Navigation Links
Facebook for molecules
Date:7/18/2013

Social media has expanded to reach an unlikely new target: molecules. Scientists at the National Institute of Standards and Technology (NIST) have created networks of molecular data similar to Facebook's recently debuted graph search feature. While graph search would allow Facebook users to find all their New York-living, beer-drinking buddies in one quick search, the NIST-designed networks could help scientists rapidly sift through enormous chemical and biological data sets to find substances with specific properties, for example all 5-ring chemicals with an affinity for enzyme A. The search approach could help speed up the development of new drugs and designer materials.

The NIST team will present their research at the upcoming American Crystallographic Association Meeting, held July 20-24 in Honolulu.

Choosing the Right Words

Molecules don't maintain their own online profiles, so a key challenge for the NIST research team was to develop a standard language for scientists to describe their research subjects. For example, one research group may describe a material's properties as glassy while another team might use the word vitreous, even though the two words have the same meaning, explained Ursula Kattner, a researcher in the Materials Science and Engineering Division at NIST.

One approach to the problem could be to define a standard set of words, but NIST scientists opted for a more flexible approach that could evolve with time. The search language they developed is similar to Indo-European languages like Sanskrit and Latin, which use short roots to build words based on a set of rules, said Talapady Bhat, a research chemist at NIST who has been leading the effort to develop a shared vocabulary for NIST's scientific databases. He gives the example of the Sanskrit word "yoga," which is based on the roots "Y(uj)", which means to join, "O", which means creator, God, or brain, and "Ga", which means motion or initiation. Similarly, scientists could take the three simple root words "red", "laser," and "light," and combine them into a single compound word "red-laser-light" that conveys a new concept. Using the root and rule-based approach will mean that scientists who know the roots can figure out the meaning of unfamiliar terms, and it also gives scientists flexibility to develop easily understandable new terms in the future.

The NIST team has already applied their root-based vocabulary rules to the chemical structures in PubChem, a "monstrous database" of millions of compounds and chemical substances, to the world wide protein data bank (PDB), and to specific NIST-based databases, said John Elliot, a biophysicist and another member of the team. While the scientific databases haven't reached a Facebook-like level of more than a billion users, they are actively used by many scientists in the NIST community and beyond.

Graphing Relationships

Once the preliminary vocabulary was established, the NIST team also worked to categorize the descriptions of molecules and scientific experiments in a hierarchical fashion that would allow a search to return comprehensive, yet precise results. A common problem with many search approaches is that they get too many results, said Elliot. Elliot described his team's approach as similar to the problem of locating the Doritos in a large Walmart store. "First you find the grocery market section, then the next level of hierarchy is snacks, after which you go to the chips section, and then you'll quickly know if they have Doritos or not," said Elliot. "So even if a store has a million products, you can find out if they have your product really quickly." The team said the hierarchical approach could also guide scientists who need to pick out key words to index in their research papers.

Organizing the huge amounts of data generated by science is a big challenge, the team said, but it has potentially huge payoffs. Effective graph searches could allow scientists to rapidly identify chemical structures and properties that are needed for the development of new drug agents or advanced materials (such as high efficiency jet turbines or flexible solar cells), results more than worthy of a Facebook like.


'/>"/>

Contact: Catherine Meyers
cmeyers@aip.org
301-209-3088
American Institute of Physics
Source:Eurekalert

Related biology news :

1. Iowa State, Ames Lab researchers invent new tool to study single biological molecules
2. New model gives hands-on help for learning the secrets of molecules
3. Weighing molecules 1 at a time
4. Nano-velcro clasps heavy metal molecules in its grips
5. Researchers develop new stamping process to pattern biomolecules at high resolution
6. A class of RNA molecules protects germ cells from damage, Penn vet researchers show
7. Dance of water molecules turns fire-colored beetles into antifreeze artists
8. How computers push on the molecules they simulate
9. How our cells cope with toxic small molecules
10. Molecules assemble in water, hint at origins of life
11. Watching molecules grow into microtubes
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:2/2/2016)... , Feb. 2, 2016 Technology Enhancements Accelerate ... an analysis of the digital and computed radiography markets ... , and Indonesia (TIM). ... and market size, as well as regional market drivers ... and discusses market penetration and market attractiveness, both for ...
(Date:2/2/2016)... 2, 2016  Based on its recent analysis ... recognizes US-based Intelligent Retinal Imaging Systems (IRIS) with ... for New Product Innovation. IRIS, a prominent cloud-based ... America , is poised to set the ... retinopathy market. The IRIS technology presents superior price-performance ...
(Date:2/1/2016)... 2016  Today, the first day of American Heart ... develop a first of its kind workplace health solution ... In the first application of Watson ... ), and Welltok will create a new offering that ... analytics, delivered on Welltok,s health optimization platform. The effort ...
Breaking Biology News(10 mins):
(Date:2/4/2016)... JUNCTION, N.J. , Feb. 4, 2016 /PRNewswire/ ... care immunotherapy leader commercializing its flagship CytoSorb® blood ... cardiac surgery patients around the world, announced that ... will present at the Source Capital Group,s 2016 ... and update on the company.  ...
(Date:2/4/2016)... , Feb. 4, 2016 Sinovac Biotech ... a leading provider of biopharmaceutical products in ... of its board of directors received on February 4, ... 2016, from a consortium comprised of PKU V-Ming ( ... Biomedicine Co., Ltd., CICC Qianhai Development ( Shenzhen ...
(Date:2/3/2016)...  Discovery Laboratories, Inc. (NASDAQ: DSCO ), ... surfactant therapies for respiratory diseases, today announced that ... award as a component of employment compensation for ... and Chief Executive Officer.  The award was approved ... 2016 and granted as an inducement material to ...
(Date:2/3/2016)... ... February 03, 2016 , ... Aerocom, a world-leading ... to the North American healthcare market. , Aerocom Healthcare, LLC will be based ... company will provide new pneumatic tube systems or expand existing systems within the ...
Breaking Biology Technology: