Presentation on the Resource Identification Pilot Project, an initiative to develop a machine-processable citation system for key research resources used in scientific studies

1. Maryann E. Martone, Ph. D.
Professor of Neuroscience, University of California, San Diego
The Resource Identification Initiative

2. What research resources are used in
biomedical research?
◦ Resources = materials, organisms, tools, data, services
What other published studies used this
resource?
Our current system for publication and citation
makes these two straightforward cases difficult

3. Access to Materials and Methods sections
Machine Readability
◦ “We used the protocol of Martone et al., 1999”
◦ Official mouse strain names not meant for computers
SMNΔ7tg/tg:Smn1−/−
◦ Non-unique, common names for resources, e.g., Enzyme
Lack of Identifiers ****
◦ Author doesn’t supply sufficient information to uniquely identify the
resource
No stock numbers, catalog numbers, model numbers, or other uniquely identifying
information

4. The following antibodies were used for
immunoblotting: -actin mAb (1:10,000 dilution, Sigma-
Aldrich); -tubulin mAb (1:10,000, Abcam); T46 mAb (specific to tau
404–441, 1:1000, Invitrogen); Tau-5 mAb (human tau 218–225,
1:1000, BD Biosciences) (Porzig et al., 2007); AT8 mAb (phospho-
tau Ser199, Ser202, and Thr205, 1:500, Innogenetics); PHF-1 mAb
(phospho-tau Ser396 and Ser404, 1:250, gift from P. Davies); 12E8
mAb (phospho-tau Ser262 and Ser356, 1:1000, gift from P.
Seubert); NMDA receptors 2A, 2B and 2D goat pAbs (C terminus,
1:1000, Santa Cruz Biotechnology)…
mAb=monoclon
al antibody

5. Hypothesis: Resources in the published literature
are not uniquely identifiable
Gather journal
articles
5 domains:
Immunology
Cell biology
Neuroscience
Developmental
biology
General biology
3 impact factors:
High
Medium
Low
84 Journals
238 papers
707 antibodies
104 cell lines
258 constructs
210 knockdown
reagents
437 model
organisms
Vasilevsky et al, PeerJ, 2013

6. The
problem is
general
across
multiple
resource
types and
disciplines
Vasilevsky et al, Peer J 2013

7. Faulty Antibodies Continue to Enter
US and European Markets, Warns Top
Clinical Chemistry Researcher-
Genome Web Daily, October 11, 2013
“…of the findings in the literature about
neuronal NF-κB are based on data garnered
with antibodies that are not selective for the
NF-κB …”
-Herkenham et al. J Neuroinflammation 2011,
8:141

8. Two pre-meetings with
editors and publishers
◦ Society for Neuroscience
◦ NIH: June, 2013
Designed pilot project
◦ Entities
◦ Procedure
◦ Infrastructure
Established working group
through FORCE11
Signed up partners
Led by: Matt Brush, Nicole
Vasilevsky, Anita Bandrowski
And more
https://www.force11.org/Resource_identification_initiative

9. ID’s should be:
◦ Machine processible (i.e.,
unique identifier that resolves
to a single resource)
◦ Outside of the paywall
◦ Uniform across journals and
publishers
Proof of principle
◦ What infrastructure would be
needed?
◦ Will authors perform the task?
◦ Can authors perform the task?
◦ Will it be useful?

10. Authors to identify 3 types of
research resources:
◦ Software /databases
◦ Antibodies
◦ Model organisms
Include RRID in methods section
Voluntary for authors
Journals did not have to modify
their submission system
Journals have flexibility in
implementation. Send request to
author at:
◦ Submission
◦ During review
◦ After acceptance
Launched February 2014: 3 month commitment
and more…

11. A single portal for
authors
◦ RRID’s = accession
numbers from
authoritative database
◦ Identifiers were
scattered over >10
different databases
◦ Very difficult to find the
identifier in some cases
Uniform format for
citation
Help desk for authors
http://scicrunch.com/resources

12. Google Scholar: Search RRID; select since 2014

13. •80 articles have appeared
to date
•15 journals
•Data set being made
available to community
•>500 RRID’s
•3 removed by
typesetting
•94% correct
•14% false negative
rate
•>200 antibodies were
added
•>75 software
tools/databases were
added
•~50 help requests
Database available at: https://www.force11.org/node/5635

14. A resolver
service has been
created
3rd party tools
are being
created to
provide linkage
between
resources and
papers
◦ Utopia prototype
◦ Text mining tools
for assigning and
validating RRID’s
http://scicrunch.com/resolver/RRID:nlx_14
4509

15. Authors are willing to adopt new types of
citations
Authors were fairly accurate at performing
the task
RRID’s resolved by search engines without
requiring specialized citation services
Citation drives registration
Clear role for repositories as authorities

16. What identifier systems should be used
◦ Accession numbers vs DOI’s
◦ Entities vs digital objects
Integrate with system for citation of data sets
and more complex research objects
What entities should be identified?
◦ All reagents and tools?
◦ Governance
Machine actionability

17. Join the Resource Identification Initiative!
◦ Authors: Add ID’s to your papers
◦ Journal Editors: It’s not too late to join!
◦ Publishers: Use RRID’s to enhance the reading
experience
Vendors:
◦ List your products in the Resource Registry
◦ Include RRID’s in your catalog
◦ Increase transparency!