Relational database mangement system for chemical structure storage, searching and retrieval

• US 5,950,192 A
• Filed: 06/26/1997
• Issued: 09/07/1999
• Est. Priority Date: 08/10/1994
• Status: Expired due to Term

• Current Assignee: Accelrys Incorporated
• Original Assignee: Oxford Molecular Group, Inc.
• Inventors: Moore, Jeffrey, Hoover, Jeffrey R., Brazil, Joanne
• Primary Examiner(s): Von Buhr, Maria N.
• Application Number:
  US08/883,165
• Time in Patent Office: 803 Days
• Field of Search: 395/496, 395/497, 395/499, 395/600, 395/603, 707/1-3, 707/100, 707/102, 707/104, 707/22, 707/27, 707/19, 707/20, 702/22, 702/27, 702/19, 702/20
• US Class Current: 1/1
• CPC Class Codes: G16C 20/40 Searching chemical structures or physicochemical data
• CPC Class Codes: G16C 20/90 Programming languages; Computing architectures; Database systems; Data warehousing
• CPC Class Codes: Y10S 707/941 Human sciences
• CPC Class Codes: Y10S 707/954 Relational
• CPC Class Codes: Y10S 707/99933 Query processing, i.e. searching

Abstract

A chemical structure search system and method are disclosed which expand the capabilities of existing systems by capitalizing on the strengths of relational database technology. The system allows the user to optimally store and search chemical structure information including information relating to multi-valued atoms, multi-typed bonds, Markush searching and various other options in a relational database management system. The system provides a complete chemical information system which includes capabilities 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 chemical structure search system 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. The system also has dynamic querying capabilities which allow the user to be notified of any new chemicals that are entered into the database that are responsive to previously run queries. Furthermore, 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.

Claims

1. A method for storing chemical structures in a relational database, comprising the following steps:

receiving the atoms of a chemical structure;

receiving the bonds between the atoms of said chemical structure;

constructing a matrix representation of said chemical structure including said atoms and said bonds;

storing said matrix in said relational database;

generating one search key for each of said atoms in said chemical structure; and

storing said search keys in said relational database.

2. The method of storing chemical structures of claim 1 further comprising the steps of:

defining a registry key number for said structure;

defining a registry key name for said structure; and

storing said registry key number and said registry key name in said relational database.

3. The method of storing chemical structures of claim 1 further comprising the steps of storing a chemical formula for each said structure in said relational database.

4. The method for storing chemical structures in a relational database according to claim 1, further comprising relating inventory information to said stored structure.

5. The method for storing chemical structures in a relational database according to claim 1, further comprising relating spectroscopic data to said stored structure.

6. The method for storing chemical structures in a relational database according to claim 1, further comprising relating clinical or biological information to said stored structure.

7. A method for searching chemical structures stored in a relational database, comprising the following steps:

inputting queries including atoms and bonds;

generating one query key for each said atom in said inputted query;

creating a query connection table derived from said inputted query;

comparing at least one said query key to one or more search keys generated for a given database structure, wherein a match is found when said at least one said query key matches at least one of said search keys in said chemical structure;

comparing said query connection table to a search connection table when said match is found;

creating a table which stores said matches of said comparisons; and

outputting the results of said inputted query.

8. The method of searching chemical structures stored in a relational database according to claim 7, wherein said step of generating one query key comprises assigning a code to each atom in said structure, said code being based on the type of atom and the type of neighboring atoms.

9. The method of searching chemical structures stored in a relational database of claim 8, further comprising the steps of:

labeling each bond with a unique letter based on an ordering of said bonds; and

storing said letters as a search query key in said relational database.

10. The method of searching chemical structures stored in a relational database according to claim 7, further comprising outputting results selected from the group consisting of inventory data, spectroscopic data, clinical data, toxicological data and biological data for the results of said inputted query.

11. The method of searching chemical structures stored in a relational database according to claim 7, wherein said search query key includes a Markush searching query.

12. The method of searching chemical structures stored in a relational database according to claim 7, wherein said search query key includes a wildcard search query.

13. A method of storing chemical structures in a relational database, comprising the following steps:

inputting a structure including atoms and bonds into a relational database of a computer;

constructing a matrix representation of each of said structures including said atoms and said bonds;

checking said stored structures for duplicates;

generating one search key for each of said atoms and said bonds in said structure; and

storing said search keys in said relational database.

14. A method for storing chemical structures in a database, comprising the following steps:

receiving each of the atoms of a chemical structure;

receiving each of the bonds between said atoms in said chemical structure;

constructing a matrix representation of said chemical structure including said atoms and said bonds;

storing said matrix in said database;

generating one search key for every one of said atoms in said chemical structure; and

storing said search keys in said database.