Reactome knowledgebase of human biological pathways and processes
Open accessAbstract
Reactome (http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets. Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome's data content and software can all be freely used and redistributed under open source terms.
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Reactome BioPAX formatted pathways are imported by the NCI/Nature Pathway Information Database (PID).
“For example, Reactome8 BioPAX formatted pathways are imported by the NCI/Nature Pathway Information Database (PID)9.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [8]
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- Authors
- Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., Kanapin, A., Lewis, S., Mahajan, S., May, B., Schmidt, E., Vastrik, I., Wu, G., Birney, E., Stein, L., & D'Eustachio, P.
- Affiliations
- Cold Spring Harbor Laboratory (US)
- Ontario Institute for Cancer Research (CA)
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-01-01
- Volume
- 37
- Issue
- Database
- Pages
- D619-D622
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC2686536
- OpenAlex
- W1999895438
- Cited by
- 873
- References
- 17
- Citations by year
- 2026: 7 · 2025: 16 · 2024: 13 · 2023: 15 · 2022: 14 · 2021: 12 · 2020: 13 · 2019: 18 · 2018: 29 · 2017: 32 · 2016: 62 · 2015: 63 · 2014: 94 · 2013: 104 · 2012: 98
- FWCI
- 38.58
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- CUNY Academic Works (City University of New York) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- European Commission
- National Institutes of Health
- National Human Genome Research Institute (U41HG003751, P41HG003751)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Reactome, biological pathways, human reactions, pathway inference, orthology prediction, high-throughput data analysis, reference citation, open source software
- MeSH terms
- Animals, Humans, Physiological Phenomena, Proteins, Software, Signal Transduction, Systems Integration, Models, Animal, Databases, Protein, Metabolic Networks and Pathways
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