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

Authors
  • Arshinoff, Bradley I1
  • Cary, Gregory A2
  • Karimi, Kamran1
  • Foley, Saoirse2
  • Agalakov, Sergei1
  • Delgado, Francisco2
  • Lotay, Vaneet S1
  • Ku, Carolyn J2
  • Pells, Troy J1
  • Beatman, Thomas R2
  • Kim, Eugene1
  • Cameron, R Andrew3
  • Vize, Peter D1
  • Telmer, Cheryl A2
  • Croce, Jenifer C4
  • Ettensohn, Charles A2
  • Hinman, Veronica F2
  • 1 Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada. , (Canada)
  • 2 Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
  • 3 Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
  • 4 Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université, CNRS, Villefranche-sur-Mer, France. , (France)
Type
Published Article
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Publication Date
Nov 17, 2021
Identifiers
DOI: 10.1093/nar/gkab1005
PMID: 34791383
Source
Medline
Language
English
License
Unknown

Abstract

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. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

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