The RGD mission to provide researchers with current genetic and genomic data, as well as the tools necessary to relate these data and information to the physiology and biology of complex phenotypes and diseases, is on task. We expanded our efforts to meet the evolving needs of the research community. As demonstrated here, we increased the biological content of RGD, explored new ways to manage and query data and made curation more efficient. Our genomics and genetic data sets continue to expand, as do the tools that enable the users to capitalize on the data.
RGD remains sensitive to the community's needs and prioritizes data curation, tool and ontology development and collaborative activities accordingly. For example, currently, there is an expressed need to develop a system for managing the genomic sequence for the rat community. While the draft rat genome sequence is 6.8X and its assembly is very good, there are no plans to finish it. Consequently, there will be a need to update the genomic sequence assembly as further research reveals inaccuracies. Given RGD's role in the rat community, it seems natural for it to fill this critical need. We are working with the genome sequence group at Baylor University to develop a system for providing continued annotation updates of the sequence.
RGD plans to annotate all genes in the rat over the next couple of years, and to convert the VCMap tool into a sequence-based tool. We anticipate RGD will serve as a ‘clearing house’ for changes to the genomic sequence as the community continues to use the data. We anticipate that results from most molecular genetics approaches will be actively tied to the genomic sequence. It will serve as a Rosetta stone between the human sequence and those of other model organisms. The curation teams at RGD have also identified new target information for incorporation, including mutant genes, alleles and full-length cDNA data, along with details on mutant, knock-out, congenic and transgenic strains.
Knowledge representation through ontology annotations will be made more sophisticated through data mining of the orthogonal relationships between the different ontologies. The resulting information should shed light on the relationships between the knowledge bases that they anchor and on the information within them. These developments will provide a more sophisticated infrastructure for the ontology system. Given that RGD's ontologies cover molecular, phenotypic and disease data, this is another avenue for bridging the distance between genomics and biomedicine.
Finally, we are continuously working towards making interactions with the RGD easier and more productive. Tools that provide visual cues to help navigate the data are under development. An infrastructure that allows the outputs of tools and reports to be input directly to other tools is also planned. A prototype system that sends queries to the Gene Annotation tool from the ontology system is being implemented. Furthermore, recognizing the diversity of communities of rat researchers, portal and portlet technologies, which allow users to customize the presentation of web data according to their needs, are also earmarked for implementation.