Open data and digital morphology

Thomas G Davies¹, Imran A Rahman^{1

2}, Stephan Lautenschlager^{1

3}, John A Cunningham¹, Robert J Asher⁴, Paul M Barrett⁵, Karl T Bates⁶, Stefan Bengtson⁷, Roger B J Benson⁸, Doug M Boyer⁹, José Braga^{10

11}, Jen A Bright^{12

13}, Leon P A M Claessens¹⁴, Philip G Cox¹⁵, Xi-Ping Dong¹⁶, Alistair R Evans¹⁷, Peter L Falkingham¹⁸, Matt Friedman¹⁹, Russell J Garwood^{5

20}, Anjali Goswami²¹, John R Hutchinson²², Nathan S Jeffery⁶, Zerina Johanson⁵, Renaud Lebrun²³, Carlos Martínez-Pérez^{1

24}, Jesús Marugán-Lobón²⁵, Paul M O'Higgins¹⁵, Brian Metscher²⁶, Maëva Orliac²³, Timothy B Rowe²⁷, Martin Rücklin^{1

28}, Marcelo R Sánchez-Villagra²⁹, Neil H Shubin³⁰, Selena Y Smith¹⁹, J Matthias Starck³¹, Chris Stringer⁵, Adam P Summers³², Mark D Sutton³³, Stig A Walsh³⁴, Vera Weisbecker³⁵, Lawrence M Witmer³⁶, Stephen Wroe³⁷, Zongjun Yin^{1

38}, Emily J Rayfield³⁹, Philip C J Donoghue⁴⁰

Affiliations

¹ School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
² Oxford University Museum of Natural History, Parks Road, Oxford OX1 3PW, UK.
³ School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
⁴ Museum of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
⁵ Dept. Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
⁶ Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK.
⁷ Dept. Palaeobiology, Swedish Museum of Natural History, PO Box 50007, 104 05 Stockholm, Sweden.
⁸ Dept. Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK.
⁹ Dept. Evolutionary Anthropology, Duke University, PO Box 90383, Biological Sciences Building, 130 Science Drive, Durham, NC 27708, USA.
¹⁰ Computer-assisted Palaeoanthropology Team, UMR 5288 CNRS-Université de Toulouse (Paul Sabatier), Toulouse, France.
¹¹ Evolutionary Studies Institute, University of Witwatersrand, Johannesburg, South Africa.
¹² School of Geosciences, University of South Florida, Tampa, FL 33620, USA.
¹³ Center for Virtualization and Applied Spatial Technologies, University of South Florida, Tampa, FL 33620, USA.
¹⁴ Dept. Biology, College of the Holy Cross, Worcester, MA 01610, USA.
¹⁵ Dept. Archaeology and Hull York Medical School, University of York, York YO10 5DD, UK.
¹⁶ School of Earth and Space Science, Peking University, Beijing 100871, People's Republic of China.
¹⁷ School of Biological Sciences, Monash University, Victoria 3800, Australia.
¹⁸ School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.
¹⁹ Dept. Earth and Environmental Sciences and Museum of Paleontology, University of Michigan, Ann Arbor, MI 48109, USA.
²⁰ School of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, UK.
²¹ Dept. Genetics, Evolution and Environment, and Dept. Earth Sciences, University College London, Gower Street, London SW17 7PL, UK.
²² Structure and Motion Lab, Dept. Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Hatfield, Hertfordshire AL9 7TA, UK.
²³ Institut des Sciences de l'Evolution de Montpellier, CC64, Université de Montpellier, campus Triolet, Place Eugène Bataillon, 34095 Montpellier cedex 5, France.
²⁴ Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, 46980 Paterna, Spain.
²⁵ Unidad de Paleontología, Dpto. Biología, Universidad Autónoma de Madrid, 28049 Cantoblanco, Spain.
²⁶ Dept. Theoretical Biology, University of Vienna, Althanstrasse 14, 1090, Austria.
²⁷ Jackson School of Geosciences C1100, The University of Texas at Austin, Austin, TX 78712, USA.
²⁸ Naturalis Biodiversity Center, Postbus 9517, 2300 RA Leiden, The Netherlands.
²⁹ Paläontologisches Institut und Museum der Universität Zürich, Karl Schmid Strasse 4, 8006 Zürich, Switzerland.
³⁰ Dept. Organismal Biology & Anatomy, University of Chicago, Chicago, IL 60637, USA.
³¹ Dept. Biology II, Ludwig-Maximilians University Munich (LMU), Großhadernerstr. 2, 82152 Planegg-Martinsried, Germany.
³² University of Washington, Friday Harbor Labs, Friday Harbor, WA 98250, USA.
³³ Dept. Earth Science and Engineering, Imperial College, London SW7 2AZ, UK.
³⁴ National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK.
³⁵ School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia.
³⁶ Dept. Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Athens, OH 45701, USA.
³⁷ School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia.
³⁸ State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.
³⁹ School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK e.rayfield@bristol.ac.uk.
⁴⁰ School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK phil.donoghue@bristol.ac.uk.

PMID: 28404779
PMCID: PMC5394671
DOI: 10.1098/rspb.2017.0194

Review

Open data and digital morphology

Thomas G Davies et al. Proc Biol Sci. 2017.

. 2017 Apr 12;284(1852):20170194.

doi: 10.1098/rspb.2017.0194. Epub 2017 Apr 12.

Authors

Affiliations

¹ School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
² Oxford University Museum of Natural History, Parks Road, Oxford OX1 3PW, UK.
³ School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
⁴ Museum of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
⁵ Dept. Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
⁶ Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK.
⁷ Dept. Palaeobiology, Swedish Museum of Natural History, PO Box 50007, 104 05 Stockholm, Sweden.
⁸ Dept. Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK.
⁹ Dept. Evolutionary Anthropology, Duke University, PO Box 90383, Biological Sciences Building, 130 Science Drive, Durham, NC 27708, USA.
¹⁰ Computer-assisted Palaeoanthropology Team, UMR 5288 CNRS-Université de Toulouse (Paul Sabatier), Toulouse, France.
¹¹ Evolutionary Studies Institute, University of Witwatersrand, Johannesburg, South Africa.
¹² School of Geosciences, University of South Florida, Tampa, FL 33620, USA.
¹³ Center for Virtualization and Applied Spatial Technologies, University of South Florida, Tampa, FL 33620, USA.
¹⁴ Dept. Biology, College of the Holy Cross, Worcester, MA 01610, USA.
¹⁵ Dept. Archaeology and Hull York Medical School, University of York, York YO10 5DD, UK.
¹⁶ School of Earth and Space Science, Peking University, Beijing 100871, People's Republic of China.
¹⁷ School of Biological Sciences, Monash University, Victoria 3800, Australia.
¹⁸ School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.
¹⁹ Dept. Earth and Environmental Sciences and Museum of Paleontology, University of Michigan, Ann Arbor, MI 48109, USA.
²⁰ School of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, UK.
²¹ Dept. Genetics, Evolution and Environment, and Dept. Earth Sciences, University College London, Gower Street, London SW17 7PL, UK.
²² Structure and Motion Lab, Dept. Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Hatfield, Hertfordshire AL9 7TA, UK.
²³ Institut des Sciences de l'Evolution de Montpellier, CC64, Université de Montpellier, campus Triolet, Place Eugène Bataillon, 34095 Montpellier cedex 5, France.
²⁴ Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, 46980 Paterna, Spain.
²⁵ Unidad de Paleontología, Dpto. Biología, Universidad Autónoma de Madrid, 28049 Cantoblanco, Spain.
²⁶ Dept. Theoretical Biology, University of Vienna, Althanstrasse 14, 1090, Austria.
²⁷ Jackson School of Geosciences C1100, The University of Texas at Austin, Austin, TX 78712, USA.
²⁸ Naturalis Biodiversity Center, Postbus 9517, 2300 RA Leiden, The Netherlands.
²⁹ Paläontologisches Institut und Museum der Universität Zürich, Karl Schmid Strasse 4, 8006 Zürich, Switzerland.
³⁰ Dept. Organismal Biology & Anatomy, University of Chicago, Chicago, IL 60637, USA.
³¹ Dept. Biology II, Ludwig-Maximilians University Munich (LMU), Großhadernerstr. 2, 82152 Planegg-Martinsried, Germany.
³² University of Washington, Friday Harbor Labs, Friday Harbor, WA 98250, USA.
³³ Dept. Earth Science and Engineering, Imperial College, London SW7 2AZ, UK.
³⁴ National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK.
³⁵ School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia.
³⁶ Dept. Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Athens, OH 45701, USA.
³⁷ School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia.
³⁸ State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.
³⁹ School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK e.rayfield@bristol.ac.uk.
⁴⁰ School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK phil.donoghue@bristol.ac.uk.

PMID: 28404779
PMCID: PMC5394671
DOI: 10.1098/rspb.2017.0194

Abstract

Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.

Keywords: computed tomography; digital data; functional analysis; phenotype; three-dimensional models; visualization.

PubMed Disclaimer

Conflict of interest statement

We declare we have no competing interests.

Comment in

Empty rhetoric over data sharing slows science.
[No authors listed] [No authors listed] Nature. 2017 Jun 12;546(7658):327. doi: 10.1038/546327a. Nature. 2017. PMID: 28617474 No abstract available.

References

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Open data and digital morphology

Affiliations

Open data and digital morphology

Authors

Affiliations

Abstract

Conflict of interest statement

Comment in

References

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MeSH terms

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