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

82%

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

SKILL.md
Quality
Evals
Security

Quality

Content

71%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, tool-dense skill body with a clear phased workflow, verified examples, and useful failure-mode guidance. Its weaknesses are inline reference material that should be split into bundle files and missing explicit validation checkpoints in the pipeline.

Suggestions

Move the KEGG pathway table (hsa00600–hsa00565 with enzymes and disease relevance) and the lipid class enrichment script into a references/ file, keeping only a summary table plus a clearly signaled link in SKILL.md.

Add an explicit validation checkpoint in Phase 0, e.g. 'Confirm the returned LIPID MAPS exact mass matches the observed precursor m/z (±ppm tolerance) before classifying'.

Reconcile the Core Tools table with the workflow: add 'PubChem_get_CID_by_compound_name' and 'LipidMaps_search_by_formula' (both used in Phase 0) or remove them from the examples.

DimensionReasoningScore

Conciseness

The body is dense with high-value, non-obvious material — tool tables, real query examples, KEGG IDs with enzymes, and verified caveats (e.g., 'classification can come back as an empty array'). Minor over-explanation keeps it from a 5: the opening 'Distinct from general metabolomics...' paragraph and parts of the Reasoning Strategy restate biology Claude largely knows.

4 / 5

Actionability

Concrete, executable tool calls with real parameters and outputs appear in every phase (e.g., 'SwissLipids_search(query="PC(16:0/18:1)") → entity_id "SLM:000088148"' and the verified FASN gene lookup). Not a 5 because a few tools used in the workflow ('PubChem_get_CID_by_compound_name', 'LipidMaps_search_by_formula') are absent from the Core Tools table and have no example output.

4 / 5

Workflow Clarity

The 5-phase pipeline (identity → classification → pathway → disease → report) is clearly sequenced with an ASCII diagram, and failure-recovery routes are documented ('If name search fails, try PubChem', 'fall back to LIPID MAPS'). Not a 5 because explicit validation checkpoints are missing — e.g., no step to confirm a returned LMSP ID's exact mass against the observed m/z before proceeding.

4 / 5

Progressive Disclosure

The single 200-line SKILL.md is well-sectioned (When to Use, Core Tools, Workflow, Limitations) but has no bundle files, so content that belongs at one level of depth is inlined: the 8-row KEGG pathway table and the lipid class enrichment script are prime candidates for a references/ file. This matches 'some structure but content that should be separate is inline' rather than the good-split anchor at 4.

3 / 5

Total

15

/

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 description with explicit 'what' and 'when' clauses, concrete actions, and domain-specific trigger keywords. The main gaps are the absence of the natural term 'lipidomics' and an unstated boundary against general metabolomics skills.

DimensionReasoningScore

Specificity

The description lists several concrete actions — 'lipid identification, lipid metabolism pathway mapping, and lipid-associated disease analysis' — grounded in named data sources (LIPID MAPS, HMDB, KEGG/Reactome, PubChem). Not a 5 because the leading phrase 'Lipid analysis' is generic and the full capability set (classification, gene/protein lookups, literature) is only implied by the resource list rather than stated as actions.

4 / 5

Completeness

It explicitly answers both questions: the 'what' is lipid analysis and lipid-disease associations using the named databases, and the 'when' is the explicit clause 'Use for lipid identification, lipid metabolism pathway mapping, and lipid-associated disease analysis (cardiovascular, diabetes, NAFLD)'. Both are concrete and explicit, matching the top anchor.

5 / 5

Trigger Term Quality

Good natural keyword coverage: 'lipid identification', 'pathway mapping', 'sphingolipid', 'eicosanoid', 'steroid', 'fatty acid', 'cardiovascular', 'diabetes', 'NAFLD'. Not a 5 because the most natural user term 'lipidomics' never appears, nor do 'mass spectrometry' or 'm/z' — phrases a user with lipidomics data would actually say.

4 / 5

Distinctiveness Conflict Risk

The lipid-specific vocabulary (LIPID MAPS, sphingolipid, eicosanoid, steroid lipid pathways) carves a clear niche with minimal conflict risk. Not a 5 because 'HMDB metabolite data' and 'PubChem chemical info' overlap with a general metabolomics skill, and the description does not state that boundary (the body reserves it for tooluniverse-metabolomics).

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

plugin/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.