Navigation Links
UF scientists encounter holes in tree of life, push for better data storage
Date:9/3/2013

GAINESVILLE, Fla. --- 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."


'/>"/>

Contact: Doug Soltis
dsoltis@botany.ufl.edu
352-273-1963
University of Florida
Source:Eurekalert

Related biology news :

1. Scientists discover new bat species in West Africa
2. Worlds scientists, researchers and nutrition experts convene to explore the benefits of mushrooms
3. Now hear this: Scientists discover compound to prevent noise-related hearing loss
4. NIH scientists describe how anthrax toxins cause illness, death
5. UCLA scientists receive $2 million grant to improve quality of donor livers for transplant
6. Cancer scientists discover novel way gene controls stem cell self-renewal
7. UK & USA scientists collaborate to design crops of the future
8. Scientists uncover the secret life of frozen soils
9. Tufts scientists develop new early warning system for cholera epidemics
10. Cattle can be a source of MRSA in people, scientists find
11. LLNL scientists make new discoveries in the transmission of viruses between animals and humans
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:8/15/2017)... , Aug. 15 2017   ivWatch LLC , a ... intravenous (IV) therapy, today announced receipt of its ISO 13485 Certification, ... by the International Organization for Standardization (ISO®). ... ivWatch Model 400 Continuous Monitoring device for the early ... "This is an ...
(Date:5/23/2017)... May 23, 2017  Hunova, the first robotic gym for the rehabilitation ... officially launched in Genoa, Italy . The first 30 ... and the USA . The technology was developed and ... by the IIT spin-off Movendo Technology thanks to a 10 million euro ... Release, please click: ...
(Date:4/19/2017)... April 19, 2017 The global ... landscape is marked by the presence of several large ... held by five major players - 3M Cogent, NEC ... accounted for nearly 61% of the global military biometric ... in the global military biometrics market boast global presence, ...
Breaking Biology News(10 mins):
(Date:10/12/2017)... New York, NY (PRWEB) , ... October 12, ... ... York Academy of Sciences today announced the three Winners and six Finalists of ... Awards are given annually by the Blavatnik Family Foundation and administered by the ...
(Date:10/12/2017)... ... October 12, 2017 , ... ... pharmaceutical and biotechnology industries to improve patient outcomes and quality of life, will ... analytical testing are being attributed to new regulatory requirements for all new drug ...
(Date:10/11/2017)... ... October 11, 2017 , ... Personal eye wash is a basic first aid supply for ... time. So which eye do you rinse first if a dangerous substance enters both eyes? ... Eye Wash with its unique dual eye piece. , “Whether its dirt and debris, ...
(Date:10/11/2017)... LAGUNA HILLS, Calif. , Oct. 11, 2017 /PRNewswire/ ... London (ICR) and University of ... tool to risk-stratify patients with multiple myeloma (MM), in a ... . The University of Leeds is ... Myeloma UK, and ICR will perform the testing services to ...
Breaking Biology Technology: