Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes
J. Brad Karpinka
2
Joshua D. Fortriede
1
Kevin A. Burns
1
Christina James-Zorn
1
Virgilio
G. Ponferrada
1
Jacqueline Lee
2
Kamran Karimi
2
Aaron M. Zorn
1
Peter D. Vize
0
2
0
University of Calgary-Biological Sciences
,
Calgary, Alberta
,
Canada
1
Cincinnati Children's Research Foundation-Division of Developmental Biology
,
Cincinnati, OH
,
USA
2
University of Calgary-Computer Science
,
Calgary, Alberta
,
Canada
Xenbase (http://www.xenbase.org), the Xenopus frog model organism database, integrates a wide variety of data from this biomedical model genus. Two closely related species are represented: the allotetraploid Xenopus laevis that is widely used for microinjection and tissue explant-based protocols, and the diploid Xenopus tropicalis which is used for genetics and gene targeting. The two species are extremely similar and protocols, reagents and results from each species are often interchangeable. Xenbase imports, indexes, curates and manages data from both species; all of which are mapped via unique IDs and can be queried in either a speciesspecific or species agnostic manner. All our services have now migrated to a private cloud to achieve better performance and reliability. We have added new content, including providing full support for morpholino reagents, used to inhibit mRNA translation or splicing and binding to regulatory microRNAs. New genomes assembled by the JGI for both species and are displayed in Gbrowse and are also available for searches using BLAST. Researchers can easily navigate from genome content to gene page reports, literature, experimental reagents and many other features using hyperlinks. Xenbase has also greatly expanded image content for figures published in papers describing Xenopus research via PubMedCentral.
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Xenbase (http://www.xenbase.org) is the Xenopus model
organism database. The frogs Xenopus laevis and Xenopus
(Silurana) tropicalis are widely used in biomedical research,
ranging from the study of cell and developmental
biology, physiology and drug screening and toxicology.
Findings from Xenopus research are highly applicable to
human health and disease modeling as key biological
processes are conserved, such as embryonic germ layer
specification, body plan patterning, angiogenesis,
neurogenesis and organogenesis. Xenopus are amenable to laboratory
study as they can be stimulated to lay eggs on demand
without seasonal restrictions, and their large robust eggs and
embryos serve as powerful in vivo systems to explore
vertebrate biology. Fertilized embryos develop externally into
tadpoles with fully differentiated organs in just a few days
when grown in a simple saline solution. Thus, this frog
model system is straightforward in observing embryonic
development and in detecting changes caused by experimental
interventions.
In the 2 years since the last update reported in NAR, the
Xenbase team has improved the sites usability by providing
a redesigned user interface, adding new content and
improving the sites performance and availability. The user
interface redesign was done with the help of professional
designers, providing Xenbase with a dynamic and easy to navigate
landing page. We have added new data types, such as
morpholinos and antibodies, as well as increasing the number of
our existing data types, such as papers, through manual
curation and automatic data harvesting. To improve the sites
speed and reduce down time, we replaced Xenbases
hardware with more up-to-date equipment, and completely
redesigned the software architecture, allowing us to move to a
virtual environment. These content, hardware and software
improvements, together with numerous bug and usability
fixes, have made the site more useful, stable and responsive.
The scientific method relies heavily on the ability of
scientists to reproduce and build upon each others results.
A fundamental principle of reproducibility is clear,
unambiguous description of the methods and material resources
used in experiments. Consistent use of standardized gene
nomenclature, as well as the tools and resources used in
Xenopus research (e.g. antibodies, morpholinos, transgene
(Tg) constructs and transgenic lines) will not only enhance
the clarity of the research to the specialist as well as the
broader model organism community, but also provide
information necessary to facilitate experimental
reproducibility. Xenbase continues to support these principles by
hosting and promoting the use of stable nomenclature
including gene names (congruent with human gene
nomenclature), miRNAs, antibodies, morpholinos, transgenic
constructs and transgenic frog lines. Our antibody database was
launched in early 2013 (1). New antibody entries are
continually added, as published, through our manual curation
pipeline, giving researchers access to antibody data
specifically from work on Xenopus. Two newly expanded features
on Xenbase further support resources commonly used in
Xenopus biomedical research: (i) the morpholino module
and (ii (...truncated)