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The Paleobiology Database application programming interface

  • Shanan E. Peters (a1) and Michael McClennen (a1)
Abstract
Abstract

The Paleobiology Database (PBDB; https://paleobiodb.org) consists of geographically and temporally explicit, taxonomically identified fossil occurrence data. The taxonomy utilized by the PBDB is not static, but is instead dynamically generated using an algorithm applied to separately managed taxonomic authority and opinion data. The PBDB owes its existence to many individuals, some of whom have entered more than 1.26 million fossil occurrences and over 570,000 taxonomic opinions, and some of whom have developed and maintained supporting infrastructure and analysis tools. Here, we provide an overview of the data model currently used by the PBDB and then briefly describe how this model is exposed via an Application Programming Interface (API). Our objective is to outline how PBDB data can now be accessed within individual scientific workflows, used to develop independently managed educational and scientific applications, and accessed to forge dynamic, near real-time connections to other data resources.

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Copyright
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
References
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Alroy J. 2008. Dynamics of origination and extinction in the marine fossil record. Proceedings of the National Academy of Sciences 105:1153611542.
Alroy J. 2010a. Geographical, environmental and intrinsic biotic controls on Phanerozoic marine diversification. Palaeontology 53:12111235.
Alroy J. 2010b. The shifting balance of diversity among major marine animal groups. Science 329:11911194.
Alroy J., Aberhan M., Bottjer D. J., Foote M., Fuersich F. T., Harries P. J., Hendy A. J. W., Holland S. M., Ivany L. C., Kiessling W., Kosnik M. A., Marshall C. R., McGowan A. J., Miller A. I., Olszewski T. D., Patzkowsky M. E., Peters S. E., Villier L., Wagner P. J., Bonuso N., Borkow P. S., Brenneis B., Clapham M. E., Fall L. M., Ferguson C. A., Hanson V. L., Krug A. Z., Layou K. M., Leckey E. H., Nuernberg S., Powers C. M., Sessa J. A., Simpson C., Tomasovych A., and Visaggi C. C. 2008. Phanerozoic trends in the global diversity of marine invertebrates. doi: 10.1126/science.1156963.
Butler R., Benson R., and Barrett P. 2013. Pterosaur diversity: untangling the influence of sampling biases, Lagerstätten, and genuine biodiversity signals. Palaeogeography, Palaeoclimatology, Palaeoecology 372:7887.
Darroch S. A. F., and Wagner P. J. 2015. Response of beta diversity to pulses of Ordovician-Silurian mass extinction. Ecology 96:532549.
Foote M. 2006. Substrate affinity and diversity dynamics of Paleozoic marine animals. Paleobiology 32:345366.
Foote M. 2014. Environmental controls on geographic range size in marine animal genera. Paleobiology 40:440458.
Foster W. J., and Twitchett R. J. 2014. Functional diversity of marine ecosystems after the Late Permian mass extinction event. Nature Geoscience 7:233238.
Finnegan S, Heim N. A., Peters S. E., and Fischer W. W. 2012. Climate change and the selective signature of the Late Ordovician mass extinction. Proceedings of the National Academy of Sciences 109:68296834.
Heim N. A., and Peters S. E. 2011a. Regional environmental breadth predicts geographic range and longevity in fossil marine genera. PLoS One 6(5), e18946. doi: 10.1371/journal.pone.0018946.
Heim N. A., and Peters S. E. 2011b. Covariation in macrostratigraphic and macroevolutionary patterns in the marine record of North America. Geological Society of America Bulletin 123:620630.
Heim N. A., Knope M. L., Schaal E. K., Wang S. C., and Payne J. L. 2015. Cope’s Rule in the evolution of marine animals. Science 347:867870.
Hendy A. J. W. 2011. Taphonomic overprints on Phanerozoic trends in biodiversity: lithification and other secular megabiases. Topics in Geobiology 32:1977.
Hopkins M. J., Simpson C., and Kiessling W. 2014. Differential niche dynamics among major marine invertebrate clades. Ecology Letters 17:314323.
Kiessling W., and Kocsis A. 2015. Biodiversity dynamics and environmental occupancy of fossil azooxanthellate and zooxanthellate scleractinian corals. Paleobiology 41:402414.
Klompmaker A. A., and Kelley P. H. 2015. Shell ornamentation as a likely exaptation: evidence from predatory drilling on Cenozoic bivalves. Paleobiology 41:187201.
Kosnik M. A., Behrensmeyer A. K., Fursich F. T., Gastaldo R. A., Kidwell S. M., Kowalewski M., Plotnick R. E., Rogers R. R., Wagner P. J., and Alroy J. 2011. Changes in the shell durability of common marine taxa through the Phanerozoic: evidence for biological rather than taphonomic drivers. Paleobiology 37:303331.
Kowalewski M., Kiessling W., Aberhan M., Fursich F. T., Scarponi D., Barbour Wood S. L., and Hoffmeister A. P. 2006. Ecological, taxonomic, and taphonomic components of the post-Paleozoic increase in sample-level species diversity of marine benthos. Paleobiology 32:533561.
Marcot J. D. 2014. The fossil record and macroevolutionary history of North American ungulate mammals: standardizing variation in intensity and geography of sampling. Paleobiology 40:238255.
Peters S. E., Zhang C., Livny M., and Ré. C. 2014. A machine reading system for assembling synthetic paleontological databases. PLoS One 9:e113523. doi: 10.1371/journal.pone.0113523.
Powell M. G., Moore B. R., and Smith T. J. 2015. Origination, extinction, invasion, and extirpation components of the brachiopod latitudinal biodiversity gradient through the Phanerozoic Eon. Paleobiology 41:330341.
Smith A. B., Lloyd G. T., and McGowan A. J. 2012. Phanerozoic marine diversity: rock record provides independent test of large-scale trends. Proceedings of the Royal Society B 279:44894495.
Tomasovych A., Fursich F. T., and Wilmsen M. 2006. Preservation of autochthonous shell beds by positive feedback between increased hardpart-input rates and increased sedimentation rates. Journal of Geology 114:287312.
Uhen M. D., Barnosky A. D., Bills B., Blois J., Carrasco M. A., Carrano M. T., Erickson G. M., Eronen J. T., Fortelius M., Graham R. W., Grimm E. C., O’Leary M. A., Mast A., Piel W. H., Polly P. D., and Säilä L. K. 2013. From card catalogs to computers: Databases in vertebrate paleontology. Journal of Vertebrate Paleontology 33:1328.
Wright N., Zahirovic S., Müller R. D. and Seton M. 2013. Towards community-driven paleogeographic reconstructions: integrating open-access paleogeographic and paleobiology data with plate tectonics. Biogeosciences 10:15291541.
Zaffos A.A., and Miller A. I. 2015. Cenozoic latitudinal response curves: individualistic changes in the latitudinal distributions of marine bivalves and gastropods. Paleobiology 41:3344.
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Paleobiology
  • ISSN: 0094-8373
  • EISSN: 1938-5331
  • URL: /core/journals/paleobiology
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