[Xenopus] How important is Xenbase to you? Respond to the NIH RFI by Sept 30.

Christina Zorn xenopus2 at gmail.com
Tue Aug 30 02:20:05 EDT 2016

The National Institutes for Health (NIH) recently announced a new *Request
for Information (RFI): Metrics to Assess Value of Biomedical Digital

All responses must be submitted by September 30, 2016.

Biomedical Digital Repository can be thought of in two general categories:
*Knowledgebase**s* and *Deposition repositories*.  Xenbase is a ‘
*Knowledgebase*’ 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unpublished (community submitted) experimental data. *Deposition
repositories*, like GenBank/NCBI, support primary research data submitted
by the data producers.

The NIH wants to understand and measure

1) the value of Xenbase and other data repositories,

2) the value of data types and data sets they contain, and

3) how important these data repositories are to your research.

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 *Xenopus* research community fall
under numerous categories, including, but not limited to:

·       Biomedical science researcher: PIs and Group Leaders, Post Docs and
Grad Students, Clinicians

·       Bioinformatician

·       Data scientist

·       Standard developer or maintainer

·       Research data repository manager

·       Library or information scientist

·       Data curator

Specifically, the NIH is seeking information on *qualitative and
quantitative metrics* such as those that describe:

·       *Utilization at multiple levels* (repository, dataset, data item).

   - Size and demand from the Xenopus community served, placed in the
         context of the overall field.
         - the frequency of access and number of downloads from Xenbase
         - The ongoing rate of data deposition and data access or download

·       *Indicators of Xenbase quality and impact*. Examples include but
are not limited to:

   - Publications from the data
         - Data citations
         - Altmetrics (i.e., metrics other than citation numbers, impact
         factor or h-index.)
         - Utilization of data sets in research studies
         - Enhanced data sharing and community collaboration around
         annotation/analysis of data sets

·       *Quality of service*.

   - Use of community-recognized standards
         - User support and training
         - Ease of data deposition and retrieval
         - Technical indicators, e.g., uptime, response time

·       *Infrastructure and governance. * Examples may include but are not
limited to:

   - Existence of an independent advisory board (note: Xenbase has an
         External Advisory Board)
         - Long-term sustainability plan

·       *Qualitative metrics* that may address many of the above
categories, such as collection of use cases or case studies

·       *Consideration of case studies demonstrating the value of the
repository.* For example, assessing the questions of:

   - If Xenbase weren’t available, how would that impact your work?
         - What are the data sharing alternatives to the Xenbase?
         - What are the implications of using these alternatives?

*Your response may also include details of your role(s) within industry,
government, or academia and your history and experiences of relevant
repositories. *

*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

To assist you in your response to the NIH, several quotes taken from
letters of support Xenbase received for our 2015 P41 grant renewal.

*“Xenbase is **an essential part of our daily research”*

“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”

*“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.”*

“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.”

“I could not imagine how my NIH-funded research would be possible without
my regular access of the Xenbase site.”

* “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.”*

*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.*

*“I truly believe that our research productivity would be seriously
compromised without access to this crucial resource.”*

“Xenbase is almost our sole access point for bioinformatics services”

*“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.”*

“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.”

“The comprehensive gene expression data available at Xenbase that includes
both temporal changes in mRNA (blots, microarrays and deep sequencing) and
spatial information (*in situ *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.”

“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.”

“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.”

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.  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]
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