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Reactome

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.

URL: http://www.reactome.org

Resource ID: nif-0000-03390     Resource Type: Resource     Version: Latest Version

Keywords

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

Comment

Access: Open
Reuse: Open
Type: Disciplinary
(info provided by re3data.org)

Listed By

re3data.org

Availability

Open unspecified license

Supercategory

Resource

Related To

Resource:WikiPathways, Resource:Gene Ontology - AmiGO, Resource:PSICQUIC, Resource:Monarch Initiative

Abbreviation

Reactome

Parent Organization

Funding Information

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

Used By

NIF Data Federation

Species

human, mouse, rat, bos taurus, zebrafish, sus scrofa, chicken, drosophila melanogaster, caenorhabditis elegans, saccharomyces cerevisiae, arabidopsis thaliana, escherichia coli, dog, others

Original Submitter

Anonymous

Version Status

Curated

Submitted On

12:00am September 21, 2010

Originated From

SciCrunch

Changes from Previous Version

First Version

Version 1

Created 5 years ago by Anonymous

Reactome knowledgebase of human biological pathways and processes.

  • 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.

Reactome: a database of reactions, pathways and 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.