Your SlideShare is downloading. ×
0
Melissa Haendel, OHSU Library
April 9, 2014
The Resource Identification
Initiative:
What are we curating anyway?
@ontowonk...
Journal guidelines for methods are often poor and
space is limited
“All companies from which materials were obtained shoul...
How identifiable are resources in the
published literature?
An experiment in reproducibility
Domains:
Immunology
Cell biology
Neuroscience
Developmental
biology
General biology
Impac...
Only ~50% of resources were identifiable
Vasilevsky et al, 2013, PeerJ
There is no correlation between impact factor and
resource identification
Journal Impact Factor
0 10 20 30 40
Fractionofre...
Resources are not more identifiable in journals
with stricter reporting requirements
http://validation.scienceexchange.com/#/cancer-biology
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 repor...
Maybe labs are just disorganized?
Meet the Urban Lab
Meet the Urban Lab
A+ organization!
The Urban lab antibodies
Of 9 antibodies published in 5 articles, only
44% were identifiable
Percentidentifiable
0%
25%
50%
75%
100%
Commerical Ab
...
Resource information is not adequately
getting into the literature, EVEN
THOUGH IT IS READILY AVAILABLE
The problem is a l...
http://www.force11.org/Resource_Identification_Initiative
Numerous endorsers https://www.force11.org/RII/SignUp
Implementa...
Promoting use of Research Resource
IDs (RRIDs) in the published literature
Antibodies
Software & Tools
Model Organisms
Pil...
Sample citation:
Polyclonal rabbit anti-
MAPK3
antibody, Abgent, Cat#
AP7251E,
RRID:AB_2140114
1.
Research
er
submits a
ma...
Potential outcomes
 Better reporting of materials and methods
 Making the literature machine readable
outside the paywal...
Be a beta tester!
http://www.antibodies-
online.com/resource-
identification-initiative/
Free gift!
Questions and issues
• Should the RRIDs be: DOIs? URIs? Nanopubs?
– Most sources do not create these
• Part of a new bibli...
Upcoming SlideShare
Loading in...5
×

Biocuration 2014 - The Resource Identification Initiative

564

Published on

Published in: Technology, Business
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
564
On Slideshare
0
From Embeds
0
Number of Embeds
2
Actions
Shares
0
Downloads
3
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Transcript of "Biocuration 2014 - The Resource Identification Initiative"

  1. 1. Melissa Haendel, OHSU Library April 9, 2014 The Resource Identification Initiative: What are we curating anyway? @ontowonka #RII
  2. 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. 3. How identifiable are resources in the published literature?
  4. 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. 5. Only ~50% of resources were identifiable Vasilevsky et al, 2013, PeerJ
  6. 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. 7. Resources are not more identifiable in journals with stricter reporting requirements
  8. 8. http://validation.scienceexchange.com/#/cancer-biology Attempting to reproduce 50 prominent cancer studies
  9. 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. 10. Maybe labs are just disorganized?
  11. 11. Meet the Urban Lab Meet the Urban Lab
  12. 12. A+ organization! The Urban lab antibodies
  13. 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. 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. 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. 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. 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. 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. 19. Be a beta tester! http://www.antibodies- online.com/resource- identification-initiative/ Free gift!
  20. 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?
  1. A particular slide catching your eye?

    Clipping is a handy way to collect important slides you want to go back to later.

×