The Paleobiology Database (PBDB) is a public resource of information on more than 1.3 million fossil occurrences and 350,000 taxonomic names. The database is designed to address fundamental questions in Earth and life science and contains information that can be of use when characterizing and predicting the distribution of energy and water resources. The PBDB is organized and operated by a multi-disciplinary, multi-institutional, international collaborative group of more than 300 paleobiological researchers.

A core objective of this NSF EAR Geoinformatics grant was to better capitalize on the more than 11 continuous person years of effort that have gone into the PBDB data entry and curation process and to establish a modern geoinformatics foundation capable of carrying the database into the future. We have accomplished these objectives by completely overhauling every aspect of the public interface of the PBDB (https://paleobiodb.org) and by provisioning the underlying databases and infrastructure with new physical hardware and software tools that improve performance and facilitate data availability, discoverability and use. The most important accomplishment in this regard was the development and public release of the PBDB Application Programming Interface (https://paleobiodb.org/data, also described at http://dx.doi.org/10.1017/pab.2015.39), which allows third party developers to independently design and build PBDB data-driven applications that are tailored to the specific and diverse needs of industry, research, and education users. The API is now deployed extensively in all three of these areas. In 2016, the PBDB transferred more than 184GB of data in response to more than 8 million individual API requests that were generated by at least 300,000 distinct users globally. Year-over-year, rates of PBDB data access and usage is on track to more than double in volume. Example apps included in the 2016 usage statistics are the commercial iOS app Mancos, the freely available geoscience mobile apps Flyover Country (http://fc.umn.edu) and Rockd (https://rockd.org), and our own Navigator web application (https://paleobiodb.org/navigator). The entire ecosystem of PBDB-utilizing web and mobile applications that now exists was made possible by the informatics work supported by this grant. The interoperability of the Paleobiology Database, measured by its data connections to other biological and geoscience databases and resources, has also improved in response to the release of the API. For example, R packages created by individuals and the rOpenSci team have been released (https://paleobiodb.org/#/resources), and some of these aim to serve non-paleontologist communities.

The Paleobiology Database is community governed, and during the course of this grant the governance structure was substantively reorganized and new leadership chosen. The PBDB is managed by the Executive Committee, which sets overall database policy, oversees matters related to the membership and access to data. The Committee consists of 12 members, including a Chair, currently held by Mark D. Uhen, and a Secretary, currently held by Matthew Clapham. Primary software development has been carried out at the University of Wisconsin-Madison under the auspices of this grant. The PBDB also has an External Advisory Board that advises the Executive Committee on Database activities and policies, promotes the use of the Database among the scientific community, and forges links to other scientific communities and the general public.

In addition to designing and releasing core infrastructure components, and reorganizing governance, we have designed, tested, and publicly released educational materials for a course in paleobiology that is designed to provide technical and analytical skills of wide utility to undergraduate students. Material for an entire semester-long course, including lab exercises that use the PBDB API, is available online (https://github.com/paleobiodb/teachPaleobiology). A number of other educational resources are also available (https://paleobiodb.org/#/resources). The PBDB website and Navigator application, developed as part of this grant activity, have also been used on campuses across the country, including in large online classes. The PBDB has also enjoyed several viral social media exposures, primarily via Instagram, that were prompted entirely by the release of our new data visualization and exploration tools. 

Facilitating primary scientific research and publication has remained the core of our mission, and since the July 2010 start date of this grant, more than 165 officially numbered scientific papers that use the database have been published (https://paleobiodb.org/#/publications); many more publications are not included in this official list but have used the PBDB in some capacity (https://scholar.google.com/citations?user=PP946k4AAAAJ). The number of publications that draws on the PBDB continues to increase steadily year-over-year.

In summary, the work accomplished over the period July 2010 to Dec. 2016, supported by this Geoinformatics grant, has met or exceeded the stated goals of better leveraging the Paleobiology Database for research, education, mentorship and interoperability. In particular, the decentralization and democratization of software development activities made possible by the development and release a public API has resulted in more efficient and widespread use of PBDB data in industry, research and in education. The potential of the new capabilities of the PBDB are only now beginning to be realized.

Last Modified: 02/07/2017
Modified by: Shanan E Peters