(Press-News.org) 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.
###
The poster 03.01.11, "Challenges and Solutions for Enabling Facebook like Graph-search on Small and Macro-molecular Structural Data," will be presented on Sunday, July 21. Abstract: http://www.amercrystalassn.org/app/session/100111
END
VIDEO:
This is a iime-lapse movie of blood progenitor cells dividing and differentiating in culture. The brightness of green fluorescence indicates the amount of the regulatory protein PU.1 present in each...
Click here for more information.
Biologists at the California Institute of Technology (Caltech) have worked out the details of a mechanism that leads undifferentiated blood stem cells to become macrophages—immune cells that attack bacteria and other foreign pathogens. ...
Designing an effective HIV/AIDS vaccine is something of a paradox: a good vaccine would be safe and look enough like HIV to kick-start the immune system into neutralizing the virus – but the problem is that this is exactly what the human immune system has trouble doing even when it's exposed to the real thing.
Now a team of researchers led by scientists at The Scripps Research Institute in La Jolla, Calif. has developed a strategy for inducing a key part of an effective immune response to HIV. By tracing the evolution of HIV-recognizing molecules called antibodies taken ...
If you squeeze a normal object in all directions, it shrinks in all directions. But a few strange materials will actually grow in one dimension when compressed. A team of chemists has now discovered a structure that takes this property to a new level, expanding more dramatically under pressure than any other known material. The finding could lead to new kinds of pressure sensors and artificial muscles.
Andrew Cairns, a graduate student at the University of Oxford and a member of the research team, will discuss the new material and its applications at the American Crystallographic ...
PROVIDENCE, R.I. – Rhode Island Hospital researchers have found that multiple factors contribute to the burden felt by caregivers of people living with Alzheimer's and other forms of dementia. These factors include the direct impact of providing care upon the caregivers' lives, guilt, and frustration or embarrassment. The study is published online in advance of print in American Journal of Geriatric Psychiatry.
The study, conducted by Beth A. Springate, Ph.D, and Geoffrey Tremont, Ph.D, of the division of neuropsychology in the department of psychiatry at Rhode Island ...
PROVIDENCE, R.I. – Rhode Island Hospital researchers have found that the absence of the Shp-2 enzyme near specialized cartilage cells can lead to the development of multiple benign cartilage tumors in mice, a model that recapitulates the rare human tumor syndrome metachondromatosis. Shp2 is an enzyme in the cell that regulates the activity of other proteins and signaling pathways. Mice lacking Shp2 formed two types of tumors: enchondromas and osteochondromas, and also developed deformed joints. The study is published online in advance of print in the journal Nature.
...
LA JOLLA, CA---- Stem cells are key to the promise of regenerative medicine: the repair or replacement of injured tissues with custom grown substitutes. Essential to this process are induced pluripotent stem cells (iPSCs), which can be created from a patient's own tissues, thus eliminating the risk of immune rejection. However, Shinya Yamanaka's formula for iPSCs, for which he was awarded last year's Nobel Prize, uses a strict recipe that allows for limited variations in human cells, restricting their full potential for clinical application.
Now, in this week's issue ...
The risk of catching some nasty germ in the Hudson River just started looking nastier. Disease-causing microbes have long been found swimming there, but now researchers have documented antibiotic-resistant strains in specific spots, from the Tappan Zee Bridge to lower Manhattan. The microbes identified are resistant to ampicillin and tetracycline, drugs commonly used to treat ear infections, pneumonia, salmonella and other ailments. The study is published in the current issue of the Journal of Water and Health.
"If you find antibiotic-resistant bacteria in an ecosystem, ...
Astronomers using NASA's Hubble Space Telescope have determined the orbital motion of two distinct populations of stars in an ancient globular star cluster, offering proof they formed at different times and providing a rare look back into the Milky Way galaxy's early days.
Researchers led by Harvey Richer of the University of British Columbia in Vancouver combined recent Hubble observations with eight years' worth of data from the telescope's archive to determine the motions of the stars in the globular cluster 47 Tucanae, which is located about 16,700 light-years away ...
As a class, people who don't drink at all have a higher mortality risk than light drinkers. But nondrinkers are a diverse bunch, and the reasons people have for abstaining affects their individual mortality risk, in some cases lowering it on par with the risk for light drinkers, according to a University of Colorado study.
Multiple studies have shown that the likelihood of dying for people who drink increases as they consume more alcohol. Those same studies have shown that a person's mortality risk also increases at the other end of the spectrum — among people who choose ...
Chronic obstructive pulmonary disease (COPD) is associated with an increased risk of developing cerebral microbleeds, according to a new study from researchers in the Netherlands. Cerebral microbleeds are a marker of cerebral small vessel disease, an important cause of age-related disability and cognitive decline.
"The connection between COPD and cerebral small vessel disease was suggested by two earlier studies, but the connection between COPD and cerebral microbleeds, the location of which can help elucidate underlying disease mechanisms, has not been studied," said ...
