Paleobiology Database Chordates

Michael McClennen1, Julian Jenkins1, Mark Uhen1, John Wieczorek2, David Bloom3

1 Paleobiology Database, , United States; 2 VertNet, , United States; 3 VertNet, 

Corresponding author(s): Michael McClennen (mmcclenn@geology.wisc.edu), Julian Jenkins (admin@paleobiodb.org), Mark Uhen (info@paleobiodb.org)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

You can cite the Paleobiology Database in several ways. First, you can cite the specific e- publication that you used (see above). Second, you can refer to a specific download from the PaleoBioDB, giving the date and parameters of the download. Here is an example:
The data were downloaded from the Paleobiology Database on 31 December, 2013, using the group name 'marine' and the following parameters: time intervals = Eocene and Oligocene, region = Europe, paleoenvironment = marine, Order = Cetacea.
In such a case, you may want to cite or acknowledge the people who contributed the bulk of the data to the database. We also strongly encourage that you create a secondary bibliography for work that uses large data sets. You can easily download all of the references that contributed to a dataset for this secondary bibliography. Many journals will accept a secondary bibliography as a supplementary material file, and this type of citation helps ensure that the hard work performed by members of our community collecting and describing fossil organisms gets acknowledged properly.

Abstract

The Paleobiology Database (PBDB) is a non-governmental, non-profit public resource for paleontological data. It has been organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. Its purpose is to provide global, collection-based occurrence and taxonomic data for organisms of all geological ages, as well data services to allow easy access to data for independent development of analytical tools, visualization software, and applications of all types. The Database’s broader goal is to encourage and enable data-driven collaborative efforts that address large-scale paleobiological questions.

Keywords: Occurrence, Literature

General description

Additional information: https://creativecommons.org/licenses/by-nc/4.0/ and http://vertnet.org/resources/norms.html

Project details

Project title: Paleobiology Database Chordates
Personnel: Julian Jenkins, Mark Uhen
Funding: ePANDDA (Enhancing Paleontological and Neontological Data Discovery API)

Interoperability between the PBDB, iDigBio, and iDigPaleo

NSF ICER 1540929 | ePANDDA on the STEPPE website

This project focuses on interactions between the PBDB and specimen-based databases, including iDigBio/iDigPaleo and individual museum collections.

The ePANDDA project will develop an application programming interface (API) to permit the exchange of data between three large, established, and well-supported databases: the Paleobiology Database, whose data are drawn from publications, and iDigBio and iDigPaleo, whose data are based on museum-held specimens. The new API, by enabling each of these databases to query the other two and synthesize the results, will allow data from all the included sources to be seamlessly accessed by users of any of them. For example, a paleontologist using the PBDB interface will be able to search a taxonomic name and receive not only a list of collection sites, but also a list of museum-held fossil and modern specimens of that taxon.

ELC (Earth-Life Consortium): Building Interoperable Cyberinfrastructure (CI) at the Interface between Paleogeoinformatics and Bioinformatics

Interoperability between the PBDB, Neotoma, Macrostrat, and six other databases

NSF ICER 1540997 | ELC project website | ELC on EarthCube

This project focuses on interactions between the PBDB and geography/environment-based databases, such as Neotoma and Macrostrat.

It will create a cyberinfrastructure for paleobiological sciences and a data exchange standard to facilitate data exchange between existing and future biological and geoscience databases. The existing databases being included in the project are the PBDB, Neotoma, Macrostrat, MioMap, the Mexican Quaternary Mammals Database, the South American Extinctions Database, and the regional nonmarine ostracode databases DAOD, NANODe, and NODE. An API and web services that serve as an interface between PBDB, Neotoma, and Macrostrat will be built, and the other databases listed will be incorporated into Neotoma by harmonizing their data structures. Extending the DarwinCore data exchange format to deal with paleobiological data and establishing a system of unique digital object identifiers (DOIs) for the collections and other objects in these databases will help to create a framework for the future sharing of data between biological and paleobiological databases.

Leveraging "Big Data" to Explore Big Ideas: Utilizing the Paleobiology Database to Provide Hands-on Research Opportunities for Undergraduates

Education curriculum development based on the PBDB

NSF DUE 1504718

Research experience for undergraduates in paleontology and data science, thanks to the public availability of the PBDB, is theoretically available to anyone at any school. However, making the interface easier to use and making lesson plans available will improve the usability of the database. This grant permits us to develop a new and more user-friendly interface for the PBDB and a library of lesson plans for undergraduate paleontology classes.

The research activities being designed as part of this project are being tested at several two-year and four-year colleges to assess their usefulness across a range of student populations and teaching modes, including both traditional classroom and distance learning. All of the lesson plans and tutorials are available on the Resources page.
Study area descriptions/descriptor: Global

Data published through GBIF: http://ipt.vertnet.org:8080/iptstrays/resource?r=pbdb_verts

Taxonomic coverage

Taxonomic ranks
Phylum: Chordata

Spatial coverage

General spatial coverage: Collections in the Paleobiology Database are assigned present-day coordinates and geological ages. These two pieces of information are combined with paleogeographic rotation models to obtain reconstructed paleogeographic positions.
Coordinates: 90°0'0''S and 90°0'0''N Latitude; 180°0'0''W and 180°0'0''E Longitude 

Methods

Method step description: Data are extracted from the published literature on fossil organisms.
Study extent description: Global
Sampling description: Data are extracted from the published literature on fossil organisms.

Datasets

Dataset description
Object name: Darwin Core Archive Paleobiology Database Chordates
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: http://ipt.vertnet.org:8080/iptstrays/archive.do?r=pbdb_verts
Publication date of data: 2018-07-12
Language: English
Licences of use: Creative Commons Attribution (CC-BY) 4.0 License

Metadata language: English
Date of metadata creation: 2017-11-05
Hierarchy level: Dataset