A Stable Isotope Data Repository as Part of Neotoma, a Paleoecological Database

BioScience Advance Access published September 16, 2015

Letters

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multiproxy analyses using disciplinespecific 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 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

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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