<div dir="ltr">
<p class="MsoNormal" style="text-align:justify;vertical-align:baseline"><span style="font-size:10pt;color:black">The National Institutes for Health
(NIH) recently announced a new <b style="mso-bidi-font-weight:normal">Request
for Information (RFI): Metrics to Assess Value of Biomedical Digital
Repositories</b>. </span><a href="http://grants.nih.gov/grants/guide/notice-files/NOT-OD-16-133.html"><span style="font-size:10pt;color:rgb(17,85,204)">http://grants.nih.gov/grants/guide/notice-files/NOT-OD-16-133.html</span></a><span style="font-size:10pt;color:black"></span></p>
<p class="MsoNormal" style="text-align:justify;vertical-align:baseline"><span style="font-size:10pt;color:black"> </span></p>
<p class="MsoNormal" style="text-align:justify;vertical-align:baseline"><span style="font-size:10pt;color:black">All responses must be submitted by
September 30, 2016.</span></p>
<p class="MsoNormal" style="vertical-align:baseline"><span style="font-size:10pt;color:black"> </span></p>
<p class="MsoNormal" style="text-align:justify;vertical-align:baseline"><span style="font-size:10pt;color:black">Biomedical Digital Repository</span><span style="font-size:10pt"> can be thought of in two general categories: <b style="mso-bidi-font-weight:normal">Knowledgebase</b></span><b style="mso-bidi-font-weight:normal"><span style="font-size:10pt;color:black">s</span></b><span style="font-size:10pt;color:black"> and </span><b style="mso-bidi-font-weight:normal"><span style="font-size:10pt">Deposition repositories</span></b><span style="font-size:10pt;color:black">.<span style="mso-spacerun:yes"> </span>Xenbase is a ‘</span><b style="mso-bidi-font-weight:
normal"><span style="font-size:10pt">Knowledgebase</span></b><span style="font-size:10pt">’ as it provides species-specific, curated findings derived
from the aggregation or analysis of a large body of published and unpublished (community
submitted) experimental data. <b style="mso-bidi-font-weight:normal">Deposition
repositories</b>, like GenBank/NCBI, support primary research data submitted by
the data producers.</span><span style="font-size:10pt;color:black"></span></p>
<p class="MsoNormal" style="vertical-align:baseline"><span style="font-size:10pt"> </span></p>
<p class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">The
NIH wants to understand and measure</span></p><p class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt"> 1) the<b style="mso-bidi-font-weight:normal">
</b>value<b style="mso-bidi-font-weight:normal"> </b>of Xenbase<b style="mso-bidi-font-weight:normal"> </b>and other data repositories, <br></span></p><p class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">2) the
value of data types and data sets they contain, and <br></span></p><p class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">3) how important these data repositories are
to your research.<span style="mso-spacerun:yes"> </span></span></p>
<p class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt"> </span></p>
<p class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt;color:black">All stakeholders with an interest in
approaches to measure and assess the value of biomedical data repositories and
decisions driven by these metrics are invited to provide information. The <i style="mso-bidi-font-style:normal">Xenopus</i> research community fall under numerous
categories, including, but not limited to:</span><span style="font-size:10pt"></span></p>
<p class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt"> </span></p>
<p class="" style="vertical-align:baseline"><span style="font-size:10pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7pt "Times New Roman""> </span></span></span><span style="font-size:10pt;color:black">Biomedical
science researcher: PIs and Group Leaders, Post Docs and<span style="mso-spacerun:yes"> </span>Grad Students, Clinicians</span></p>
<p class="" style="vertical-align:baseline"><span style="font-size:10pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7pt "Times New Roman""> </span></span></span><span style="font-size:10pt;color:black">Bioinformatician</span></p>
<p class="" style="vertical-align:baseline"><span style="font-size:10pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7pt "Times New Roman""> </span></span></span><span style="font-size:10pt;color:black">Data scientist</span></p>
<p class="" style="vertical-align:baseline"><span style="font-size:10pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7pt "Times New Roman""> </span></span></span><span style="font-size:10pt;color:black">Standard
developer or maintainer</span></p>
<p class="" style="vertical-align:baseline"><span style="font-size:10pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7pt "Times New Roman""> </span></span></span><span style="font-size:10pt;color:black">Research data
repository manager</span></p>
<p class="" style="vertical-align:baseline"><span style="font-size:10pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7pt "Times New Roman""> </span></span></span><span style="font-size:10pt;color:black">Library or
information scientist</span></p>
<p class="" style="vertical-align:baseline"><span style="font-size:10pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7pt "Times New Roman""> </span></span></span><span style="font-size:10pt;color:black">Data curator</span></p>
<p class="MsoNormal" style="vertical-align:baseline"><span style="font-size:10pt"> </span></p>
<p class="MsoNormal" style="text-align:justify;vertical-align:baseline"><span style="font-size:10pt">Specifically,
</span><span style="font-size:10pt">the
NIH is seeking information on <b style="mso-bidi-font-weight:normal">qualitative
and quantitative metrics</b> such as those that describe: </span></p>
<p class="MsoNormal" style="text-align:justify;vertical-align:baseline"><span style="font-size:10pt"> </span></p>
<p class="" style="text-align:justify;vertical-align:baseline"><span style="font-size:10pt;font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7pt "Times New Roman"">
</span></span></span><b style="mso-bidi-font-weight:normal"><span style="font-size:10pt">Utilization at multiple levels</span></b><span style="font-size:10pt"> (repository, dataset, data item).</span></p>
<ul type="disc"><ul type="circle"><ul type="square"><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">Size and demand from the Xenopus
community served, placed in the context of the overall field.</span></li><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">the frequency of access and
number of downloads from Xenbase</span></li><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">The ongoing rate of data
deposition and data access or download</span></li></ul></ul></ul>
<p class="MsoNormal" style="margin-left:0in"><span style="font-size:10pt;font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7pt "Times New Roman"">
</span></span></span><b style="mso-bidi-font-weight:normal"><span style="font-size:10pt">Indicators of Xenbase quality and impact</span></b><span style="font-size:10pt">. Examples include but are not limited to:</span></p>
<ul type="disc"><ul type="circle"><ul type="square"><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">Publications from the data</span></li><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">Data citations</span></li><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">Altmetrics (i.e., <span class="">metrics other than citation numbers, impact factor or
h-index.)</span></span></li><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">Utilization of data sets in
research studies</span></li><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">Enhanced data sharing and
community collaboration around annotation/analysis of data sets</span></li></ul></ul></ul>
<p class="MsoNormal" style="margin-left:0in"><span style="font-size:10pt;font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7pt "Times New Roman"">
</span></span></span><b style="mso-bidi-font-weight:normal"><span style="font-size:10pt">Quality of service</span></b><span style="font-size:10pt">.
</span></p>
<ul type="disc"><ul type="circle"><ul type="square"><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">Use of community-recognized
standards</span></li><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">User support and training</span></li><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">Ease of data deposition and
retrieval</span></li><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">Technical indicators, e.g.,
uptime, response time</span></li></ul></ul></ul>
<p class="MsoNormal" style="margin-left:0in"><span style="font-size:10pt;font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7pt "Times New Roman"">
</span></span></span><b style="mso-bidi-font-weight:normal"><span style="font-size:10pt">Infrastructure and governance. </span></b><span style="font-size:10pt"> Examples may include but are not limited to:</span></p>
<ul type="disc"><ul type="circle"><ul type="square"><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">Existence of an independent
advisory board (note: Xenbase has an External Advisory Board)</span></li><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">Long-term sustainability plan</span></li></ul></ul></ul>
<p class="MsoNormal" style="margin-left:0in"><span style="font-size:10pt;font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7pt "Times New Roman"">
</span></span></span><b style="mso-bidi-font-weight:normal"><span style="font-size:10pt">Qualitative metrics</span></b><span style="font-size:10pt">
that may address many of the above categories, such as collection of use cases
or case studies</span></p>
<p class="MsoNormal" style="margin-left:0in"><span style="font-size:10pt;font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7pt "Times New Roman"">
</span></span></span><b style="mso-bidi-font-weight:normal"><span style="font-size:10pt">Consideration of case studies demonstrating the value of the
repository.</span></b><span style="font-size:10pt"> For example,
assessing the questions of:</span></p>
<ul type="disc"><ul type="circle"><ul type="square"><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">If Xenbase weren’t available,
how would that impact your work?</span></li><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">What are the data sharing
alternatives to the Xenbase?</span></li><li class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt">What are the implications of
using these alternatives?</span></li></ul></ul></ul>
<p class="MsoNormal" style="vertical-align:baseline"><b style="mso-bidi-font-weight:normal"><span style="font-size:10pt">Your response may
also include details of your role(s) within industry, government, or academia
and your history and experiences of relevant repositories. </span></b></p>
<p class="MsoNormal" style="vertical-align:baseline"><b style="mso-bidi-font-weight:normal"><span style="font-size:10pt"> </span></b></p>
<p class="MsoNormal" style="vertical-align:baseline"><b style="mso-bidi-font-weight:normal"><span style="font-size:10pt">We ask that you
respond to this NIH RFI immediately to express you support for Xenbase and
other data repositories and knowledgebases, and explain how the data that
Xenbase collates, curates and displays supports your research.</span></b></p>
<span style="font-size:10pt;font-family:Cambria"><br style="" clear="all">
</span>
<p class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt;color:blue">To assist you in your response to the NIH, several quotes taken from
letters of support Xenbase received for our 2015 P41 grant renewal. <br></span></p><p class="MsoNormal" style="margin-right: -0.5in;"><br><span style="font-size:10pt;color:blue"></span><span style="font-size:10pt"></span></p>
<p class="MsoNormal" style="text-align:center" align="center"><b style="mso-bidi-font-weight:
normal"><i style="mso-bidi-font-style:normal"><span style="font-size:10pt">“Xenbase
is </span></i></b><b style="mso-bidi-font-weight:normal"><i style="mso-bidi-font-style:
normal"><span style="font-size:10pt">an essential
part of our daily research”</span></i></b></p><p class="MsoNormal" style="text-align:center" align="center"><br><b style="mso-bidi-font-weight:normal"><i style="mso-bidi-font-style:
normal"><span style="font-size:10pt"></span></i></b><b style="mso-bidi-font-weight:normal"><i style="mso-bidi-font-style:normal"><span style="font-size:10pt"></span></i></b></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size:10pt;font-family:Arial">“Xenbase is an efficiently organized central database
and community web site that gives my research team access to many diverse types
of data including gene sequence, expression and function data, morpholino and
antibody support. It has become the first place I go to for all my
bioinformatic analyses. It provides a number of unique search tools tailored to
the Xenopus specific information that I need and allows me to efficiently
navigate to many other web sites”</span></p><p class="MsoNormal" style="text-align:justify"><br><span style="font-size:10pt;font-family:Arial"></span><span style="font-size:10pt;font-family:Times"></span></p>
<p class="MsoNormal" style="text-align:center" align="center"><i style="mso-bidi-font-style:
normal"><span style="font-size:9pt;font-family:Calibri">“Xenbase is a prime example of how species-specific data can be seamlessly
linked to external (government) resources for comparisons across species. As
computer processing speeds increase, centralized databases like Xenbase are
indispensable for storing, accessing, and maintaining compliance for grants and
publications.”</span></i></p><p class="MsoNormal" style="text-align:center" align="center"><i style="mso-bidi-font-style:
normal"><span style="font-size:9pt;font-family:Calibri"><br></span></i></p>
<p class="MsoNormal" style=""><span style="font-size:10pt;font-family:"Abadi MT Condensed Light"">“Xenbase provides critical information on Xenopus
genes that we cannot get from any other source. It is also the only place where
all of the different data from Xenopus is integrated, so we can find not only
genes but all of the sequences, publications and biological information on them
very easily.”</span></p><p class="MsoNormal" style=""><span style="font-size:10pt;font-family:"Abadi MT Condensed Light""><br></span></p>
<p class="MsoNormal" style="margin-bottom:12pt;text-align:justify"><span style="font-size:10pt;font-family:Calibri">“I could not imagine how my NIH-funded research would be possible
without my regular access of the Xenbase site.”</span><span style="font-size:10pt;font-family:Times"></span></p>
<p class="MsoNormal" style="text-align:center" align="center"><b style="mso-bidi-font-weight:
normal"><span style="font-size:10pt;font-family:"Apple Symbols""><span style="mso-spacerun:yes"> </span>“Xenbase is a critical partner in bringing
large scale data sets and resources (assembled EST expression data, time series
expression profiles, the Xenopus Orfeome, etc.) to the community.”</span></b></p><p class="MsoNormal" style="text-align:center" align="center"><b style="mso-bidi-font-weight:
normal"><span style="font-size:10pt;font-family:"Apple Symbols""><br></span></b></p>
<p class="MsoNormal" style="text-align:center" align="center"><i style="mso-bidi-font-style:
normal"><span style="font-size:10pt;font-family:Arial">We routinely use
Xenbase to blast our DNA sequences, to search for published Xenopus genes, to
review gene expression data, to identify key reagents, such as antibodies, and
to find new and old protocols.</span></i></p><p class="MsoNormal" style="text-align:center" align="center"><i style="mso-bidi-font-style:
normal"><span style="font-size:10pt;font-family:Arial"><br></span></i></p>
<p class="MsoNormal" style=""><b style="mso-bidi-font-weight:normal"><span style="font-size:8pt;font-family:Ayuthaya">“I truly believe that our research productivity would be
seriously compromised without access to this crucial resource.”</span></b></p><p class="MsoNormal" style=""><b style="mso-bidi-font-weight:normal"><span style="font-size:8pt;font-family:Ayuthaya"><br></span></b></p>
<p class="MsoNormal" style="text-align:center" align="center"><span style="font-family:"Franklin Gothic Medium"">“Xenbase is almost our sole access
point for bioinformatics services”</span></p><p class="MsoNormal" style="text-align:center" align="center"><span style="font-family:"Franklin Gothic Medium""><br></span></p>
<p class="MsoNormal" style="text-align:justify"><i style="mso-bidi-font-style:
normal"><span style="font-size:10pt;font-family:"Times New Roman"">“We have
recently carried out a genome-wide ChIP-seq and RNA-seq investigation …where
access to the services provided by Xenbase was absolutely instrumental for the
analysis of our raw data and then the interpretation of the identified targets.”</span></i></p><p class="MsoNormal" style="text-align:justify"><br><i style="mso-bidi-font-style:
normal"><span style="font-size:10pt;font-family:"Times New Roman""></span></i><i style="mso-bidi-font-style:normal"><span style="font-size:10pt;font-family:Times"></span></i></p>
<p class="MsoNormal" style="text-align:center" align="center"><span style="font-size:11pt;font-family:"Book Antiqua"">“Not only is
Xenbase useful for frog-specific information, but much of the general
information on gene function, synteny and links to disease resources and gene
information in other organisms is superior to other model organism web pages.”</span></p><p class="MsoNormal" style="text-align:center" align="center"><span style="font-size:11pt;font-family:"Book Antiqua""><br></span></p>
<p class="MsoNormal" style="text-align:center" align="center"><span style="font-size:9pt;font-family:Calibri">“The comprehensive gene
expression data available at Xenbase that includes both temporal changes in
mRNA (blots, microarrays and deep sequencing) and spatial information (<i>in
situ </i>hybridization) is indispensible to our efforts to interpret the data
we have collected in these important studies. Indeed, my students and I use
Xenbase nearly daily.”</span></p><p class="MsoNormal" style="text-align:center" align="center"><span style="font-size:9pt;font-family:Calibri"><br></span></p>
<p class="MsoNormal" style=""><span style="font-family:"Gloucester MT Extra Condensed"">“Higher education also benefits greatly from Xenbase. I am based at the
largest public university in the US, with over 82,000 students. Resources such
as Xenbase are valuable tools in our undergraduate courses…. Graduate students
take full advantage of databases such as Xenbase. Laboratories making use of
Xenbase allow us to train the next generation to make full use of the genomics
revolution.”</span></p><p class="MsoNormal" style=""><span style="font-family:"Gloucester MT Extra Condensed""><br></span></p><p class="MsoNormal" style=""><span style="font-family:"Gloucester MT Extra Condensed""><br></span></p>
<p class="MsoNormal" style=""><span style="font-size:10pt;font-family:"American Typewriter"">“Another measure of the value of Xenbase emerges
when I ask myself ‘What would I do without it?’ …. not having Xenbase … would
be a serious setback with numerous implications for our own research and for
the community, as Xenbase has become a focal point for us.”</span><span style="font-size:10pt;font-family:"American Typewriter""></span></p>
<p class="" style="text-align:justify"><span style="font-family:Chalkboard">We have
entered a new age in molecular genetics and genomics in which masses of
biological data (e.g., sequence information, in situ images, annotation of the
genes) are acquired and required to be hosted in a systematic fashion for the
Xenopus community.<span style="mso-spacerun:yes"> </span>My current research is
funded by three NIH grants and we use Xenbase routinely. It provides a number
of unique search tools tailored to the Xenopus specific information that I need
and allows me to efficiently navigate to many other [data] sites. </span><span style="font-family:Chalkboard"></span></p>
<p class="MsoNormal" style=""><span style="font-family:Chalkboard"> </span></p>
<p class="MsoNormal" style=""><span style="font-size:10pt;font-family:"Andale Mono""> </span></p>
<p class="MsoNormal" style="text-align:center" align="center"><i style="mso-bidi-font-style:
normal"><span style="font-size:9pt;font-family:Times"> </span></i></p>
<p class="MsoNormal" style="margin-right: -0.5in;"><span style="font-size:10pt"> </span></p>
</div>