Access to and integration of biological information continues to be a critical problem in biology. This is particularly clear in genome informatics. Annotations of genome sequences are distributed across many databases, each with their own different protocols for extracting the desired information. Attempting to integrate data from these different repositories is a challenging task, and one that both lab and computational biologists working with genomic data face often. To address this problem, we propose to significantly extend and enhance the Distributed Annotation System (DAS). DAS is an existing specification for sharing distributed annotations of biological sequences. DAS allows researchers to integrate biological information from many different sources via standardized queries and responses across the Web. DAS has gained momentum over the last two years as a method for serving, accessing, and viewing annotations of the human genome and a number of model organism genomes. However, since DAS's inception there have been a number of requests for clarifications, enhancements, extensions, and sometimes complete overhauls of the DAS system. For example, the most frequent request is for a better representation of the richness of possible annotations of biological sequence. Also, new technologies have appeared since DAS was first created that allow for more formal specification of """"""""web services"""""""". We propose to address many of these requests and produce a new version of DAS, DAS2. Specifically, we intend to advance DAS2 as a standard by 1) Creating and documenting a DAS 2.0 specification. This will include a formal specification as well as a less formal explanation of the spec. A tutorial, FAQ, and collection of cookbook-style examples will also be included as documentation; 2) Providing a freely available open-source implementation of a DAS2 compatibility checker; 3) Providing a freely available open-source implementation of a DAS2 server, including and API to support layering a DAS server on top of standard relational databases; 4) Providing a freely available open-source implementation of a DAS2 client that supports visualization and integration of annotation data from multiple DAS2 servers (and legacy DAS 1.x servers); 5) Providing access to Ensembl genome annotations via a DAS2 server; 6) Liaising with a number of other popular genome databases to promote accessibility of their data via DAS2 protocol; and 7) Liaising with the bioMOBY project to establish bioMOBY as a registry service for DAS2 servers (and discovery service for DAS2 clients). The work in this proposal will be performed as a collaboration between Affymetrix, CSHL, and Sanger Center, with consulting provided by Dalke Scientific. ? ?

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Project (R01)
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Special Emphasis Panel (ZRG1)
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Bonazzi, Vivien
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Affymetrix, Inc.
Santa Clara
United States
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Helt, Gregg A; Nicol, John W; Erwin, Ed et al. (2009) Genoviz Software Development Kit: Java tool kit for building genomics visualization applications. BMC Bioinformatics 10:266