Multi-paradigm knowledge-bases

• US 20020194187A1
• Filed: 05/16/2002
• Published: 12/19/2002
• Est. Priority Date: 05/16/2001
• Status: Abandoned Application

• Current Assignee: ISIS Pharmaceuticals Incorporated
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Sherman, Daniel A., Blanford, Ronald P., Goates, Alan, Do, Karen A., Warren, Robin, McNeil, John
• Application Number:
  US10/150,668
• Publication Number:
  US 20020194187A1
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: G06N 5/022 Knowledge engineering; Knowledge acquisition
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 Ontologies; Annotations
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures

Abstract

Knowledge-bases are disclosed. In accordance with preferred embodiments, such knowledge-bases comprise pluralities of knowledge-elements as well as pluralities of knowledge-relationships dynamically forming the relationships among the knowledge-elements. Such knowledge-base may be assessed to determine knowledge syntheses of utility per se or to capture further knowledge-elements for augmentation of the knowledge-base. In accordance with a preferred embodiment, the knowledge-base is used to exert operative control over one or more manipulable device.

Claims

1. An irrelational knowledge-base comprising:

an irrelational knowledge-element for retaining knowledge, said knowledge-element retaining a knowledge;

a control element for enforcing a paradigm rule-set; and

a relationship modulator for modulating a relation among knowledge-elements.

2. The knowledge-base according to claim 1 wherein the relationship modulator dynamically establishes said relationships according to said paradigm rule-set.

3. The knowledge-base according to claim 1 wherein the paradigm rule-set is pseudo-hyperbolic.

4. The knowledge-base according to claim 1 wherein the control element enforces integrity of the paradigm within the knowledge-base and among the knowledge elements.

5. The irrelational knowledge-base according to claim 1 wherein said irrelational knowledge-elements are comprised of at least one relational knowledge-element.

6. The irrelational knowledge-base according to claim 5 wherein said at least one relational knowledge-element is a relational database.

7. The irrelational knowledge-base according to claim 6 wherein said relational database contains records pertaining to a plurality of bimolecular sequences and wherein said paradigm rule-set within said relational database is hierarchical.

8. The irrelational knowledge-base according to claim 1 wherein the relationship is established in the code pre-compile.

9. The irrelational knowledge-base according to claim 1 wherein at least one knowledge element is further comprised of biomolecular data.

10. The irrelational knowledge-base according to claim 9 wherein said biomolecular data comprises a data selected from the group consisting essentially of;

Gene, Sequence, Experiment, Starting Material, Treatment, Endpoint and Gene Group.

12. The examiner according to claim 10 further comprising:

d. a dynamic display modulator in communication with a display device and a user command designator, said display modulator modulating communication with said display device, said display modulator communicating display changes to the display device; and

said user command designator communicating a user command to said dynamic examiner where said designator receives user commands and communicates said commands to the dynamic examiner.

14. A computer system comprising an irrelational knowledge-base according to claim 1.

15. The computer system according to claim 14 further comprising an examiner of the irrelational knowledge-base according to claim 10.

11. An examiner of an irrelational knowledge-base providing a multi-paradigmatical examination of the knowledge-base, said examiner comprising:

a. an interpreter of said knowledge-base for designation of knowledge-elements, said interpreter generating a knowledge-element;

b. a relationship-modulator for modulating formation of a relationship among knowledge-elements; and

c. a communication-modulator for modulating knowledge-element communication.

18. The database management system according to claim 17 wherein said query servicing mechanism further comprises:

a reference generating mechanism for generating a user-defined reference to aggregated fact data generated by the aggregation module; and

a query processing mechanism for processing a given query statement, wherein, upon identifying that the given query statement is on said user-defined reference,

communicates with said aggregation module over an interface therebetween to retrieve portions of aggregated fact data pointed to by said reference that are relevant to said given query statement.

19. The database management system of claim 17, wherein said aggregation module includes a query handling mechanism for receiving query statements, and wherein communication between said query processing mechanism and said query handling mechanism is accomplished by forwarding the given query statement to the query handling mechanism of the aggregation module.

20. The database management system of claim 19, wherein said query handling mechanism extracts knowledge-element data from the received query statement and forwards the knowledge-element data to the storage handler;

and wherein the storage handler accesses said knowledge-element data of the irrelational multi-dimensional data store based upon the forwarded knowledge-element data and returns the retrieved data back to the query servicing mechanism for communication to the user.

21. The database management system of claim 17, wherein said aggregation module includes a data loading mechanism for loading at least fact data from the knowledge-base store, an aggregation engine for aggregating the fact data and a storage handler for storing the fact data and resultant aggregated fact data in the irrelational multidimensional data store.

22. The database management system of claim 21, wherein said aggregation module includes control logic that, upon determining that the irrelational multi-dimensional data store does not contain data required to service the given query statement, controls the data loading mechanism and aggregation engine to aggregate at least fact data required to service the given query statement and controls the aggregation module to return the aggregated data back to the query servicing mechanism for communication to the user.

23. The database management system of claim 22, further comprising a data analysis engine.

24. The database management system of claim 23, for use as an enterprise wide data warehouse that interfaces to a plurality of information technology systems.

25. The database management system of claim 17, for use as a database store in an informational database system.

26. The database management system of claim 17, wherein said knowledge data is biological data.

27. The database management system of claim 17, wherein said query statements are generated by a query interface in response to communication of a natural language query communicated from a client machine.

28. The database management system of claim 27, wherein said client machine comprises a web-enabled browser to communicate said natural language query to the query interface.

29. The database management system of claim 17, wherein said interface that provides communication between said query processing mechanism and said aggregation module comprises a standard interface.

13. A method of forming a knowledge-base comprising:

i) providing an organizational paradigm for describing knowledge;

ii) providing irrelational knowledge-elements for acquiring knowledge and retaining said acquired knowledge,

iii) acquiring knowledge into the knowledge-elements; and

iv) allowing the knowledge-elements to establish inter-element relationships according to said organizational paradigm.

16. A method of forming a knowledge-base comprising:

i) providing an organizational paradigm for describing knowledge;

ii) providing irrelational knowledge-elements for retaining knowledge,

iii) acquiring knowledge into the knowledge-elements; and

iv) defining a build order rule-set through a user input whereby inter-element relationships are established.

17. A database management system comprising:

a knowledge-base store storing knowledge data;

an aggregation module, operatively coupled to the knowledge-base store, for aggregating the knowledge data and storing the resultant aggregated data in an irrelational multi-dimensional data store; and

a query servicing mechanism, operatively coupled to the aggregation module, for servicing query statements generated in response to user input.

30. In a database management system comprising a knowledge-base data store storing knowledge-data at least of a member of the group consisting of;

irrelational, relational or non-relational data, a method for aggregating the knowledge data and providing query access to the aggregated data comprising the steps of;

providing an integrated aggregation module, operatively coupled to the relational data store, for aggregating the knowledge-data and storing the resultant aggregated data in an irrelational data store;

in response to user input, generating a reference to aggregated fact data generated by the aggregation module; and

processing a given query statement generated in response to user input, wherein, upon identifying that the given query statement is on said reference, communicating with said integrated aggregation module over an interface operably coupled thereto to retrieve from the integrated aggregation module portions of aggregated knowledge-data pointed to by said reference that are relevant to said given query statement.

31. The method of claim 30, further comprising the step of extracting knowledge-element data from the received query statement and forwards the knowledge-element data to the storage handler;

and

wherein the storage handler accesses said knowledge-element data of the irrelational multi-dimensional data store based upon the forwarded knowledge-element data and returns the retrieved data back to the query servicing mechanism for communication to the user.

32. The method of claim 30, wherein said aggregation module includes a data loading mechanism for loading at least fact data from the knowledge-base store, an aggregation engine for aggregating the fact data and a storage handler for storing the fact data and resultant aggregated fact data in the irrelational multi-dimensional data store.

33. The method of claim 32, wherein said aggregation module, upon determining that the irrelational multi-dimensional data store does not contain data required to service the given query statement, controls the data loading mechanism and aggregation engine to aggregate at least fact data required to service the given query statement and controls the aggregation module to return the aggregated data back to the user.

34. The method of claim 30, wherein said database management system is used as an enterprise wide data warehouse that interfaces to a plurality of information technology systems.

35. The method of claim 30, wherein said database management system is uses as a database store in an informational database system.

36. The method of claim 35, wherein said informational database system is a bioinformatics program.

37. The method of claim 30, wherein said query statements are generated by a query interface in response to communication of a natural language query communicated from a client machine.

38. The method of claim 37, wherein said client machine comprises a web-enabled browser to communicate said natural language query to the query interface.

39. The method of claim 38, wherein said interface that is operably coupled to said aggregation module comprises a standard interface.

40. The method of claim 39, wherein said standard interface is selected from the group consisting of OLDB, OLE-DB, ODBC, SQL, JDBC.