Updates to the Largest Markush Search Databases: MMS and MARPAT

[tweetmeme source=”Intellogist” only_single=false] Do you know the best resources for searching Markush chemical structures in patent documents? If you need to freshen up your Markush search skills, then you’re in luck.  Intellogist Reports on two of the largest sources of Markush data, Merged Markush Service (MMS) and MARPAT on STN, have both been fully updated, and we’ll look at some of the most important recent changes to these databases. The Merged Markush Service (MMS) is a generic chemical structure file which is linked to two bibliographic data files, the Derwent World Patents Index, produced by Thomson Derwent, and the Pharm (formerly Pharmsearch) file, produced by the French Patent Office (INPI).  MARPAT, produced by CAS and FIZ-Karlsruhe,  contains only patents which have been indexed into the CAplus database and which generically disclose/claim chemical structures.

Last week we looked at major updates to the STN platform, on which you can search MARPAT.  The content of the MARPAT database has undergone a lot of recent improvements, with new country coverage, more structure images, and additional backfile coverage from 1987 added to the file. Meanwhile, users can now search the MMS file through a new platform produced by ChemAxon.  After the jump, we’ll look at updates to both the search features and content of MARPAT and MMS.

Updates to MMS

The updated MMS Intellogist Report includes many new features available on ChemAxon’s JChem search platform:

  • Full Search on JChem: After a user has linked the JChem platform to the MMS database, they can conduct a Markush structure search through the JChem interface. First, users must define the domain of the query: searching the entire database is the default domain, but users can also choose to conduct the search within specific lists of records. The user then selects to add a “detail field.” Under the “detail field” menu, they select the “vmns” option, and from the “vmns” menu they select “Markush structure.” Users can upload a structure query drawn in MarvinSketch. Users then define the search type (i.e. full structure or substructure), and they define other structure query options (stereochemistry, atom matching, tautomer, and vague bond). Finally, users can add additional search terms in text fields, connected by Boolean operators to the structure query, in order to further narrow the search.

The chemical structure search form on JChem.

  • Chemical Structure Drawing with MarvinSketch: Chemical structures in JChem can be drawn using MarvinSketch, the “integrated structure drawing tool of JChem.” MarvinSketch is similar in use and functionality to Questel’s TOPFRAG program, since both programs allow users to draw chemical structures through a graphical interface and define attributes for certain elements of the structure.  However, unlike TOPFRAG, MarvinSketch doesn’t generate code representing the structure query which needs to be pasted into a command line. The MarvinSketch structure drawings can be uploaded directly to the query form on JChem. Users choose to “Add detail field” and then select a “Markush structure” drawn in MarvinSketch to be added as a term in the query.

Drawing chemical structures on MarvinSketch.

  • View Focus on JChem: From the Markush structure hit list, users can select to view the enumerations (specific chemical structures) that correspond with the selected Markush structure. Users can select the “colouring” option to highlight the relevant R-groups in the enumerations.

When viewing structure enumerations, users can highlight the relevant R-groups.

  • Analyzing Results in JChem: Users can analyze the list of enumerations of a selected Markush structure in ChemAxon’s JChem by selecting the “Filter” tab in the enumerated structure menu.  In the “Chemical terms filter” editor, users can select predefined chemical term filters listed under the “Favourites” drop-down menu.  Users can also manually enter their own chemical term expressions into the editor form. Suggested chemical terms will automatically appear as the user types.

Users enter the desired chemical terms and select “OK” to filter the enumerations.

Updates to MARPAT

While the search interface options for MMS have changed, MARPAT has a number of content updates that are described fully in the updated MARPAT Intellogist Report:

  • Broader patent authority coverage: Since January 2010, CAS has added four new patenting authorities to its available coverage in CA/CAplus (which has equivalent country coverage to MARPAT, as described in the Data Coverage Summary section on the MARPAT Intellogist Report).  The new patenting authorities covered in MARPAT include the Philippines (PH), Costa Rica (CR), Malaysia (MY), and the Eurasian Patent Organization (EA).  As of April 2012, 63 authorities are covered by CAS.
  • More structure graphics: In January 2012, CAS and STN announced that over 79,000 structure graphics would become available on MARPAT and CA/CAplus on STN and SciFinder. Structure graphics are now available for more than 75 percent of MARPAT records.
  • Enhanced MARPAT backfile: In March 2012, it was announced that additional backfile coverage from 1987 for English, German, and Japanese-language patent documents were being added to the MARPAT file.

Read the updated Intellogist Report to also learn about new MARPAT search options, such as MARPAT on SciFinder!

These are just a few of the major highlights for both the updated MMS and MARPAT Intellogist Reports.  Read the full reports to get the latest information on these invaluable Markush search tools!

Which updates to MMS and MARPAT do you find the most useful for searching generic chemicals in patent documents?  Let us know in the comments!

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This post was contributed by Joelle Mornini. The Intellogist blog is provided for free by Intellogist’s parent company Landon IP, a major provider of patent searches, trademark searches, technical translations, and information retrieval services.


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