2014-02-25T10:00:29-08:00
Resource:Reactome
Reactome
curated
http://www.reactome.org
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. These include 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 rationale behind Reactome is to convey the rich information in the visual representations of biological pathways familiar from textbooks and articles in a detailed, computationally accessible format. 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.
Category:P41 HG003751
Category:LSHG-CT-2005-518254
Category:GM080223
Category:R01-GM100039
nif-0000-03390
Resource:Reactome
2014-02-07T00:00:00
21082427, 21067998
Resource
Resource:NCBI BioSystems Database
Resource:hiPathDB - human integrated Pathway DB with facile visualization
Resource:FlyMine
Resource:Pathway Interaction Database
Resource:MOPED - Model Organism Protein Expression Database
Resource:Pathway Commons
Resource:PSICQUIC Registry
Resource
ENFIN)
(FP6
European Union
National Human Genome Research Institute
Supporting Agency
SuperCategory
Others
Human
Species
Resource:PSICQUIC
Resource:Monarch Initiative
Resource:AmiGO
Resource:NIF Data Federation
Resource:WikiPathways
RelatedTo
PMID
ModifiedDate
Label
Protein-protein interaction
Visualization
Ortholog
Metabolism
Apoptosis
Translation
Transcriptional regulation
Immune function
Signaling
Small molecule
Complex
Protein
Nucleic acid
Reaction
Interaction
Gold standard or authority
Pathway
Keywords
New York University School of Medicine; New York; USA
Resource:European Bioinformatics Institute
Resource:Cold Spring Harbor Laboratory
Resource:Ontario Institute for Cancer Research
Is part of
Id
Book
Web service
Data analysis service
Database
Has role
Grant
File:Reactome.PNG
ExampleImage
Definition
DefiningCitation
CurationStatus
Open unspecified license
Availability
Abbrev