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MORPHOSOURCE: ARCHIVING AND SHARING 3-D DIGITAL SPECIMEN DATA

Published online by Cambridge University Press:  27 April 2017

Doug M. Boyer ,
Gregg F. Gunnell ,
Seth Kaufman  and
Timothy M. McGeary
Doug M. Boyer
Affiliation:
Duke University, Department of Evolutionary Anthropology, Biological Sciences Building, 130 Science Drive, Durham, North Carolina 27708, USA, 〈dmb65@duke.edu〉
Gregg F. Gunnell
Affiliation:
Duke Lemur Center, Division of Fossil Primates, 1013 Broad Street, Durham, North Carolina 27705, USA, 〈gregg.gunnell@duke.edu〉
Seth Kaufman
Affiliation:
PO Box 672, Greenport, New York 11944, USA, 〈seth@whirl-i-gig.com〉
Timothy M. McGeary
Affiliation:
Duke University Library Information Technology Services, Durham, North Carolina 27708, USA, 〈tim.mcgeary@duke.edu〉
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Abstract

Advancement of understanding in paleontology and biology has always been hindered by difficulty in accessing comparative data. With current and burgeoning technology, the severity of this hindrance can be substantially reduced. Researchers and museum personnel generating three-dimensional (3-D) digital models of museum specimens can archive them using internet repositories that can then be explored and utilized by other researchers and private individuals without a museum trip. We focus on MorphoSource, the largest web archive for 3-D museum data at present. We describe the site, how to use it most effectively in its current form, and best practices for file formats and metadata inclusion to aid the growing community wishing to utilize it for distributing 3-D digital data. The potential rewards of successfully crowd sourcing the digitization of museum collections from the research community are great, as it should ensure rapid availability of the most important datasets. Challenges include long-term governance (i.e., maintaining site functionality, supporting large amounts of digital storage, and monitoring/updating file to prevent bit rot, which is the slow and random corruption of electronic data over time, and data format obsolescence, which is the problem of data becoming unreadable or ineffective because of the loss of functional software necessary for access), and utilization by the community (i.e., detecting and minimizing user error in creating data records, incentivizing data sharing by researchers and institutions alike, and protecting stakeholder rights to data, while maximizing accessibility and discoverability).

MorphoSource serves as a proof-of-concept of how these kinds of challenges can be met. Accordingly, it is generally recognized as the most appropriate repository for large, raw datasets of fossil organisms and/or comparative samples. Its existence has begun to transform data transparency standards because journal reviewers, editors, and grant officers now often suggest or require that 3-D data be made available through this site.

Type
Research Article
Information
The Paleontological Society Papers , Volume 22: Virtual Paleontology , September 2016 , pp. 157 - 181
Copyright
Copyright © 2017, The Paleontological Society 

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References

Archivematica, 2016, Archivematica [online software]: https://www.archivematica.org/en/ (accessed 8 September 2016).Google Scholar
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Wheeler, D.L., 2005, GenBank: Nucleic Acids Research, v. 33 (Database Issue), p. D34–D38.Google Scholar
Berger, L.R., Hawks, J., de Ruiter, D.J., Churchill, S.E., Schmid, P., Delezene, L.K., Kivell, T.L., Garvin, H.M., Williams, S.A., DeSilva, J.M., Skinner, M.M., Musiba, C.M., Cameron, N., Holliday, T.W., Harcourt-Smith, W., Ackermann, R.R., Bastir, M., Bogin, B., Bolter, D., Brophy, J., Cofran, Z.D., Congdon, K.A., Deane, A.S., Dembo, M., Drapeau, M., Elliott, M.C., Feuerriegel, E.M., Garcia-Martinez, D., Green, D.J., Gurtov, A., Irish, J.D., Kruger, A., Laird, M.F., Marchi, D., Meyer, M.R., Nalla, S., Negash, E.W., Orr, C.M., Radovcic, D., Schroeder, L., Scott, J.E., Throckmorton, Z., Tocheri, M.W., VanSickle, C., Walker, C.S., Wei, P., and Zipfel, P., 2015, Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa: eLife, v. 4, art. e09560, DOI: 10.7554/eLife.09560.Google Scholar
Bloch, J.I., Woodruff, E.D., Wood, A.R., Rincon, A.F., Harrington, A.R., , Morgan, G.S., Foster, D.A., Montes, C., Jaramillo, C.A., Jud, N.A., Jones, D.S., and MacFadden, B.J., 2016, First North American fossil monkey and early Miocene tropical biotic interchange: Nature, v. 533 (7602): 243–246, DOI: 10.1038/nature17415. http://www.nature.com/nature/journal/v533/n7602/abs/nature17415.html#supplementary-information.Google Scholar
Boyer, D.M., 2008, Relief index of second mandibular molars is a correlate of diet among prosimian primates and other euarchontan mammals: Journal of Human Evolution, v. 55, p. 1118–1137.Google Scholar
Boyer, D.M., Kirk, E.C., Silcox, M.T., Gunnell, G.F., Gilbert, C.C., Yapuncich, G.S., Allen, K.L., Welch, E., Bloch, J.I., Gonzales, L.A., Kay, R.F., and Seiffert, E.R., 2016, Internal carotid arterial canal size and scaling in Euarchonta: Re-assessing implications for arterial patency and phylogenetic relationships in early fossil primates: Journal of Human Evolution, v. 97, 123–144, DOI: http://dx.doi.org/10.1016/j.jhevol.2016.06.002.Google Scholar
Broo, J., and Mahoney, J., 2015, Chewing on change: exploring the evolution of horses in response to climate change: http://www.paleoteach.org/chewing-on-change-exploring-the-evolution-of-horses-in-response-to-climate-change (accessed June 2016).Google Scholar
California Digital Library, 2016, EZID: University of California, Office of The President, http://ezid.cdlib.org (accessed June 2016).Google Scholar
Copes, L.E., Lucas, L.M., Thostenson, J.O., Hoekstra, H.E., and Boyer, D.M., 2016, A collection of non-human primate computed tomography scans housed in MorphoSource, a repository for 3D data: Scientific Data, v. 3, art. 160001, DOI: 10.1038/sdata.2016.1.Google Scholar
Corel Corporation, 1991, WinZip [computer software]: http://winzip.com/index.html (accessed 13 September 2016).Google Scholar
Datacite, 2016, Cite Your Data: https://www.datacite.org/services/cite-your-data.html (accessed March 2016).Google Scholar
Dryad Data Development Team, 2014, Dryad: http://datadryad.org (accessed June 2016).Google Scholar
Duraspace Organization, 2016, Fedora Commons, Apache 2 license: http://fedorarepository.org (accessed June 2016).Google Scholar
Evans, A.R., Wilson, G.P., Fortelius, M., and Jernvall, J., 2007, High-level similarity of dentitions in carnivorans and rodents: Nature, v. 445, p. 78–81.Google Scholar
Fulwood, E. L., Boyer, D.M., and Kay, R.F., in press, Stem members of Platyrrhini are distinct from Catarrhines in at least one derived cranial feature: Journal of Human Evolution.Google Scholar
Ginsparg, P., 1991, ArXiv: Cornell University Library [online software], http://arxiv.org (accessed 13 September 2016).Google Scholar
Google, 2016, Google Scholar: https://scholar.google.com (accessed June 2016).Google Scholar
Grant, C., 2016, PaleoTeach: http://www.paleoteach.org/ (accessed June 2016).Google Scholar
Grant, C.A., MacFadden, B.J., Antonenko, P., and Perez, V.J., 2017, 3-D fossils for K–12 education: A case example using the giant extinct shark Carcharocles megalodon: The Paleontological Society Papers, v. 22, p. 197–209.Google Scholar
Hydra Partners, 2016, Project Hydra, Apache 2 license: http://projecthydra.org (accessed June 2016).Google Scholar
iDigBio, 2016, iDigBio: Integrated Digitized Biocollections: https://www.idigbio.org/ (accessed June 2016).Google Scholar
Jernvall, J., Fortelius, M., Evans, G., Evans, A.E., Pljusnin, I., and Kauhanen, J., 2016, MorphoBrowser: http://morphobrowser.biocenter.helsinki.fi/ (accessed June 2016).Google Scholar
Klimpel, P., 2012, Free knowledge based on Creative Commons Licenses: Consequences, risks and side-effects of the license module ‘non-commercial use only – NC’, in Djordjevic, V., Weitzmann, J.H., and Otto, P., eds., Wikimedia Germany–Association for the Advancement of Free Knowledge: http://openglam.org/files/2013/01/iRights_CC-NC_Guide_English.pdf (accessed May 2016).Google Scholar
Lebrun, R., and Orliac, M.J., 2017, MorphoMuseuM: An online platform for publication and storage of virtual specimens: The Paleontological Society Papers, v. 22, p. 183–195.CrossRefGoogle Scholar
Marigó, J., Roig, I., Seiffert, E.R., Moyà-Solà, S., and Boyer, D.M., 2016, Astragalar and calcaneal morphology of the middle Eocene primate Anchomomys frontanyensis (Anchomomyini): Implications for early primate evolution: Journal of Human Evolution, p. 91, v. 122–143.CrossRefGoogle ScholarPubMed
MIT Libraries, 2016, APls for Scholarly Resources [Internet]: http://libguides.mit.edu/apis (accessed 3 October 2016).Google Scholar
NAE and NRC (National Academy of Engineering and National Research Council), 2014, STEM Integration in K-12 Education: Status, Prospects, and an Agenda for Research: National Academies Press, Washington, DC, 180 p.Google Scholar
NGSS (Next Generation Science Standards), 2016, Next Generation Science Standards: http://www.nextgenscience.org (accessed June 2016).Google Scholar
O’Leary, M.A., and Kaufman, S.G., 2012, MorphoBank 3.0: Web application for morphological phylogenetics and taxonomy: http://www.morphobank.org (accessed 13 September 2016).Google Scholar
Owen, R., 1843, Glossary: Lectures on the Comparative Anatomy and Physiology of the Invertebrate Animals Delivered at the Royal College of Surgeons in 1843, p. 379.CrossRefGoogle Scholar
Pavlov, I., 1999, 7zip [computer software]: http://www.7-zip.org/ (accessed 13 September 2016).Google Scholar
Researchgate GMBH, 2016, ResearchGate: https://www.researchgate.com (accessed June 2016).Google Scholar
Roshal, E., and Roshal, A., 1995, WinRAR [computer software]: http://rarlab.com/ (accessed 13 September 2016).Google Scholar
Seiffert, E.R., Boyer, D.M., and Costeur, L., 2015, Tarsal morphology of Caenopithecus, a large adapiform primate from the middle Eocene of Switzerland: PeerJ, v. 3, p. e1036, DOI: 10.7717/peerj.1036.Google Scholar