The document discusses the Resource Identification Initiative (RII) which aims to improve reproducibility in scientific research by promoting the use of Research Resource Identifiers (RRIDs) in published literature. An experiment analyzing over 800 biological resources across multiple journals found that only about 50% were identifiable. The RII is developing standards and tools to integrate RRIDs into the publishing workflow so that resources are consistently and uniquely identified in a machine-readable way. This could help credit data contributions, enable data reanalysis, and improve reproducibility overall. A pilot project is underway to test the inclusion of RRIDs in publications.

1. Melissa Haendel, OHSU Library
April 9, 2014
The Resource Identification
Initiative:
What are we curating anyway?
@ontowonka #RII

2. Journal guidelines for methods are often poor and
space is limited
“All companies from which materials were obtained should
be listed.” - A well-known journal
Reproducibility is dependent at a minimum, on
using the same resources. But…

3. How identifiable are resources in the
published literature?

4. An experiment in reproducibility
Domains:
Immunology
Cell biology
Neuroscience
Developmental
biology
General biology
Impact factors:
High
Medium
Low
84 Journals
248 papers
707 antibodies
104 cell lines
258 constructs
210 knockdown
reagents
437 model
organisms
Reporting Guidelines:
Stringent
Satisfactory
Loose

5. Only ~50% of resources were identifiable
Vasilevsky et al, 2013, PeerJ

6. There is no correlation between impact factor and
resource identification
Journal Impact Factor
0 10 20 30 40
Fractionofresourcesidentified
0.0
0.2
0.4
0.6
0.8
1.0 Antibodies
Cell Lines
Constructs
Knockdown reagents
Organisms

7. Resources are not more identifiable in journals
with stricter reporting requirements

8. http://validation.scienceexchange.com/#/cancer-biology
Attempting to reproduce 50 prominent cancer studies

9. Even for some of the highest profile papers, we still
have to go back to the authors to identify resources
Resources reported in the 50 Reproducibility
Initiative studies show similar results
Vasilevsky et al., 2013, PeerJ
Reproducibility Initiative
http://shar.es/BSsab

10. Maybe labs are just disorganized?

11. Meet the Urban Lab
Meet the Urban Lab

12. A+ organization!
The Urban lab antibodies

13. Of 9 antibodies published in 5 articles, only
44% were identifiable
Percentidentifiable
0%
25%
50%
75%
100%
Commerical Ab
identifiable
Catalog number
reported
Source organism
reported
Target uniquely
identifiable

14. Resource information is not adequately
getting into the literature, EVEN
THOUGH IT IS READILY AVAILABLE
The problem is a lack of standards,
review, and tools

15. http://www.force11.org/Resource_Identification_Initiative
Numerous endorsers https://www.force11.org/RII/SignUp
Implementation of the new standard http://biosharing.org/bsg-000532

16. Promoting use of Research Resource
IDs (RRIDs) in the published literature
Antibodies
Software & Tools
Model Organisms
Pilot project runs from February – April
RRIDs should be:
Machine Readable
Consistent across publishers and
journals
Free to generate and access
Resources:

17. Sample citation:
Polyclonal rabbit anti-
MAPK3
antibody, Abgent, Cat#
AP7251E,
RRID:AB_2140114
1.
Research
er
submits a
manuscri
pt for
publicatio
n
2. Editor or
Publisher
asks for
inclusion of
RRID
3. Author goes to
Research
Identification
Portal to locate
RRID
4. RRID is
included
in
Methods
section
and
as
Keyword
Publishing Workflow

18. Potential outcomes
 Better reporting of materials and methods
 Making the literature machine readable
outside the paywall
 Reduce the curation load
 Change how we utilize the literature –
observations span journals and formats
 Credit and citation tracking for contributions
of resources
 Better retrospective reanalysis of data
 Ability for authors to subscribe to resources
and semantically similar entities

19. Be a beta tester!
http://www.antibodies-
online.com/resource-
identification-initiative/
Free gift!

20. Questions and issues
• Should the RRIDs be: DOIs? URIs? Nanopubs?
– Most sources do not create these
• Part of a new bibliographic type?
– For pilot, going into keywords to be outside paywall
• What is the best way to incorporate the RIID portal
into the publishers workflow?
– Provide text-mined checklist when author submits?
• How to best synchronize and coordinate
nomenclature with authoritative sources aggregated
in the RII Portal?
• How to utilize the RII Portal in dataset contribution to
data repositories?