Echinobase: a resource to support the echinoderm research community

Abstract

Echinobase (www.echinobase.org) is a model organism knowledgebase serving as a resource for the community that studies echinoderms, a phylum of marine invertebrates that includes sea urchins and sea stars. Echinoderms have been important experimental models for over 100 years and continue to make important contributions to environmental, evolutionary, and developmental studies, including research on developmental gene regulatory networks. As a centralized resource, Echinobase hosts genomes and collects functional genomic data, reagents, literature, and other information for the community. This third-generation site is based on the Xenbase knowledgebase design and utilizes gene-centric pages to minimize the time and effort required to access genomic information. Summary gene pages display gene symbols and names, functional data, links to the JBrowse genome browser, and orthology to other organisms and reagents, and tabs from the Summary gene page contain more detailed information concerning mRNAs, proteins, diseases, and protein-protein interactions. The gene pages also display 1:1 orthologs between the fully supported species Strongylocentrotus purpuratus (purple sea urchin), Lytechinus variegatus (green sea urchin), Patiria miniata (bat star), and Acanthaster planci (crown-of-thorns sea star). JBrowse tracks are available for visualization of functional genomic data from both fully supported species and the partially supported species Anneissia japonica (feather star), Asterias rubens (sugar star), and L. pictus (painted sea urchin). Echinobase serves a vital role by providing researchers with annotated genomes including orthology, functional genomic data aligned to the genomes, and curated reagents and data. The Echinoderm Anatomical Ontology provides a framework for standardizing developmental data across the phylum, and knowledgebase content is formatted to be findable, accessible, interoperable, and reusable by the research community.

Keywords: biocuration; database; echinoderm; genomics; knowledgebase; model organism; ontology.

Fig. 1.

The Echinobase landing page.

Fig. 2.

Gene Search options from the landing page. A) Direct search using the search bar. B) Gene Search using the drop-down menu. C) Search for genes link from the Genes & Expression block. D) Both the drop-down and the link take users to the Search Genes page.

Fig. 3.

A sample gene page shows all of the information gathered and displayed on the Summary tab. Species-agnostic information such as gene symbol, synonyms, molecular function, and disease associations are displayed at the top, while species-specific content is arranged in vertical columns below this more general content. Other tabs can be used to access more specific supporting information. Note that the gene in this example is orthologous S. purpuratus, L. variegatus, P. miniata, and A. planci. The species displayed, and the order in which they are displayed, can be set by users using the dropdowns on top of each column.

Fig. 4.

The ECAO serves as a scaffold that can have data attached to it using spatial and temporal dimensions. A) The anatomy can be searched, and items are organized in a hierarchy of spatial structures. B) The developmental stages are arranged in a temporal hierarchy.