dkNET Webinar: Discover the Latest from dkNET - Biomed Resource Watch Presenter: Jeffrey Grethe, PhD, dkNET Principal Investigator, University of California San Diego Abstract The dkNET (NIDDK Information Network) team is announcing an exciting new service - Biomed Resource Watch (BRW, https://scicrunch.org/ResourceWatch), a knowledge base for aggregating and disseminating known problems and performance information about research resources such as antibodies, cell lines, and tools. We aggregate trustworthy information from authorized sources such as Cellosaurus, Antibody Registry, Human Protein Atlas, ENCODE, and many more. In addition, BRW includes antibody specificity text mining information extracted from the literature via natural language processing. BRW provides researchers and curators an easy-to-use interface to report their claims about a specific resource. Researchers can check information about a resource before planning their experiments via BRW-enhanced Resource Reports. This new service aims to help improve efficiency in selecting appropriate resources, enhancing scientific rigor and reproducibility, and promoting a FAIR (Findable, Accessible, Interoperable, Reusable) research resource ecosystem in the biomedical research community. Join us for a webinar to introduce the following resources & topics: 1. An overview of dkNET 2. How Resource Reports benefit you 3. Biomed Resource Watch 3.1 Navigating Biomed Resource Watch 3.2 How to Submit a Claim Upcoming webinars schedule: https://dknet.org/about/webinar

1. An NIDDK Resource dknet.org
Discover the Latest from dkNET
- Biomed Resource Watch
Jeffrey S. Grethe, Ph.D.
dkNET Webinar Series
June 2, 2023

2. An NIDDK Resource dknet.org
About dkNET
• Research resource information portal for biomedical researchers
• Information network to connect DK researchers and NIH-funded
centers
• Funded by National Institute of Health (NIH) - National Institute of
Diabetes and Digestive and Kidney Diseases (NIDDK)
• Developed and maintained by the FAIR Data Informatics Laboratory
(fdilab.org) at UCSD (Supports major informatics projects in
biomedicine)

3. An NIDDK Resource dknet.org
5 AREAS IN THE PORTAL
● dkNET provides:
○ Resource Reports: helps researchers find and evaluate resources
○ Authentication Reports: assists researchers in preparing NIH authentication plans
○ FAIR Data Services: assists researchers in finding data repositories and standards
for preparing data management plans
○ Discovery Portal: connects researchers to more than 200 biomedical databases
○ Hypothesis Center: powerful tools for data mining and hypothesis generation of
FAIR ‘omics data

4. An NIDDK Resource dknet.org
dkNET Portal https://dknet.org

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How is dkNET Helping Researchers?
Construct a
hypothesis
Ask a question
Do background
research
Plan
experiments
Collect and
analyze data Publish
results
Discovery Portal Hypothesis Center Resource Reports
Authentication
Reports
Information
Material
Data
Tools
Funded grant and
funding opportunities
Literature
Tutorials
Resource Reports
Hypothesis Center
FAIR Data Resources
Data Management
Data Repositories
Resource Reports
Cite RRID
Track Resources
Resource Identification
Authentication plans
NIH Mandates on Rigor
and Reproducibility for
grant submission
SPP
MMPC
•
•
•

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An NIDDK Resource
Research resource identifiers
Identification of key biological resources

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An NIDDK Resource
Why were RRIDs introduced

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An NIDDK Resource
How common is this?
Papers are
currently poor at
identifying the
simplest part of
the paper, the
materials used
Vasilevsky 2013

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An NIDDK Resource
RRIDs are:
● Unique identifiers for
research resources
● Search friendly
● Provided by independent
community registries who
track a single type of
resource
RRID:AB_1855196
Fothergill LJ et al. Cell and Tissue Research. 375 (2) 359-69, 2019.

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An NIDDK Resource
Why were RRIDs created?
Tracking
Who used these mice?
Rigor and Transparency
New Guidelines Authenticate:
Antibodies, Cell lines, Organisms
RRIDs answer both needs
“...Blueprint IC were briefed on the
neuromouse project .. publication
generated using this resource- (It
was 4 - believe)- to the extent NIF
could offer a strategy for
monitoring/tracking this resource
that would be extremely valuable…”
Nov 2011
Resource Identification Initiative

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● RRIDs in use across major publishers:
○ Cell Press, Elsevier, Wiley, Nature, Science
● 2019: JATS standard (Journal Article Tag Suite)
● Part of Materials Design Analysis Reporting (MDAR) Checklist
for Authors
● Part of the new ARRIVE Essential 10 reporting checklist
Significant Growth of RRID Adoption
2,350+
Distinct
Journals
90,000 Distinct Resources Identified
620,000 RRID Citations in Literature
55,000 page views per month *
20,400 sessions per month
750,000 resolver hits per month
> 1,000,000
RIN/RRID Pageviews per Year*
(Webpage + API)
Journals with RRID annotations

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Recent Journals/Publisher

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https://grants.nih.gov/grants/guide/rfa-files/RFA-DA-18-014.html
RRIDs are requested
in several RFAs
(NIDA & NIDDK)

14. dknet.org
An NIDDK Resource
Resource Information Network
Ecosystem of information about key biological resources

15. dknet.org
An NIDDK Resource
Resource Reports
Find antibodies, organisms, cell lines, tools
and services, plasmids, biosamples that are:
● the most cited
● validated or recommended
● used by others near me
I’m publishing a
paper, and would
like to find RRIDs for
citing key resources.
Construct a
hypothesis
Ask a question
Do background
research
Plan
experiments
Collect and
analyze data
Publish
results
I’m planning my
experiments, and
would like to find and
evaluate key
resources.

16. dknet.org
An NIDDK Resource
Resource Reports
Report includes:
● Citations of usage
and mentions
● Who is using them?
● Do they have issues?
● How do they
compare?
● Is anyone near me
familiar with them?

17. An NIDDK Resource dknet.org
Making Resources FAIR
• dkNET’s Resource Information Network (RIN) is a unique data set and suite of
associated services and tools
• Research Resource Identifiers (RRIDs) are the foundation of the RIN
• RRIDs enable aggregation of information about key biomedical research resources
• RRIDs have major impact on resources:
• Findability
• Identifiability
• Trackability
• Improved rigor and reproducibility
FAIR is not just for data!

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An NIDDK Resource
WARNING! Problematic Research Resources
“Not one of my published papers has led to a retraction
by a journal or scientist. Less than 10 corrections have
been issued, when each false line I discovered affects
the conclusions of hundreds or thousands of papers.”
● Reagent problems in the biomedical
literature have been estimated to cost the
NIH $10B each year as papers that are not
reproducible swamp the scientific literature
● Key reagents such as antibodies can be
tracked down less than 50% of the time.

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RRIDs associated with a lower reported use of
problematic cell lines
Babic Z, et al. eLIFE 2019; 8:e41676 DOI: 10.7554/eLife.41676

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An NIDDK Resource
Resources Rating and Alerts
RRIDs provide us with an
opportunity to alert
researchers to issues with a
particular resource at time of
publication
dkNET aggregates information from multiple sources about
known issues with these resources

21. dknet.org
An NIDDK Resource
Biomed Resource Watch
Aggregation of information about key biological resources

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Biomed Resource Watch https://scicrunch.org/ResourceWatch
• Resource performance
information for
research resources
• Aggregation from
varied sources
• Community
contribution
• Information from
advanced text mining
algorithms

23. An NIDDK Resource dknet.org
Biomed Resource Watch (BRW)
Alerts RRID
Sources and
metadata
Literature
Collaborators
Validation & Ratings
Antibody Watch
Core Facilities
Authorized sources
Community sources
Text mining from the literature
about antibody specificity
Individual researchers
NEW

24. An NIDDK Resource dknet.org
NLP - Antibody Specificity Information
● Text mining antibody specificity from the
literature by deep learning.
● 33,712 papers from 2018 – 2021 with RRID
mentions processed.
● 5,241 found to contain antibody RRIDs.
● 163 claims of non-specific antibodies identified.
Hsu C-N, et al.PLOS Computational Biology. 2021 May
27;17(5):e1008967.

25. An NIDDK Resource dknet.org
A Knowledgebase for Communicating Resource Information
Provide resource validation and
performance Information

26. An NIDDK Resource dknet.org
dkNET is partnering with YCharOS
YCharOS Inc. is an open science
company with the mission of
characterizing commercially
available reagent antibodies for
every human protein. Directly works
with vendors as partners

27. An NIDDK Resource dknet.org
Aggregate Trustworthy Information From Various Resources
NEW
● Bulk Upload
Implementation
● New data addition

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Connecting dkNET to BRW

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Allow Contributions From Researchers
Resources Submission Types
Antibodies Validation, discontinued, and issues
such as non-specific
Cell Lines Validation, discontinued, issues,
contaminated, misidentified,
misclassified
Tools Validation, issues, discontinued
Information Accepted Report an issue or validation information?
It's easy! Follow these steps:

30. An NIDDK Resource dknet.org
Submission Instructions and Tutorials
Submission
instruction
based on
resource
type

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Submission and Curator Dashboard Implementation
Streamline submissions:
Curator can use easy-to-use
dashboard to monitor and
manage the submission and
communicate easily

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Walk-through of Biomed Resource Watch

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Starting from Biomed Resource Watch
AB_2315049 https://scicrunch.org/ResourceWatch

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Resource Information Webpage

35. An NIDDK Resource dknet.org
Confirm the resource

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Submission Form

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Report Information from dkNET

38. An NIDDK Resource dknet.org
Login to Confirm

39. An NIDDK Resource dknet.org
Submission Form

40. dknet.org
An NIDDK Resource
Questions?