Reactome is a collaborative, open-source database of human pathways and reactions, developed by the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine, and the European Bioinformatics Institute. The database provides a comprehensive, manually curated, peer-reviewed resource for biological pathways and processes. It includes detailed annotations of human proteins, genes, small molecules, and pathways, cross-referenced with various databases such as UniProt, NCBI EntrezGene, Ensembl, KEGG Compound, ChEBI, PubMed, and GO. The Reactome data model generalizes the concept of a reaction to include a wide range of biological processes, including signaling, metabolism, transcriptional regulation, apoptosis, and synaptic transmission. The database has expanded significantly in the past two years, with new tools for data aggregation and analysis. The Reactome website has been redesigned to support quick access to data and tools, and the Pathway Browser has been developed to provide a more interactive and dynamic visualization of pathways. The Pathway Browser is based on the Systems Biology Graphical Notation (SBGN) and allows for zooming, scrolling, and highlighting of events and molecules. It integrates molecular interaction data from various sources, including the Reactome Functional Interaction Network and external databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT, and STRING. Reactome also supports pathway annotation and analysis in other species by making orthology-based inferences of pathways in non-human species using Ensembl Compara. The database has been extended to include manually curated data sets for model organisms such as Gallus (chicken), Drosophila (fruit fly), and rice. The Reactome data model has been extended to include manual curation of pathways in model organisms, with Gallus Reactome and the Drosophila pathway database being examples of such efforts. The Reactome database also provides tools for pathway and expression analysis, including ID mapping, pathway assignment, and overrepresentation analysis. These tools allow users to analyze user-supplied data sets and visualize the results in pathway diagrams. The database is also integrated with other bioinformatics resources and is available under a Creative Commons Attribution 3.0 Unported License. Reactome is part of the BioPAX Consortium and has been integrated with the Gene Set Enrichment Analysis (GSEA) group at the Broad Institute. The database is also used for ontology development and is linked to many online bioinformatics databases.Reactome is a collaborative, open-source database of human pathways and reactions, developed by the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine, and the European Bioinformatics Institute. The database provides a comprehensive, manually curated, peer-reviewed resource for biological pathways and processes. It includes detailed annotations of human proteins, genes, small molecules, and pathways, cross-referenced with various databases such as UniProt, NCBI EntrezGene, Ensembl, KEGG Compound, ChEBI, PubMed, and GO. The Reactome data model generalizes the concept of a reaction to include a wide range of biological processes, including signaling, metabolism, transcriptional regulation, apoptosis, and synaptic transmission. The database has expanded significantly in the past two years, with new tools for data aggregation and analysis. The Reactome website has been redesigned to support quick access to data and tools, and the Pathway Browser has been developed to provide a more interactive and dynamic visualization of pathways. The Pathway Browser is based on the Systems Biology Graphical Notation (SBGN) and allows for zooming, scrolling, and highlighting of events and molecules. It integrates molecular interaction data from various sources, including the Reactome Functional Interaction Network and external databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT, and STRING. Reactome also supports pathway annotation and analysis in other species by making orthology-based inferences of pathways in non-human species using Ensembl Compara. The database has been extended to include manually curated data sets for model organisms such as Gallus (chicken), Drosophila (fruit fly), and rice. The Reactome data model has been extended to include manual curation of pathways in model organisms, with Gallus Reactome and the Drosophila pathway database being examples of such efforts. The Reactome database also provides tools for pathway and expression analysis, including ID mapping, pathway assignment, and overrepresentation analysis. These tools allow users to analyze user-supplied data sets and visualize the results in pathway diagrams. The database is also integrated with other bioinformatics resources and is available under a Creative Commons Attribution 3.0 Unported License. Reactome is part of the BioPAX Consortium and has been integrated with the Gene Set Enrichment Analysis (GSEA) group at the Broad Institute. The database is also used for ontology development and is linked to many online bioinformatics databases.