Open-source, open access, manually curated and peer-reviewed pathway database with pathway annotations authored by expert biologists, in collaboration with Reactome editorial staff, and cross-referenced to many bioinformatics databases including NCBI Entrez Gene, Ensembl and UniProt databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI small molecule databases, PubMed, and Gene Ontology. 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 signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism. Reactome provides an intuitive website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. A tool that allows the comparison of pathways between human and any of the other species inferred from Reactome by orthology is included. Visualization of Reactome data is facilitated by the Pathway Browser, a Systems Biology Graphical Notation (SBGN)-based interface, that supports zooming, scrolling and event highlighting. It exploits the PSIQUIC web services to overlay molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, ChEMBL, BioGRID and iRefIndex. The whole content of the Reactome can be downloaded as a MySQL database dump. A SOAP based Web Services API is also available to access the Reactome data. Additionally, the complete Reactome textbook of biological pathways and processes can be downloaded.
Resource Type: Resource
Version: Latest Version
pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard
(info provided by re3data.org)
Open unspecified license
WikiPathways, AmiGO, PSICQUIC, Monarch Initiative
NHGRI, European Union, FP6, ENFIN, Ontario Research Fund, European Molecular Biology Laboratory, P41 HG003751, LSHG-CT-2005-518254, GM080223, R01-GM100039
Additional Resource Types
Database, Data Analysis Service
NIF Data Federation
human, mouse, rat, bos taurus, zebrafish, sus scrofa, chicken, drosophila melanogaster, caenorhabditis elegans, saccharomyces cerevisiae, arabidopsis thaliana, escherichia coli, dog, others
Created 1 month ago by Christie Wang
Created 2 months ago by Christie Wang
Created 2 months ago by Christie Wang
Created 5 years ago by Anonymous
- D'Eustachio P
- Methods Mol. Biol.
- 2011 18
The Reactome Knowledgebase is an online, manually curated resource that provides an integrated view of the molecular details of human biological processes that range from metabolism to DNA replication and repair to signaling cascades. Its data model allows these diverse processes to be represented in a consistent way to facilitate usage as online text and as a resource for data mining, modeling, and analysis of large-scale expression data sets over the full range of human biological processes.
- Croft D
- Nucleic Acids Res.
- 2011 23
Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice.