Reactome: a database of reactions, pathways and biological processes

Reactome: a database of reactions, pathways and biological processes

2011, Vol. 39, Database issue | David Croft, Gavin O'Kelly, Guanming Wu, Robin Haw, Marc Gillespie, Lisa Matthews, Michael Caudy, Phani Garapati, Gopal Gopinath, Bijay Jassal, Steven Jupe, Irina Kalatskaya, Shahana Mahajan, Bruce May, Nelson Ndegwa, Esther Schmidt, Veronica Shamovsky, Christina Yung, Ewan Birney, Henning Hermjakob, Peter D'Eustachio and Lincoln Stein
Reactome is an open-source, manually curated bioinformatics database that describes human pathways and biological processes. The database has recently been updated with a new web interface featuring improved tools for pathway browsing and data analysis. The Pathway Browser, based on Systems Biology Graphical Notation (SBGN), supports interactive visualization, zooming, scrolling, and event highlighting. It integrates molecular interaction data from various sources, such as IntAct, BioGRID, ChEMBL, RefIndex, MINT, and STRING, to overlay curated pathways. Reactome also offers tools for ID mapping, pathway assignment, and overrepresentation analysis of user-supplied data sets. To support pathway annotation in non-human species, Reactome uses orthology-based inferences, leveraging Ensembl Compara to identify orthologs of curated human proteins in 20 other species. The database includes pathways for 5272 human proteins and 3504 macromolecular complexes in 3847 reactions organized into 1057 pathways. New higher-order topics, such as transcriptional regulation and GPCR signaling, have been added. The Reactome data model has been extended to support pathway curation in model organisms like chicken, Drosophila, and rice. The redesigned website provides intuitive access to tools and resources, and the Pathway Analysis tool offers powerful functionalities for integrating experimental data with published literature and biological databases.Reactome is an open-source, manually curated bioinformatics database that describes human pathways and biological processes. The database has recently been updated with a new web interface featuring improved tools for pathway browsing and data analysis. The Pathway Browser, based on Systems Biology Graphical Notation (SBGN), supports interactive visualization, zooming, scrolling, and event highlighting. It integrates molecular interaction data from various sources, such as IntAct, BioGRID, ChEMBL, RefIndex, MINT, and STRING, to overlay curated pathways. Reactome also offers tools for ID mapping, pathway assignment, and overrepresentation analysis of user-supplied data sets. To support pathway annotation in non-human species, Reactome uses orthology-based inferences, leveraging Ensembl Compara to identify orthologs of curated human proteins in 20 other species. The database includes pathways for 5272 human proteins and 3504 macromolecular complexes in 3847 reactions organized into 1057 pathways. New higher-order topics, such as transcriptional regulation and GPCR signaling, have been added. The Reactome data model has been extended to support pathway curation in model organisms like chicken, Drosophila, and rice. The redesigned website provides intuitive access to tools and resources, and the Pathway Analysis tool offers powerful functionalities for integrating experimental data with published literature and biological databases.
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