Integrated Publishing Toolkit(IPT)

free and open access to biodiversity data

Paleobiology Database

Latest version published by Paleobiology Database on Nov 3, 2017 Paleobiology Database

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.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 1,310,925 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Downloads

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

Data as a DwC-A file download 1,310,925 records in English (119 MB) - Update frequency: biannually
Metadata as an EML file download in English (15 KB)
Metadata as an RTF file download in English (13 KB)

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

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.

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is Paleobiology Database. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: bb5b30b4-827e-4d5e-a86a-825d65cb6583.  Paleobiology Database publishes this resource, and is itself registered in GBIF as a data publisher endorsed by U.S. Geological Survey.

Keywords

Occurrence; Specimen

Contacts

Who created the resource:

Michael McClennen
Chief Informaticist
Paleobiology Database +1-608-262-5366
https://paleobiodb.org

Who can answer questions about the resource:

Julian Jenkins
Geoinformaticist/Data Scientist
Paleobiology Database US
https://paleobiodb.org

Who filled in the metadata:

Julian Jenkins
Geoinformaticist/Data Scientist
Paleobiology Database US
https://paleobiodb.org
Mark Uhen
Executive Committee Chair
Paleobiology Database US
https://paleobiodb.org

Who else was associated with the resource:

Point Of Contact
Julian Jenkins
Geoinformaticist
Paleobiology Database
https://paleobiodb.org
Programmer
David Bloom
Programmer
John Weiczorek
Information Architect
Museum of Vertebrate Zoology at UC Berkeley

Geographic 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.

Bounding Coordinates South West [-90, -180], North East [90, 180]

Taxonomic Coverage

Mollusca 33% Brachiopoda 13% Arthropoda 10% Mammalia 8% Cnidaria 5% Radiolaria 4% Foraminifera 3% Bryozoa 2% Echinodermata 2%

Phylum  Mollusca,  Brachiopoda,  Arthropoda,  Cnidaria,  Foraminifera,  Bryozoa,  Echinodermata
Class  Mammalia
Strain  Radiolaria

Project Data

The Paleobiology Database is a public database of paleontological data that anyone can use, maintained by an international non-governmental group of paleontologists. You can explore the data online in the Navigator, which lets you filter fossil occurrences by time, space, and taxonomy, and displays their modern and paleogeographic locations; or you can download the data to your own computer to do your own analyses.

Title Paleobiology Database
Identifier PBDB
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 Description Global

The personnel involved in the project:

Metadata Provider
Julian Jenkins
Principal Investigator
Mark Uhen

Sampling Methods

Data are extracted from the published literature on fossil organisms.

Study Extent Global

Method step description:

  1. Data are extracted from the published literature on fossil organisms.