Open data and digital morphology

Thomas G. Davies; Imran A. Rahman; Stephan Lautenschlager; John A. Cunningham; Robert J. Asher; Paul M. Barrett; Karl T. Bates; Stefan Bengtson; Roger B.J. Benson; Doug M. Boyer; José Braga; Jen A. Bright; Leon P.A.M. Claessens; Philip G. Cox; Xi Ping Dong; Alistair R. Evans; Peter L. Falkingham; Matt Friedman; Russell J. Garwood; Anjali Goswami; John R. Hutchinson; Nathan S. Jeffery; Zerina Johanson; Renaud Lebrun; Carlos Martínez-Pérez; Jesús Marugán-Lobón; Paul M. O’Higgins; Brian Metscher; Maëva Orliac; Timothy B. Rowe; Martin Rücklin; Marcelo R. Sánchez-Villagra; Neil H. Shubin; Selena Y. Smith; J. Matthias Starck; Chris Stringer; Adam P. Summers; Mark D. Sutton; Stig A. Walsh; Vera Weisbecker; Lawrence M. Witmer; Stephen Wroe; Zongjun Yin; Emily J. Rayfield; Philip C.J. Donoghue

doi:10.1098/rspb.2017.0194

Open data and digital morphology

Thomas G. Davies, Imran A. Rahman, Stephan Lautenschlager, John A. Cunningham, Robert J. Asher, Paul M. Barrett, Karl T. Bates, Stefan Bengtson, Roger B.J. Benson, Doug M. Boyer, José Braga, Jen A. Bright, Leon P.A.M. Claessens, Philip G. Cox, Xi Ping Dong, Alistair R. Evans, Peter L. Falkingham, Matt Friedman, Russell J. Garwood, Anjali GoswamiJohn R. Hutchinson, Nathan S. Jeffery, Zerina Johanson, Renaud Lebrun, Carlos Martínez-Pérez, Jesús Marugán-Lobón, Paul M. O’Higgins, Brian Metscher, Maëva Orliac, Timothy B. Rowe, Martin Rücklin, Marcelo R. Sánchez-Villagra, Neil H. Shubin, Selena Y. Smith, J. Matthias Starck, Chris Stringer, Adam P. Summers, Mark D. Sutton, Stig A. Walsh, Vera Weisbecker, Lawrence M. Witmer, Stephen Wroe, Zongjun Yin, Emily J. Rayfield, Philip C.J. Donoghue

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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.

Original language	English
Article number	20170194
Journal	Proceedings of The Royal Society of London Series B: Biological Sciences
Volume	284
Issue number	1852
DOIs	https://doi.org/10.1098/rspb.2017.0194
Publication status	Published - 12 Apr 2017
Externally published	Yes

Bibliographical note

Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

Keywords

Computed tomography
Digital data
Functional analysis
Phenotype
Three-dimensional models
Visualization

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10.1098/rspb.2017.0194Licence: CC BY

Published versionFinal published version, 317 KBLicence: CC BY

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Davies, T. G., Rahman, I. A., Lautenschlager, S., Cunningham, J. A., Asher, R. J., Barrett, P. M., Bates, K. T., Bengtson, S., Benson, R. B. J., Boyer, D. M., Braga, J., Bright, J. A., Claessens, L. P. A. M., Cox, P. G., Dong, X. P., Evans, A. R., Falkingham, P. L., Friedman, M., Garwood, R. J., ... Donoghue, P. C. J. (2017). Open data and digital morphology. Proceedings of The Royal Society of London Series B: Biological Sciences, 284(1852), Article 20170194. https://doi.org/10.1098/rspb.2017.0194

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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",

author = "Davies, {Thomas G.} and Rahman, {Imran A.} and Stephan Lautenschlager and Cunningham, {John A.} and Asher, {Robert J.} and Barrett, {Paul M.} and Bates, {Karl T.} and Stefan Bengtson and Benson, {Roger B.J.} and Boyer, {Doug M.} and Jos{\'e} Braga and Bright, {Jen A.} and Claessens, {Leon P.A.M.} and Cox, {Philip G.} and Dong, {Xi Ping} and Evans, {Alistair R.} and Falkingham, {Peter L.} and Matt Friedman and Garwood, {Russell J.} and Anjali Goswami and Hutchinson, {John R.} and Jeffery, {Nathan S.} and Zerina Johanson and Renaud Lebrun and Carlos Mart{\'i}nez-P{\'e}rez and Jes{\'u}s Marug{\'a}n-Lob{\'o}n and O{\textquoteright}Higgins, {Paul M.} and Brian Metscher and Ma{\"e}va Orliac and Rowe, {Timothy B.} and Martin R{\"u}cklin and S{\'a}nchez-Villagra, {Marcelo R.} and Shubin, {Neil H.} and Smith, {Selena Y.} and Starck, {J. Matthias} and Chris Stringer and Summers, {Adam P.} and Sutton, {Mark D.} and Walsh, {Stig A.} and Vera Weisbecker and Witmer, {Lawrence M.} and Stephen Wroe and Zongjun Yin and Rayfield, {Emily J.} and Donoghue, {Philip C.J.}",

note = "Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.",

year = "2017",

month = apr,

day = "12",

doi = "10.1098/rspb.2017.0194",

language = "English",

volume = "284",

journal = "Proceedings of The Royal Society of London Series B: Biological Sciences",

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Davies, TG, Rahman, IA, Lautenschlager, S, Cunningham, JA, Asher, RJ, Barrett, PM, Bates, KT, Bengtson, S, Benson, RBJ, Boyer, DM, Braga, J, Bright, JA, Claessens, LPAM, Cox, PG, Dong, XP, Evans, AR, Falkingham, PL, Friedman, M, Garwood, RJ, Goswami, A, Hutchinson, JR, Jeffery, NS, Johanson, Z, Lebrun, R, Martínez-Pérez, C, Marugán-Lobón, J, O’Higgins, PM, Metscher, B, Orliac, M, Rowe, TB, Rücklin, M, Sánchez-Villagra, MR, Shubin, NH, Smith, SY, Starck, JM, Stringer, C, Summers, AP, Sutton, MD, Walsh, SA, Weisbecker, V, Witmer, LM, Wroe, S, Yin, Z, Rayfield, EJ & Donoghue, PCJ 2017, 'Open data and digital morphology', Proceedings of The Royal Society of London Series B: Biological Sciences, vol. 284, no. 1852, 20170194. https://doi.org/10.1098/rspb.2017.0194

TY - JOUR

T1 - Open data and digital morphology

AU - Davies, Thomas G.

AU - Rahman, Imran A.

AU - Lautenschlager, Stephan

AU - Cunningham, John A.

AU - Asher, Robert J.

AU - Barrett, Paul M.

AU - Bates, Karl T.

AU - Bengtson, Stefan

AU - Benson, Roger B.J.

AU - Boyer, Doug M.

AU - Braga, José

AU - Bright, Jen A.

AU - Claessens, Leon P.A.M.

AU - Cox, Philip G.

AU - Dong, Xi Ping

AU - Evans, Alistair R.

AU - Falkingham, Peter L.

AU - Friedman, Matt

AU - Garwood, Russell J.

AU - Goswami, Anjali

AU - Hutchinson, John R.

AU - Jeffery, Nathan S.

AU - Johanson, Zerina

AU - Lebrun, Renaud

AU - Martínez-Pérez, Carlos

AU - Marugán-Lobón, Jesús

AU - O’Higgins, Paul M.

AU - Metscher, Brian

AU - Orliac, Maëva

AU - Rowe, Timothy B.

AU - Rücklin, Martin

AU - Sánchez-Villagra, Marcelo R.

AU - Shubin, Neil H.

AU - Smith, Selena Y.

AU - Starck, J. Matthias

AU - Stringer, Chris

AU - Summers, Adam P.

AU - Sutton, Mark D.

AU - Walsh, Stig A.

AU - Weisbecker, Vera

AU - Witmer, Lawrence M.

AU - Wroe, Stephen

AU - Yin, Zongjun

AU - Rayfield, Emily J.

AU - Donoghue, Philip C.J.

N1 - Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

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N2 - 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.

AB - 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.

KW - Computed tomography

KW - Digital data

KW - Functional analysis

KW - Phenotype

KW - Three-dimensional models

KW - Visualization

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U2 - 10.1098/rspb.2017.0194

DO - 10.1098/rspb.2017.0194

M3 - Article

C2 - 28404779

AN - SCOPUS:85017538431

SN - 0962-8452

VL - 284

JO - Proceedings of The Royal Society of London Series B: Biological Sciences

JF - Proceedings of The Royal Society of London Series B: Biological Sciences

IS - 1852

M1 - 20170194

ER -

Open data and digital morphology

Abstract

Bibliographical note

Keywords

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