Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Reference data and database search

Reactome

Explore curated metabolic and signaling reactions with literature-linked pathway context.

Platform-independentWeb applicationFree web service
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Overview

Reactome organizes molecules and reactions into pathways through expert curation and review. It offers interactive maps, downloads and programmatic services.

What can this tool do?

Structure-database searching

Common uses

  • Place annotated metabolites in reaction context.
  • Trace pathway assertions to supporting literature.

Scientific fit

Primary function

Reference data and database search

Data compatibility

Inputs

Compound list or annotations, Molecular structures

Outputs

Pathway or reaction data, Compound list or annotations

Input formats

Other, Molecular identifiers, pathways or species

Output formats

Other, Pathway maps and downloadable reaction data

Scope and considerations

Designed for

  • Place annotated metabolites in reaction context.

Not designed for

  • Measuring pathway activity or metabolic flux from a database diagram.

Important requirements

  • Recognized molecular identifiers and an appropriate species context.

Considerations

  • Check whether a pathway is directly curated or computationally inferred and preserve database-release information.

Access and documentation

Primary access

Open-source, open-access resource; data and software license details are available on the site.

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. Ragueneau E, Gong C, Sinquin P, et al. The Reactome Knowledgebase 2026. Nucleic Acids Res 54, D673-D681 (2026). doi:10.1093/nar/gkaf1223

Software and documentation citations

  • Reactome team. What is Reactome? Official database, evidence model and access documentation. Documentation

Related tools

WikiPathwaysComplementary to · Find and contribute biological pathway diagrams and machine-readable pathway knowledge.ChEBIComplementary to · Look up curated chemical entities, names and ontology relationships.MetaboSignalComplementary to · Explore relationships between genes and metabolites in combined metabolic and signaling networks.RaMP-DBComplementary to · Integrated metabolite, gene/protein, reaction, ontology and pathway resource for metabolomics and multi-omics pathway analysis.

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