Output and Publications


ZooArchNet: A “Meeting of the Minds” Workshop, April 17-18, 2017, University of Florida, Gainesville. 

Participants: Kitty Emery (Florida Museum of Natural History) Robert Guralnick (Florida Museum of Natural History), Michelle LeFebvre (Florida Museum of Natural History), Laura Brenskelle (Florida Museum of Natural Hisotry/ University of Florida), John Wieczorek (Jante Consultants), Edward Davis (University of Oregon), Suzanne Pilaar-Birch (University of Georgia)


2017. Brenskelle, J. Wieczorek, R.Guralnick, K. Emery, M. LeFebvre. Extending Darwin Core to Incorporate Data About Material Condition and Absolute Deep Time.” Biodiversity Informatics Standards (TDWG). Ottawa, Canada. October 2017.

Abstract: As part of efforts to mobilize zooarchaeological collections data, there is a strong need for new terms that can extend the Darwin Core standard in order to describe material condition, preparation history, and chronology. These data are important for understanding the full context of specimens from an array of natural and cultural heritage disciplines, especially those involving deep time, such as paleontology and zooarchaeology. These disciplines offer pre- and early Anthropocene biodiversity baselines to recognize and understand the deep history of human-environment interactions and use this information for research and conservation. They also provide an invaluable perspective about climate change in the past, thus providing insight into future climate change and impacts on ecology and biodiversity.

We propose two new extensions: one for chronology, and one for material condition. While Darwin Core does currently accommodate data about lithostratigraphy, the chronology extension will allow for sharing of absolute dates and dating protocols. Absolute dates increase global comparisons between datasets and are often the primary chronology associated with biodiversity data from archaeological sites. Additionally, the material condition extension will provide proper means for sharing data that, thus far, have been lumped under the Darwin Core term ‘preparations’, which limits their discoverability to users. This includes data about skeletal elements, taphonomy, and preparation history. Here we present these two extensions to Darwin Core and open the discussion about improving the proposed terms and definitions in the extensions we developed.

E. Kansa, S. Whitcher Kansa. “Context, Linked Data, and Reproducible Research in Archaeology.” ZooArchNet: A “Meeting of the Minds” Workshop. Gainesville, Florida. April 2017.

Abstract: In archaeology, digital data comes in many different forms that serve different purposes. Most data still remain isolated, usually trapped on the hard drives of individual investigators. Even if data do enter repositories, idiosyncrasies in data formats, data models, and vocabularies mean data typically lack connection with other datasets. Researchers have long recognized these problems, leading to the perennial call for archaeologists to adhere to common “standards.”

However, archaeology is a dynamic field, with evolving research designs and theoretical priorities. We will achieve little if we sacrifice interpretive freedom at the altar of (apparent) interoperability by imposing standards that codify certain models and perspectives that should be contested. Instead, meaningful interoperability can be achieved in a more “bottom-up” manner, through modes of data publishing that make meaning more explicit and formally described.

Linked Data methods allow for the computational modelling of connections between concepts. Rather than attempting to force adoption of predetermined standards, Linked Data makes annotation to common standards feasible. This promotes greater dynamism and flexibility, as researchers can develop and apply new standards to suit new research questions using Linked Data. Case studies in Open Context (http://opencontext.org) involving zooarchaeological data from Epi-Paleolithic through Chalcolithic Anatolia and archaeological site data from North America, will illustrate research outcomes from linking several individual datasets. These examples will show how Linked Data methods can make data integration and resulting interpretations more reproducible and contestable.

2016. Brenskelle, R. Guralnick, J. Wieczorek. “Building Linked Open DataFor Zooarchaeological Specimens and Their Context.” Biodiversity Informatics Standards (TDWG). Santa Clara de San Carlos, Alajuela, Costa Rica. December 2016.

Abstract: Zooarchaeological collections data present special challenges for mobilization into global biodiversity networks, given the critical importance that human site context plays in interpretation.  At the same time, faunal remains are biological samples that can be represented using existing standards.  Here we present a means to use a linked open data framework to connect cultural context and specimen data in order  to support integrated global change research.  We demonstrate this approach using a subset of the zooarchaeological holdings of the Florida Museum of Natural History as a case study.  We show how these datasets can be expressed using Darwin Core, especially information relating to excavation, chronology, and cultural provenience.  We also have developed means to share context information with Open Context, an archaeoinformatics project that is well established in the community.  We discuss the importance of linked open data frameworks in representing zooarchaeological data, and the importance for future development of Darwin Core extensions to further appropriately capture contents rather than relegating this content to container fields such as dynamicProperties in Darwin Core. Many of the concepts required to share zooarchaeological data have conceptual overlap with paleontological data, and we argue it is timely and needed to fully connect biological, paleontological, and archaeological data together most efficiently for broad scientific use.

2016. Emery, S. Kansa, R. Guralnick. “Mobilizing Zooarchaeology Data Between Bioinformatics and Archaeoinformatics.” Paper  presented at the International Committee Meetings of the ICAZ, Zhengzhou, China. October 2016.

Abstract: Re-use of very large zooarchaeological datasets has recently opened the door to new and exciting research capable of tackling the grand challenges of our science. However, two obstacles stand in the way of taking full advantage of the potential for big-data zooarchaeological research. 1. Zooarchaeological data is increasingly accessible as a result of the move to data publication through open-access archaeological data publishers such as Open Context and Neotoma, and data archiving in archaeological data repositories such as tDAR and the Archaeology Data Service. Despite this, even the open-access publishers and archives are still data silos because there does not yet exist a means for communication among the repositories, let alone among the private databases of the many zooarchaeological researchers. 2. Biodiversity informatics has made impressive strides in scientific research on openly accessible and interoperable distributed data provisioned by a biodiversity data network represented by the Global Biodiversity Information Facility (GBIF) and associated worldwide nodes and portals (for example, iDigBio, VertNet, and the like in the US). However, this valuable network so far provides only paleontological and neontological data and thus is missing the vital zooarchaeological data that represents the long history of human-environment interaction.

ZooArchNet is a collaborative project between archaeoinformatics and bioinformatics that will provide not only a bridge between the biodiversity distributed data network and the developing archaeoinformatics infrastructure, but also a linking mechanism among the many new archaeological repositories and data publication facilities such as Open Context. This presentation will discuss the benefits and challenges of such a system, and the experiments that we are currently conducting to mobilize a subset of zooarchaeological data from the Florida Museum of Natural History representing several millennia of prehistory in Florida while bridging between the biodiversity network (represented by VertNet) and the developing world of archaeoinformatics (represented by Open Context).


2017. Brenskelle, L. “Studying the Interactions of Climate, Biodiversity and humans.” Biodiversity Blog, University of Florida Biodiversity Institute, November 3, 2017. https://biodiversity.institute.ufl.edu/2017/11/studying-the-interactions-of-climate-biodiversity-and-humans/.

2016. “Building a Zooarchaeology Network and the Value of Linked Open Data.”  VertNet Blog, December 12, 2016. http://blog.vertnet.org/post/154388885926/building-a-zooarchaeology-network-and-the-value-of.