Data processing: database and file management or data structures – Database design – Data structure types
Reexamination Certificate
1999-02-16
2001-10-16
Von Buhr, Maria N. (Department: 2171)
Data processing: database and file management or data structures
Database design
Data structure types
C702S027000
Reexamination Certificate
active
06304869
ABSTRACT:
FIELD OF THE INVENTION
The present invention relates to a relational database management system that stores, searches and retrieves chemical structure information quickly and easily.
BACKGROUND OF THE INVENTION
Chemical and pharmaceutical industries and chemical-related government agencies commonly maintain large chemical substance databases. These entities often provide structure-searching capabilities in association with such databases. Recently, these organizations have been standardizing their databases using relational database management systems (RDBMS) such as the Oracle Relational Database Management System by Oracle Corporation, World Headquarters, 500 Oracle Pkwy., Redwood Shores, Calif. 94065.
The advantages of integrating chemical structure information into an RDBMS include: a closer integration with other related chemical data, efficiency in both storage and retrieval of chemical structure data, and better access to the chemical structure data by other related applications.
Unfortunately, chemical information systems have traditionally been built using specialized database technology requiring, in many cases, hundreds of thousands of lines of custom computer code. Systems of this type are often both difficult to maintain, and difficult to adapt to changing hardware technologies. These maintenance problems, coupled with a lack of portability of these highly specialized systems, often lead to large investments of time and money being allocated to relatively short-lived systems.
The introduction of relational database technology provides an opportunity to transfer a large amount of the database management responsibility from the specialized database systems described above to a standard widely-accepted technology. However, relational technology has typically not been used as the basis for chemical information systems. This is due to the fact that there are problems inherent in any attempt to cast a chemical structure searching system problem into structured query language (SQL)—the standard language of relational databases. These problems include difficulty in storing and representing chemical structures in a database. No chemical information system has yet been implemented using only relational technology as its database component.
Several systems have attempted to achieve this goal but, as more fully explained below, none have been able to develop a purely relational database management system which is able to search and retrieve chemical structure information easily and quickly.
For example, Molecular Access System (MACCS) and Integrated Scientific Information System (ISIS) are both created by Molecular Design Ltd., MDL Information Systems, 14600 Catalina Street, San Leandro, Calif. 94577. These systems provide a stand-alone chemical information system wherein chemical structures are stored as hierarchical structures. However, these systems require large amounts of custom code, and are not maintained in a relational database. Accordingly, they do not have the advantages of relational technology listed above.
While it is true that these systems can be interfaced to a relational database management system such as the Oracle Database Management System noted above, it must be done using additional custom code and software that converts hierarchical structures to the relational tables needed for such a database. Therefore, it is difficult to incorporate the advantages of relational technology into the MACCS and ISIS systems. Moreover, the conversion software slows down overall performance speed.
In summary, these systems do not provide the advantages and capabilities existing in the present invention.
The present invention overcomes the above-listed problems and additionally has the following advantages: (1) development and maintenance costs will be greatly reduced by using a commercial database package. Accordingly, development efforts and benefits can be more effectively directed toward aspects of system design, and improvements in the underlying database technology will be automatically transferred to the chemical information system. This shift of focus away from database development concentrates the development and maintenance efforts on improving the search strategy and the user interface, which are the highly visible aspects of the system; (2) interfacing with other information systems will be simplified since relational databases are already used to store much of the non-structural chemical data used in research and commercial settings; and (3) portability will be much less of a design drawback since the amount of custom programming is minimal and can easily be adapted to numerous types of technology. Therefore, the portability responsibilities are mostly shouldered by the database manufacturer itself, and not by the developer of the chemical storage system.
SUMMARY OF THE INVENTION
The present invention overcomes the shortfalls in the art by developing a chemical structure search system which expands the capabilities of existing systems by capitalizing on the strengths of relational database technology.
The present invention allows the user to optimally store and search the chemical structure information using various search strategies such as multi-valued atoms, multi-typed bonds, Markush searching and various other options in a relational database management system.
Furthermore, it provides a complete chemical information system which includes modules for:
(1) exact structure searching;
(2) substructure searching;
(3) key searching;
(4) chemical name searching;
(5) molecular formula searching;
(6) registration of new molecules;
(7) structure import/export; and
(8) data editing.
Additionally, the present invention allows the routine integration of chemical structure data with other related information such as inventory, spectroscopic data and clinical data via standard relational database methods to allow better usage of all types of chemical information in both commercial and research settings.
By taking advantage of the data manipulation capabilities of relational technology, this system will also introduce dynamic querying capabilities which will allow the user to be notified of any new chemicals that are entered into the database that are responsive to previously run queries. This provides the functionality of relational views for chemical structure information.
Additionally, structure classes can also be implemented which allow the user to store certain types of information about particular types of chemical structures such as steroids. Accordingly, users can later call up this information in a quick and efficient manner without re-entering or performing previously run queries.
With these and other objects, advantages and features of the invention that may become apparent, the nature of the invention may be more clearly understood by reference to the following detailed description of the invention, the appended claims and the several drawings attached hereto.
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Brazil Joanne
Hoover Jeffrey R.
Moore Jeffrey
Dickenstein Shapiro Morin & Oshinsky LLP
Oxford Molecular Group, Inc.
Von Buhr Maria N.
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