Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Reference data and database search

ChEBI

Look up curated chemical entities, names and ontology relationships.

Platform-independentWeb applicationFree web service
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Overview

ChEBI connects chemical structures to classes and biological roles through a maintained ontology, supporting consistent naming and interoperability.

What can this tool do?

Structure-database searching

Common uses

  • Map metabolite names to stable chemical identifiers.
  • Group compounds by chemical class or biological role.

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, Text, formula or structure queries

Output formats

SDF, Other, SDF and ontology downloads

Scope and considerations

Designed for

  • Map metabolite names to stable chemical identifiers.

Not designed for

  • Direct identification of a measured mass-spectrometry feature.

Important requirements

  • A chemical name, formula, identifier or structure query.

Considerations

  • An ontology role describes curated knowledge, not evidence that a function occurs in the current experiment.

Access and documentation

Primary access

Open-access EBI database; use the resource policies for redistribution.

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. Malik A, Arsalan M, Moreno C, et al. ChEBI: re-engineered for a sustainable future. Nucleic Acids Res 54, D1768-D1778 (2026). doi:10.1093/nar/gkaf1271

Software and documentation citations

  • ChEBI team. Chemical Entities of Biological Interest: database and ontology documentation. EMBL-EBI. Documentation

Related tools

PubChemComplementary to · Search chemical structures, identifiers, properties and contributed annotations.ReactomeComplementary to · Explore curated metabolic and signaling reactions with literature-linked pathway context.HMDBComplementary to · Find chemical, biological and spectral reference information for human metabolites.

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