D696 Nucleic Acids Research, 2011, Vol. 39, Database issue change or statistical values) and shows how expression/ abundance levels affect reactions and pathways in living organisms (Figure 3). Again, the results are provided in a tabular format. Results from both the pathway and ex- pression analysis results can be downloaded as a spread- sheet or tab- and comma-separated formats. The colored pathway diagrams can be downloaded in publication quality format. The molecular overlay and context sensi- tive menu features are also enabled in the colored pathway diagrams, providing links from user-supplied experimental data to Reactome pathways and MIs and networks. Other collaborations and data exports In collaboration with NCBI, Reactome annotations of pathways are being deposited into the NCBI BioSystems database, a large data repository for cataloguing mol- ecules (nucleic acids, proteins, small molecules, drugs, etc.) that interact in biological systems (28). Reactome is part of the BioPAX Consortium to develop a data-exchange language to describe pathways, reactions and interactions (29). We have partnered with Gene Set Enrichment Analysis (GSEA) group at the Broad Institute to expand the collection of curated gene sets in the Molecular Signatures Database (MSigDB) to include Reactome’s high-quality pathway data (30). Reactome participated in this year’s Google Summer of Code program, collaborating with WikiPathways (31). The in- tegration of pathway and interaction data has been a key element of the Reactome redevelopment. We have provided a new ﬁle format for the exchange of binary interaction data, based upon the PSI-MITAB format (32). In response to user requests, we recently changed the representation of protein modiﬁcations in Reactome to the PSI-MOD standard (33). We continue to support the use of Reactome data for ontology development with our relationships with the Gene and Protein Ontology groups. Reactome web pages link out to many online bioinformatics databases. This year, additional cross- references to RSCB Protein Data Bank (34), Comparative Toxicogenomics Database (35), DockBlaster (36), BioGPS (37) and dbSNP (38) have been added to the protein pages. Reactome software and data are now distributed under the terms of a Creative Commons Attribution 3.0 Unported License, that grants parties the non-exclusive right to use, distribute and create derivative works based on Reactome, provided that the software and information is correctly attributed to CSHL, OICR and EBI. ACKNOWLEDGEMENTS We are grateful to the many researchers who have volun- teered to be external authors and reviewers. Development of the Reactome data model and ﬂy and chicken databases is a collaborative project and this work beneﬁted greatly from our interactions with Carl Schmidt, Mark Williams and Michael Ashburner. 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