Letters
A Stable Isotope Data Repository as
Part of Neotoma, a Paleoecological
Database
We agree with Pauli and colleagues
that the time is right for a comprehensive database that stores and serves stable isotope data. As they point out, the
uses of stable isotope data are many,
with applications in biology, ecology,
physiology, forensic sciences, climatology, paleontology, and archaeology.
Perhaps the authors’ most important
observation is that limits to progress
are not in data acquisition but rather
in data exchange. We suggest that the
ability to not only exchange stable
isotope data but also to visualize their
intersection with other types of biological, ecological, and paleo- or archaeological data will add immeasurably to
the advancement of research in these
disciplines (e.g., Pilaar Birch 2013).
To that end, we discuss here the
potential of an IsoBank within the
Neotoma Paleoecological Database
(www.neotomadb.org), already a
National Science Foundation–­
recognized database consortium,
which stores and serves subsidiary
paleobiological databases spanning the
Miocene to the present day, including
pollen, vertebrate, plant macrofossil,
diatom, and ostracod data. A stable
isotope database is currently being
created within Neotoma and will provide open access to chronologically
and geographically referenced isotopic
data. Therefore, it provides the perfect
format for the type of data exchange
cited by the authors and offers a means
toward two additional goals: data standardization and integration.
Neotoma has a centralized structure
that facilitates interdisciplinary multiproxy analyses using discipline-specific
data sets (Graham 2012). Each constituent database is administered by an
advisory panel that sets standards, format, and quality controls. Appointed
data stewards upload data using the
program Tilia, which automatically
checks for errors in order to prevent
database corruption. Data is accessed
through the Neotoma Explorer, which
allows for multiple combinations of
data to be served at one time. It is
http://bioscience.oxfordjournals.org
possible to map individual parameters,
such as the geographic distribution of
a given mammalian taxa at a specific
time interval, along with elevation and
vegetation overlays. These displays of
data can be animated to show change
through time. Numerical stratigraphic
data can be graphed based on an internal age model in either continuous
curves or discrete discontinuous bar
graphs. Data can be downloaded into
various software packages for analysis
and manipulation, and Neotoma also
has R modules to assist with downloading and importing data (Goring
et al. 2015).
The idiosyncratic nature of isotope
data noted by Pauli and colleagues
contributes to a lack of standardization in isotopic data analysis, curation,
and dissemination. By instituting a
standardized database format, such as
already exists in Neotoma and Tilia,
it is our hope that data practices in
stable isotope research become more
cohesive. A unified structure in data
sharing should foster standards in
data recording and analysis, increasing reproducibility and the potential
for integration with other data sets.
Neotoma is designed for the direct
storage of metadata with data and can
be linked with repositories such as
GenBank and Arctos, and its format
makes it easy to visualize and crossreference multiple data sets in time
and space. We envision it as perfectly
poised to serve the need for robust,
multiproxy, linked, standardized databases that will make groundbreaking
integrated ecological and biological
research possible in the future.
SUZANNE E. PILAAR BIRCH
RUSSELL W. GRAHAM
Suzanne E. Pilaar Birch (sepbirch@
uga.edu) is a joint assistant professor
in the Departments of Anthropology
and Geography and the Director of
the Quaternary Isotope Paleoecology
Laboratory at the University of Georgia,
in Athens. Russell W. Graham is a professor in the Department of Geosciences and
the Director of the Earth and Mineral
Sciences Museum at Pennsylvania State
University, in State College.
References cited
Graham RW. 2012. Neotoma: A multidisciplinary and relational database for terrestrial paleoecological datasets for the
Pliocene, Pleistocene, and Holocene.
Quaternary International 279, 280: 175–176.
doi:10.1016/j.quaint.2012.08.255.
Goring S, Dawson A, Simpson G, Ram K,
Graham R, Grimm E, Williams J. 2015.
Neotoma: A programmatic interface to the
Neotoma Paleoecological Database. Open
Quaternary 1: 1–17. doi:10.5334/oq.ab.
Pauli JN, Steffan SA, Newsome SD. 2015. It is
time for IsoBank. BioScience 65: 229–230.
Pilaar Birch SE. 2013. Stable isotopes in zooarchaeology: An introduction. Archaeological
and Anthropological Sciences 5: 81–83.
doi:10.1007/s12520-013-0126-7.
doi:10.1093/biosci/biv133
Response to Pilaar Birch and Graham
We are delighted that our call for
IsoBank, a database for stable isotope
data, has generated interest among
our colleagues, and we applaud Pilaar
Birch and Graham for offering in their
letter the Neotoma Paleoecological
Database as a potential repository. Their suggestion is promising
and should be explored. We encourage continued discussions of potential archives, including Neotoma, as
well as museum-based databases (e.g.,
Arctos) that house modern, historical,
archaeological, and paleontological
specimens. Any archive should facilitate cross-linkage among databases,
thereby encouraging and supporting
interdisciplinary research. Once the
home for IsoBank has been identified, there are many details to be considered; most prominently are those
relating to metadata indexing and data
acquisition.
As Pilaar Birch and Graham identify, the “idiosyncratic nature of isotope data . . . contributes to a lack of
standardization in isotopic data analysis, curation, and dissemination.” With
their current development of a stable
isotope database linked to Neotoma,
it is important that the community
comes to a consensus on the necessary metadata that will be required to
control for data quality and therefore
enhance accessibility. Such metadata
should include—but are not limited
October 2015 / Vol. 65 No. 10 • BioScience 953