Public Data Archiving in Ecology and Evolution: How well are we doing?
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The document discusses the importance of public data archiving in ecology and evolution, emphasizing the need for scientists to make their data accessible to the public to improve reproducibility and collaboration. Despite the growing trend in data deposition due to policies like the Joint Data Archiving Policy, many researchers remain hesitant to share their data due to concerns about competition and misinterpretation. Strategies for enhancing public data archiving include improving communication between data generators and users, increasing recognition of archived data, and providing better metadata and education on best practices.
![“63% of PIs were against PDA as currently required”
“41% of respondents said that they have avoided
publishing in journals that require [PDA]”
“53% intend to avoid publishing in [journals requiring
PDA] in the future”
“A key concern is that [PDA] will be a disincentive
both for the initiation of long-term studies, and for
maintenance of ongoing studies.”](https://image.slidesharecdn.com/binningosnioosymposiumtoshare-171213095931/85/Public-Data-Archiving-in-Ecology-and-Evolution-How-well-are-we-doing-14-320.jpg)
Public Data Archiving in Ecology and Evolution: How well are we doing?
- 1. Public Data Archiving in Ecology and Evolution How well are we doing? Dr. Sandra A. Binning @binsan5
- 3. Are publications the only useful research output?
- 4. What about DATA? Do scientists have an obligation to make their data freely available? Big push in the biological sciences for Public Data Archiving “The data and its analysis are the scientific product. The paper is just an advertisement.” Richard McElreath McElreath R (2016) Statistical rethinking: A Bayesian course with examples in R and Stan. CRC Press: 469 pp
- 5. What is Public Data Archiving? (Figure from Reichman et al 2011 Science) The process of storing data and associated metadata in a repository that is open to the public and where data can be accessed and downloaded freely by a third party.
- 6. Why do it? • avoids data loss from hardware malfunction/obsolescence or from researchers moving on to different projects or retiring • encourages good metadata production to ensure that datasets are interpretable • increases the ability to evaluate and reproduce studies • increases opportunities for teaching and learning • encourages a stronger sharing culture • improves the return per research dollar • increased citations and collaborations (Huang & Qiao 2011 TREE, Molloy 2011 PLOS Biol, Piwowar et al 2011 Nature, Reichman et al 2011 Science, Tenopir et al 2011 PLOS One, Whitlock 2011 TREE, Whitlock et al 2010 Am Nat)
- 7. Most research is paid for by….. Data as a public good? TAXPAYERS in the form of government grants and salaries So, who really “owns” the data?
- 8. Joint Data Archiving Policy (JDAP) http://datadryad.org/pages/jdap
- 9. Journals that require data archiving Examples: •The American Naturalist •Biological Journal of the Linnean Society •Biology Letters •BMC Ecology •BMC Evolutionary Biology •BMJ •BMJ Open •Ecological Applications •Ecological Monographs •Ecology •Ecosphere •Evolution •Evolutionary Applications •Frontiers in Ecology and the Environment •Functional Ecology •Genetics •Heredity … http://datadryad.org/pages/jdap
- 10. Data archiving trends in Ecology & Evolution? Data deposition has increased considerably in Dryad and other repositories. (Vision 2013 figshare) Members of the JDAP consortium have tripled since its inception in 2011. (Magee et al 2014 PLOS One) Enforcing Public Data Archiving policies has had a positive effect on data deposition rates. (Vines et al 2013 FASEB Journal, Magee et al 2014 PLOS One)
- 11. The problem… Many researchers harbour concerns about making their data publicly available. This is particularly true in fields such as ecology and evolutionary biology, where datasets are often complex, have a long shelf life, and can be used to test multiple hypotheses.
- 12. Why are researchers reluctant to archive/share their data? • Proper data archiving takes time (away from publishing). • Competition for publications - fear of being “scooped”. • Concerns about data misinterpretation / misuse. • Lack of recognition for Public Data Archiving.
- 13. Benefits vs. Costs • avoids data loss from hardware malfunction/obsolescence or from researchers moving on to different projects or retiring • encourages good metadata production to ensure that datasets are interpretable • increases the ability to evaluate and reproduce studies • increases opportunities for teaching and learning • encourages a stronger sharing culture • improves the return per research dollar • increased citations and collaborations • funded by taxpayers Good for scientific community But costs are to individual researchers
- 14. “63% of PIs were against PDA as currently required” “41% of respondents said that they have avoided publishing in journals that require [PDA]” “53% intend to avoid publishing in [journals requiring PDA] in the future” “A key concern is that [PDA] will be a disincentive both for the initiation of long-term studies, and for maintenance of ongoing studies.”
- 15. Are we filling up ‘empty archives’? (Nelson 2009 Nature) Most journals and databases don’t verify the quality of archived data beyond basic checks like ensuring that a data availability statement and a valid DOI number are provided in the paper. (Noor et al 2006 PLOS Biol, Costello et al 2013 TREE)
- 16. What’s happening in molecular biology? It’s not looking good… 1) Ioannidis et al 2008 Nat Gen: Review of microarray studies : - only 2 of 18 were reproducible 2) Gilbert et al 2014 Mol Ecol: Review of pop genetics studies: - 30% of analyses irreproducible - 35% of datasets insufficiently described
- 18. PDA in E&E – how well are we doing? We assessed 100 non-molecular studies in journals either have adopted the Joint Data Archiving Policy (JDAP) or have a strong data archiving policy. Completeness criterion Reusability criterion
- 19. Joint Data Archiving Policy (JDAP) “data supporting the results in the paper should be archived in an appropriate public archive” http://datadryad.org/pages/jdap
- 20. Data completeness score Meets JDAP requirements Does not meet JDAP requirements (Roche et al 2015; PLOS Biol)
- 21. Data reusability score (Roche et al 2015; PLOS Biol)
- 22. Bad archiving examples • SPSS files archived • Files archived in language other than English with no metadata • Too much data! • Only data (no description) • Principle components without raw data
- 23. Data completeness - results More than half (56%) of studies did not meet the minimum requirement of JDAP or strong archiving policies passfail (Roche et al 2015; PLOS Biol)
- 24. Data reusability - results passfail Even more (64%) of studies were archived in a way that partially or entirely prevented reuse (Roche et al 2015; PLOS Biol)
- 25. How do we increase high quality participation?
- 26. How do we increase participation?
- 27. 1. Encourage communication between data generators and re-users (Roche et al 2014 PLOS Biol) How do we increase high quality participation?
- 28. 1. Encourage communication between data generators and re-users 2. Disclose data re-use ethics (Roche et al 2014 PLOS Biol) How do we increase high quality participation?
- 29. 1. Encourage communication between data generators and re-users 2. Disclose data re-use ethics 3. Encourage increased recognition of publicly archived data (Roche et al 2014 PLOS Biol) How do we increase high quality participation?
- 30. 1. Encourage communication between data generators and re-users 2. Disclose data re-use ethics 3. Encourage increased recognition of publicly archived data 4. Facilitate more flexible embargoes on archived data (Roche et al 2014 PLOS Biol) How do we increase high quality participation?
- 31. • Be mindful of PDA • Provide detailed metadata • Use descriptive file names • Archive unprocessed data • Use standard file formats (i.e. .txt, .csv) • Facilitate data aggregation • Perform quality control How do we increase high quality participation? Key recommendations to improve PDA practices
- 32. Public Data Archiving: The way forward? • Not everyone is on board • “Empty archives” are a problem in E&E • Willful omission • Lack of knowledge • Solutions • Acknowledge fears and try to alleviate them • Enforcement, reward, flexibility • Educate researchers as to best practices • Recognize individual efforts to increase transparency
- 33. Many thanks to Ainsley Seago, Luke Holman, Scott Keogh, Pat Backwell, Andrew Cockburn, Todd Vision, Mark Hahnel, the Evolutionary Ecology Reading group at the Australian National University and the Eco-Ethology and Cognitive Sciences lab groups at the University of Neuchatel. Image / illustration credits: A. Seago, Google@binsan5