Arshinoff BI et al. (2022), Echinobase: leveraging an extant model organism...

XB-ART-58644

Nucleic Acids Res 2022 Jan 07;50D1:D970-D979. doi: 10.1093/nar/gkab1005.

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Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms.

Arshinoff BI , Cary GA , Karimi K , Foley S , Agalakov S , Delgado F , Lotay VS , Ku CJ , Pells TJ , Beatman TR , Kim E , Cameron RA , Vize PD , Telmer CA , Croce JC , Ettensohn CA , Hinman VF .

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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.

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Species referenced: Xenopus tropicalis Xenopus laevis

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	Figure 1. The Echinobase landing page and portal. A central feature of the page is an animated ânews sliderâ 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 âtilesâ of grouped content, e.g. âGenes and Expressionâ, âGenome Browsersâ and âBLASTâ aggregate commonly used tools and content.
	Figure 2. The Echinobase Gene Page. The top section of the page contains species agnostic information such as gene symbols, names and functions. It also contains synonyms, where legacy symbols and short names are stored and make genes locatable via database searches. The synonyms are also used to link Gene Pages to matched terms in the literature section. Due to the large amount of content aggregated on Gene Pages, much of the data is sorted into âtabsâ at the top of the page (orange arrow). Where a tab contains content, this is indicated by a numeral or icon. A transcriptional profile for the gene is also present, currently only for S. purpuratus, and will be expanded to additional species as data becomes available. The species specific content is arranged in vertical columns, each topped by a drop down menu that enables the user to define the content of that column (red arrow). In this example the third column header has been selected, displaying the three options for its content. The â+â symbol highlighted by the green arrow allows additional columns to be displayed. As we will be adding both a fourth species and paralogs to the display options in the near future, the ability to customize the data viewed will become even more important. Where we store and integrate multiple genome versions, for example for S. purpuratus, the user can also select which genome version is displayed as a gene model via a drop-down menu, and which genome version is linked to the Gene Page in JBrowse. This is only the case when we have integrated multiple versions, and this is only the case in some species. As different genome builds (e.g. S. purpuratus v3.1 and v5.0) have different sets of gene models, not all genes will be available in all genome versions. When this happens the number of available genomes will change in the user display. The chromosome maps and gene model exon/intron graphics are generated dynamically from database content by JavaScript, and selecting a new genome version will dynamically display the new gene structure for the selected version. The rocket icon that appears adjacent to many sequence based hyperlinks will load the corresponding sequence into BLAST, while the magnifying glass icon will open the sequence in a display window.
	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 âechinodermataâ, 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.
	Supplemental Figure 1. The Xenbase and Echinobase software stacks. The majority of code is shared between the two resources and features developed for one site benefit the other (light green). When features are resource specific, conditional code is utilized as indicated by dark green. Database content is mostly unique to each resource, except for shared content such as core ontologies (e.g. GO), disease relationships, human protein-protein interaction data etc. Double ended arrows indicate database queries.

References [+] :

Alliance of Genome Resources Consortium, The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. 2019, Pubmed