ACS Publications has recently launched a dynamic new web delivery system, hosting 34 ACS peer-reviewed research journals on a fully integrated web platform rich with new features and functionality. The new website provides a state-of-the-art online experience for information discovery, interactivity and research productivity for scientists and professionals worldwide. A Flash-based demonstration available at http://pubs.acs.org/flashdemo showcases many of the features and benefits of the new site.

That’s all well and good, but boy do they make you jump through digital hoops to get registered and up and running. First off, I had several duplicate emails making the announcement and telling me to login at pubs.acs.org to set my e-alerts (I only want ASAPs but I seem to be getting ToCs now as well). You cannot then just login with your membership number, you have to register as a user, but that happens on www.acs.org which is announced via a popup dialog box that has to be closed before you can then re-enter the new URL instead of simply redirecting.

There are several more steps but once you’re in, correcting errors in your work address seems to involve starting entry from scratch so I abandoned that update with my old zipcode intact. Just as I thought I’d got through the last hoop and clicked the link in the confirmation email, I get a “network error” on attempting to login. Not a fun experience, I have to say, but at least they’ve got a nice flash video, and once you’re in it should be well worth the effort…

Defining chemical definitions - Chemists Catherine Castillo-Colaux and Alain Krief of the University Notre-Dame de la Paix, Namur, Belgium, describe the different stages involved in the collaborative construction of an organic chemical ontology - a glossary of definitions and relationships - by chemists. Writing in the International Journal of Knowledge and Learning, they reveal their experiences, as chemists as opposed to computer scientists, in learning how to build a collaborative ontology and how to use the ontology software to do so. In so doing they show how chemists can work together on essentially computer science projects that benefit the chemistry community.

The chemists were working on building EnCOrE, a freely accessible net-based encyclopaedia of organic chemistry. They had selected what they thought to be adequate tools and strategies for transferring chemical knowledge into an electronic format but the whole process proved to be “far from easy”.

“The initial expectation that selected hypertext links would solve the problem proved to be inaccurate,” the researchers explain, “since those links were too numerous and too static. We also found that even the more elaborated XML language was inadequate, since we had too many interconnected contexts related to a single paragraph.”

The way forward was to adopt an ontological approach. An ontology, in the informatics and computing, as opposed to philosophical sense, is a formal explicit description of all the concepts in a given field. So an organic chemical ontology would include details of carbon, compounds, reactions, bonds, etc. An ontology contains Classes, or concepts, Slots, roles or properties, and Facets, role restrictions and together with a set of individual instances of classes, represents the sum of knowledge for the subject in question. It is the complete dictionary, taxonomy and semantics of the field formalised so that it is machine readable.

“We have been attracted by their efficiency to organise the inherent concepts within a domain or a subdomain and to ensure consistency between the different modules of our encyclopaedia,” the researchers explain.

The researchers outline the aches and pains they experienced in developing their ontology using various collaborative and Grid tools and ultimately the successes.

It took us quite a lot of time to become acquainted with and to understand ontology building. Our goal, as ‘chemists who are neophytes in ontology’ was not only to create an ontology of organic chemistry but also to find the important steps to enable ourselves as well as other chemists to be able to do so. It implies finding the best way to learn this new field.

Given the failures of certain approaches to ontology building, the team carefully analysed the different problems encountered and have devised a new protocol they say will help other chemists develop ontologies for their own purposes and in their own fields.

“This way, we believe, the chemist or the expert in general can work at his/her own rhythm and find the right support at the right moment,” the researchers say, “The success of this protocol indeed deals with its capacity to allow the participant to learn and at the same time to work. Use of the appropriate tool seems to be essential for success.”

Catherine Castillo Colaux, Alain Krief (2008). Protocols for building an organic chemical ontology International Journal of Knowledge and Learning, 4 (2/3) DOI: 10.1504/IJKL.2008.020652

A $2 egg-beater could save lives in developing countries, according to a report from the UK’s Royal Society of Chemistry. A piece of inexpensive plastic tubing taped to a handheld egg-whisk could be used as an ad hoc centrifuge for separating out blood plasma in a matter of minutes and allow life-saving diagnostic medical tests to be carried out much faster and at far less cost than with conventional lab-based centrifuge equipment.

George Whitesides and colleagues at Harvard University, USA, say the plasma obtained is easily good enough to use in tests to detect diseases such as Hepatitis B and cysticercosis, a parasitic infection of the nervous system.

“The object was to separate serum [plasma] from blood using readily-obtained materials in a resource-constrained environment,” explains Whitesides. The equipment can be bought from shops for around two dollars. It needs no special training to use, no electricity or maintenance, and can be sterilised with boiling water and reused. The user can even prepare several samples at once – just by taping more lengths of tubing to the beater.

This simple DIY approach to diagnostics contrasts starkly with the bulky, and fragile commercial centrifuges, that cost thousands of dollars and require extensive operator training. Given that it is Blog Action Day on poverty, it is rather timely that this new, simple technology is announced today.

“This technique is simple and works remarkably well,” says Doug Weibel, an expert in microbiology at the University of Wisconsin-Madison, US. “This technique complements several other ’simple solutions’ that the Whitesides group has developed to tackle point-of-care diagnostics in resource-poor settings.”

Amy P. Wong, Malancha Gupta, Sergey S. Shevkoplyas, George M. Whitesides (2008). Egg beater as centrifuge: isolating human blood plasma from whole blood in resource-poor settings Lab on a Chip DOI: 10.1039/b809830c

My latest feature article was published recently in Nature Reviews Drug Discovery. In it I discuss the issues surrounding the next phase of the US National Institutes of Health roadmap in which the Molecular Libraries Initiative (MLI) becomes the Molecular Libraries Program (MLP) with what appears to be a deficit of cheminformatics.

You can subscribe to the print edition of Nature Reviews Drug Discovery, which I can, of course, highly recommend, courtesy of Chemspy. It’s free to qualifying professionals in North America and some selected international readers. There’s a quick form to fill in but free if you make the effort to do that.

(2008). Dealing with a data dilemma. Nature Reviews Drug Discovery, 7(8), 632-633. DOI: 10.1038/nrd2649

As of October, the UK Department of Health is updating the health warnings and information taglines it includes on packets of cigarettes and other tobacco products because, despite a nationwide ban on smoking in the workplace (buildings and vehicles), smoking remains an incredibly popular pastime. As of October 1, 2008, they are also going to force tobacco manufacturers to include graphic images of cadavers and diseased body parts to be printed on packaging.

Anyway, in case you couldn’t think of a reason not to stop smoking, here are the fifteen top warnings:

1. Smokers die younger
2. Smoking clogs the arteries and causes heart attacks and strokes
3. Smoking causes fatal lung cancer
4. Smoking is highly addictive, don’t start
5. Stopping smoking reduces the risk of fatal heart and lung diseases
6. Smoking can cause a slow and painful death
7. Smoking causes aging of the skin
8. Smoking can damage sperm and decreases fertility
9. Smoking may reduce the blood flow and cause impotence
10. Smoking contains benzene, nitrosamines, formaldehyde and hydrogen cyanide
11. Smoking when pregnant harms your baby
12. Protect children, don’t make them breathe your smoke
13. Smoking costs a packet

Actually #13 is one I added to the list of warnings. #14 would have to be smoking causes global warming, but that is perhaps laboring the point a little too much. More information here.

(American Society for Biochemistry and Molecular Biology) A new study has shown that an investigational drug, R207910, is quite effective at killing latent bacteria. This revelation suggests that R207910 may lead to improved and shortened treatments for this globally prevalent disease.

(American Society for Biochemistry and Molecular Biology) Researchers have uncovered a gene in corals that responds to day/night cycles, which provides some tantalizing clues into how symbiotic corals work together with their plankton partners.

(Crop Science Society of America) Representatives Norman Dicks (D-WA) and Ralph Regula (R-OH) will be presented with the first USGS Coalition Leadership Award on Monday evening, Sept. 15, 2008. The USGS Coalition is an alliance of 70 organizations united by a commitment to the continued vitality of the unique combination of biological, geological, hydrological and mapping programs of the US Geological Survey.

(Universidad de Granada) They have used a simulated layer system with the Transmission Line Matrix Modelling method, which is able to hide, in certain frequencies, the objects placed in an electromagnetic simulator. This research work has been carried out by scientists of the University of Granada in collaboration with researchers of the Massachusetts Institute of Technology, and has been recently published in two papers in the prestigious journal Optics Express.

(Physikalisch-Technische Bundesanstalt (PTB)) The new magnetic resonance tomograph which is delivered to its new location on Sept. 11, will be the only one of the modern 7 tesla generation in the world, in which a metrology institute is also involved. And for the first time in the world, cardiovascular research carried out on such a device is now also to play an important role.