ChemAxon: Revolutionizing Generic Chemical Structure Searches

Searching for Markush structures is a difficult task, and professional searchers need training and experience to search competently for Markush structures in the MMS database.  Markush structures originate in patent claims (Markush claims) for generic chemical compounds, and a single Markush structure could correspond to thousands of different specific chemical structures (enumerations).  The Merged Markush Service (MMS) was created in 1998, after the merger of two generic structure databases owned by Thomson Derwent and the French Patent Office (INPI).  Until recently, the MMS file was only accessible via the Questel Imagination platform or the STN Express platform, and both platforms require command line searching in order to draw, search, and display structures.  The chemical drawing tool Topfrag is available through Questel, but this program must be purchased.

Luckily, users now have a third option for searching MMS: through JChem  and MarvinSketch, created by  ChemAxon.  Thomson Reuters recently partnered with ChemAxon to make Markush DARC (MMS) records available on the JChem platform.  Continue reading to discover the unique search, display, and analytic capabilities of ChemAxon products!

Are your chemical structure searches catching Markush claims?

There are only a few commercial information providers that can cope with the challenge of querying the chemical information disclosed in Markush structure claims in patents.   If you’re not familiar with Markush patent claims,  they are patent claims which describe generic patent structures that could include many different interchangeable parts.  These complex patent claims can disclose hundreds of different potential chemical compounds by describing them in generic ways.  For an example, see the chemical structure searching section of our Best Practices wiki article on Chemistry and Pharmaceuticals Searching.

Some chemical information companies have been interested in creating registries of known chemical substances that exist anywhere (not just in patent art).  For example, the Chemical Abstracts Service has a well-known file of chemical substances called CAS REGISTRY, and the ChemSpider database is a newer service which aggregates publicly available chemical data from the web into a single repository.  But searching Markush claims is not just a matter of querying a database of known structures.  To conduct a successful Markush search, a search engine must be able to search through the patent claim language and understand all the possible compounds that may be covered by structures described in  generic chemical terms.   For example, how would you teach a computer to understand that a patent which claims a compound substituted by “an alkyl, an alkoxy, hydroxy, or amino,” is a good match for the specific chemical structure you drew as a query?