I list a few questions here with regards to enabling Chemical Knowledge Integrated Environments. If a collective set of affirmatives could be given, we could have tremendous benefit to both the chemical and pharmaceutical industries and the academic world of research:
Can we effectively, quickly and easily exchange chemical information in context?
Can we exchange chemical knowledge between chemists? Between chemists and other disciplines? Automatically between systems? Across the life science product life cycle?
Do we have a standard universally agreed format for the description of chemical structures and analytical information?
Can desktop applications receive all relevant chemical information alerts from global sources that are personalised to my interests?
Can scientists working with varied and heterogenous applications easily exchange chemical information in collaborative research and development systems?
Do we have a Chemical Semantic Web?
Chemical Markup Language (CML) originally developed by Peter-Murray Rust in the 90s offers an enabling universal chemical language platform to aid the positive answering of the above questions. His research continues today at the Unilever Centre for Molecular Informatics at Cambridge, UK. We however need much greater agreement by commercial and open source solution providers to such a standard, accompanied by application support, to move towards chemical knowledge integrated environments. Worker productivity enabled by personalised knowledge management tools first requires such a semantic environment and in drug discovery and life science product management, chemical information is an essential ingredient.
Once we have such chemical information described, captured and classified, it should be possible to include it in XML-supporting collaborative systems and in communication between agents and systems. In publishing activities driven by blogging we could include such chemically smart information, including tracebacks to chemical information in individual blog posts or group-based wikis. Peter-Murray Rust and Henry Rzepa (UCL) point out the possibilities opened up by CMLRSS (Chemical Markup Language, Really Simple Syndication) feeds in the article available at http://www.ch.ic.ac.uk/rzepa/rss/ with guidance on setting up a channel available at http://wwmm.ch.cam.ac.uk/moin/CmlRss.
An implemetation example demonstrating the promise of the approach is given by the
MDB (Metalloprotein Database and Browser) at the Scripps Institute. The URL for the RSS file takes the form: http://metallo.scripps.edu/services/api.php?func=metallopdb&metal=zn&count=12&format=rss
This in fact is a dynamically generated RSS feed, resulting for a query fed to the (MySQL) database of metalloproteins, with the output being formatted in RSS. Installing this will alert the user to any new (in this case Zinc-containing) metalloproteins recently added.
Barry Hardy
Douglas Connect
www.douglasconnect.com
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