A stage and anatomy ontology for embryogenesis in indirect-developing echinoderms

Developmental and anatomical ontologies are fundamental tools for standardizing biological data. They facilitate the reproducibility of experiments and the integration of information across laboratories and animal species. They underpin digital curation, dissemination and analysis of diverse biological data, including gene expression patterns and phenotypes associated with pharmacological, molecular and genetic perturbations. As such, ontologies are cornerstones of model organism knowledgebases. Echinoderms have been prominent developmental biology models for more than a century and are widely used to address evolutionary questions; however, no formalized ontology has been produced for any echinoderm. Here, based on direct observations of living embryos of five species, representing euechinoids, cidaroids and sea stars, we provide developmental and anatomical ontologies for the embryogenesis of indirect-developing echinoderms. Moreover, we leverage these ontologies to create a 'pan-echinoderm' developmental and anatomical ontology, which we show will support comparative analyses across the phylum. These resources will be important for the curation of data from multiple species by Echinobase and Marimba, two public knowledgebases of echinoderm genomics and invertebrate marine models, respectively. They will greatly enhance the use and value of echinoderms as model organisms for biological research.