Rice Genetics IV - IRRI books - International Rice Research Institute

Bioinformatics workshopThe Bioinformatics Workshop was arranged to promote contacts with the rice communityattending the IRGS. Graham McLaren, Richard Bruskiewich, and MichaelJackson focused on three general questions during the workshop:1. What are our current objectives for bioinformatics development within therice research community?2. What additional formal collaborative framework do we need to establish withinthe rice bioinformatics research community to achieve those objectives?3. On what specific technical areas should the rice bioinformatics communityfocus and who is willing to assume responsibility to coordinate developmentin those specific areas?There was a general agreement on the goal for bioinformatics of seamlessly linkinginformation from genome to phenotype. The initial objective of linking islands ofinformation from different disciplines was agreed upon, and the need to develop userfriendlyspecialist interfaces for different users was discussed. There was a call foron-line compilation and curation of rice genetics literature and a comprehensive databaseon publicly available rice expressed sequence tags.Other areas identified for development were the inclusion of more image data indatabases and for graphical user interfaces. The need to develop tools to locate, manage,and display the anticipated large quantities of natural variation in sequence datawas also identified. This was seen as essential for the process of allele mining ingermplasm collections.There was an agreement that the rice bioinformatics community will have to collaborateto develop standard vocabularies and data exchange protocols.The idea of federated curation of databases was discussed, but the technical andorganizational issues of enabling fully queriable, distributed databases may constrainthis approach for the near future. Database links or tunnels were considered the mostpractical short-term mechanism of linking.For the third point, the need to improve and standardize rice genome annotationwas briefly discussed, as was the need to canvass opinions among the rice community.To facilitate this process, IRRI has set up a rice bioinformatics Web page and E-mail list at http://www.cgiar.org/irri/bioinformatics/.487