Report:MMS/Feature Comparison/Between MARPAT and MMS
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Features that differ between MARPAT and MMS
MMS and MARPAT, another generic chemical structure search database produced by CAS, are similar databases. As they are both independently produced Markush structure search databases, no Markush search is really complete unless the searcher has consulted at least both of these sources. However, there are some substantive differences between the two systems. A summary of the best known differences is presented below.
- Earliest dates of coverage: MARPAT indexing extends back to 1988 (with some backfile from 1987 added), while some segments of MMS extend back to 1978, and the French special medicine patents series reaches back to 1961. However, MARPAT now also contains some extracted Markush structures from INPI data back to 1961.[1]
- Number of countries covered: Although a direct comparison is not possible given the lack of current coverage information for the systems, we know that MARPAT offers indexed coverage of 63 patenting authorities as of 2012, while MMS offered coverage of about 29 sources from the Derwent World Patents Index (including 2 closed sources of technical disclosures) as of 2001 (updated coverage data of MMS could not be provided by the Thomson help desk, although we list 34 authorities treated with MMS indexing in the Data Coverage Summary).
- Applying translation: In MMS, translation attributes must be explicitly declared for each node. This is in contrast to MARPAT, where narrow translation is inferred unless otherwise defined by the user.[2]
- Automatic variability: MMS requires users to apply free sites when they wish to allow non-hydrogen attachment points in a structure query. In MARPAT, however, the default setting is open variability on any node.
- Ring isolation: MARPAT offers an “isolated ring” attribute that users can apply to any ring structures in their search queries. If used, this attribute will ensure that fused ring systems will not be included in the answer set. In contrast, if free sites are applied by the user to an MMS query, there is no way the user can designate that the free sites should not allow fused ring structures.[2] Some workarounds for this problem are available.
- Carbonyl carbon treatment: The two systems differ in their treatment of carbonyl carbons. While MARPAT treats a carbonyl carbon as a regular part of a carbon chain, MMS treats it as a chain-terminating node. The result is that MARPAT can sometimes result in giving ester hits, when only ether hits are desired. (There are possible workarounds in MARPAT to counter-act this effect.)[2]
- Viewing search hits: In MMS, the “view focus” command highlights where the hit occurred in the larger record structure, and users can also use the "Relevant R-Groups" option in the JChem Markush hitlist. In MARPAT, the graphical Markush structures that caused the hit, and their various fragments of interest, are highlighted in red within the session transcript (no need or ability to open the structure drawing in a separate window). The enhanced display in MARPAT with assembled query-focused fragments also improves the user's ability to quickly assess structure relevancy.
- Structure input function: In MARPAT/STN, structure queries may be prepared before log-on and uploaded into the system quickly once the connection has been made. In MMS, structures must be input using the MMS command language, which is less intuitive than the structure drawing tool. One workaround with MMS is to use Thomson’s Markush TOPFRAG or ChemAxon's MarvinSketch software to draw the structure; the TOPFRAG software will automatically generate MMS-ready commands in a script that can be pasted into MMS to immediately communicate the structure. However, TOPFRAG costs around $1,500, so users must be searching MMS fairly regularly to make the savings in connect-hour charges on MMS worthwhile. Structures drawn in [[|MarvinSketch|MarvinSketch]] can be loaded directly into the query form, and MarvinSketch is included in the purchase of the JChem software.
- Structure input function: In MARPAT/STN, structure queries may be prepared before log-on and uploaded into the system quickly once the connection has been made. In MMS, structures must be input using the MMS command language, which is less intuitive than the structure drawing tool. One workaround with MMS is to use Thomson’s Markush TOPFRAG or ChemAxon's MarvinSketch software to draw the structure; the TOPFRAG software will automatically generate MMS-ready commands in a script that can be pasted into MMS to immediately communicate the structure. However, TOPFRAG costs around $1,500, so users must be searching MMS fairly regularly to make the savings in connect-hour charges on MMS worthwhile. Structures drawn in [[|MarvinSketch|MarvinSketch]] can be loaded directly into the query form, and MarvinSketch is included in the purchase of the JChem software.
Editor's Note:A final difference between the two services would be timeliness. Although exact data is not known, it is believed that MARPAT provides fully indexed records more quickly than MMS.
Limitations of MARPAT vs. MMS
The following section contains subjective comments about the system that represent our editor's opinions, and should not be viewed as fact. Editor's opinions include positive and negative judgments about the product written in consideration of wider context, including related products and the industry at large. Further subjective information is presented in clearly labeled "Editor's Notes" throughout the report.
In practice there are many differences between the two systems, but the main one to be concerned with is content coverage. There is a high degree of overlap in content between MARPAT and MMS, but neither provides the elusive “complete collection.” Therefore any “complete” search would query both databases. Both systems provide a high degree of control when it comes to defining the variability in a Markush query structure, though they use slightly different tools and commands to exert that control.
One difference where the editors believe MARPAT is superior, apart from its general “feel,” is in its ability to more easily pinpoint exactly how a queried structure “fits” a Markush answer with the FQHIT display field. The enhanced FQHIT display automatically assembles the query-relevant fragments in their correct placement in the chemical structure, thereby giving a visual demonstration of how the structure fits the query. In order to see where in a document a hit originates using MMS, the searcher must “back out” of the main application to execute a “view focus” command. MARPAT allows the searcher to gather that information more quickly and in a more streamlined fashion. However, the new interface of the JChem software offers features like viewing "Relevant R-Groups" that improve the ability to see how the structure fits the query in MMS.
Another difference, this time in favor of MMS, is that it has a standardized way in which it treats carbonyl carbons. Essentially their standardization is in line with observed organic chemical equilibria between possible conformers in a normalized bonding relationship. The editors are not aware of such a standard in the construction of MARPAT records.
A third difference between the systems relates to match level and translation. In MMS, translation must be explicitly declared for each node. This is a disadvantage when compared to MARPAT, where match levels are set by default to approximate the narrow translation function. In fact, a 2001 article by Berks comparing the systems, states “Translation functions are almost identical in function in MMS and MARPAT – the difference is the level of effort users must input to manage the system’s interpretation of the query – here, MMS is more work.” [2]
Finally, Berks also notes another feature in MARPAT that allows easier control of variability than is available in MMS. Any MARPAT ring node, or is given one additional right-click menu item, “Ring Isolation.” Here rings can be defined as isolated, embedded, or isolated/embedded. Isolated rings are restricted from sharing bonds with other rings, whereas embedded rings are required to do so. The default setting for all rings is isolated/embedded which allows either. No such ring isolation attribute exists in MMS, though one can envision possible workarounds.
