Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

Arlin Stoltzfus, Brian O'Meara, Jamie Whitacre, Ross Mounce, Emily L Gillespie, S Kumar, Dan F Rosauer, Rutger A Vos

Research output: Non-textual formData set/Database

Abstract

BACKGROUND: Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote data sharing reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing phylogenetic trees and associated data in a way that promotes re-use. RESULTS: Here we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find that the technical infrastructure is available to support rudimentary archiving, but the frequency of archiving is low. Currently, most phylogenetic knowledge is not easily re-used due to a lack of archiving, lack of awareness of best practices, and lack of community-wide standards for formatting data, naming entities, and annotating data. Most attempts at data re-use seem to end in disappointment. Nevertheless, we find many positive examples of data re-use, particularly those that involve customized species trees generated by grafting to, and pruning from, a mega-tree. CONCLUSIONS: The technologies and practices that facilitate data re-use can catalyze synthetic and integrative research. However, success will require engagement from various stakeholders including individual scientists who produce or consume shareable data, publishers, policy-makers, technology developers and resource-providers. The critical challenges for facilitating re-use of phylogenetic trees and associated data, we suggest, include: a broader commitment to public archiving; more extensive use of globally meaningful identifiers; development of user-friendly technology for annotating, submitting, searching, and retrieving data and their metadata; and development of a minimum reporting standard (MIAPA) indicating which kinds of data and metadata are most important for a re-useable phylogenetic record.
Original languageEnglish
PublisherDryad Digital Repository
DOIs
Publication statusPublished - 2012

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Stoltzfus, A. (Author), O'Meara, B. (Author), Whitacre, J. (Author), Mounce, R. (Author), Gillespie, E. L. (Author), Kumar, S. (Author), ... Vos, R. A. (Author). (2012). Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. Data set/Database, Dryad Digital Repository. https://doi.org/10.5061/dryad.h6pf365t
Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. Stoltzfus, Arlin (Author); O'Meara, Brian (Author); Whitacre, Jamie (Author); Mounce, Ross (Author); Gillespie, Emily L (Author); Kumar, S (Author); Rosauer, Dan F (Author); Vos, Rutger A (Author). 2012. Dryad Digital Repository.

Research output: Non-textual formData set/Database

Stoltzfus, A, O'Meara, B, Whitacre, J, Mounce, R, Gillespie, EL, Kumar, S, Rosauer, DF & Vos, RA, Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis, 2012, Data set/Database, Dryad Digital Repository. https://doi.org/10.5061/dryad.h6pf365t
Stoltzfus A (Author), O'Meara B (Author), Whitacre J (Author), Mounce R (Author), Gillespie EL (Author), Kumar S (Author) et al. Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis Dryad Digital Repository. 2012. https://doi.org/10.5061/dryad.h6pf365t
Stoltzfus, Arlin (Author) ; O'Meara, Brian (Author) ; Whitacre, Jamie (Author) ; Mounce, Ross (Author) ; Gillespie, Emily L (Author) ; Kumar, S (Author) ; Rosauer, Dan F (Author) ; Vos, Rutger A (Author). / Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. [Data set/Database].
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title = "Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis",
abstract = "BACKGROUND: Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote data sharing reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing phylogenetic trees and associated data in a way that promotes re-use. RESULTS: Here we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find that the technical infrastructure is available to support rudimentary archiving, but the frequency of archiving is low. Currently, most phylogenetic knowledge is not easily re-used due to a lack of archiving, lack of awareness of best practices, and lack of community-wide standards for formatting data, naming entities, and annotating data. Most attempts at data re-use seem to end in disappointment. Nevertheless, we find many positive examples of data re-use, particularly those that involve customized species trees generated by grafting to, and pruning from, a mega-tree. CONCLUSIONS: The technologies and practices that facilitate data re-use can catalyze synthetic and integrative research. However, success will require engagement from various stakeholders including individual scientists who produce or consume shareable data, publishers, policy-makers, technology developers and resource-providers. The critical challenges for facilitating re-use of phylogenetic trees and associated data, we suggest, include: a broader commitment to public archiving; more extensive use of globally meaningful identifiers; development of user-friendly technology for annotating, submitting, searching, and retrieving data and their metadata; and development of a minimum reporting standard (MIAPA) indicating which kinds of data and metadata are most important for a re-useable phylogenetic record.",
author = "Arlin Stoltzfus and Brian O'Meara and Jamie Whitacre and Ross Mounce and Gillespie, {Emily L} and S Kumar and Rosauer, {Dan F} and Vos, {Rutger A}",
note = "When using this data, please cite the original article: Stoltzfus A, O'Meara B, Whitacre J, Mounce R, Gillespie EL, Kumar S, Rosauer DF, Vos RA (2012) Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Research Notes 5: 574. doi:10.1186/1756-0500-5-574 Additionally, please cite the Dryad data package: Stoltzfus A, O'Meara B, Whitacre J, Mounce R, Gillespie EL, Kumar S, Rosauer DF, Vos RA (2012) Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. Dryad Digital Repository. doi:10.5061/dryad.h6pf365t",
year = "2012",
doi = "10.5061/dryad.h6pf365t",
language = "English",
publisher = "Dryad Digital Repository",

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TY - ADVS

T1 - Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

AU - Stoltzfus, Arlin

AU - O'Meara, Brian

AU - Whitacre, Jamie

AU - Mounce, Ross

AU - Gillespie, Emily L

AU - Kumar, S

AU - Rosauer, Dan F

AU - Vos, Rutger A

N1 - When using this data, please cite the original article: Stoltzfus A, O'Meara B, Whitacre J, Mounce R, Gillespie EL, Kumar S, Rosauer DF, Vos RA (2012) Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Research Notes 5: 574. doi:10.1186/1756-0500-5-574 Additionally, please cite the Dryad data package: Stoltzfus A, O'Meara B, Whitacre J, Mounce R, Gillespie EL, Kumar S, Rosauer DF, Vos RA (2012) Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. Dryad Digital Repository. doi:10.5061/dryad.h6pf365t

PY - 2012

Y1 - 2012

N2 - BACKGROUND: Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote data sharing reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing phylogenetic trees and associated data in a way that promotes re-use. RESULTS: Here we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find that the technical infrastructure is available to support rudimentary archiving, but the frequency of archiving is low. Currently, most phylogenetic knowledge is not easily re-used due to a lack of archiving, lack of awareness of best practices, and lack of community-wide standards for formatting data, naming entities, and annotating data. Most attempts at data re-use seem to end in disappointment. Nevertheless, we find many positive examples of data re-use, particularly those that involve customized species trees generated by grafting to, and pruning from, a mega-tree. CONCLUSIONS: The technologies and practices that facilitate data re-use can catalyze synthetic and integrative research. However, success will require engagement from various stakeholders including individual scientists who produce or consume shareable data, publishers, policy-makers, technology developers and resource-providers. The critical challenges for facilitating re-use of phylogenetic trees and associated data, we suggest, include: a broader commitment to public archiving; more extensive use of globally meaningful identifiers; development of user-friendly technology for annotating, submitting, searching, and retrieving data and their metadata; and development of a minimum reporting standard (MIAPA) indicating which kinds of data and metadata are most important for a re-useable phylogenetic record.

AB - BACKGROUND: Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote data sharing reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing phylogenetic trees and associated data in a way that promotes re-use. RESULTS: Here we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find that the technical infrastructure is available to support rudimentary archiving, but the frequency of archiving is low. Currently, most phylogenetic knowledge is not easily re-used due to a lack of archiving, lack of awareness of best practices, and lack of community-wide standards for formatting data, naming entities, and annotating data. Most attempts at data re-use seem to end in disappointment. Nevertheless, we find many positive examples of data re-use, particularly those that involve customized species trees generated by grafting to, and pruning from, a mega-tree. CONCLUSIONS: The technologies and practices that facilitate data re-use can catalyze synthetic and integrative research. However, success will require engagement from various stakeholders including individual scientists who produce or consume shareable data, publishers, policy-makers, technology developers and resource-providers. The critical challenges for facilitating re-use of phylogenetic trees and associated data, we suggest, include: a broader commitment to public archiving; more extensive use of globally meaningful identifiers; development of user-friendly technology for annotating, submitting, searching, and retrieving data and their metadata; and development of a minimum reporting standard (MIAPA) indicating which kinds of data and metadata are most important for a re-useable phylogenetic record.

UR - http://dx.doi.org/10.5061/dryad.h6pf365t

U2 - 10.5061/dryad.h6pf365t

DO - 10.5061/dryad.h6pf365t

M3 - Data set/Database

PB - Dryad Digital Repository

ER -