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tooluniverse-lipidomics

Analyzes lipid identification, pathway mapping, and lipid-disease associations using LIPID MAPS, HMDB, and KEGG.

1.7k|254|Updated Mar 3, 2025
Search Tags:#metabolism#biomarker#disease association#lipidomics#kegg pathways#lipid maps#sphingolipid
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-lipidomics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-lipidomics
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-lipidomics
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-lipidomics

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pandas, scipy.

What problem does it solve?

Interpreting lipidomics results requires navigating specialized classification systems, lipid-specific metabolic pathways, and scattered disease association data. This Skill provides a structured pipeline that resolves lipid identities, classifies them under the LIPID MAPS 8-category system, maps them to KEGG lipid metabolism pathways, and retrieves evidence-graded disease associations.

Core Features & Use Cases

  • Lipid Identity Resolution: Search LIPID MAPS, HMDB, and PubChem by name, abbreviation, or mass to obtain IDs, exact masses, and structural classifications.
  • Pathway Mapping: Connect lipids to KEGG pathways such as sphingolipid metabolism (hsa00600), arachidonic acid metabolism, and steroid biosynthesis, including pathway enzymes.
  • Disease Association Analysis: Retrieve lipid-disease and enzyme-disease links from CTD, DisGeNET, and HMDB with evidence grading, plus lipid class enrichment analysis via Fisher's exact test.
  • Use Case: Given a list of significantly changed lipids from an experiment, classify each by LIPID MAPS category, map them to affected pathways like sphingolipid metabolism, and identify associated diseases such as Niemann-Pick or Alzheimer's with supporting literature.

Quick Start

Ask the agent to identify the lipid ceramide, map it to its KEGG metabolic pathways, and list its associated diseases with evidence.

Frequently Asked Questions about tooluniverse-lipidomics

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I identify a lipid from its name or mass?▼

Use LipidMaps_search_by_name with a generic class name like ceramide or sphingomyelin to get the LIPID MAPS ID, exact mass, and classification. Species-level abbreviations like Cer(d18:1/16:0) may return no results, so search the generic name first and filter by chain length.

How do I map lipids to KEGG metabolic pathways?▼

Use kegg_search_pathway with a keyword such as sphingolipid or glycerolipid to find pathway IDs like hsa00600, then call KEGG_get_pathway_genes to retrieve the enzymes involved, such as SMPD1 and CERS1-6 for sphingolipid metabolism.

What diseases are associated with altered lipid metabolism?▼

Query CTD_get_gene_diseases and DisGeNET_search_gene for lipid metabolism enzymes, and HMDB_get_metabolite for metabolite-disease links. Examples include ceramide elevation in Alzheimer's and insulin resistance, and sphingomyelin depletion in Niemann-Pick disease.

When should I use lipidomics instead of general metabolomics analysis?▼

Use this lipidomics workflow when analyzing lipids, since they require the LIPID MAPS classification system and specialized pathways like sphingolipid and eicosanoid metabolism. For amino acids, sugars, and organic acids, use the general metabolomics skill instead.

Can this skill process raw mass spectrometry data?▼

No, it interprets already-identified lipids rather than raw spectra. Perform identification first with tools like LipidSearch, MS-DIAL, or LipiDex, then use this workflow for classification, pathway mapping, and disease association analysis.

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