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hmdb-database
Look up any metabolite in the Human Metabolome Database (HMDB) via REST API across 220,000+ entries. Use when: user asks 'what is this metabolite', needs an HMDB ID, wants metabolite pathways or disease associations, queries a metabolite database, or needs cross-references to KEGG/PubChem/ChEBI. Triggers: metabolite lookup, HMDB search, metabolite properties, metabolite spectra, metabolite biomarker, compound information, metabolite concentration, biofluid metabolites, serum metabolites, urine metabolites.
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// RATINGS
Not yet listed on ClawHub or SkillsMP
// README
metabolism-skills
Curated AI agent skills for metabolism and metabolomics research. Built for Claude Code.
Why
Metabolism-related skills are scattered across multiple repositories and represent only 1.6% of the scientific AI agent ecosystem (Claw4Science, 2026). This project aggregates the best existing skills and fills gaps with original contributions, providing a single entry point for metabolomics researchers.
Installation
# Add all skills
npx skills add dailycafi/metabolism-skills
# Or copy specific skills
cp -r skills/metabolomics-analysis/xcms-preprocessing ~/.claude/skills/
Skill Catalog
Mass Spectrometry Data Processing (ms-data-processing/)
| Skill | Tool | Description |
|---|---|---|
| pyopenms | pyOpenMS | LC-MS/MS data processing, untargeted metabolomics pipeline |
| matchms | matchms | Mass spectral similarity matching and compound identification |
| gcms-processing | XCMS/matchms | GC-MS deconvolution, NIST matching, retention index calculation |
| nmr-metabolomics | nmrglue/speaq | 1D/2D NMR processing, binning, metabolite identification |
| format-conversion | msConvert | RAW/WIFF/mzML/mzXML format conversion |
| spatial-metabolomics | pyimzML | MALDI-MSI/DESI-MSI ion imaging and spatial analysis |
Metabolic Modeling (metabolic-modeling/)
| Skill | Tool | Description |
|---|---|---|
| cobrapy | COBRApy | Constraint-based modeling: FBA, FVA, gene knockouts, flux sampling |
Metabolomics Analysis (metabolomics-analysis/)
| Skill | Tool | Description |
|---|---|---|
| xcms-preprocessing | XCMS (R) | Peak detection, alignment, gap filling |
| msdial-preprocessing | MS-DIAL | Untargeted metabolomics preprocessing |
| metabolite-annotation | Various | Metabolite identification and annotation |
| normalization-qc | R | QC, normalization, batch correction |
| statistical-analysis | R | Univariate/multivariate statistical analysis |
| pathway-mapping | MetaboAnalystR | KEGG/Reactome pathway enrichment |
| targeted-analysis | Various | Targeted metabolomics quantification |
| lipidomics | lipidr (R) | Lipidomics data analysis |
| pharmacometabolomics | RDKit | Drug metabolite profiling, CYP450 prediction, ADME |
| clinical-metabolomics | Python | IEM screening, newborn screening, clinical reporting |
Pathway Analysis (pathway-analysis/)
| Skill | Tool | Description |
|---|---|---|
| bioservices | bioservices (Python) | KEGG, Reactome, UniProt, STRING integration |
Databases (databases/)
| Skill | Tool | Description |
|---|---|---|
| hmdb | REST API | Human Metabolome Database (220k+ metabolites) |
| metabolights | REST API | EMBL-EBI MetaboLights repository |
| metabolomics-workbench | REST API | NIH Metabolomics Workbench (4,200+ studies) |
| metabolomics-workbench-api | REST API | Metabolomics Workbench endpoint reference |
| kegg-api | REST API | KEGG pathway/compound database |
| reactome-api | REST API | Reactome pathway database |
| string-api | REST API | STRING protein interaction network |
Multi-Omics Integration (multi-omics/)
| Skill | Tool | Description |
|---|---|---|
| mofa-integration | MOFA2 (R) | Multi-Omics Factor Analysis |
| mixomics-analysis | mixOmics (R) | Multivariate integration (sPLS, DIABLO) |
| data-harmonization | R | Cross-platform data harmonization |
| similarity-network | SNFtool (R) | Similarity Network Fusion |
| mgwas-integration | PLINK/coloc | Metabolite-gene association and Mendelian randomization |
| microbiome-metabolomics | mmvec/mixOmics | Host-microbiome metabolite interactions |
Systems Biology (systems-biology/)
| Skill | Tool | Description |
|---|---|---|
| flux-balance-analysis | COBRApy | FBA for genome-scale models |
| metabolic-reconstruction | CarveMe/gapseq | Genome-scale model reconstruction |
| context-specific-models | COBRApy | Tissue/condition-specific models (GIMME/iMAT) |
| gene-essentiality | COBRApy | Gene essentiality prediction |
| model-curation | memote | Model quality assessment and curation |
| isotope-flux-analysis | IsoCor/COBRApy | 13C metabolic flux analysis and isotope correction |
| network-visualization | Escher/Cytoscape | Metabolic network maps with flux overlay |
Credits & Attribution
This project curates skills from the open-source community. Every aggregated skill has an upstream field in its SKILL.md frontmatter linking to the original source.
| Source Repository | License | Skills |
|---|---|---|
| K-Dense-AI/claude-scientific-skills | MIT | cobrapy, pyopenms, bioservices, database API references |
| wu-yc/LabClaw | MIT | matchms, metabolomics-workbench |
| GPTomics/bioSkills | MIT | 17 skills (metabolomics, multi-omics, systems-biology) |
See LICENSES/NOTICE.md for full per-skill attribution.
Roadmap
See docs/ROADMAP.md for future planned skills and improvement ideas.
Contributing
- Fork the repo
- Create a skill directory under the appropriate domain
- Write a
SKILL.mdwith real, runnable code blocks - Submit a pull request
License
Original contributions are MIT licensed. Aggregated skills retain their original licenses. See LICENSES/ for details.
// HOW IT'S BUILT
KEY FILES