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ePANDDA: EarthCube IA: Collaborative Proposal: Enhancing Paleontological and Neontological Data Discovery API 
NSF Award # 1541028 


ABSTRACT

Understanding future environmental change requires researchers to access and integrate data from the geological and biological sciences, in order to answer questions about how environmental change will affect life on Earth. In many cases the data needed to answer these questions already exists but, unfortunately, technology has not kept pace with research needs. This places increasing demands on researchers, who have to search for and download data from multiple separate online databases; compile published information from many different literature sources; and track down specimens housed in museum and other collections scattered around the world. The time needed to search and retrieve this information is enormous and, once found, the data often have to be standardized before they can be used. This project will tackle this problem by developing software tools to connect three established, well-supported, and critically important data sources: the Paleobiology Database (PBDB, paleontological, literature based), iDigPaleo (paleontological, specimen based) and iDigBio (neontological, specimen based). This project will allow users of any one of these databases to access and query the others at the same time, returning a much richer, combined set of data to the user. Connecting these resources will open up a whole host of research questions that are currently difficult to answer, even by multiple researchers working as a team. The development of this system will allow scientists to ask and answer new research questions affecting fields as diverse as biogeographic/niche modeling, systematics, functional morphology, evolutionary biology, ecology, climatology, conservation biology, oceanography, and petroleum geology. This project will fundamentally change the nature of the research questions that can be addressed by the scientific community.

The connectivity between modern and fossil, and specimen and literature-based resources does not currently exist. The digital infrastructure provided by the composite ePANDDA application programming interfaces (APIs) will streamline and normalize data acquisition, including retrieval from disparate data sources, and will facilitate coordination with future data initiatives. Rather than creating another portal for the aggregation of data, ePANDDA will unify results that normally would have required multiple searches on numerous platforms. For the researcher, this eliminates a significant barrier to data collection and processing. Researchers will now have the ability to collaborate across disciplinary boundaries to study earth system processes and the nature of biotic response to environmental change across both space and time. Linking publications to specimens will enrich the potential of museum collections and augment their value for both research and education. The ePANDDA project also provides an opportunity to build collaborative programs that leverage existing education and outreach activities in addition to the primary research goals.

PIs: 
Jocelyn Sessa and Neil Landman (American Museum of Natural History) 
Gil Nelson (Florida State University)
Mark Uhen (George Mason University)
Dena Smith (STEPPE)
Susan Butts, Larry Gall, Talia Karim and Christopher Norris (Yale Peabody Museum)

Dates: Sept 1, 2015–Oct. 31, 2017

Developers:
Michael McClennen - PBDB programmer & ePANDDA API creator at UW-Madison University
Seth Kaufman - iDigPaleo & ePANDDA API programmer in New York City
Noel Heim - PBDB & ePANDDA app programmer at Stanford University
Jon Lauters - iDigBio developer at Florida State University
Valerie Syverson - PBDB programmer at UW-Madison University
Alex Thompson - iDigBio/ACIS IT
Harry Shyket - Programmer/web developer at Yale University Peabody Museum
David Iler - STEPPE webmaster in Boulder

Resources:

Paleobiology Database-

PBDB Navigator overview https://www.youtube.com/watch?v=db2He3pJco

And a longer explanation by Dr. Mark Uhen of PBDB https://www.youtube.com/watch?v=ntNfVLYjnA

iDigBio-

Introduction to iDigBio https://vimeo.com/67570758

Webinar of a demonstration of the iDigBio portal https://idigbio.adobeconnect.com/_a1130716096/p6tpc4c9r06/

iDigBio API wiki page https://www.idigbio.org/wiki/index.php/IDigBio_API

And a link to the portal https://www.idigbio.org/portal

iDigPaleo-

iDigPaleo on the iDigBio Paleontology Digitization webinar series slideshow: https://www.idigbio.org/wiki/images/4/49/Norris_and_butts.pdf

video: https://idigbio.adobeconnect.com/_a1130716096/p8jdq825bl6/?launcher=false&fcsContent=true&pbMode=normal

iDigPaleo background from the iDigBio TCN summit slideshow: https://www.idigbio.org/wiki/images/d/d6/IDigBioSummitV_FossilInsectTCN_KarimButts.pdf

video: https://idigbio.adobeconnect.com/_a1130716096/p1h85oyt5lw/?launcher=false&fcsContent=true&pbMode=normal (iDigPaleo presentation starts at 52:33)

Courtesy of the NYU Health Science Library- Data Sharing and Management Snafu in 3 Short Acts: https://www.youtube.com/watch?v=N2zK3sAtr-4 "everything you need is in the paper"