CtrlK
BlogDocsLog inGet started
Tessl Logo
SkillPublic

tooluniverse-lipidomics

Lipid analysis and lipid-disease associations using LIPID MAPS classification, HMDB metabolite data, KEGG/Reactome lipid pathways (sphingolipid, eicosanoid, steroid, fatty acid), and PubChem chemical info. Use for lipid identification, lipid metabolism pathway mapping, and lipid-associated disease analysis (cardiovascular, diabetes, NAFLD).

Quality

86%

Does it follow best practices?

Run evals on this skill

Adds up to 20 points to the overall score

View guide
SecuritybySnyk

Passed

No findings from the security scan

The canonical home for this skill is tooluniverse-lipidomics in mims-harvard/ToolUniverse

SKILL.md
Quality
Evals
Security

Quality

Content

82%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 strong, fact-dense tool-use skill: it gives executable tool calls with real example outputs, a clearly sequenced 5-phase pipeline with fallback chains for lookup failures, and honest limitations. Its main weaknesses are mild — some duplicated reasoning across sections and reference-grade tables kept inline.

Suggestions

Deduplicate the LIPID MAPS category→biological-context mapping: it appears in both the Reasoning Strategy and Phase 1; state it once and cross-reference.

Move the 8-row KEGG pathway table and the verified SwissLipids example outputs into a references/ file (e.g. PATHWAYS.md) to slim the main body toward an overview, and add an explicit error-recovery step for Phases 2–3 (what to do when a KEGG or CTD lookup returns nothing).

DimensionReasoningScore

Conciseness

The body is dense with genuinely non-obvious look-up facts Claude cannot reliably know (KEGG pathway IDs like hsa00600, 'm/z 184 for phosphocholine', enzyme-disease pairs, SwissLipids' empty-classification caveat), so most tokens earn their place. Minor redundancy: the SP→apoptosis/neurodegeneration, GP→membrane-remodeling mapping appears in both the Reasoning Strategy and Phase 1, and Key principles 2–4 restate Reasoning Strategy points, and the intro paragraph largely re-covers the frontmatter description. Fits anchor 4 ('efficient; minor instances that could be trimmed') rather than 3 because the padded content is a small fraction of a fact-heavy document, and rather than 5 because the duplication is real.

4 / 5

Actionability

Concrete, copy-paste-ready invocations with parameters and real outputs throughout: 'LipidMaps_search_by_name(query="ceramide")', 'SwissLipids_search(query="PC(16:0/18:1)") → entity_id "SLM:000088148"', and a runnable pandas enrichment snippet in Phase 4. Operational gotchas ('Species-level abbreviations like "Cer(d18:1/16:0)" may return 0 results', 'classification can come back as an empty array [] ... fall back to LIPID MAPS') make the guidance executable rather than descriptive. Not below 5: the only nit is an unused fisher_exact import in the Phase 4 snippet, which does not block execution or coverage of the common case.

5 / 5

Workflow Clarity

A clear Phase 0→4 pipeline is shown as a diagram and then per-phase with concrete steps, and Phase 0 includes explicit fallback loops ('If name search fails, try PubChem', SwissLipids when LIPID MAPS misses, and the empty-classification fallback). Fits anchor 4 ('clear sequence with most checkpoints present; minor validation gaps') rather than 5 because there is no explicit validation of intermediate results in Phases 2–3 beyond the general 'Always verify via HMDB or CTD', and no error-recovery guidance if a KEGG/CTD lookup returns nothing.

4 / 5

Progressive Disclosure

No bundle files exist, and the skill is organized into well-labeled sections (When to Use, Core Tools table, Workflow, Limitations) that make the ~200-line single file navigable. Fits anchor 4 ('good structure; most content appropriately placed') rather than 3 because the inline content (tool table, KEGG pathway table) is genuinely overview-level, but not 5 because some reference-worthy detail (the 8-row KEGG pathway table, the verified SwissLipids examples) would slim the main body if split into a references file, and no one-level-deep reference files are provided to absorb it.

4 / 5

Total

17

/

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 well-constructed description with an explicit 'Use for' trigger clause, concrete named actions, and a clearly bounded lipidomics niche. The main gaps are the missing headline term 'lipidomics' (the word users most naturally say) and a generic opening action ('Lipid analysis').

Suggestions

Add the term 'lipidomics' to the description (e.g. 'Lipidomics analysis...') — it is the most natural user keyword and currently appears only in the body, not the frontmatter.

Replace the generic opening 'Lipid analysis' with concrete actions (e.g. 'Identify lipids, classify them via LIPID MAPS, map them to metabolic pathways, and find lipid-disease associations'), and either drop Reactome or name the concrete Reactome-based action.

DimensionReasoningScore

Specificity

Concrete actions are named — 'lipid identification, lipid metabolism pathway mapping, and lipid-associated disease analysis' — anchored to specific resources ('LIPID MAPS classification, HMDB metabolite data, KEGG/Reactome lipid pathways ..., and PubChem chemical info'). Fits anchor 4 ('lists several specific actions; minor gaps') rather than 5 because the opening action 'Lipid analysis' is generic, 'Reactome' is listed as a source without any concrete Reactome-based action, and the scope of 'PubChem chemical info' is left vague.

4 / 5

Completeness

Both halves are explicit: the 'what' is 'Lipid analysis and lipid-disease associations using LIPID MAPS classification, HMDB metabolite data, KEGG/Reactome lipid pathways ..., and PubChem chemical info', and the 'when' is an explicit trigger clause 'Use for lipid identification, lipid metabolism pathway mapping, and lipid-associated disease analysis (cardiovascular, diabetes, NAFLD)' with concrete trigger phrases. Matches anchor 5 and is clearly above anchor 4, whose 'when' would be less specific.

5 / 5

Trigger Term Quality

Good natural-phrase coverage: users would plausibly say 'lipid identification', 'pathway mapping', 'lipid metabolism', and disease-area terms 'cardiovascular, diabetes, NAFLD', plus class names 'sphingolipid, eicosanoid, steroid, fatty acid'. Fits anchor 4 ('good keyword coverage; a few natural terms missing') rather than 5 because the single most natural user term — 'lipidomics' — is absent (the body's own When-to-Use examples include 'Map my lipidomics results'), along with synonyms like 'lipid profiling' or 'lipid biomarkers'.

4 / 5

Distinctiveness Conflict Risk

Clear niche — lipid-specific classification (LIPID MAPS), lipid pathways, lipid-disease associations — with distinct triggers, but it shares general-purpose databases (HMDB, KEGG, PubChem) with a general metabolomics skill, creating minor overlap risk for queries like 'metabolite disease associations'. Fits anchor 4 ('mostly distinct; minor overlap risk with closely related skills') rather than 5 because the description itself draws no boundary against general metabolomics (the boundary lives only in the body's 'Not this skill' note).

4 / 5

Total

17

/

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

plugins/tooluniverse/skills/tooluniverse-lipidomics/SKILL.md

Reviewed

Table of Contents

Is this your skill?

If you maintain this skill, you can claim it as your own. Once claimed, you can manage eval scenarios, bundle related skills, attach documentation or rules, and ensure cross-agent compatibility.