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.