Chemistry on the web JUPITER IMAGES JUPITER

Surfing Web2O The rapid evolution of the world wide web is creating fresh opportunities – and challenges – for chemistry. Richard Van Noorden reports

46 | Chemistry World | December 2007 www.chemistryworld.org

CW12.07.Web.indd 46 22/11/2007 08:50:34 As chemical reactions go, it was collaboration and speedy access to interest, riffing around the culture In short a complete failure. ‘Contents of information on an unimaginable of lab-based chemistry, blogs such the reaction flask decomposed. scale.  The internet is as Paul Docherty’s Totally Synthetic Aborted’, Drexel University chemist ‘Mainstream chemistry has no becoming flooded provide useful summaries of the Jean-Claude Bradley and students tradition of openness and electronic with free chemical latest organic syntheses, effectively recorded the day after an attempt collaboration. This is a bottom-up information: from blogs acting as global online journal clubs to synthesise a catechol aldehyde movement, largely composed of to videos and databases where researchers all over the world from adrenaline on 24 January 2006. young researchers,’ explains Peter  Linking this data chip in with constructive criticism. But the experiment has acquired a Murray-Rust, a chemical informatics together and interacting As blogger Andrew Sun argues, the peculiar honour: Bradley chose it academic at the University of via the ‘social web’ blogosphere’s content is a product to be the first written in his group’s Cambridge, UK, and a keen advocate could revolutionise the of its authors, and it would surely new online laboratory notebook, in of what he terms ‘Open Chemistry’. practice and teaching of change if more chemistry professors which all experimental data is made But as Murray-Rust also admits: chemistry bothered to blog – as happens, to an public and freely available to web ‘chemistry is the best subject to do  So-called ‘Open extent, in other sciences. users – a concept he later christened this with, but the hardest to sell Chemistry’ faces many Indeed, a few chemists are ‘Open Notebook Science’. it to’. The open chemistry model challenges: not least using blogs to discuss their own Bradley’s idea is simple: most has to prove its worth alongside maintaining data quality research, as well as comment on failed experiments are discarded, trusted, high-quality subscription and co-existing with others’. Bradley’s Open Notebook yet their data could be useful to databases and journals. It has to trusted subscription works on a ‘wiki’ (a site that any someone else. Even published show its volunteered data can be databases user can edit quickly – the name papers don’t always sufficiently useful and high-quality. And it has to derives from a Hawaiian word for explain the workings behind a capture the enthusiasm and support ‘fast’), but he discusses higher-level successful experiment. In contrast, of chemists who are, Murray-Rust thinking about the project on a all Bradley’s research and raw data says, generally apathetic about the related blog. A few Open Notebook is now documented transparently possibilities Open Chemistry offers. converts, including Cameron and almost in real-time. Anyone can Neylon of Southampton University, see it, comment on it, and use it; and Bloggers ahead UK, are attempting Bradley-like the internet is the perfect vehicle for Murray-Rust takes heart from the online records, and discovering hosting it. irreverent spirit of the fast-growing the difficulties of keeping a faithful Open Notebook Science is just one chemical blogosphere: the hundreds up-to-date log. Many researchers of many new routes for chemical of online diaries where chemists working in cheminformatics information to appear on the grumble, gossip, joke, argue, inform regularly discuss their own research internet. From searchable molecular and inspire. Writers across the directly on blogs – prominent databases to the user-editable chemical sciences post anything among them Murray-Rust, and Wikipedia; from video recordings from personal experiences as a Egon Willighagen at Wageningen of experimental protocols to the post-doc to commentaries on the University in the Netherlands. informal news, gossip and argument latest published articles, or reports In his spare time, Willighagen posted on chemistry blogs; a huge on drug discovery and software runs Chemical blogspace, a site amount of chemistry can now be technology. They dissect gossip that automatically picking useful retrieved at no cost. would a few years ago have been information out of the blogs which The emphasis on user-generated confined to laboratory corridors or regularly discuss research in the content, shared amongst online the departmental tea-room. Readers core chemical sciences. social networks, is typical of Web 2.0, relish the blogosphere’s witty Some websites collect chemistry the umbrella term for the current opinions and (occasional) reasoned information submitted voluntarily evolutionary stage of the world wide analysis, made all the more frank by by other researchers. The most web. In this ‘social web’, swamps the internet’s easy anonymity. famous of these, of course, is of data could be powerfully linked The blogosphere has a loyal Wikipedia – the user-editable together. Search engines can trawl following, but few chemistry encyclopaedia. ‘Chemistry is an it to pick out whatever another user professors write blogs; most authors ideal subject for recording factual asks for. And user ‘tagging’, together are graduate students or postdocs. information and Wikipedia will with underlying machine-readable As Open Chemistry supporter soon become acknowledged as descriptions, means that related Steve Bachrach explained about the primary chemical reference information can be easily linked. a year ago when interviewed for Peter Murray-Rust: for undergraduate study,’ insists For example, clicking on a molecule web-based chemistry magazine, avid supporter of Murray-Rust. Less well-known are could eventually bring up not just a Reactive Reports: ‘I don’t have the Open Chemistry such websites as Organic Syntheses, 3D picture and a list of properties, time to read random thoughts a database of protocols for organic but also the related online articles, by random individuals. I barely chemists, and Synthetic Pages, a experiments, videos and blog posts have time to keep up with the similar, smaller, database which that refer to it. traditional literature in my field. The records the personal experiences Many web users are already blogosphere just seemed to me to of chemists attempting particular familiar with this potential. They be filled with the rantings of people reactions. post videos to YouTube; they read who have nothing better to do with blogs; they use social networking their time.’ Though there is some ChemTube sites like MySpace and Facebook. information to be found, Bachrach But as scientists are discovering, But chemists are only just catching now concedes, he still contests that the internet allows communication on to the possibilities. Some are sure most chemistry blogs have little beyond the limits of a traditional that linking free chemical data on the content in them useful to the busy printed journal article. Thanks to web will revolutionise the culture researcher. high-capacity broadband internet, it and practice of chemistry, aiding While many post for fun and is easy to watch video and audio clips

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CW12.07.Web.indd 47 22/11/2007 08:51:11 Chemistry on the web Blogroll Andre Garcia’s nascent Chemmunity – which asks chemists to take part There are hundreds of blogs related to chemistry In The Pipeline in ‘a global collaboration to solve on the internet. Chemistry World’s own blog (www. corante.com/pipeline interesting and novel chemistry chemistryworld.org/blog), which brings you news, Insightful and stylish analysis from Derek Lowe – questions. We will take a chemistry opinion and discussion on the chemical sciences, Chemistry World columnist and medicinal chemist question from hypothesis to peer- lists some of our favourites, including: – keeping readers up to speed on the development reviewed chemical paper with all and culture of drug discovery. Chemmunity participants in the Totally Synthetic author list or acknowledgements.’ totallysynthetic.com/blog post doc ergo propter doc First up for the 15 members who’d The journal club taken global. Paul Docherty propterdoc.blogspot.com signed up by mid-November guides organic chemists through the latest Charts the ups and downs of life as an ex-pat is to work out an unusual syntheses in a beautifully presented, high quality postdoc in Canada. Chemistry’s very own Bridget phenomenon in the crystallisation of blog which attracts plenty of informed comment. Jones? hexaiodobenzene. Many chemoinformatics Chembark The Sceptical Chymist researchers and web-technology blog.chembark.com blogs.nature.com/thescepticalchymist enthusiasts are excited by With the atmosphere of a lab group’s night out Editors working at Nature and its research the prospects of chemistry in the pub, Paul Bracher coordinates irreverent journals post interviews and their analysis of communication in internet-based chemistry gossip. developments in chemistry and chemical biology. virtual worlds, such as Second Life. This online world already hosts a few islands of chemistry activity, of experiments or lectures, often on videos of their own experiments where chemists can gather to discuss video-sharing sites like the Google- on sites such as the Journal of science, aided by virtual rotating owned YouTube, where anyone is Visualised Experiments and SciVee: molecules, conference papers and encouraged to post content. both video-sharing sites that videos. Chemistry videos – with their directly target scientists, not the crowd-drawing explosions and general public. SciVee promotes the Data drive bright colours – attract a popular idea of launching a video or audio But the greatest source of following on YouTube. Hundreds presentation along with a published established free information for of chemistry educational initiatives paper, which it calls a ‘pubcast’ research chemists on the internet are use YouTube to upload videos; – much like giving a conference talk the 60+ small open-access journals so many that each risks being which is accessible to all internet- (see p12), some delayed open-access swamped by competing content. The users. Meanwhile, this year has seen archived journals and, especially, the observer interested in the explosive a proliferation of podcasts from free online chemistry databases that consequences of shaking Mentos chemistry journals and science Volunteered free aggregate together information on mints in Coca Cola can take their magazines, including Chemistry chemistry content is millions of molecules. pick of over 10 000 YouTube clips, World, which highlight the latest flooding the social web PubChem, ‘the granddaddy of all for example, although a ratings discoveries in the chemical sciences. free chemistry databases’, as former system helps to sort out the most Chemists are also actively medicinal chemist Rich Apodaca eye-catching examples. researching together in online puts it, allows users to search In July this year chemists working forums, though numbers are almost 11 million compounds. It is on a European nanoscience research small. Medicinal chemistry maintained by the National Center project, called Nano2Hybrids, is a noted frontrunner: for Biotechnology Information began recording their progress with The Synaptic Leap is just (NCBI), part of the United States a series of weekly video diaries, one website that promotes National Institutes of Health, and intended both to inform researchers collaborative biomedical takes data from over 80 sources, and explain to the general public research, focusing on building including subscription-access what being a scientist is like. The communities for diseases such journals such as Nature Chemical project works in partnership with as malaria and tuberculosis. Biology. Other free online the Vega Science Trust, established Bradley’s Open Notebook databases provide particular by buckyball-discoverer and former Science research also looks useful molecular details: RSC president Harry Kroto in into the synthesis of anti- NMRShiftDB contains over 1994. It freely broadcasts a variety malarial agents – as he 20 000 NMR spectra for of science programmes over the explains, collaborative organic compounds, internet, including interviews and involvement in this while ChemExper recorded lectures from Nobel prize kind of research and eMolecules link a winners. can only work molecule searcher to Indeed, many universities now where intellectual commercial suppliers. post audio and video of research property SureChem picks out discoveries and chemistry lectures squabbling is less more than 7 million online, in some cases free to access. important, because chemical structures ‘Whether chemistry professors like little profit can held under US and it or not, students will be using these be made from the European patents. And tools,’ says Bradley. results. medicinal chemists Innovative web content aimed One of the most are particularly well solely at professional scientists has speculative projects supplied with numerous arrived a little more slowly. But includes free databases for drug researchers are beginning to post blogger Mitch discovery. 48 | Chemistry World | December 2007 www.chemistryworld.org

CW12.07.Web.indd 48 22/11/2007 08:52:10 Project Prospect of course, customised RSS (Really One effective example of how the web can Simple Syndication) feeds can enhance content has been provided this year by automatically trawl users’ favourite the RSC’s Project Prospect, whereby electronic information resources to gather the journal articles are enriched with extra computer- latest updates into one place. readable metadata. It means readers can click And yet, Bachrach insists, on named compounds, scientific concepts and the biggest problem is cultural experimental data in an article to download – persuading chemists that they structures, understand topics, or link through to would benefit from access to other electronic databases like Iupac’s Gold Book. people’s data is not easy, particularly The applause for this project – which recently as many chemists already have marked up its 1000th paper and won the 2007 access to paid-for databases. ALPSP/Charlesworth Award for Publishing ‘Chemistry is a conservative subject,’ Innovation – has demonstrated the potential fumes Murray-Rust. ‘The chemical of machine-readable articles. For the moment, example. information market is now holding authors are not asked to provide anything special Still, the project may help to bolster the tiny back opportunities.’ when submitting the material; the work falls to numbers of those chemists aware of how the web Bachrach agrees, pointing out that the technical editors. As yet, Prospect lacks the can enhance chemistry. ‘The average head of the because some established journals interactivity that would allow users to add extra average chemistry department probably thinks we refuse pre-published submissions, he data to a molecule’s pop-up information box, for are just playing games,’ concedes Murray-Rust. would never publish original research on a blog or wiki. And chemists need their work to appear in those journals, All have to compete against journal articles, so for the moment because they determine career the authority – and guaranteed the search engine’s power is limited. progress as viewed by university quality – of subscription journals Still, Murray-Rust’s own faculty and funding bodies. and databases. Elsevier’s Beilstein CrystalEye project is aggregating But while the kinetics may be slow database, and CAS (the chemical x-ray crystal structures, from the for open chemistry supporters, the abstracts service, a division of the CIFs (crystallographic information thermodynamics are on their side. American Chemical Society (ACS)) files) that publishers demand as The next generation of professional along with its delivery services supplementary material for online chemists are far more likely to be SciFinder and STN, are still the articles. These don’t fall under in tune with web-based chemistry, undisputed gold standards. copyright laws, so it is possible to treating blogs and social networking build up a free online database of sites as professional tools in the Revolution in bits crystal structures, even though they same manner as email. For Open Open chemistry advocates are belong to closed-access papers. Chemistry advocates, the inevitable frustrated by the way chemical data Turning vast quantities of online passage of time may be enough to is fragmented between different data into a useful resource poses usher in their revolution. Or, as closed databases. They reluctantly two significant problems. First, Bachrach puts it: ‘We may concede that gaining ‘Open Access’ maintaining quality is crucial. No simply have to wait for the to chemistry journals is a tough chemist wants to be faced with dinosaurs to die.’ cause to fight (see p12). But ‘Open hundreds of incorrect chemical Web references and further reading Data’ is quite a different proposition structures, or directed to blog posts Open Notebook Science: usefulchem.blogspot. – publishers could well restrict of drivel, but that is the inevitable com; usefulchem.wikispaces.com access to journal papers while result of allowing search engines Peter Murray Rust (blog): wwmm.ch.cam.ac.uk/ still freeing online records of their to pick through unchecked data. blogs/murrayrust Reactive Reports: reactivereports.com molecules and spectra, for example. This is exactly what publishers Chemical blogspace (summary of chemistry The possible benefits of and database owners guarantee to blogs): cb.openmolecules.net this approach to the chemical avoid by paying staff to oversee their Wikipedia Chemistry portal: en.wikipedia. community are already apparent, via publications, although some Open org/wiki/Portal:Chemistry Organic Syntheses: orgsyn.org an online service called ChemSpider, Chemistry advocates point to the Synthetic Pages: syntheticpages.org which launched in March 2007. success of Wikipedia as proof that Nano2hybrids: nano2hybrids.net It promises chemists free access community editing can establish Vega Science Trust: vega.org.uk to almost 18 million compounds, acceptable levels of quality control. SciVee: scivee.tv sourced from free chemistry The second problem is making Chemistry World podcast: chemistryworld. ‘Mainstream org/podcast databases. Plans are to turn the the data searchable. Google Journal of Visualised Experiments: jove.com service into a search engine – a searches only by plain text, which chemistry has The Synaptic Leap: thesynapticleap.org chemical version of Google – which is not always ideal for the chemical Chemmunity: chemmunity.com no tradition Second Life: secondlife.com automatically ‘spiders’ across community. They need a chemical PubChem: pubchem.ncbi.nlm.nih.gov web chemistry publications and version of the XML metadata of openness ChemSpider: chemspider.com databases looking for structures, that, unseen, holds the regular CrystalEye: wwmm.ch.cam.ac.uk/crystaleye much as Google trawls through the internet together. Many computer and electronic Project Prospect: rsc.org/Publishing/Journals/ ProjectProspect text of the internet. chemists are developing machine- collaboration. P Murray-Rust, Nature Precedings, 2007, in CAS doesn’t permit web search readable languages that represent press (open access manuscript): precedings. engines to scour its database, even molecular structures – systems We may simply nature.com/documents/1200/version/1 though searchers would have to include SMILES, Chemical Mark-up have to wait for P Ertl and S Jelfs, Curr. Top. Med. Chem., 2007, pay for any CAS information they Language (the chemical version of 7, 1491 the dinosaurs Thirty-two free chemistry databases (Rich Apo- were pointed towards. Indeed, ACS HTML) and the Iupac International daca blog): depth-fi rst.com/articles/2007/01/24/ doesn’t allow Google to index its Chemical Identifier (Inchi). And to die’ thirty-two-free-chemistry-databases www.chemistryworld.org Chemistry World | December 2007 | 49

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