Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

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

04.09.2013
When it comes to public access, the tree of life has holes.

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.

"There are ambiguities with the alignments, you have to make certain judgment calls, and so an alignment that I do is not going to be the same as an alignment that somebody else does," said lead author Bryan Drew, a postdoctoral researcher in UF's biology department. "It's hard to assess a publication's validity in a lot of cases if you don't have access to the alignments. To me, that's the biggest problem with all of this."

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.

"A lot of the authors I contacted said their data was in TreeBASE, but they were unaware of the next step needed after acceptance by the journal – the researchers didn't know they had to go back into TreeBASE and actually make the data available to the public," Drew said.

Elizabeth Kellogg, a professor in the department of biology at the University of Missouri-St. Louis who was not involved with the study, said she is not surprised about the large amount of missing information.

"They're absolutely right that when people are publishing papers, you want to document your results as much as you can," Kellogg said. "But many journals aren't requiring that extra step, so some researchers are only submitting the minimum to have their studies published. "There are databases for archiving, but some of their interfaces are somewhat cumbersome, and if you haven't previously done this, it can appear to be a daunting task."

Study co-authors include Romina Gazis and David Hibbett of Clark University, Patricia Cabezas of Brigham Young University, Kristen Swithers and Laura A. Katz of Smith College, Keith Crandall of George Washington University, and Jiabin Deng and Roseanna Rodriguez of UF. The National Evolutionary Synthesis Center in Durham, N.C., is leading NSF's "Open Tree of Life" project. For more information visit http://www.opentreeoflife.org

Doug Soltis | EurekAlert!
Further information:
http://www.ufl.edu
http://www.opentreeoflife.org

More articles from Studies and Analyses:

nachricht Real-time feedback helps save energy and water
08.02.2017 | Otto-Friedrich-Universität Bamberg

nachricht The Great Unknown: Risk-Taking Behavior in Adolescents
19.01.2017 | Max-Planck-Institut für Bildungsforschung

All articles from Studies and Analyses >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Breakthrough with a chain of gold atoms

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

Im Focus: DNA repair: a new letter in the cell alphabet

Results reveal how discoveries may be hidden in scientific “blind spots”

Cells need to repair damaged DNA in our genes to prevent the development of cancer and other diseases. Our cells therefore activate and send “repair-proteins”...

Im Focus: Dresdner scientists print tomorrow’s world

The Fraunhofer IWS Dresden and Technische Universität Dresden inaugurated their jointly operated Center for Additive Manufacturing Dresden (AMCD) with a festive ceremony on February 7, 2017. Scientists from various disciplines perform research on materials, additive manufacturing processes and innovative technologies, which build up components in a layer by layer process. This technology opens up new horizons for component design and combinations of functions. For example during fabrication, electrical conductors and sensors are already able to be additively manufactured into components. They provide information about stress conditions of a product during operation.

The 3D-printing technology, or additive manufacturing as it is often called, has long made the step out of scientific research laboratories into industrial...

Im Focus: Mimicking nature's cellular architectures via 3-D printing

Research offers new level of control over the structure of 3-D printed materials

Nature does amazing things with limited design materials. Grass, for example, can support its own weight, resist strong wind loads, and recover after being...

Im Focus: Three Magnetic States for Each Hole

Nanometer-scale magnetic perforated grids could create new possibilities for computing. Together with international colleagues, scientists from the Helmholtz Zentrum Dresden-Rossendorf (HZDR) have shown how a cobalt grid can be reliably programmed at room temperature. In addition they discovered that for every hole ("antidot") three magnetic states can be configured. The results have been published in the journal "Scientific Reports".

Physicist Dr. Rantej Bali from the HZDR, together with scientists from Singapore and Australia, designed a special grid structure in a thin layer of cobalt in...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Booth and panel discussion – The Lindau Nobel Laureate Meetings at the AAAS 2017 Annual Meeting

13.02.2017 | Event News

Complex Loading versus Hidden Reserves

10.02.2017 | Event News

International Conference on Crystal Growth in Freiburg

09.02.2017 | Event News

 
Latest News

Microhotplates for a smart gas sensor

22.02.2017 | Power and Electrical Engineering

Scientists unlock ability to generate new sensory hair cells

22.02.2017 | Life Sciences

Prediction: More gas-giants will be found orbiting Sun-like stars

22.02.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>