Reactome

Reactome
Title	Reactome
Producer	European Bioinformatics Institute; Cold Spring Harbor Laboratory; Ontario Institute for Cancer Research
Country	United Kingdom; United States; Canada
Languages	English
Discipline	Molecular biology; Biochemistry; Systems biology
Depth	Expert-curated pathway database
Formats	BioPAX; SBML; PSI-MI; GMT; JSON
Cost	Free

Reactome Reactome is an expert-curated, open-access pathway database that maps molecular processes in human biology and selected model organisms. It integrates curated literature with computational inference to represent signaling, metabolic, and regulatory events, serving researchers in National Institutes of Health, European Molecular Biology Laboratory, Broad Institute, European Bioinformatics Institute, and translational groups at Cold Spring Harbor Laboratory, Ontario Institute for Cancer Research, and university centers. The resource interfaces with major bioinformatics infrastructures such as UniProt, Gene Ontology, Ensembl, KEGG, and PubMed to provide interoperable pathway knowledge for biomedical research and clinical translation.

Overview

Reactome provides a structured repository of molecular events expressed as reactions, pathways, and biological processes that can be navigated, downloaded, and analyzed. Its content is organized hierarchically to enable exploration from high-level processes (for example, Apoptosis, Cell cycle, Immune system) down to individual molecular interactions involving proteins, small molecules, complexes, and post-translational modifications. The platform supports exchange formats recognized by resources like BioPAX, SBML, and PSI-MI, and interoperates with identifier resources such as UniProt, Ensembl, and RefSeq to maximize reuse across projects at institutions like National Center for Biotechnology Information and European Bioinformatics Institute.

Data Model and Curation

The Reactome data model represents biology as reactions and pathways, each defined by participants, catalysts, regulators, and compartmental localization linked to controlled vocabularies and ontologies from sources such as Gene Ontology and ChEBI. Curation is performed by domain experts and professional curators following protocols comparable to standards used by UniProt curators and annotation workflows at EMBL-EBI. Each entry cites experimental evidence drawn from primary literature indexed in PubMed and cross-references authoritative databases like PDB for structural data, Pfam for domain annotations, and InterPro for motif mapping. Quality control employs peer review mechanisms similar to editorial practices at journals including Nature, Science, and Cell and uses software tools developed in collaboration with computational groups at European Molecular Biology Laboratory and university bioinformatics cores.

Content and Coverage

Reactome emphasizes comprehensive coverage of human pathways with inferred orthology-based projections to model organisms such as Mus musculus, Rattus norvegicus, Drosophila melanogaster, Saccharomyces cerevisiae, and Caenorhabditis elegans. Its pathway catalog spans metabolism (e.g., pathways curated with references to Glycolysis, Tricarboxylic acid cycle), signal transduction (including MAPK signaling pathway, PI3K-Akt signaling pathway), immune responses (for example, Toll-like receptor signaling pathway, Complement cascade), and disease-related processes (notably Cancer, Neurodegenerative disease, Cardiovascular disease). Cross-links to disease ontologies and clinical resources such as OMIM, ClinVar, and Human Phenotype Ontology support translational interpretation and variant annotation used by clinical genetics groups at hospitals and research centers.

Tools and Resources

Reactome provides web-based visualization and analysis tools inspired by and integrated with platforms like Cytoscape, Pathway Commons, and NDEx. Interactive pathway diagrams include features for overlaying gene expression or proteomics datasets from consortia such as The Cancer Genome Atlas and ProteomicsDB and support identifier mapping to sources like HGNC and Entrez Gene. Programmatic access is available via RESTful services and bulk downloads in formats used by workflow systems at Galaxy Project and Nextflow, enabling integration with pipelines developed at institutions like Sanger Institute and Broad Institute. Training materials and APIs facilitate reuse by bioinformatics cores in universities and biotech companies including those collaborating with European Bioinformatics Institute.

Applications and Impact

Researchers use Reactome for pathway enrichment analysis, mechanistic interpretation of omics datasets, drug target prioritization, and modeling of cellular networks in studies published in journals such as Nature Genetics, Genome Research, and PLoS Biology. Clinical researchers leverage Reactome annotations alongside variant databases like ClinVar and cohort resources such as UK Biobank to interpret disease mechanisms and biomarker discovery. Integration with systems biology tools developed by groups at EMBL-EBI and Broad Institute supports predictive modeling and hypothesis generation in translational projects involving collaborators from Stanford University, Harvard Medical School, Massachusetts Institute of Technology, and industry partners. The resource informs educational activities at universities and training programs at organizations including Cold Spring Harbor Laboratory.

History and Governance

Launched as a collaborative initiative involving groups at Cold Spring Harbor Laboratory and European Bioinformatics Institute, Reactome evolved through partnerships with institutions such as Ontario Institute for Cancer Research and funding agencies including Wellcome Trust and National Institutes of Health. Governance combines scientific oversight by external expert advisors and operational management by curatorial teams within institutions like European Molecular Biology Laboratory and EMBL-EBI. Development has followed community standards fostered by consortia such as BioPAX and Gene Ontology Consortium, with contributions from researchers at universities and research centers worldwide. Ongoing stewardship includes community curation, periodic releases, and collaborative projects with initiatives like Pathway Commons and Global Alliance for Genomics and Health to ensure sustainability and interoperability.

Category:Biological databases