Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New curation tool a boon for genetic biologists

22.06.2011
With the BeeSpace Navigator, University of Illinois researchers have created both a curation tool for genetic biologists and a new approach to searching for information.

The project was a collaboration between researchers at the Institute for Genomic Biology and the department of computer science. Led by Bruce Schatz, professor and head of medical information science at the U. of I., the team described the software and its applications in the web server issue of the journal Nucleic Acids Research.

When biologists need information about a gene or its function, they turn to curators, who keep and organize vast quantities of information from academic papers and scientific studies. A curator will extract as much information as possible from the papers in his or her collection and provide the biologist with a detailed summary of what’s known about the gene – its location, function, sequence, regulation and more – by placing this information into an online database such as FlyBase.

“The question was, could you make an automatic version of that, which is accurate enough to be helpful?” Schatz said.

Schatz and his team developed BeeSpace Navigator, a free online software that draws upon databases of scholarly publications. The semantic indexing to support the automatic curation used the Cloud Computing Testbed, a national computing datacenter hosted at U. of I.

While BeeSpace originally was built around literature about the bee genome, it has since been expanded to the entire Medline database and has been used to study a number of insects as well as mice, pigs and fish.

The efficiency of BeeSpace Navigator is in its specific searches. A broad, general search of all known data would yield a chaotic myriad of results – the millions of hits generated by a Google search, for example. But with BeeSpace, users create “spaces,” or special collections of literature to search. It also can take a large collection of articles on a topic and automatically partition it into subsets based on which words occur together, a function called clustering.

“The first thing you have to do if you have something that’s simulating a curator is to decide what papers it’s going to look at,” Schatz said. “Then you have to decide what to extract from the text, and then what you’re going to do with what you’ve extracted, what service you’re going to provide. The system is designed to have easy ways of doing that.”

The user-friendly interface allows biologists to build a unique space in a few simple steps, utilizing sub-searches and filters. For example, an entomologist interested in the genetic basis for foraging as a social behavior in bees would start with insect literature, then zero in on genes that are associated in literature with both foraging and social behavior – a specific intersection of topics that typical search engines could not handle.

This type of directed data navigation has several advantages. It is much more directed than a simple search, but able to process much more data than a human curator. It can also be used in fields where there are no human curators, since only the most-studied animals like mice and flies have their own professional curators.

Schatz and his team equipped the navigator to perform several tasks that biologists often perform when trying to interpret gene function. Not only does the program summarize a gene, as a curator would, but it also can perform analysis to extrapolate functions from literature.

For example, a study will show that a gene controls a particular chemical, and another study will show that chemical plays a role in a certain behavior, so the software makes the link that the gene could, in part, control that behavior.

BeeSpace can also perform vocabulary switching, an automatic translation across species or behaviors. For example, if it is known that a specific gene in a honeybee is analogous to another gene in a fruit fly, but the function of that gene has been documented in much more detail in a fruit fly, the navigator can make the connection and show a bee scientist information on the fly gene that may be helpful.

“The main point of the project is automatically finding out what genes do that don’t have known function,” Schatz said. “If a biologist is trying to figure out what these genes do, they’re happy with anything. They want to get as much information as possible.”

The BeeSpace Navigator, now in its fourth version, is available free online. Overview documentation is available online as well.

The National Science Foundation supported this work as the bioinformatics flagship of the Frontiers in Integrative Biological Research program.

Liz Ahlberg | EurekAlert!
Further information:
http://www.illinois.edu

Further reports about: BeeSpace Cloud Computing Navigator fruit fly social behavior

More articles from Life Sciences:

nachricht Researchers identify potentially druggable mutant p53 proteins that promote cancer growth
09.12.2016 | Cold Spring Harbor Laboratory

nachricht Plant-based substance boosts eyelash growth
09.12.2016 | Fraunhofer-Institut für Angewandte Polymerforschung IAP

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Electron highway inside crystal

Physicists of the University of Würzburg have made an astonishing discovery in a specific type of topological insulators. The effect is due to the structure of the materials used. The researchers have now published their work in the journal Science.

Topological insulators are currently the hot topic in physics according to the newspaper Neue Zürcher Zeitung. Only a few weeks ago, their importance was...

Im Focus: Significantly more productivity in USP lasers

In recent years, lasers with ultrashort pulses (USP) down to the femtosecond range have become established on an industrial scale. They could advance some applications with the much-lauded “cold ablation” – if that meant they would then achieve more throughput. A new generation of process engineering that will address this issue in particular will be discussed at the “4th UKP Workshop – Ultrafast Laser Technology” in April 2017.

Even back in the 1990s, scientists were comparing materials processing with nanosecond, picosecond and femtosesecond pulses. The result was surprising:...

Im Focus: Shape matters when light meets atom

Mapping the interaction of a single atom with a single photon may inform design of quantum devices

Have you ever wondered how you see the world? Vision is about photons of light, which are packets of energy, interacting with the atoms or molecules in what...

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

Researchers identify potentially druggable mutant p53 proteins that promote cancer growth

09.12.2016 | Life Sciences

Scientists produce a new roadmap for guiding development & conservation in the Amazon

09.12.2016 | Ecology, The Environment and Conservation

Satellites, airport visibility readings shed light on troops' exposure to air pollution

09.12.2016 | Health and Medicine

VideoLinks
B2B-VideoLinks
More VideoLinks >>>