Data Publication for UC Davis Publish or Perish


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Intro presentation for panel on going beyond publishing journal articles. UC Davis "Publish or Perish?" Event, 13 Feb 2014. Sorry about missing gradient on some of slides!

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Data Publication for UC Davis Publish or Perish

  1. 1. Data Publication Etcetera at the CDL Carly Strasser & John Kratz California Digital Library @carlystrasser Publish or Perish, UC Davis February 2014
  2. 2. Back in the day… From Wikimedia Commons From
  3. 3. Back in the day… Curie Newton Da Vinci Darwin
  4. 4. Research has Better changed Worse
  5. 5. From Flickr by John Jobby So much data! From wikimedia Such Internet! So many tools!
  6. 6. Research has changed Worse
  7. 7. From Flickr by US Army Environmental Command From Flickr by deltaMike From Flickr by DW0825 From Flickr by Flickmor Courtesey of WHOI Digital data C. Strasser
  8. 8. LIMNOLOGY and OCEANOGRAPHY: METHODS Limnol. Oceanogr.: Methods 5, 2007, 241–249 © 2007, by the American Society of Limnology and Oceanography, Inc. Laser ablation ICP-MS analysis of larval shell in softshell clams (Mya arenaria) poses challenges for natural tag studies C.A. Strasser, S.R. Thorrold, V.R. Starczak, and L.S. Mullineaux Woods Hole Oceanographic Institution, Woods Hole, MA 02543 Abstract Ideas, data, analysis We investigated whether laser ablation inductively coupled plasma mass spectrometry (ICP-MS) could be used to quantify larval shell compositions of softshell clams, Mya arenaria. The composition of aragonitic otoliths has been used as a natural tag to identify natal habitat in connectivity studies of fish. If it is possible to measure larval shell reliably, this technique could also be applied to marine bivalves. To determine whether the first larval shell (prodissoconch I) could be measured independent of underlying material, we conducted laboratory experiments in which larval M. arenaria were exposed to enrichments of the stable isotope 138Ba during different stages in shell development. We were unable to isolate the chemical signature of the prodissoconch I from subsequent life stages in all combinations of shell preparation and instrument settings. Typical instrument settings burned through the prodissoconch I on a post-settlement juvenile and at least 9 d of second larval shell (prodissoconch II) growth. Our results suggest instrumental and technical improvements are needed before laser ablation ICP-MS can be useful for connectivity studies that require analysis of larval shell on a post-settlement M. arenaria juvenile. Laser burn-through is potentially a problem in any connectivity study where it is necessary to assay the small amounts of shell material that are deposited before a larva disperses away from its natal location. Most marine benthic invertebrate life cycles include a planktonic larval phase that facilitates dispersal among adult populations (Thorson 1950). Connectivity, or the degree to which geographically separated populations exchange individuals, is an important factor in the spatial population dynamics of many marine organisms (Moilanen and Nieminen 2002). An understanding of connectivity in marine benthic populations is important because of the role spatial dynamics play in fisheries management and the design and implementation of marine protected areas. However, studying larval dispersal is challenging due to small larval sizes, high dilution rates, and high larval mortality rates (Thorson 1950, 1966). In recent years, the use of artificial and natural tags to track marine larvae has been explored (e.g., Levin 1990; Thorrold et al. 2002). One type of natural tag that may be useful for identifying natal origins is elemental signatures recorded in biogenic Acknowledgments This work was supported by NSF project numbers OCE-0241855 and OCE-0215905. Special thanks to Henry Lind of the Eastham Department of Natural Resources for supplying clams and culturing expertise, and to Diane Adams, Benjamin Walther, Travis Elsdon, Anne Cohen, Dale Leavitt, Phil Alatalo, and Susan Mills for helpful discussions. We also thank D. Zacherl and an anonymous reviewer for their helpful comments. carbonate. This technique relies on the observation that some elements are incorporated into the calcium carbonate matrix in amounts that are related to the dissolved concentrations and physical properties of the ambient water (e.g., Bath et al. 2000; Elsdon and Gillanders 2003; Fowler et al. 1995; Thorrold et al. 1997; Vander Putten et al. 2000). Provided water chemistry or temperature is significantly different among natal habitats, such variation can serve as a natural tag, or signature, of the geographic origin of organisms. The use of geochemical signatures in fish otoliths as natural tags for population studies is well established (Campana and Thorrold 2001). Recent efforts have expanded the use of elemental tags to invertebrates including decapods (DiBacco and Levin 2000), gastropods (Zacherl et al. 2003), bivalves (Becker et al. 2005), and cephalopods (Arkhipkin et al. 2004). Most studies attempting to obtain time-resolved elemental signatures from calcified tissues have used laser ablation inductively coupled plasma mass spectrometry (ICP-MS). Conventional solution-based ICP-MS analyses are generally more precise than laser ablation assays but lack the ability to resolve elemental signatures from individual life stages (Campana et al. 1997). Laser ablation ICP-MS is particularly useful for larval studies because it allows the core of an otolith or the larval shell of a juvenile bivalve to be targeted. Yet, surprisingly few studies have empirically tested the effective spatial resolution of laser 241 Provenance
  9. 9. “Reproducibility Crisis” “Digital Dark Age” “Erosion of Trust”
  10. 10. Can we fix science? v t h e w ay we o m m u n i c ate c our Change nothing Change everything
  11. 11. incentivize sharing, reproducibility work within publishing take advantage of new tools paradigm Change nothing Change everything
  12. 12. We are in the midst of a culture shift. What will scholarly communication look like in 10 years? From Flickr by Leo Reynolds
  13. 13. From Flickr by cdsessums notebook science source content access data government repository knowledge
  14. 14. Enable data sharing Explore new tools to help change system Think about code sharing Encourage new incentives Work with libraries, publishers and researchers Build tools
  15. 15. Create and manage persistent identifiers ARKs, DOIs, etc. Platform for publishing + repository for OA publications
  16. 16. “Data Publication” John Kratz, CLIR Postdoc
  17. 17. What does “data publication” mean? Data are 1. Available 2. Citable 3. Trustworthy* *peer reviewed? certified?
  18. 18. Available | Citable | Trustworthy “Email me!” CC-0 on web Publish means to “make public”. You should not have to email the author. The data doesn’t have to be open access. Where to publish?
  19. 19. Repository choices…
  20. 20. Repository choices… Repositories for data General content Non-institutional Institutional Discipline-specific
  21. 21. Available | Citable | Trustworthy Simple case… Data citations should be in reference list. Five-element citation: author, year, title, publisher, identifier Boettiger C, Dushoff J, Weitz JS (2009). Data from: Fluctuation domains in adaptive evolution. Theoretical Population Biology. Published in Dryad. doi:10.5061/dryad.j8n0p7vc
  22. 22. Available | Citable | Trustworthy More complicated… Deep data citation: what if you want to cite a subset? Dynamic data: how to create a reliable citation when a dataset is changing?
  23. 23. Available | Citable | Trustworthy Technical VS. Scientific Package review: data + paper Sometimes consider impact and/or novelty Guidelines provided From Flickr by Percival Lowell
  24. 24. What does a data publication look like? From Flickr by subsetsum 1.  Traditional article: Data published alongside a traditional journal article. Example: Supplemental material hosted by the journal publisher. Available + citable. Review is up to the journal
  25. 25. What does a data publication look like? From Flickr by subsetsum 2.  Data paper: Data published alongside a descriptive “data paper”. Most require data be in a trusted repository. All have a component of peer review. What they are NOT: results, analysis, conclusions. Examples: •  •  Standalone journals: Nature Scientific Data, Geoscience Data Journal, Ecological Archives Journals that publish data papers: GigaScience, F1000 Research, Internet Archaeology
  26. 26. What does a data publication look like? From Flickr by subsetsum 3.  Standalone data: Data published without a related journal article. Rich metadata (structured or unstructured) Examples: •  Open Context •  NASA PDS Peer Review Data •  figshare (but no validation)
  27. 27. ? Change nothing Change everything
  28. 28. Code! Beyond Data… Workflows! …? From Flickr by Klearchos Kapoutsis
  29. 29. From  Flickr  by  dotpolka   Scholarly communication is changing – for the better.
  30. 30. Big thanks to John Kratz, CLIR Postdoc Website Email Tweet Slides @carlystrasser