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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, Bradley I. and Cary, Gregory A. and Karimi, Kamran and Foley, Saoirse and Agalakov, Sergei and Delgado, Francisco and Lotay, Vaneet S. and Ku, Carolyn J. and Pells, Troy J. and Beatman, Thomas R. and Kim, Eugene and Cameron, R. Andrew and Vize, Peter D. and Telmer, Cheryl A. and Croce, Jenifer C. and Ettensohn, Charles A. and Hinman, Veronica F. (2022) Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms. Nucleic Acids Research, 50 (D1). D970-D979. ISSN 0305-1048. PMCID PMC8728261. doi:10.1093/nar/gkab1005. https://resolver.caltech.edu/CaltechAUTHORS:20211208-951158000

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/nar/gkab1005DOIArticle
http://www.echinobase.org/Related ItemEchinobase
http://www.xenbase.org/Related ItemXenbase
http://gmod.org/Related ItemGMOD, The Generic Model Organism Database project
http://legacy.echinobase.org/Related ItemLegacy Echinobase
https://github.com/olsonanl/FastOrthoRelated ItemFastOrtho
https://www.echinobase.org/gene/static/geneNomenclature.jspRelated ItemEchinobase gene nomenclature guidelines
https://www.echinobase.org/anatomy/ecao.do?method=displayRelated ItemThe ECAO
http://obofoundry.org/ontology/ecao.htmlRelated ItemThe ECAO at the OBO Foundry
http://www.ncbi.nlm.nih.gov/pmc/articles/pmc8728261/PubMed CentralArticle
ORCID:
AuthorORCID
Karimi, Kamran0000-0001-5733-9409
Foley, Saoirse0000-0002-1791-2837
Pells, Troy J.0000-0002-2340-5356
Beatman, Thomas R.0000-0003-3246-3002
Cameron, R. Andrew0000-0003-3947-6041
Vize, Peter D.0000-0001-8026-0424
Telmer, Cheryl A.0000-0002-7649-3134
Croce, Jenifer C.0000-0001-7092-0257
Ettensohn, Charles A.0000-0002-3625-0955
Hinman, Veronica F.0000-0003-3414-1357
Additional Information:© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 13 August 2021. Revision received: 05 October 2021. Accepted: 13 October 2021. Published: 17 November 2021. Features used in Echinobase are derived from the work of many active and past Xenbase, SpBase and Echinobase developers and contributors. These individuals are listed in the ‘About’ page on each resource's landing page. Training and support from the Xenbase curatorial team at Cincinnati Children's Hospital was essential in building this resource, as was advice from the Echinobase Scientific Advisory Board. The contents of Echinobase are solely the responsibility of the authors and do not necessarily represent the official views of the National Institutes of Health. unding for Echinobase is provided by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) [P41HD095831]; this work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation [ACI-1548562]; specifically, it used the Bridges system, which is supported by NSF [ACI-1445606], at the Pittsburgh Supercomputing Center (PSC) via allocation request MCB200030; J.C.C. is funded by the Centre National de la Recherche Scientifique (CNRS) and benefited from the European project ‘Coordinated Research Infrastructures Building Enduring Life Science Services’ (CORBEL) [H2020-INFRADEV-4-2014-2015 RIA]. Funding for open access charge: NICHD [P41HD095831]. DATA AVAILABILITY: Echinobase; http://www.echinobase.org Xenbase; http://www.xenbase.org GMOD, The Generic Model Organism Database project; http://gmod.org Legacy Echinobase, a VM running the previous generation Echinobase; http://legacy.echinobase.org FastOrtho, orthology prediction tool; https://github.com/olsonanl/FastOrtho Echinobase gene nomenclature guidelines; https://www.echinobase.org/gene/static/geneNomenclature.jsp The ECAO; https://www.echinobase.org/anatomy/ecao.do?method=display The ECAO at the OBO Foundry; http://obofoundry.org/ontology/ecao.html Conflict of interest statement. None declared.
Funders:
Funding AgencyGrant Number
NIHP41HD095831
NSFACI-1548562
NSFACI-1445606
Centre National de la Recherche Scientifique (CNRS)H2020-INFRADEV-4-2014-2015 RIA
Issue or Number:D1
PubMed Central ID:PMC8728261
DOI:10.1093/nar/gkab1005
Record Number:CaltechAUTHORS:20211208-951158000
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20211208-951158000
Official Citation:Bradley I Arshinoff, Gregory A Cary, Kamran Karimi, Saoirse Foley, Sergei Agalakov, Francisco Delgado, Vaneet S Lotay, Carolyn J Ku, Troy J Pells, Thomas R Beatman, Eugene Kim, R Andrew Cameron, Peter D Vize, Cheryl A Telmer, Jenifer C Croce, Charles A Ettensohn, Veronica F Hinman, Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D970–D979, https://doi.org/10.1093/nar/gkab1005
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:112307
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:10 Dec 2021 20:12
Last Modified:01 Feb 2022 22:57

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