Published July 12, 2023 | Version 1.0
Dataset Open

BioDeepTime: database and compilation code

  • 1. GeoZentrum Nordbayern, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Loewenichstr. 28, 91054 Erlangen, Germany
  • 2. ICBM - Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Schleusenstrasse 1, Wilhelmshaven, 26382, Germany
  • 3. University of St Andrews, St Andrews, KY16 9TH, United Kingdom; Guia Marine Lab, MARE, Faculty of Science of the University of Lisbon, 939, Estrada do Guincho, Cascais 2750-374, Portugal
  • 4. Department of Geography, University of Wisconsin-Madison, 550 N. Park Street, Madison, WI 53706; Department of Earth and Environmental Sciences, Syracuse University, 141 Crouse Dr, Syracuse, NY 13210
  • 5. Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
  • 6. MARUM – Center for Marine Environmental Sciences University of Bremen Leobener Strasse 8 28359 Bremen, Germany
  • 7. State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing 210008, China
  • 8. Natural History Museum, University of Oslo, Oslo, 0562, Norway
  • 9. Department of Earth and Planetary Sciences, Yale University, 210 Whitney Ave, New Haven, CT 06511
  • 10. Department of Geoscience, University of Wisconsin – Madison, Madison, WI 53706
  • 11. University of St Andrews, St Andrews, KY16 9TH, United Kingdom
  • 12. Museum für Naturkunde, Invalidenstraße 43, Berlin, D-10115, Germany
  • 13. Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, United Kingdom
  • 14. Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Universitätsstraße 30, Bayreuth, 95447, Germany
  • 15. University of British Columbia, Vancouver, BC V6T1Z4, Canada
  • 16. Earth Science Institute, Slovak Academy of Sciences, Bratislava, 84005, Slovakia
  • 17. Department of Geography, University of Wisconsin-Madison, 550 N. Park Street, Madison, WI 53706
  • 18. School of Biological Sciences, Area of Ecology and Biodiversity, Swire Institute of Marine Science, Institute for Climate and Carbon Neutrality, Musketeers Foundation Institute of Data Science, and State Key Laboratory of Marine Pollution, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong SAR, China
  • 19. Department of Integrative Biology & Museum of Paleontology, University of California, Berkeley, Valley Life Sciences Building, Berkeley, CA 94720-4780, USA
  • 20. Yale Peabody Museum, 170 Whitney Ave, New Haven, CT, 06511


The archive includes copies, compilation code, documentation and temporary data files for the BioDeepTime database.

Deposited files:

  • Relational database in SQLite format:
  • Denormalized database in zipped .csv format:
  • Denormalized database in zipped .parquet (v1.0) format:
  • Denormalized database in .rds (R version 4.0) format: biodeeptime.rds.
  • Description of tables and columns:
  • Database schema: schema.pdf.
  • Synonymy of sources: Synonymy of sources.xlsx.
  • Change log and known issues:
  • Compilation files:
  • References in .csv format: references.csv
  • References in .rds format: references.rds
  • Reference bibtex entries: references.bib
  • Bchron ages calculated for Neotoma: neotoma_bchron.rds

This repository accompanies the study BioDeepTime: a database of biodiversity time series for modern and fossil assemblages by Smith et al. (In Press).


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