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.
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Biocuration 2014 - The Resource Identification Initiative
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…
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
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
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?