Echinobase: a resource to support the echinoderm research community

Area of Science:

• Marine Biology
• Developmental Biology
• Genomics

Background:

• Echinoderms (sea urchins, sea stars) are vital model organisms in biological research.
• These marine invertebrates contribute significantly to environmental, evolutionary, and developmental studies.
• A centralized, up-to-date resource is crucial for the echinoderm research community.

Purpose of the Study:

• To introduce the third-generation Echinobase knowledgebase.
• To provide a centralized platform for echinoderm genomic and functional data.
• To enhance data accessibility, interoperability, and reusability for researchers.

Main Methods:

• Developed a gene-centric knowledgebase based on the Xenbase design.
• Integrated genomes, functional genomic data, reagents, and literature for echinoderms.
• Implemented the JBrowse genome browser and the Echinoderm Anatomical Ontology.

Main Results:

• Echinobase features gene-centric pages with summary information and detailed data tabs.
• Provides 1:1 orthologs for key echinoderm species (e.g., Strongylocentrotus purpuratus, Lytechinus variegatus).
• Offers JBrowse tracks for visualizing functional genomic data and standardized developmental data.

Conclusions:

• Echinobase serves as a vital resource for annotated genomes, orthology, and functional data.
• The knowledgebase supports research in developmental gene regulatory networks and other fields.
• Content is formatted for findability, accessibility, interoperability, and reusability (FAIR principles).