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!

1. Data Publication
Etcetera at the CDL
Carly Strasser & John Kratz
California Digital Library
@carlystrasser
Publish or Perish, UC Davis
February 2014

2. Back in the day…
From Wikimedia Commons
From ahswhg.wikispaces.com

3. Back in the day…
Curie
Newton
Da Vinci
classicalschool.blogspot.com
Darwin

4. Research has Better
changed
Worse

5. From Flickr by John Jobby
So much
data!
From wikimedia
Such
Internet!
So many
tools!

6. Research has
changed
Worse

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. 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. “Reproducibility Crisis”
“Digital Dark Age”
“Erosion of Trust”

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. incentivize sharing,
reproducibility
work within
publishing take advantage
of new tools
paradigm
Change
nothing
Change
everything

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. From Flickr by cdsessums
notebook
science
source
content
access
data
government
repository
knowledge

15. 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

16. Create and manage
persistent identifiers
ARKs, DOIs, etc.
Platform for publishing +
repository for OA
publications

17. “Data Publication”
John Kratz, CLIR Postdoc

18. What does “data
publication” mean?
Data
are
1. Available
2. Citable
3. Trustworthy*
*peer reviewed? certified?

19. 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?

20. Repository choices…

21. Repository choices…
Repositories
for data
General content
Non-institutional
Institutional
Discipline-specific

22. 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

23. 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?

24. Available | Citable | Trustworthy
Technical VS. Scientific
Package review: data +
paper
Sometimes consider
impact and/or novelty
Guidelines provided
From Flickr by Percival Lowell

25. 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

26. 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

27. 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)

28. ?
Change
nothing
Change
everything

29. Code!
Beyond Data…
Workflows!
…?
From Flickr by Klearchos Kapoutsis

30. From
Flickr
by
dotpolka
Scholarly
communication is
changing – for the
better.

31. Big thanks to John Kratz, CLIR Postdoc
Website
Email
Tweet
Slides
carlystrasser.net
carlystrasser@gmail.com
@carlystrasser
slideshare.net/carlystrasser