Report:MMS/Major Recent Updates
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Major Recent Updates
See the Intellogist update policies for more information.
- VMN import improvements: (Documentation)
- VMNs of type "display" are now read.
- VMN abbreviated group list has been extended: carbon chains up to 50 members have been added.
- AV (abnormal valence) property is now stored in atom property and not set as atom valence. The VMN valence representation will be revised in a later version.
- Deuterium and tritium count property is handled properly in VMN (added as D and T ligands for non-homology atoms). D and T are transposed during the import in comparison to the VMN, as this represents the correct information in the majority of the MMS database.
- Correcting incorrect atom types in VMNs: C0 is transformed to CHK; C1 is transformed to C; homology groups in ring are transformed to XX
- Attachment bond type is set to parent R-atom bond type if different.
- VMN import option is available for switching off corrections: (Documentation)
- Valence property is now handled correctly in Markush searches.
The following Markush-related changes were implemented for Instant JChem 5.11.0:
- Added Markush structure enumeration to JChem tables.
- Marvin Services are available in JChem Cartridge through the jc_evaluate operator.
- New Standardizer action: Create group. User defined abbreviated groups can be specified. The create group standardization process consists of three steps: substructure match, grouping, and contracting group.
- Error handling and logging improvements in JChem Cartridge.
According to the Questel website:
The *MDARCLIST command has been reactivated in the Questel bibliographic system. Once again, this command can be used to audit the CN numbers in your saved CN lists in DWPI/WPIL. In this way, you can make sure that all of the Derwent CNs have been found in DWPI/WPIL. If there are Derwent CNs that are not found, you should report them to Thomson directly or to the Questel Help Desk at email@example.com, and we will direct your request to Thomson and send the corresponding Derwent accession numbers to you.
To execute *MDARCLIST properly, you need to make sure that your POP AUDIT setting is set for AUDIT OFF.
To check your POP settings in the Questel bibliographic files, type POP.
To change your audit setting, type POP AUDIT OFF.
A transcript is also presented on the MMS News page to show "how to change your POP setting and execute *MDARCLIST from an MMS saved CN list."
According to the ChemAxon News, new features for Marvin 5.9 include:
- Document to Structure supports Microsoft Office formats (doc, xls, ppt, etc...)
- Drawing electron flow arrow in a reaction is enabled
- Copy to Clipboard and Export Prediction to PDF actions have been added to NMR Predictor Beta
New features for Instant JChem 5.9 include:
- More SQL logging options have been added (Details in the documentation)
- Ability to parse text in PDF files and import structures
- Customizable tooltip for widgets and tables
- JChem Manager connection window has been changed. It provides built-in JDBC driver names and database url examples for the databases supported by ChemAxon.
- Standardizer's tautomerize action has become notably faster for large molecules.
- Speed up molecule tables for several query features (charge, isotope, radical, tautomer, atom list, (R) and (rb) query properties).
- Reaction Library has been expanded with 33 new reactions.
For a list of all updates to JChem, visit this page on the ChemAxon website.
According to a ChemAxon press release:
TIBCO Software Inc. and ChemAxon, a leader in providing chemical software development platforms and desktop applications for the biotechnology and pharmaceutical industries, today announced the full integration of the TIBCO Spotfire® Analytics Platform with ChemAxon’s Instant JChem data management application. Through this integration, new levels of visualization, analysis and exploration will be available to the life science community.
Designed specifically for end users, Instant JChem is ChemAxon’s desktop chemistry solution that allows scientists to manage and search chemical structures and related information. Through JChem, scientists can create, explore and share chemical and non-chemical data stored in local and remote databases. With this integration, Instant JChem’s data generation and management capabilities are now fully exposed to the TIBCO Spotfire Analytics Platform, bringing scientists new levels of chemical search, analysis and visualization capabilities in order to speed and refine the analytic process.
Using TIBCO Spotfire, chemists can evaluate an ever-increasing amount of data derived from screening, ADME, and chemistry research efforts focusing on compound series. This allows them to take full advantage of the information to make the best decisions regarding the prioritization of which compounds to synthesize. TIBCO Spotfire easily accommodates new information and allows chemists to spot trends in complex datasets through the use of multiple linking visualizations and chemical structure viewing.
- Search options can now be specified during Markush enumeration
- Added ability to just show R-groups in R-group decomposition
- Search Engine
- Markush descriptors are loaded into structure cache, resulting in better screening performance.
- Fingerprint is used for Markush structures in case of homology translation off.
- Search option for using SSSR or CSSR in SMARTS matching has been added.
- Explicit hydrogen is now allowed to be used in structural key molecules.
- Markush Viewer
- R-group tree is colored if the displayed Markush structure is a colored searching result.
- The loaded file opens with expanded R-group tree on the first level.
- The Nesting View highlights the appropriate tree node.
- R-group decomposition handles queries with both defined and undefined R-groups.
- For the Markush Viewer, new display options of molecule properties and size costumization are implemented. See more information here.
- The number of timouting searches has been reduced for complex queries in case of Markush search.
- MarkushViewer: New desktop application and GUI component to visualize Markush structures in organized ways.
- New query features for Markush search: New atom query properties, and explicit hydrogen atom matching to implicit hydrogen atoms are implemented for Markush search.
- Option for homology translation: Broad and narrow homology translations are now switchable. The new default is "off", which handle homology groups as pseudo atoms. Narrow refers to query side and broad refers to target side (Markush) homology groups. Switched off broad translation provides more relevant Markush hits.
- Significant speed-up of Markush search in database due to new screening methods, and new default value of homology translation search option. For Markush tables, the new screening descriptor tables require 38% increase of database storage.
- HaltOnError option to JChem Search Options: The new default is not to stop at errors for Markush tables, but continue search processing further records.
For Instant JChem 5.6, the following Markush search and display features were upgraded:
- Added homology group search options - Options for controlling whether homology groups are searched for Markush structures.
- Improved handling of chemical terms filter - User is warned when chemical terms filter is specified but can't be used as enumerated structures will not be distinct structures.
- Expand homology groups is off by default - Homology groups are not expanded be default during enumeration (previously they were expanded by default).
- Options for 2D cleaning - User can specify options for 2D cleaning during enumeration to allow generation of nicer structures.
- New stereo types support in structure searching: syn, anti, atrop, allene, cumulene
- Search performance enhancements: R-group search and database Markush search
- Support for large Markush structures (up to thousands of R-group definitions)
Users can now utilize ChemAxon features to search and view MMS records through an alternate interface. According to the ChemAxon website,"Markush Search is an add-on to JChem Base and Instant JChem and allows the registration of generic structures into the database as well as substructure and full structure searching in their enumerated libraries (without enumeration of library members)." The ChemAxon website explains that "with the recent addition of Markush DARC format import, now it is possible to handle records from the MMS (Merged Markush Service) patent database."
In August 2008, new display formats were added for DWPI records. More details about these new display formats may be found on the Questel website, at http://www.questel.com/en/News/mms_news.htm
A major improvement to the system architecture was completed with the migration onto a UNIX platform in early 2005. This enhancement improved search times tremendously.
- ↑ "JChem history of changes: New features and improvements, Bugfixes." ChemAxon website, http://www.chemaxon.com/jchem/changes.html. Accessed September 25, 2012.
- ↑ "Instant JChem Changes." ChemAxon website, https://www.chemaxon.com/instantjchem/Release_Notes_Cumulative.html. Accessed September 25, 2012.
- ↑ "JChem history of changes: New features and improvements, Bugfixes." ChemAxon website, http://www.chemaxon.com/jchem/changes.html. Accessed August 16, 2012.
- ↑ "JChem Release Notes." ChemAxon website, http://www.chemaxon.com/jchem/release_notes.html. Accessed July 1, 2012.
- ↑ "Merged Markush Service (MMS) News ." Questel website, http://www.questel.com/News/mms_news.htm. Accessed April 9, 2012.
- ↑ 6.0 6.1 "News ChemAxon." Email, http://us4.campaign-archive1.com/?u=367e81e89570b31a401d1b039&id=8b2a18b8ea&e=2172fe4dbc. Accessed March 12, 2012.
- ↑ "JChem Release Notes." http://www.chemaxon.com/jchem/release_notes.html. Accessed March 5, 2012.
- ↑ "TIBCO Spotfire and ChemAxon to Deliver Integrated Solution for Chemical Science Community." February 2012. ChemAxon website, http://www.chemaxon.com/news/tibco-spotfire-and-chemaxon-to-deliver-integrated-solution-for-chemical-science-community/. Accessed February 21, 2012.
- ↑ "Instant JChem Changes." ChemAxon website, http://www.chemaxon.com/instantjchem/Release_Notes_Cumulative.html. Accessed January 30, 2012.
- ↑ "JChem Changes." ChemAxon website, http://www.chemaxon.com/jchem/changes.html. Accessed January 17, 2012.
- ↑ "JChem Changes." ChemAxon website, http://www.chemaxon.com/jchem/changes.html. Accessed November 10, 2011.
- ↑ "JChem Release Notes." ChemAxon website, http://www.chemaxon.com/jchem/release_notes.html. Accessed October 31, 2011.
- ↑ "Feature Parade for Instant JChem 5.6.0." ChemAxon website, http://www.chemaxon.com/instantjchem/features/ijc_5_6_0.html#markush. Accessed October 31, 2011.
- ↑ "JChem and Marvin 5.5 launched." ChemAxon website, http://www.chemaxon.com/news/jchem-and-marvin-5-5-launched/. Accessed June 13, 2011.
- ↑ "Markush Search Add-on." ChemAxon website, http://www.chemaxon.com/products/markush-search-add-on/. Accessed June 1, 2011.