Mining the Scientific Literature and Building a Pan-Echinoderm Gene Expression Database

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CURATION COMPONENT- ABSTRACT Echinoderms (sea urchins and their allies) are a pre-eminent model 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. Data on genes, genomes, and gene expression are fundamental to all aspects of modern developmental biology, including GRN biology. 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 (including GRNs) in other 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. During this project period, Curate has two overarching goals: 1) the curation of scientific literature related to echinoderm development, and 2) the development of a comprehensive gene expression database, including the formulation of an anatomical ontology for echinoderm embryos that will serve as a framework for the annotation of gene expression data. Literature curation will allow users to effectively mine information from the large body of published studies on echinoderm development, and the bibliography of published papers will serve as a backbone to which all curated biological data can be attributed. Among the most important classes of biological data are those pertaining to spatial and temporal patterns of gene expression during development. A wealth of gene expression data has been generated for sea urchins and other echinoderms in recent years, and there is a pressing need to curate these data and to develop new tools that will allow scientists to take full advantage of this information. Our curation efforts will be supported through a collaboration with Xenbase, which will provide a suite of data entry, storage, and analysis tools that are well-suited to our needs. Through its activities, Curate will extend the capabilities of Echinobase and thereby greatly enhance its utility to the research community.