Transcript of "Biocuration 2014 - The Resource Identification Initiative"
Melissa Haendel, OHSU Library
April 9, 2014
The Resource Identification
What are we curating anyway?
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…
How identifiable are resources in the
An experiment in reproducibility
104 cell lines
Only ~50% of resources were identifiable
Vasilevsky et al, 2013, PeerJ
There is no correlation between impact factor and
Journal Impact Factor
0 10 20 30 40
Resources are not more identifiable in journals
with stricter reporting requirements
Attempting to reproduce 50 prominent cancer studies
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
Of 9 antibodies published in 5 articles, only
44% were identifiable
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
Numerous endorsers https://www.force11.org/RII/SignUp
Implementation of the new standard http://biosharing.org/bsg-000532
Promoting use of Research Resource
IDs (RRIDs) in the published literature
Software & Tools
Pilot project runs from February – April
RRIDs should be:
Consistent across publishers and
Free to generate and access
Polyclonal rabbit anti-
antibody, Abgent, Cat#
2. Editor or
3. Author goes to
Portal to locate
4. RRID is
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
Better retrospective reanalysis of data
Ability for authors to subscribe to resources
and semantically similar entities
Be a beta tester!
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
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