dkNET poster presentation at the Endocrine Society's Annual Meeting on April 1-4, 2016, Boston, MA

1. The NIDDK Information Network - A Community Discovery Portal for Researchers:
Finding Data, Materials, and Tools Relevant to Your Research
Ko-Wei Lin, James Go, Yueling Li, Anita Bandrowski, Jeffrey S. Grethe, Maryann E. Martone
University of California San Diego, Center for Research in Biological Systems, School of Medicine, La Jolla, CA, USA
Support Reproducible Research
v For detailed information, please check our website
(https://dknet.org) or our article in PLoS ONE (DOI:
10.1371/journal.pone.0136206).
Abstract
Get Involved in dkNETCommunity
1. Users cansearchNIDDKrelatedresourcesusing dkNET Portal.
2. Stay upto date with notification alerts (New!)
a. Researchers: Find out when new relevant data are added.
b. Resource Providers: Find out when people are using your
resource.
Use Cases:
1. What clinical trial dataset s of polycystic kidney disease are
available?
2. Find mouse models of diet-­‐inducedobesity.
3. Look forfunding opportunities for type 1 diabetes.
4. Are there validatedant ibodie sagainst TR(Thyroidhormone
receptor) alpha isoform?
5. Are there chemical reagents for imaging the digest ive
system?
Connect to the Broader
Biomedical Community
1. dkNET is built on a collaborative community data platform
(SciCrunch.org). Under More Re sources, users can search
hundreds of m illionsof items from more than 200 addit ional
biomedical databases.
The
NIDDK
Information
Network
(dkNET)
portal
is
funded
in
part
by
the
NIDDK
under
grant
U24DK097771
Find What You Need
for Your Research
• Open
an
account
-­‐ join
the
community
• Find
research
resources
using
dkNET
• Subscribe
to
notification
alerts
• Follow
us
on
Twitter
@dkNET_Info
• Community
calendar
and
blog
• Sign
up
for
our
e-­‐mail
list
• Contact
us
at
info@dknet.org
• Make
your
resource
available
through
dkNET:
we
help
scientists
find
and
reuse
your
resources
and
data.
• Let
us
know
what
you’re
doing:
we
post
events,
funding
opportunities,
or
tutorials
for
your
center.
• Find
out
who
is
using
your
resources:
we
have
tools
to
track
mentions
in
the
literature.
User
Resource
Provider
What Can dkNET Do for You ?
1
Category
and
Subcategory
Search
Information
Sort
or
filter
by
keywordsFilter
results
using
different
facets
in
table
view
1. Journal e ditors, publication authors, and re source providers
can find Research Resource Identifiers (RRIDs) via the dkNET
portalfor citing resources (e.g., antibodies, model organisms,
software) inthe literature.
2. Using RRIDspromotes data reuse andreproducibility.
Users
can
search
resources
and
find
citation
guidelines
for
RRIDs
by
clicking
Cite
This
Using
RRIDs
in
published
papers
helps
standardize
resource
identification
1
2
Check
community
source
list,
news
and
events,
funding
opportunities
under
ABOUT
Find
dkNET community
resources
by
filtering
different
categories
and
subcategories
1
1
2 Login
to
edit
this
resource
or
subscribe
to
new
mentions
Users
can
discover
more
by
searching
under
under
More
Resources
1
SUN-764
TheNIDDK Information Network(dkNET;https://dknet.org) is an open community
resourcefor basic and clinical investigators in metabolic,digestiveand kidneydisease.
dkNET’s portal facilitates access to acollection of diverseresearch resources (i.e.the
multitude of data, software tools, materials, services, projects and organizations
availableto researchers) that advancethemissionoftheNational Instituteof Diabetes
and DigestiveandKidneyDiseases (NIDDK).Mostoftheseresources areaccessiblevia
web-­‐accessibledatabases or web portals,each developed,designed and maintained
bynumerous differentprojects,organizations andindividuals.
While many of the large government funded databases, maintained by agencies
such as NIH’s National Center for Biotechnology Information and the European
Bioinformatics Institute, arewell known to researchers, many more that have been
developed by and for the biomedical research community are unknown or
underutilized. One problem in discoveringthese resources is the nature of dynamic
databases,which areconsidered part of the“hidden” web,that is,content that is not
easilyaccessed bysearch engines.dkNETfunctions as aResourceand DataDiscovery
Index (i.e. a “search enginefor data and resources”), searching across millions of
database records contained in hundreds of biomedical databases and resources
developed and maintainedbyindependentprojects around theworld.dkNETmakes it
easyto find research resources relevantto your work,through aconcept based search
interface across NIDDK communityresources, e.g. Nuclear Receptor SignalingAtlas,
GenitoUrinary Molecular Anatomy Project, Diabetic Complications Consortium, to
name afew,as well as general biomedical resources. Through thenovel data ingest
process used indkNET,additional datasources can easilybeincorporated,allowingit
to scalewith thegrowth of digital dataandtheneeds of thedkNETcommunity.
In addition to search across data sources, dkNET provides the abilityto search
across aResourceRegistry,acurated catalogof thousands of research resources,and
the Literature, a searchable index across literature viaPubMed and full text articles
from theOpen Access literature.Buildingon dkNET’s coreinfrastructure,Wehavealso
worked to implement standards, most recently by brokering deals with major
publishers to improveresearchreproducibilitybyprovidingdatacuration andresearch
resource identification standards (http://scicrunch.org/resources) within their
publication pipelines.
Here,weprovidean overview of thedkNETportal and show how dkNETcan be
used to address avarietyof usecases that involvesearchingfor research resources.
Wewill also provideinformation on how researchers can get involvedwith dkNETand
associated effortssuchas theresearch resourceidentification initiative.
dkNET Challenge
Your Feedback Helps
Try
it
now!
Use
dkNET to
answer
any
one
of
five
questions
and
give
us
feedback!
Q1.
Funding
Opportunities
Find
funding
opportunity
announcements
related
to
obesity
that
expire
in
2016.
Q2.
Research
Materials
Can
you
find
validated
monoclonal
antibodies
against
Thyroid
Stimulating
Hormone
Receptor
(TSHR)
or
thyrotropin receptor?
Q3.
Clinical
Trials
How
many
clinical
trial
datasets
related
to
type
1
diabetes
are
available?
Q4.
Model
Organisms
Can
you
find
animal
models
of
polycystic
kidney
disease?
Q5.
Research
Resource
Identifier
(RRIDs)
You
are
required
to
use
RRIDs
when
publishing
a
paper.
Can
you
find
the
RRID
(Antibody
ID)
for
a
mouse
anti-­‐human
Glucagon-­‐like
peptide
1
receptor
(GLP1R)
antibody?
Your
opinions
or
suggestions
will
play
an
important
role
in
helping
us
to
build
better
tools
to
serve
the
community.
Survey
link:
https://www.surveymonkey.com/r/dknet
Keep You Up to Date with
the NIDDK Community