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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)

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

Related To

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

Abbreviation

Reactome

Parent Organization

Supercategory

Resource

Resource PubMed IDs

PMID: 15642094, PMID: 15642104, PMID: 16515723, PMID: 17101041, PMID: 17367534, PMID: 19067749, PMID: 19288185, PMID: 19455256, PMID: 19811689, PMID: 19828068, PMID: 20333223, PMID: 20358275, PMID: 20643908, PMID: 20664637, PMID: 20671204, PMID: 20807400, PMID: 20979611, PMID: 21186182, PMID: 21234354, PMID: 21478484, PMID: 21691773, PMID: 21712192, PMID: 21785142, PMID: 21785143, PMID: 21897858, PMID: 21929785, PMID: 21930502, PMID: 21999653, PMID: 22012987, PMID: 22025670, PMID: 22087225, PMID: 22120663, PMID: 22135291, PMID: 22303341, PMID: 22359512, PMID: 22523603, PMID: 22548703, PMID: 22577488, PMID: 22591066, PMID: 22654671, PMID: 22655260, PMID: 22724003, PMID: 22784567, PMID: 22815860, PMID: 22839973, PMID: 22916088, PMID: 22961259, PMID: 22982105, PMID: 23029552, PMID: 23046449, PMID: 23155061, PMID: 23162564, PMID: 23180722, PMID: 23209772, PMID: 23269912, PMID: 23272104, PMID: 23339624, PMID: 23354516, PMID: 23355459, PMID: 23382686, PMID: 23432914, PMID: 23497562, PMID: 23566118, PMID: 23575280, PMID: 23656885, PMID: 23691139, PMID: 23703215, PMID: 23724895, PMID: 23750284, PMID: 23762101, PMID: 23799003, PMID: 23803311, PMID: 23814041, PMID: 23825635, PMID: 23936158, PMID: 23983798, PMID: 24009678, PMID: 24096697, PMID: 24098495, PMID: 24196483, PMID: 24196705, PMID: 24243840, PMID: 24252331, PMID: 24270789, PMID: 24271396, PMID: 24278029, PMID: 24284405, PMID: 24287435, PMID: 24350286, PMID: 24428872, PMID: 24446963, PMID: 24460644, PMID: 24511209, PMID: 24522610, PMID: 24531128, PMID: 24610234, PMID: 24647608, PMID: 24679154, PMID: 24688456, PMID: 24723850, PMID: 24893065, PMID: 24901787, PMID: 24951798, PMID: 24978043, PMID: 25123454, PMID: 25255318, PMID: 25299225, PMID: 25368508, PMID: 25379146, PMID: 25392995, PMID: 25427715, PMID: 25500563, PMID: 25525469

Funding Information

NHGRI, European Union, FP6, ENFIN, Ontario Research Fund, European Molecular Biology Laboratory, P41 HG003751, LSHG-CT-2005-518254, GM080223, R01-GM100039

Curation Status

curated

Listed By

re3data.org

Availability

Open unspecified license

Resource Status

Last checked up;

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