- Reactome is a freely accessible, open-source knowledgebase of curated biological pathways and reactions, designed to provide researchers with a detailed and structured view of molecular and cellular processes.
- Developed initially at the Cold Spring Harbor Laboratory and now maintained by an international consortium led by the European Bioinformatics Institute (EBI), Reactome serves as both a database and a tool for systems biology research. It focuses on representing biological knowledge in a structured, computable form that links molecular entities such as proteins, small molecules, and nucleic acids to the reactions and pathways in which they participate.
- Unlike many databases that emphasize broad coverage, Reactome prioritizes high-quality manual curation, relying on domain experts and curators to extract information from the primary literature. Each entry in Reactome is backed by experimental evidence and linked to supporting publications, ensuring transparency and reliability. This detailed annotation is organized into a hierarchy of events, ranging from simple molecular reactions (such as binding, phosphorylation, or transport) to complex, multi-step biological pathways (such as cell cycle progression, immune signaling, or metabolism). The hierarchical structure allows researchers to zoom in from high-level pathways to fine-grained molecular interactions.
- Reactome covers a wide range of biological processes, including signal transduction, gene expression, DNA replication and repair, metabolism, immune system function, and disease-related pathways. Importantly, Reactome also includes disease modules that illustrate how normal biological processes are altered in pathological conditions such as cancer, infectious diseases, and neurodegenerative disorders. By linking molecular perturbations to disease outcomes, Reactome provides a valuable framework for translational and clinical research.
- The database is accompanied by a powerful visualization and analysis platform. Its web interface allows users to explore pathway diagrams that are interactive, hierarchical, and searchable. Users can upload their own datasets (such as gene expression or proteomics results) to perform pathway enrichment analysis, overlay experimental data on curated pathways, and identify significantly impacted biological processes. Reactome also supports programmatic access through APIs and is integrated with other bioinformatics resources, including UniProt, Ensembl, and ChEBI, making it highly interoperable within the life sciences ecosystem.
- Reactome has become a standard tool for omics data interpretation and systems biology, particularly in pathway enrichment and network-based analyses. Its structured, machine-readable data model (using standards such as BioPAX and SBML) makes it well-suited for computational modeling and integration into automated pipelines. Additionally, Reactome collaborates with other pathway resources as part of initiatives like WikiPathways and Pathway Commons, helping to ensure harmonization and comprehensive coverage across the pathway knowledge domain.
- In summary, Reactome is a rigorously curated, interactive, and versatile pathway database that provides deep insights into molecular mechanisms and their alterations in disease. By combining expert curation, detailed annotation, visualization tools, and integration with external resources, it serves as a vital resource for researchers seeking to connect molecular data with biological function. Its emphasis on accuracy, usability, and interoperability makes it a cornerstone in systems biology, functional genomics, and translational research.
