.

4 / 5

Progressive Disclosure

A single-level, well-organized document: clear section headers, consistent per-registry tables, and a summary 'Choosing Among the Five' table that aids navigation, with no nested or buried references. It scores 4 rather than 5 because at ~95 lines it exceeds the under-50-line simple-skill exception, and the per-registry 'Verified live' details are candidates for a separate reference file.

4 / 5

Total

16

/

20

Passed

Description

100%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.

An exemplary description: concrete, third-person, comprehensive over both 'what' and 'when', with natural verbatim trigger phrases and clearly bounded scope. It is dense but every clause carries information, so verbosity is not penalized.

DimensionReasoningScore

Specificity

Enumerates multiple concrete discovery targets — "bioinformatics software tool, biomedical REST API, R/Bioconductor package, CRAN package, or training material" — each mapped to a named registry with its search dimensions ("by keyword, EDAM topic, or EDAM operation"). Coverage across the skill's full scope is comprehensive, exceeding the "several specific actions; minor gaps" of a 4.

5 / 5

Completeness

Explicitly answers both: what ("Discover which ... exists for a task, before writing analysis code or building a pipeline", with the five covered registries) and when ("Use when someone asks ..."). Concrete trigger phrases match the 5 anchor exactly; it is not merely an implicit or partial 'when' as at 4.

5 / 5

Trigger Term Quality

Four verbatim natural trigger phrases ("is there an existing tool/package for X", "what software does [analysis]", "find an API for Y", "is there a tutorial on Z") plus natural nouns like "tutorial", "API", and "package" give comprehensive coverage of how users actually phrase these requests. No common variation is obviously missing for this domain.

5 / 5

Distinctiveness Conflict Risk

A clear niche — discovering existing bioinformatics resources across five named registries "before writing analysis code or building a pipeline" — with trigger phrases that would not fire for general coding, document, or data-retrieval skills. Overlap risk with adjacent tooluniverse skills is minimal because the discovery-vs-execution boundary is stated.

5 / 5

Total

20

/

20

Passed

Validation

100%

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-bioinformatics-resource-discovery/SKILL.md

Reviewed

Table of Contents

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