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hmdb-database

combined

Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification. Access the Human Metabolome Database (HMDB) to search metabolites by name/structure/ID and extract chemical/biological/clinical fields when you need metabolomics research data or automated HMDB XML mining.

When to use

• This skill should be used when performing metabolomics research, clinical chemistry, biomarker discovery, or metabolite identification tasks.
• You need to look up a metabolite by **common name** (e.g., “Caffeine”) and retrieve its HMDB entry data.
• You have an **HMDB ID** (e.g., `HMDB0000001`) and want to extract standardized chemical/biological/clinical fields for downstream analysis.
• You want to build a **local, scriptable pipeline** to mine the HMDB XML dump instead of manually browsing the website.
• You need to **map HMDB identifiers** to external resources (e.g., KEGG, PubChem, ChEBI) for integration tasks.
• You are preparing metabolomics datasets and need **pathway/enzyme/transporter** annotations from HMDB entries.

When not to use

• commercial use without explicit permission
• web scraping

Skill page

Conflict

The two copies cover the same HMDB task but with materially different procedures. The aipoch copy is a local, scriptable pipeline that downloads the HMDB XML dump and parses it with a Python HMDBParser using xml.etree.ElementTree, with an optional pandas dependency and a reference file for field mapping. The FreedomIntelligence copy is a broader reference that emphasizes the web interface, spectral searches, downloadable formats (XML, SDF, FASTA, TXT, CSV/TSV), licensing/citation requirements, lack of a public REST API, R/Bioconductor hmdbQuery, and common research workflows. Neither copy is a strict reproduction of the other; crowning one would hide the alternative access path and constraints.