D74 Nucleic Acids Research, 2008, Vol. 36, Database issue Figure 4. Statistics of chains. (a) Distribution of number of common genes in a chain. (b) Distribution of total number of genes in a chain. (c) Subset of (b). Figure 5. Screenshot of the phenotype browser. DOWNLOADS We have made the CMGSDB schema, scripts and raw data freely available under the GPL. Only the software for computing chains is not included. The download package is available at https://bioinformatics.cs.vt.edu/cmgs/ CMGSDB/download.php. Using this package, a user with proper hardware and software resources (including PostgreSQL and Perl) can locally set up an exact replica of CMGSDB’s back end. The data is downloaded at runtime dynamically over the Internet. Scripts prepare the data and populate the database. This includes the integration of phenotypes from various sources. All data in CMGSDB (except data related to chains) is available for download as ﬂat ﬁles in download page. CONCLUDING REMARKS The integration of RNAi data and the application of data mining within CMSGDB provides the user with enhanced abilities to interpret raw C. elegans data. Unlike existing C. elegans resources, CMGSDB integrates RNAi data from multiple discrete sources. Using chains, users can discover new associations and relationships in the data that can be tested experimentally. A very meaningful future direction is to further consolidate the phenotypes to support alternate sets of phenotypes. This could be done by identifying very similar phenotypes as the same or by choosing a level of specialization in the phenotype tree. During the next 2 years of the CMGS project, additional data mining and modeling capabilities will be added. been implemented using the PHP TreeView class and is dynamically linked to individual phenotype pages and to other biots. Figure 5 illustrates the phenotype browser with the tree view on the left. ACKNOWLEDGEMENTS This work is supported by NSF-ITR Grant-0428344 for the CMGS project. We also thank the two anonymous reviewers for their very useful suggestions. Funding to pay