skills.rest
dailycafi
dailycafiCOMMUNITY
Explore all skills by this author →
𝕏@dailycafiGitHub

bio-metabolomics-pathway-mapping

Map metabolites to KEGG, Reactome, and SMPDB pathways with enrichment and topology analysis.

7|Updated Apr 5, 2026
Search Tags:#metabolomics#enrichment#reactome#kegg#pathway-mapping#smpdb#metaboanalystr
One-click install
npx skills add https://github.com/dailycafi/metabolism-skills --skill bio-metabolomics-pathway-mapping
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-metabolomics-pathway-mapping
Source: https://github.com/dailycafi/metabolism-skills/tree/main/skills/metabolomics-analysis/pathway-mapping
Command: npx skills add https://github.com/dailycafi/metabolism-skills --skill bio-metabolomics-pathway-mapping

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Relate metabolite lists to biological pathways to enable interpretation of metabolomics results and identify affected biological processes.

Core Features & Use Cases

  • Map metabolites to KEGG, Reactome, and SMPDB pathways and perform enrichment and topology analysis.
  • Visualize results on pathway maps, export enrichment/topology reports, and integrate with downstream interpretation workflows.
  • Support meta-analytic workflows with MetaboAnalystR and related tools for advanced pathway analyses.

Quick Start

Map your list of metabolites to biological pathways and run enrichment analysis to identify affected pathways.

Frequently Asked Questions about bio-metabolomics-pathway-mapping

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

FAQPage Schema
How do I map a list of metabolites to biological pathways for enrichment analysis?▼

Metabolomics pathway mapping connects your metabolite list to KEGG, Reactome, and SMPDB databases to identify affected biological processes. It calculates enrichment scores and pathway impact, returning structured results for downstream interpretation and reporting.

What's the best way to perform pathway topology analysis on metabolomics data?▼

Pathway topology analysis on metabolomics data is performed using MetaboAnalystR to calculate pathway impact values. The Skill maps metabolites to KEGG, Reactome, and SMPDB pathways, generating topology reports for visualization and interpretation of affected biological processes.

Can I use MetaboAnalystR with KEGG, Reactome, and SMPDB mappings simultaneously?▼

Yes, you can use MetaboAnalystR with KEGG, Reactome, and SMPDB mappings simultaneously. The Skill integrates all three pathway databases to perform comprehensive enrichment and topology analysis on your metabolite list.

Does metabolomics pathway mapping support exporting enrichment reports for downstream interpretation?▼

Metabolomics pathway mapping supports exporting enrichment and topology reports for downstream interpretation workflows. Results are returned in a structured format suitable for visualization, reporting, and integration with meta-analytic workflows.

Why use SMPDB and Reactome alongside KEGG for metabolite enrichment analysis?▼

Using SMPDB and Reactome alongside KEGG for metabolite enrichment analysis provides broader pathway coverage across different biological processes. This multi-database approach ensures more comprehensive identification of affected pathways and actionable results.

Related Skills

Explore More Data & Analytics Skills→
LeonChaoXLeonChaoX
783

hmdb-database

Retrieve metabolite records from the Human Metabolome Database by identifiers and biological context.

Community
Intermediate
Yezez9Yezez9

reactome-database

Query Reactome REST API for pathway enrichment and gene-pathway mapping.

Community
Intermediate
zongtingweizongtingwei
25

pathway-analysis

Automate pathway enrichment and interpretation across multi-omics gene lists.

Community
Advanced
jaechang-hitsjaechang-hits
298

gseapy-gene-enrichment

Perform GSEA and ORA on gene lists with Enrichr pathway lookups.

Community
Intermediate