Reactome

Reactome is a free online database of biological pathways.[1][2][3] It is manually curated and authored by PhD-level biologists, in collaboration with Reactome editorial staff. The content is cross-referenced to many bioinformatics databases. The rationale behind Reactome is to visually represent biological pathways in full mechanistic detail, while making the source data available in a computationally accessible format.

Reactome is maintained by an international multidisciplinary team from OICR, OHSU, EMBL-EBI and NYULMC, with expertise in pathway curation and annotation, software development, and training and outreach, dedicated to providing the research community with openly accessible biological pathway knowledge. The Reactome team is led by Lincoln Stein (OICR). Peter D'Eustachio (NYULMC), Henning Hermjakob (EMBL-EBI), Guanming Wu (OHSU). The Reactome helpdesk can be reached via email.

Reactome: a database of reactions, pathways and biological processes.
The Reactome logo
Content
DescriptionReactome: a database of reactions, pathways and biological processes.
Contact
Primary citationPMID 37941124
Access
Data formatBioPAX
SBML
Websitehttps://reactome.org
Download URLhttps://reactome.org/download-data
Web service URLhttps://reactome.org/ContentService/
Miscellaneous
Licensehttps://reactome.org/license
Data release
frequency		https://reactome.org/about/release-calendar

The website can be used to browse pathways and submit data to a suite of data analysis tools. The underlying data is fully downloadable in a number of standard formats including PDF, SBML, Neo4j GraphDB, MySQL, PSI-MITAB, and BioPAX. Pathway diagrams use a Process Description (PD) Systems Biology Graphical Notation (SBGN)-based style.

The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. Examples of biological pathways in Reactome include signal transduction, innate and acquired immune function, transcriptional regulation, programmed cell death and classical intermediary metabolism.

The pathways represented in Reactome are species-specific, with each pathway step supported by literature citations that contain an experimental verification of the process represented. If no experimental verification using human reagents exists, pathways may contain steps manually inferred from non-human experimental details, but only if an expert biologist, named as Author of the pathway, and a second biologist, names as Reviewer, agree that this is a valid inference to make. The human pathways are used to computationally generate by an orthology-based process derived pathways in other organisms.

  1. ^ Croft, D.; O'Kelly, G.; Wu, G.; Haw, R.; Gillespie, M.; Matthews, L.; Caudy, M.; Garapati, P.; Gopinath, G.; Jassal, B.; Jupe, S.; Kalatskaya, I.; Mahajan, S.; May, B.; Ndegwa, N.; Schmidt, E.; Shamovsky, V.; Yung, C.; Birney, E.; Hermjakob, H.; d'Eustachio, P.; Stein, L. (2010). "Reactome: A database of reactions, pathways and biological processes". Nucleic Acids Research. 39 (Database issue): D691–D697. doi:10.1093/nar/gkq1018. PMC 3013646. PMID 21067998.
  2. ^ Joshi-Tope, G.; Gillespie, M.; Vastrik, I.; d'Eustachio, P.; Schmidt, E.; De Bono, B.; Jassal, B.; Gopinath, G.; Wu, G.; Matthews, L.; Lewis, S.; Birney, E.; Stein, L. (2004). "Reactome: A knowledgebase of biological pathways". Nucleic Acids Research. 33 (Database issue): D428–D432. doi:10.1093/nar/gki072. PMC 540026. PMID 15608231.
  3. ^ Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P (2014). "The Reactome pathway knowledgebase". Nucleic Acids Res. 42 (Database issue): D472–7. doi:10.1093/nar/gkt1102. PMC 3965010. PMID 24243840.