Update: CML, Chem4Word, CheTA, OREChem, Lensfield


dictated to Arcturus

Our group has been making tremendous progress over the last few months and I will be posting many posts which detail what we have done and where the resources are. As almost everything that we do is open. Here are some of the things that I expect to be talking about.

  • Chemical Markup Language (CML). The work with chem4word has not only been tremendously valuable in developing the architecture and functionality of the system but also has given us great confidence in CML. We now have a schema (cmllite) which covers all the main features of molecules and is extensible. This has been widely tested on our own software (JUMBO, OPSIN, OSCAR,) and also for importing sources such as Pubchem. This means that we can now have access to a very large number of molecules in CML. To give information on CML we shall be devoting a special blog to it. We shall also revitalise the CML website and Home page.
  • Chem4word. Again there has been tremendous progress here Joe Townsend is now running this is a global activity. We hope to have a special blog devoted to chem4word and mechanisms for keeping the community in touch.
  • CheTA, OSCAR and OPSIN. CheTA is our JISC funded project with NACTEM and we have been making very good progress. Oscar is now being refactored with a project sponsored by OMII. OPSIN is the leading open source name2structure converter and achieves 97% correctness on do IUPAC names in Pubchem. We are now using these to automate our reading of the chemical literature.
  • Lensfield and OREchem. Orechem is a collaborative project with Cornell, Penn State, Indiana University, Southampton and funded by Microsoft. An important sub project is to be able to compute the world’s chemical literature automatically. We are building a pipeline based on RDF which will automate the conversion of crystal structures into CML, high throughput computation with quantum mechanical programs, conversion to RDF and publication with a SPARQL endpoint. Lensfield is Jim Downing’s supervision for a new generation of automatic scientific computation. It’s based on functional programming and is derived from the ideas of the make utility.
  • AMY. Our “Star Trek” vision of an artificially-intelligent chemistry laboratory. It’s not science fiction. It will soon be science fact. Also JISC funded.

More in detail on all of these.

This entry was posted in Uncategorized. Bookmark the permalink.

3 Responses to Update: CML, Chem4Word, CheTA, OREChem, Lensfield

  1. Pingback: Science in the Open » Blog Archive » Capturing and connecting research objects: A pitch for @sciencehackday

  2. Hello this is kind of of off topic but I was wondering if blogs use WYSIWYG editors or if you have to manually code with HTML. I’m starting a blog soon but have no coding knowledge so I wanted to get advice from someone with experience. Any help would be greatly appreciated!

Leave a Reply

Your email address will not be published. Required fields are marked *