dkNET poster presentation at the Experimental Biology 2019 on April 6-9, 2019 in Orlando, FL.

1. • dkNET (The NIDDK Information Network, https://dknet.org) is an
open community resource portal for researchers in diabetes,
digestive, endocrine, obesity, metabolic, kidney, and urologic disease
fields.
• dkNET provides access to a collection of diverse research resources,
including data, information, materials, organisms, tools, funding
opportunities, literature, services, and events that advance the
mission of the National Institute of Diabetes and Digestive and
Kidney Diseases (NIDDK).
• The use of problematic resources such as contaminated or
misidentified cell lines and crossCreactive antibodies lead to
reproducibility problems. Research has shown that about twenty
percent of published studies use contaminated cell lines. Many
factors, including the ability to easily retrieve alert information,
result in continued use of these resources wasting both time and
money.
• dkNET supports Research Resource Identifiers (RRIDs) to ensure that
reagent and tools are properly identified within published studies.
RRIDs allow dkNET to aggregate and provide in depth information
about how resources are used and information on known problems.
• dkNET continuously updates its data sources, providing researchers
upCtoCdate information about research resources.
• The newly designed dkNET portal includes many new tools and
services that can assist researchers in finding and selecting the
appropriate resources for their research and in supporting efforts to
improve rigor and reproducibility.
• The new portal contains four service areas : Resource Reports,
Discovery Portal, Rigor & Reproducibility Support, and Hypothesis
Center.
dkNET&(NIDDK&Information&Network):&Research&Tools&That&Assist&Scientists&in&Improving&the&Rigor&and&Reproducibility&of&Their&Research
Ko-Wei Lin, Anita E. Bandrowski, Tom Gillespie, James Go, Vicky Guo, Stephanie Hagstrom, Chun-Nan Hsu, Ibrahim B. Ozyurt,
Jeffrey S. Grethe, and Maryann E. Martone
Center for Research in Biological Systems, School of Medicine, University of California San Diego, La Jolla, CA, USA
! ForLdetailedLinformation,LpleaseLgoLto https://dknet.org
! NeedLhelp?LContactLinfo@dknet.org
! CheckLoutLsomeLofLourLpublications:L
• dkNETLarticleLinLPLoSLONEL(DOI:L10.1371/journal.pone.0136206)
• RRIDLarticlesLinLNeuronL(DOI:L10.1016/j.neuron.2016.04.030)LandL
eLIFEL(DOI:10.7554/eLife.41676)
What&is&dkNET?
Get&Involved&in&the&dkNET&Community
Resource&Reports&J Usage&and&Citation&Metrics
• Research Resource Identifiers (RRIDs) are persistent and unique identifiers
for research resources, and the use of RRIDs help promote reuse and
reproducibility.
• RRIDs currently appear in over 8000 papers across 600 biomedical
journals, including Endocrine Society Journals, Nature, Elsevier, BMC,
Frontiers, Cell Press, and Wiley. RRIDs provide a unique means for
disseminating information about resource performance.
• Analysis of cell lines in published papers using RRIDs vs those didn’t use
RRIDs, showed the reported use of contaminated cell lines is significantly
lower in papers with RRIDs than in the average paper, suggesting that
making researchers aware of problematic resources may decrease their
usage.
• dkNET used RRIDs, to develop several tools, such as Resource Reports and
Reproducibility Reports, to help scientists enhance research rigor and
reproducibility. dkNET used RRIDs, text mining and data aggregation to
track resource use and provide information on resource performance.
dkNETLisLfundedLinLpartLbyL
theLNIHLNIDDKLunderLgrantL
U24DK097771
Research&Resource&Identifiers&(RRIDs)
• Sign&up&for&our&eJmail&list
• Open&an&account&J join&the&community
• Find&and&get&information&on&research&
resources&using&dkNET
• Track&resources&via&collections
• Follow&us&on&Twitter&@dkNET_Info
• Community&calendar&and&blog
• 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&Help&You&With&Your&Research? Summary
Your&Feedback&Helps
Your opinions or suggestions will play an
important role in helping us to build
better tools to serve the community.
Join our Beta test or fill in online survey.
https://goo.gl/EY2LNf
Introduction&of&Resource&Reports
• Newly&designed&Discovery&Portal&connectsLresearchersLtoLmoreLthanL
200LbiomedicalLdatabasesLandLmillionsLofLresourcesLandLLiterature.L
ResearchersLcanLalsoLexploreLcommunityLresourcesLthatLareLhighlyL
relevantLtoLtheLdiseaseLfieldsLinLNIDDK’sLmission.
• FAIR&data&resources&provideLinformationLaboutLdataLmanagementL
plansLandLaLlistLofLsuggestedLdataLrepositories.L
• Hypothesis&Center:&dkNETLisLpartneringLwithLthe SignalingLPathwaysL
ProjectL(SPP)LknowledgeLbase,LwhichLhasLdevelopedLaLpowerfulLnewL
metaCanalysisLplatformLforLdiverseL‘omicsLdata,LallowingLresearchersL
toLmodelLsignalingLeventsLtoLgenerateLorLtestLresearchLhypotheses.L
ExamplesLofLuseLcase:L
(1) SearchLforLlistLofLgenesLwithLimportantLrolesLinLreceptors,L
enzymes,Lorgans,LandLtissuesL
(2) SearchLnovelLsignalingLpathwaysLusingLregulationLreports
What&questions&can&
resource&report&answer?
1. Resource&Information&–IsLthisLaL
contaminatedLcellLlines?LWhatLareL
theLvalidatedLapplicationsLforLthisL
antibodies?LHowLtoLciteLthisL
resourceLproperly?
2. Usage&and&Citation&Metrics&– WhoL
elseLusedLthisLresource?LWhichL
papersLmentionedLthisLresource?
3. Ratings&and&Alerts&– AreLthereL
ratingLorLvalidationLinformationL
availableLforLmyLantibodies?L
4. Collaborator&Network&&C AreLthereL
researchersLwhoLusedLthisL
resourceLnearLmyLinstitution?
Start&Checking&and&Tracking&Your&Resources&in&3&Steps
1. Usage and Citation Metrics – Resource Usage Report provides
researchers a simple way to explore citations of the use of this resource.
The citation information is updated automatically as the RRIDCbased text
mining pipeline finds new papers that cite the resources from biomedical
literature (Table 1, 2). Researchers can view a yearly distribution chart and
a full list of articles. Information about what resources have been used
together is also shown in this section.
1
2 4
3
2
Find&
resources&
at&dkNET
Learn&about&your&
resources&using&
Resource&Reports
Sign&up&for&a&free&account&
to&track&these&resources&
using&Collection&feature&or&
to&create&Reproducibility&
Reports.
dkNET&provides&
authentication&
information,&
resource&
information&
and&alerts.
Search&for&a&list&
of&genes&with&
important&roles&
in&PPAR&
(peroxisome&
proliferatorJ
activated&
receptors)&family&
in&mouse&
metabolic&
system
Explore&More&at&dkNET&3.0
A&search&of&dkNET&(April&
4,&2019)&showed&a&list&of&
problematic&cell&lines&
(contaminated&and/or&
misidentified&cell&lines).
What’s in Resource Reports?
1. Resource Information – A detailed overview of each resource, including
documented problems with the resource, organisms, target antigen and
validated applications for antibodies, proper citation, etc. dkNET updates
its data from community resource registries, such as the Cellosaurus,
Antibody Registry, the SciCrunch Registry and a variety of organism
repositories.
3. Rating and Alerts – dkNET provides information on resource ratings,
validation, and provides alerts for problematic resources when available.
Currently, dkNET aggregates information from Cellosaurus, Antibody
Registry, ENCODE, Human Protein Atlas, NITRC, and resource centers such
as the Intestinal Stem Cell Consortium (ISCC).
4. Collaborator Network – dkNET provides researchers a search tool to find
a list of researchers by locations. Research can find collaborators near
their location or at a specific institution, city or state.
1
4
3
2
Yearly&
distribution&
chart
Mention&
list
A&list&of&resources&that&
have&been&frequently&
mentioned&with&this&
resources
Reproducibility&Reports&
Support&Reproducible&Research&using&RRIDs&and&dkNET&Tools&Now!&
• RRIDsLandLtheLassociatedLtoolsLandLservicesLatLdkNETLmakeLitLeasierL
forLtrackingLandLdisseminationLofLinformationLonLresourceL
performance.
• FindLRRIDsLforLyourLresourcesLviaLResourceLReports.LRememberLtoL
includeLRRIDsLinLyourLproposalLandLpublications.
• CheckLResourceLReportsLbeforeLplanningLexperimentsLorLpurchasingL
resources,LandLafterLpublications.
• CheckLauthenticationLplansLviaLReproducibilityLReportsLbeforeL
submittingLgrantLproposalsLorLplanningLexperiments.
• For submitting grant or planning experiments, dkNET helps researchers to
create authentication plans/reports for cell lines and antibodies easily.
• Researchers can save resources for projects, obtain their RRIDs, retrieve
metadata information, and generate authentication plans for proposal
submission or for use in the laboratory.
• dkNET continuously updates data sources and researchers can check for
problematic resources.
Resource&alerts
Suggested&Authentication&Plans