hmdb-database
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
77
70%
Does it follow best practices?
Impact
89%
1.17xAverage score across 3 eval scenarios
Passed
No known issues
Optimize this skill with Tessl
npx tessl skill review --optimize ./scientific-skills/hmdb-database/SKILL.mdEvaluation results
77%
34%Metabolite Property Lookup Tool in R
R programmatic HMDB access
Uses hmdbQuery package
0%
15%
BiocManager install instruction
0%
100%
No REST API calls
0%
80%
No web scraping
53%
80%
Correct HMDB ID format
100%
100%
Results saved to CSV
100%
100%
README documents package install
100%
100%
Retrieves multiple metabolites
100%
100%
100%
Local HMDB Integration for Metabolomics Platform
HMDB dataset download and format selection
XML for comprehensive data
100%
100%
SDF for cheminformatics
100%
100%
CSV/TSV for pipeline
100%
100%
Download over repeated queries
100%
100%
Downloads URL
100%
100%
Version tracking
100%
100%
Cross-database IDs
100%
100%
Python plan script
100%
100%
Format justifications
100%
100%
92%
6%Unknown Metabolite Identification from LC-MS Data
Metabolite identification workflow
Spectral search tools
100%
75%
Multiple evidence types
100%
100%
MW check
100%
100%
Retention time check
100%
75%
MS-MS fragmentation check
100%
100%
Biological plausibility
100%
93%
SMPDB for pathways
0%
83%
Worked example applied
100%
100%
Experimental vs predicted data
75%
100%
Biofluid/specimen filter
100%
100%
- Repository
- K-Dense-AI/claude-scientific-skills
- Commit
71add64
- Evaluated
- Agent
- Claude Code
- Model
- Claude Sonnet 4.6
Table of Contents
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