Searching generic structures

An alternative to retrieval by means of an atom list is a structure search performed by means of a user-defined generic group which contains only chlorine... 

We should not minimize the effects that electronic searching of patents has had on the business of research. In 1990, CAS introduced MARPAT, which is a database of Markush (generic) structures found in patent documents [1]. This database provided a valuable tool for patent searching in a more comprehensive way than had been available previously. In 1995, CAS launched SciFinder, which provided access to the patent literature for chemists on their desktops. Using the SciFinder interface, one may search for research topics, authors, companies, or structures/reactions. From a practical viewpoint, SciFinder did more to enhance the searching capabilities of the medicinal chemist than any other tool. Even today, SciFinder continues to provide a first pass through the patent literature when chemists want to include patents in their searching. Indeed, when a search is performed, patent references are included in the answer set. Only very recently have there been additional tools to search the patent literature that have found widespread use. 

MPHARM is a companion database to the bibliographic PHARM. It contains the specific and generic structure records for compounds disclosed in patents included in the bibliographic database. Compound numbers located in MPHARM can be searched in PHARM to retrieve the corresponding bibliographic records (100). 

WPIM (World Patents Index Markush), produced by Derwent Publications, Ltd., contains the specific and generic structure records for compounds in the patents included in Derwent Sections B (Farmdoc), C (Agdoc), and E (Chemdoc) since 1987. Sources include patents from 29 industrialized countries as well as European and PCT patents and also items from Research Disclosure and International Technology Disclosures. The compound numbers of relevant references found in WPIM can be searched in Derwent s WPI database to retrieve the corresponding bibliographic information. 

Fig. 7. Nontrivial overlap between two simple com- Fig. 8. Substructure search of generic structures, binatorial libraries.

Another searching capability is required by the need to find a partial structure or substructure in a database that includes generic structures. The ability to do a substructure search is standard in modem chemical structure information systems. The problem is more complicated when generic structures must be searched, yet even more necessary since the generic might represent millions of specific structures. The query in Fig. 8 is compared with the generic structure to find the set of specific structures. 

Anon. Markush or Generic Structures. J. Chem. Inf. Comput. Sci. 1991 31(1) 1. A brief summary of the conceptual basis of generic chemical structures in patents and the terminology used in discussing it. Written as an introduction to a special issue of the journal devoted to the use of Markush structures in the patent literature and the databases that allow searching of Markush structures. 

Attachments Any type of file information that can be attached to a section similar to e-mail attachments. Examples are texts in a generic format, chemical structures, spectra, chromatograms, and images. These attachments should be searchable using the appropriate search functionality, such as full-text search, structure search, or spectrum. 

Another typical sitnation in the R D phase is that the scientist does not know enough about a structure to store this in a conventional structure database. In this case, generic structures can be used, which contain some placeholders (e.g., residues, superatoms, molecular masses, labels) on a part of the structure instead of the not yet known atoms or groups. An ELN in the research environment needs to provide means for storing this information and searching for it in combination with the known structure query features. 

Substructure searching methods, then as now, retain pride of place in interest. Here, the advances are especially strongly evident many of the papers this week report on the operations of in-house and public structure and data retrieval systems, now very widespread in industry. Fourteen years ago, the ICI and BASF systems were two of a few operational search systems in industry, with Richard Feldmann s forerunner of the Chemical Information System(CIS) at the National Institutes of Health. The ICI CROSSBOW system, though, depended for some of its functions on the use of notations at the user interface, which restricted its use somewhat, as chemists wereunwilling to learn to encode structures for input. The performance of the BASF system was remarkable for the time, yet had already been in operation for over five years, and even included some generic structure storage and search capabilities. 

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