Presented to ALPSP annual meeting 2011 in Oxfordshire UK during a session entitled "Abort Retry Fail? Data and the scholarly literature"

1. Research data and scholarly publications:Going from casual acquaintances to something more Todd Vision Dept of Biology, University of North Carolina at Chapel Hill and the U.S. National Evolutionary Synthesis Center ALPSP, September 2011 Abort, Retry, Fail? Data and the scholarly literature

4. Peer-to-peer ‘sharing’ fails Wicherts and colleagues requested data from from 141 articles in American Psychological Association journals. “6 months later, after … 400 emails, [sending] detailed descriptions of our study aims, approvals of our ethical committee, signed assurances not to share data with others, and even our full resumes…” only 27% of authors complied Wicherts, J.M., Borsboom, D., Kats, J., & Molenaar, D. (2006). The poor availability of psychological research data for reanalysis. American Psychologist, 61, 726-728.

5. Time of publication Specific details General details Retirement or career change Information Content Accident Death Time (Michener et al. 1997)

6. Bumpus HC (1898) The Elimination of the Unfit as Illustrated by the Introduced Sparrow, Passer domesticus. Biological Lectures from the Marine Biological Laboratory: 209-226.

8. n=3824 Source: Publishing Research Consortium, http://publishingresearch.net

10. Taxonomy of data archiving benefits Modified from Beagrie et al. (2009) Keeping Research Data Safe 2 10

11. Joint Data Archiving Policy (JDAP) Data are important products of the scientific enterprise, and they should be preserved and usable for decades in the future. As a condition for publication, data supporting the results in the article should be deposited in an appropriate public archive. Authors may elect to embargo access to the data for a period up to a year after publication. Exceptions may be granted at the discretion of the editor, especially for sensitive information. Whitlock, M. C., M. A. McPeek, M. D. Rausher, L. Rieseberg, and A. J. Moore. 2010. Data Archiving. American Naturalist. 175(2):145-146.

12. The long tail of orphan data in “small science” after B. Heidorn “Most of the bytes are at the high end, but most of the datasets are at the low end” – Jim Gray Specialized repositories (e.g. GenBank, PDB) Volume Orphan data Rank frequency of datatype

13. Smit E (2011) Abelard and Héloise: Why Data and Publications Belong Together. D-Lib Magazine doi:10.1045/january2011-smit

14. The End To make data archiving and reuse standard part of research and publishing. The Means Enable low-burden data archiving at the time of manuscript submission. Promote researcher benefits from data archiving. Promote responsible data reuse. Empower journals, societies & publishers in shared governance. Ensure sustainability and long-term preservation. The Scope Data underlying peer-reviewed articles in basic and applied biosciences.

15. Integrated Submit manuscript

16. Integrated Submit manuscript Prompt author Manuscript metadata

17. Integrated Submit manuscript Submit data Prompt author Manuscript metadata

18. Integrated Submit manuscript Submit data Prompt author Manuscript metadata Review passcode Peer review

19. Integrated Submit manuscript Submit data Prompt author Manuscript metadata Review passcode Peer review Acceptance notification Curation Data DOI Production

20. Integrated Submit manuscript Submit data Prompt author Manuscript metadata Review passcode Peer review Acceptance notification Curation Data DOI Production Article metadata Curation

21. Integrated Submit manuscript Submit data Prompt author Manuscript metadata Review passcode Peer review Acceptance notification Curation Data DOI Production Article metadata Curation Article Publication Data publication Article DOI/final metadata harvested

23. Non-integrated Integrated Submit manuscript Submit data Prompt author Manuscript metadata Review passcode Peer review Submit data Acceptance notification Curation Data DOI Production Article metadata Curation Article Publication Data publication Article DOI/final metadata harvested

24. Non-integrated Integrated Submit manuscript Submit data Prompt author Manuscript metadata Review passcode Peer review Submit data Acceptance notification Curation Data DOI Production Author includes data DOI Data DOI Article metadata Curation Article Publication Data publication Article DOI/final metadata harvested

25. Non-integrated Integrated Submit manuscript Submit data Prompt author Manuscript metadata Review passcode Peer review Submit data Acceptance notification Curation Data DOI Production Author includes data DOI Data DOI Article metadata Curation Article Publication Data publication Article publication DOI/final metadata harvested Article DOI/final metadata harvested

26. Dryad relative to Supplementary Online Materials * A few publisher SOM sites are exceptions to the general rule ** Practices differ among publishers, see Smit (2011), doi:10.1045/january2011-smit 26

27. Article citation Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA (2011) Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes. PLoS ONE 6(3): e18011. doi:10.1371/journal.pone.0018011 Data citation Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA (2011) Data from: Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes. Dryad Digital Repository. doi:10.5061/dryad.8384

28. Rebbeck CA, Leroi AM, Burt A (2011) Mitochondrial capture by a transmissible cancer. Science 331, 303

30. Number of data packages

31. 20 papers from Delsuc and Douzery going back to 2002

32. By now, downloaded >1000X

33. Fulfilling the role of a journal

35. Does sharing imply that it need be altruistic? For a set of 85 cancer microarray clinical trials 48% had publicly available data These received 85% of the article citations Independent of journal impact factor, publication date, author nationality Piwowar H, et al. (2007) Sharing Detailed Research Data Is Associated with Increased Citation Rate. PLoS ONE 2(3): e308.

36. Does sharing imply that it need be altruistic? For a set of 85 cancer microarray clinical trials 48% had publicly available data These received 85% of the article citations Independent of journal impact factor, publication date, author nationality Piwowar H, et al. (2007) Sharing Detailed Research Data Is Associated with Increased Citation Rate. PLoS ONE 2(3): e308.

37. Data policies among bioscience journals IF=3.6 IF=6.0 IF=4.5 n=70 Piwowar HA, Chapman WW (2008) A review of journal policies for sharing research data. Presented at ELPUB2008, Nature Precedings hdl:10101/npre.2008.1700.1

38. The value proposition For researchers Increase the impact of, and citations to, published research. Preserve and make data available to verify published results, to refine methodologies, and to repurpose. Free researchers from the burden of data preservation and access. For journals, publishers and societies Free journals from the burden of managing supplemental data Increase the discoverability, impact, and integrity of articles Increase their value to the community they serve. For funders A cost-effective mechanism to make research more accessible Leverage existing investments in order to enable new science

39. Sustainability and governance Business model Long-term preservation requires a long-term organization In Dryad’s case, a membership-based nonprofit Revenue received from a broad array of ‘customers, including journals, societies, publishers, and researchers Deposit charges Paid upfront, when the majority of costs are incurred Ensure free access to the data in perpetuity Allow revenue to naturally scale with costs (i.e. volume of deposits) Distribute costs fairly among stakeholders Governance 12 member Board of Directors nominated, elected by Membership Membership serves in advisory capacity, and is a community of practice

40. Costs Moderate economies of scale are required At 10K packages/yr, <$50/deposit, depending on curation What are the costs for SOM? Journal of Clinical Investigation: $300 flat fee Ecological Archives: $250 <10Mb, more fees beyond that FASEB: $100 per file Beagrie N, Eakin-Richards L, Vision TJ (2009) Business models and cost estimation: Dryad repository case study. iPRES 2010

41. Proposed payment plans Journal-based annual fee based on all research articles published/yr (~$25/per*) covers any deposits from the journal (even from prior yrs) Voucher-based pay in advance for some number of deposits (<$50/per deposit) Pay-as-you-go: be invoiced retrospectively for deposits (>$50/per deposit) Author-pays Author pays online at time of deposit Journal can still facilitate archiving through submission integration *These are rates for Members, which include a 10% discount

42. What is the return on investment? A rigorous framework is lacking But we can look at comparators Marginal cost of data archiving $50/article is <2% of of publication costs (>$2.5K) And 0.2% of grant costs/article (~$25K) Is the data worth 2% of the research investment? Using DNA microarray data in GEO as a model 2,711 submissions in 2007 Data reused by 3rd parties in >1,150 articles Vision (2011) Open data and social contract of scientific publishing. BioScience, 60(5):330-330 Piwowar H, Vision TJ, Whitlock MC (2011) Data archiving is a good investment. Nature 473:285

44. http://datadryad.org http://blog.datadryad.org http://datadryad.org/wiki http://code.google.com/p/dryad dryad-users@nescent.org @datadryad Dryad

45. A very incomplete list of contributors JDAP: M. Whitlock DryadUS. R. Scherle, E. Feinstein, J. Greenberg, H. Piwowar, P. Schaeffer DryadUK: B. Hole, Max Wilkinson, D. Shotton Sustainability planning: N. Beagrie, L. Eakin-Richards