Report:MARPAT on STN/Chemical Structure Tools/Verifying the Query
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Verifying the Query
The STN structure drawing tool allows users to apply a number of “invisible” attributes to structures, involving ring/chain designations for atoms and bonds, isolated/embedded designations for ring systems (see the STN Express 8.4 User Guide section on structure drawing menus for more information), and “match level" specifications for Markush structure searches. Because these terms cannot be readily assessed by viewing the structure in the drawing window, STN Express gives users the ability to verify that these attributes have been properly assigned. This verification option is available to users attempting to save a finished structure.
As the verification feature runs, it highlights appropriate portions of the structure drawing and informs the user of their status. Features of bonds, atoms, ring systems, G-groups, and stereochemistry are all examined during this verification process. In the figure below, a user is asked to verify that the nodes in the query have the appropriate match level designations. The same process will allow the user to verify the bonds and ring system properties via separate steps.
The user should check to verify that these designations have been assigned appropriately to the structure in accordance with the search objectives. Failure to do so may result in a search that is improperly defined, returns too many false hits, or excludes potential relevant hits. The figure below shows the verification dialog window, listing the features of the structure that will be examined during the verification process.
Editor's Note:The verification process in the STN Express structure drawing tool requires the user to study and approve the query before it is saved. This method can be contrasted with the MMS version of verification, where the structure query is built during an online session, and then put through a verification process by the system itself. The MMS version of verification is not transparent, and is performed by the MMS search system itself with a certain level of artificial chemical intelligence.
While any verification steps can be beneficial to the user, in cases where searching on an incorrect structure can be very costly to the user, user-verification steps that are built into the process are very desirable. When comparing the two different approaches taken by STN and MMS, it seems as though the ability to draw and verify the structure query offline offered by STN is the approach more likely to catch structure-drawing errors.
