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

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

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.

Keywords:
evolution, phylogeny, data sharing, bioinformatics, standards, synthesis, data re-use, trees, sharing, archiving, metadata

Cite this dataset as:
Stoltzfus, A., O'Meara, B., Whitacre, J., Mounce, R., Gillespie, E., Kumar, S., Rosauer, D., 2012. Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. Dryad Digital Repository. https://doi.org/10.5061/dryad.h6pf365t.

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Publication details

Publication date: 2012
by: Dryad Digital Repository

Version: 1

DOI: https://doi.org/10.5061/dryad.h6pf365t

URL for this record: https://researchdata.bath.ac.uk/id/eprint/382

Related articles

Stoltzfus, A., O'Meara, B., Whitacre, J., Mounce, R., Gillespie, E. L, Kumar, S., Rosauer, D. F and Vos, R. A, 2012. Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Research Notes, 5(1), p.574. Available from: https://doi.org/10.1186/1756-0500-5-574.

Contact information

Please contact the Research Data Service in the first instance for all matters concerning this item.

Contact person: Arlin Stoltzfus

Departments:

Faculty of Science
Biology & Biochemistry