ENHANCED ECHINOBASE: A COMMUNITY GENOMICS RESEARCH RESOURCE FOR THE FUTURE Overall Summary Echinobase (Echinobase.org) is a database that houses all of the diverse genomic data types produced by biologists working with echinoderms. It is accessed through a website that allows scientists to search, view and download a range of datatypes to empower their own research. Echinoderms are one of only three major phyla within the deuterostomes, and therefore the species within this clade encompass a large taxonomic diversity of body plans. Species of echinoderms are powerful model systems for understanding the processes by which the genome controls development. For example, they have uniquely contributed to understanding how gene expression is regulated in time and space and how networks of interacting genes, or Gene Regulatory Networks (GRNs) control development. The proposal here will migrate current Echinobase data to a customized clone of Xenbase with underlying Chado schema. As a consequence, Echinobase will inheriting enhanced database functionality, web application capabilities, and performance upgrades, all at a fraction of the cost of doing this independently. A key added feature obtained through this work will be database modules that support curation and searches of gene expression data, and thus effort is proposed to curate gene expression data to exploit this important capability. The look and feel of Echinobase will however be unique, and be tailored to its user base. A further goal of this proposal is to develop an echinoderm embryological anatomy schema using controlled vocabularies, and to improve identification of orthologous genes, not only among echinoderms but also to common reference proteomes. These initiatives follow emerging best practices, and hence ensure that Echinobase data can be readily shared with other resources. The assembly and annotation of echinoderm genomes, including the identification of both genic and noncoding regulatory features, will also be improved. Significant improvements to the curation of these genic and nongenic elements are also proposed. The new resource will also support an interactive module to model GRNs. These enhancements are directed at providing data types to support research for which the echinoderms have known strengths and where they can contribute uniquely to reveal the mechanistic links between the genome and development. The goal is to integrate these components to allow a user to readily navigate through these different data types in the different species. Changes will also be made throughout, to make this resource more useable, e.g. by controlling vocabularies, improving website design, and by providing training and workshops, in order to increase the usefulness of the resource. The improvements suggested throughout this proposal have wide community support as evidenced by results of our survey and community White Paper, boh referenced in the component, and 34 attached letters of support. 1
Echinobase is database for all genomic data types of the phylum Echinodermata, accessible via web browser, and enabling scientists to search, view, and download selected data to empower their own research. This facilitates research that explains how genomes control developmental process, which is needed to understand how genetic variations lead to birth, or other, defects.
