Mining Information from Echinoderm Genomes and the Scientific Literature

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SUMMARY CURATION Mining Information from Echinoderm Genomes and the Scientific Literature Echinoderms (sea urchins and their allies) are valuable models for analysis of the genomic control of embryonic development. For example, the most complete gene regulatory networks (GRNs) for development that we have for any animal have recently been solved for sea urchin embryos. Comparative studies across echinoderms are elucidating the evolution of gene regulatory programs. Data on genes, genomes, and gene expression are fundamental to all aspects of modern developmental biological research. Effective access to these data has become vital not only to members of the echinoderm research community but to a broader audience studying developmental processes in many model systems. The activities of Echinobase are essential in order to ultimately apply this scientific information to human development and disease. Model organism databases enhance the value of research by consolidating and storing data, integrating different types of information and representing it in useful ways, and linking similar kinds of data across organisms. Echinobase was created to enhance the value of scientific data related to the genes and genomes of sea urchins and other echinoderms and to serve as a centralized, definitive resource for information related to these important model organisms. The Curate Component (Curate) plays a central role in the overall mission of Echinobase by identifying, extracting, and organizing scientific data. All of our curation efforts are supported through a close collaboration with Xenbase, which provides a suite of data entry, storage, and analysis tools that are well-suited to our needs. During this project period, Curate has three major goals: 1) to curate echinoderm genomes, including the provision of accurate, orthology-based names to echinoderm genes and the improved annotation of current echinoderm gene models; 2) to curate an extensive scientific literature related to echinoderm development, including the ongoing assembly of a bibliography of published papers that serves as a backbone to which all curated biological data are attributed, and the curation of a wealth of information from these papers related to gene expression patterns, morpholinos, antibodies, guide RNAs (gRNAs), and cis-regulatory elements (CREs); 3) to enhance the current echinoderm developmental ontology, which provides a foundation for almost all of our curation efforts, by expanding the ontology to include representatives of additional classes of echinoderms and additional life history stages and by incorporating into Echinobase additional static content derived from the developmental ontology. By achieving these goals, Curate will vastly enhance the utility of Echinobase to the community of researchers who study echinoderm development and ensure that echinoderm-related information is readily accessible to biologists who work with other model organisms, including vertebrates.