Echinobase will be undergoing a hardware update June 13 and 14, 2023 and therefore will be unavailable those days.
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Echinobase (www.echinobase.org) is a third generation web resource supporting genomic research on echinoderms. The new version was built by cloning the mature Xenopus model organism knowledgebase, Xenbase, refactoring data ingestion pipelines and modifying the user interface to adapt to multispecies echinoderm content. This approach leveraged over 15 years of previous database and web application development to generate a new fully featured informatics resource in a single year. In addition to the software stack, Echinobase uses the private cloud and physical hosts that support Xenbase. Echinobase currently supports six echinoderm species, focused on those used for genomics, developmental biology and gene regulatory network analyses. Over 38 000 gene pages, 18 000 publications, new improved genome assemblies, JBrowse genome browser and BLAST + services are available and supported by the development of a new echinoderm anatomical ontology, uniformly applied formal gene nomenclature, and consistent orthology predictions. A novel feature of Echinobase is integrating support for multiple, disparate species. New genomes from the diverse echinoderm phylum will be added and supported as data becomes available. The common code development design of the integrated knowledgebases ensures parallel improvements as each resource evolves. This approach is widely applicable for developing new model organism informatics resources.
Figure 1. The Echinobase landing page and portal. A central feature of the page is an animated ‘news slider’ that presents a slide show of community news and new features of the resource. A horizontal navigation menu shared between all Echinobase pages provides consistency, and large ‘tiles’ of grouped content, e.g. ‘Genes and Expression’, ‘Genome Browsers’ and ‘BLAST’ aggregate commonly used tools and content.
Figure 3. Echinobase literature pages. This screenshot illustrates a paper that has been processed by automated systems only, so all links, identified genes, authors and anatomy terms, figures and legends etc. were added by machine-based methods. The only organism detected by these tools was ‘echinodermata’, and a curator must annotate this page to include the species in the title, Heliocidaris erythrogramma, add additional genes, experimental reagents (morpholinos etc.), curate the gene expression patterns in the figures etc. When this is done all these data will also be displayed on this page. Authors with Echinobase community pages are hyperlinked, as are terms in the abstract and figure legends matching genes/synonyms, anatomy/synonyms etc. When text matches more than one target, selecting the link will display a disambiguation page.