Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Reference data and database search

HMDB

Find chemical, biological and spectral reference information for human metabolites.

Platform-independentWeb applicationFree web service
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Overview

The Human Metabolome Database links compound records to biological context and experimental or predicted analytical information. Evidence types vary across entries.

What can this tool do?

Structure-database searching

Common uses

  • Look up synonyms and structures for human metabolites.
  • Review available spectral and biological evidence for an annotation.

Scientific fit

Primary function

Reference data and database search

Data compatibility

Inputs

Compound list or annotations, Molecular structures

Outputs

Compound list or annotations, Molecular structures

Input formats

Other, Names, identifiers, structures or spectral queries

Output formats

Other, Metabolite records and selected downloads

Scope and considerations

Designed for

  • Look up synonyms and structures for human metabolites.

Not designed for

  • Assuming every listed compound has been experimentally measured in the study population.

Important requirements

  • A compound name, identifier, structure or compatible analytical query.

Considerations

  • Distinguish measured information from predictions and expected metabolites; inspect the source supporting each field.

Access and documentation

Primary access

Publicly accessible database; check HMDB download and commercial-use terms before bulk reuse.

Evidence and review

Documentation-based editorial review on 7 September 2026. Scope and limitations summarize the linked official sources; software execution and developer verification were not assessed.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. Wishart DS, Guo A, Oler E, et al. HMDB 5.0: the Human Metabolome Database for 2022. Nucleic Acids Res 50, D622-D631 (2022). doi:10.1093/nar/gkab1062

Related tools

ChEBIComplementary to · Look up curated chemical entities, names and ontology relationships.PubChemComplementary to · Search chemical structures, identifiers, properties and contributed annotations.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-09-08 · Entry update

    Audit core publications across existing tools

    View change · Entry at this revision
  2. 2026-09-07 · First committed entry

    Add 50 documented metabolomics resources

    View change · Entry at this revision

Full GitHub history