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Resource:Reactome

Name: Resource:Reactome
Description: 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.
Parent Organization: Resource:Ontario Institute for Cancer Research, Resource:Cold Spring Harbor Laboratory, Resource:European Bioinformatics Institute, New York University School of Medicine; New York; USA
Supporting Agency: NHGRI, European Union, (FP6, ENFIN)
Related to: Resource:WikiPathways, Resource:NIF Data Federation, Resource:Gene Ontology - AmiGO, Resource:Monarch Initiative, Resource:PSICQUIC
Resource Type(s): Database, Data analysis service, Web service, Book
Keywords: Pathway, Gold standard or authority, Interaction, reaction, nucleic acid, protein, complex, small molecule, signaling, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction
Grant: P41 HG003751, LSHG-CT-2005-518254, GM080223, R01-GM100039
Abbreviation: Reactome
Resource: Resource
URL: http://www.reactome.org
PMID: PMID 21082427, 21067998
Availability: Open unspecified license
Id: nif-0000-03390
Organism: Human, Others
Link to OWL / RDF: Download this content as OWL/RDF

Categories related to Resource:Reactome

Resource:FlyMine, Resource:MOPED - Model Organism Protein Expression Database, Resource:NCBI BioSystems Database, Resource:PSICQUIC Registry, Resource:Pathway Commons, Resource:Pathway Interaction Database, Resource:hiPathDB - human integrated Pathway DB with facile visualization

Curation status: Curated

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Notes

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Contributors

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Facts about Resource:ReactomeRDF feed
AbbrevReactome  +
AvailabilityOpen unspecified license  +
CurationStatuscurated  +
DefiningCitationhttp://www.reactome.org  +
DefinitionOpen-source, open access, manually curated 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.
pathways and processes can be downloaded.
ExampleImageReactome.PNG  +
GrantCategory:P41 HG003751   +, Category:LSHG-CT-2005-518254   +, Category:GM080223   +, and Category:R01-GM100039   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +, Data analysis service  +, Web service  +, and Book  +
Idnif-0000-03390  +
Is part ofResource:Ontario Institute for Cancer Research  +, Resource:Cold Spring Harbor Laboratory  +, Resource:European Bioinformatics Institute  +, and New York University School of Medicine; New York; USA  +
KeywordsPathway  +, Gold standard or authority  +, Interaction  +, Reaction  +, Nucleic acid  +, Protein  +, Complex  +, Small molecule  +, Signaling  +, Immune function  +, Transcriptional regulation  +, Translation  +, Apoptosis  +, Metabolism  +, Ortholog  +, Visualization  +, and Protein-protein interaction  +
LabelResource:Reactome  +
ModifiedDate7 February 2014  +
PMID21082427, 21067998  +
Page has default formThis property is a special property in this wiki.Resource  +
RelatedToResource:WikiPathways  +, Resource:NIF Data Federation  +, Resource:Gene Ontology - AmiGO  +, Resource:Monarch Initiative  +, and Resource:PSICQUIC  +
SpeciesHuman  +, and Others  +
SuperCategoryResource  +
Supporting AgencyNHGRI  +, European Union  +, (FP6  +, and ENFIN)  +