Scientists encounter holes in tree of life, push for better data storage

"A new study co-authored by University of Florida researchers shows about 70 percent of published genetic sequence comparisons are not publicly accessible, leaving researchers worldwide unable to get to critical data they may need to tackle a host a problems ranging from climate change to disease control. Scientists are using the genetic data to construct the largest open-access tree of life as part of the National Science Foundation's $5.6-million Assembling, Visualizing and Analyzing the Tree of Life project. Understanding organismal relationships is increasingly valuable for tracking the origin and spread of emerging diseases, creating agricultural and pharmaceutical products, studying climate change, controlling invasive species and establishing plans for conservation and ecosystem restoration. The study appearing today in PLoS Biology describes a significant challenge for the project, which is expected to produce an initial draft tree by the end of the year. It highlights the need for developing more effective methods for storing data for long-term use and urges journals to adopt more stringent data-sharing policies. "I think what we need is a major change in our mindset about just how important it is to deposit your data -- this has to be a standard part of what we do," said co-author Doug Soltis, a distinguished professor at the Florida Museum of Natural History on the UF campus and UF's biology department. "Because if it's not there, it's lost forever. These are really, really important for long-term use, as we're seeing now in our efforts to build a tree." Estimates of the amount of missing data were based on 7,539 peer-reviewed studies about animals, fungi, seed plants, bacteria and various microscopic organisms. Soltis said the missing genetic data has required project collaborators to contact hundreds of researchers to request information, or attempt to reproduce the sequence alignments and analyses, which is extremely labor intensive ... Challenges include complicated mechanisms for uploading data and inconsistencies between journals -- some require or strongly recommend data be stored in an online database and others do not, Drew said. The most widely used, publicly accessible databases include GenBank, TreeBASE and Dryad. Most journals require DNA sequences be deposited in GenBank, but comparatively few require the sequence alignments to be publicly archived. When study co-authors emailed researchers to obtain missing information, a majority did not respond, and the co-authors were rarely successful in retrieving the data ..."