System and method for parsing and/or exporting data from one or more multi-relational ontologies

• US 7,493,333 B2
• Filed: 05/05/2005
• Issued: 02/17/2009
• Est. Priority Date: 09/03/2004
• Status: Expired due to Fees

• Current Assignee: Bio Wisdom Limited
• Original Assignee: BioWisdom Ltd. (Instem Plc)
• Inventors: Davis, Benjamin, Blue, Neil Andrew Miller, Eldridge, Matthew David, Hill, Robin Duncan, Gardner, Stephen Philip, McMenamin, Conor
• Primary Examiner(s): Vital; Pierre M.
• Assistant Examiner(s): Nofal; Christopher P
• Application Number:
  US11/121,965
• Publication Number:
  US 20060053170A1
• Time in Patent Office: 1,384 Days
• Field of Search: 707/1, 707/3, 707/9, 707/10, 707/101, 707/102, 707/104.1, 709/202, 709/217, 709/224, 715/513, 715/769, 715/804, 715/863, 715/866, 717/106, 717/120, 717/146, 704/4, 704/9, 706/45
• US Class Current: 1/1
• CPC Class Codes: G06F 16/353 into predefined classes
• CPC Class Codes: G06F 16/358 Browsing; Visualisation therefor
• CPC Class Codes: G06F 16/367 Ontology
• CPC Class Codes: G06F 16/38 Retrieval characterised by using metadata, e.g. metadata not derived from the content or metadata generated manually
• CPC Class Codes: Y10S 707/99943 Generating database or data structure, e.g. via user interface
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing

Abstract

The invention relates to a system and method for parsing and/or exporting one or more multi-relational ontologies. The system may apply a set of export constraints to one or more master ontologies to produce a redacted data subset. The redacted data subset may then be exported to a specified location or application.

Claims

1. A computer-implemented system for parsing and exporting data from one or more multi-relational ontologies, the system comprising:

one or more master multi-relational ontologies including a plurality of individual assertions, wherein an individual assertion comprises a first concept, a second concept, and a relationship between the first concept and the second concept, wherein at least one concept in a first assertion of the plurality of individual assertions is a concept in at least a second assertion of the plurality of assertions, wherein one or more relationships in the plurality of individual assertions comprise relationships unconstrained by any hierarchical arrangement of concepts, and wherein each of individual assertions of the one or more master multi-relational ontologies is associated with a confidence weight that is an indication of the confidence in the truth of the assertion;

an export module that;

receives a selection of two or more concepts from the plurality of assertions of the one of the one or more master multi-relational ontologies,

applies one or more path-finding constraints to the two or more concepts to yield a subset of individual assertions from the plurality of assertions, wherein the path finding constraints identify one or more individual assertions from the plurality of individual assertions of the one or more master multi-relational ontologies that connect, directly or indirectly, the two or more concepts,

receives a selection of a starting concept from the subset of individual assertions, and

applies one or more expansion parameters to the starting concept to yield a redacted subset of assertions from the subset of individual assertions, wherein the one or more expansion parameters include one or more selectable characteristics of the subset of individual assertions, and wherein the redacted subset of assertions includes at least one assertion that includes the starting concept; and

a storage device that stores the redacted subset of assertions as individual assertions,

wherein the export module outputs the redacted subset of assertions to a predetermined location in a predetermined format.

2. The system of claim 1, wherein one or more of the path-finding constraints or the expansion parameters are derived from a user profile associated with a specific user, wherein the user profile identifies one or more characteristics of assertions to be included in one or more of the subset of individual assertions or the redacted subset of assertions.

3. The system of claim 2, wherein the user profile includes information regarding access rights of the specific user, such that at least one of the one or more characteristics of the assertions to be included in one or more of the subset of individual assertions or the redacted subset of assertions is the specific user'"'"'s right to access any given assertion.

4. The system of claim 2, wherein the user profile includes information regarding one or more personal themes of the specific user, wherein a personal theme defines the one or more characteristics of the assertions to be included in one or more of the subset of assertions or the redacted subset of assertions according to a specific goal defined by the user.

5. The system of claim 1, wherein one or more of the path-finding constraints or the expansion parameters include information regarding one or more of identified concepts or identified relationships from the plurality of individual assertions of the master multi-relational ontologies.

6. The system of claim 1, wherein one or more of the path-finding constraints or the expansion parameters include information regarding one or more of:

concept types of one or more concepts from the plurality of individual assertions of the one or more master multi-relational ontologies or relationship types of one or more relationships from the plurality of individual assertions of the one or more master multi-relational ontologies.

7. The system of claim 1, wherein one or more of the path-finding constraints or expansion parameters include information regarding one or more data sources from which one or more of the plurality of individual assertions of the one or more master multi-relational ontologies were derived.

8. The system of claim 1, wherein one or more of the path-finding constraints or expansion parameters include information regarding one or more data source types from which one or more of the plurality of individual assertions of the one or more master multi-relational ontologies were derived.

9. The system of claim 1, wherein each of the assertions of the plurality of individual assertions of the one or more master multi-relational ontologies is associated with a curator that is a person or routine that operated on each assertion prior to inclusion into the one or more master multi-relational ontologies, wherein one or more of the path-finding constraints or expansion parameters specify at least one curator, such that one or more of the assertions of one or more of the subset of individual assertions or the redacted subset of assertions are associated with the at least one curator.

10. The system of claim 1, wherein one or more of the path-finding constraints or expansion parameters include information regarding confidence weights, such that one or more assertions in one or more of the subset of individual assertions or redacted subset of assertions is selected based at least in part on its associated confidence weight.

11. The system of claim 1, wherein the path-finding constraints include assertions from the plurality of individual assertions of the one or more master multi-relational ontologies that form a predetermined number of best paths between the two or more selected concepts.

12. The system of claim 1, wherein one or more of the path-finding constraints or the expansion parameters includes user access rights, such that one or more of the subset of individual assertions or the redacted subset of assertions include only assertions to which a particular user is permitted access.

13. The system of claim 12, wherein the user access rights include the particular user'"'"'s data source permissions, such that one or more of the subset of individual assertions or the redacted subset of assertions include only assertions derived from data sources to which the particular user is permitted access.

14. The system of claim 1, wherein the storage device stores evidence information underlying each assertion of the redacted subset of assertions along with the redacted subset of assertions.

15. The system of claim 14, wherein the evidence information includes one or more documents containing information supporting the validity of each assertion of the redacted subset of assertions.

16. The system of claim 1, wherein the export module outputs the redacted subset of assertions to a remote database.

17. The system of claim 1, wherein the export module outputs the redacted subset of individual assertions to one or more computer applications.

18. The system of claim 1, wherein the export module outputs the redacted subset of individual assertions to one or more computer applications, and wherein a user interacts with the redacted subset of individual assertions through the one or more computer applications.

19. The system of claim 18, wherein the one or more computer applications bi-directionally link the user to an ontology navigation application.

20. The system of claim 1, wherein each of the assertions of the plurality of individual assertions of the one or more master multi-relational ontologies is associated with one or more pieces of evidence underlying the plurality of assertions, each piece of evidence being associated with a data source from a plurality of data sources, wherein each of one or more users are associated with access rights to the plurality of data sources, and wherein one or more of the path-finding constraints or the expansion parameters include the access rights of at least one of the one or more users, such that one or more of the subset of individual assertions or the redacted subset of assertions includes only assertions supported by evidence associated with data sources to which the at least one of the one or more users has access rights.

21. The system of claim 20, wherein the export module further outputs at least one of the one or more pieces of evidence associated with the redacted subset of assertions, wherein only the pieces of evidence associated with the data sources to which the user has access rights is output.

22. The system of claim 9, wherein curator operation on an assertion includes approval of inclusion of the assertion in the one or more master multi-relational ontologies.

23. A computer-implemented method for parsing and exporting data from one or more multi-relational ontologies, the method comprising:

selecting two or more concepts from one or more master multi-relational ontologies, wherein the one or more master ontologies include a plurality of individual assertions, wherein an individual assertion comprises a first concept, a second concept, and a relationship between the first concept and the second concept, wherein at least one concept in a first assertion of the plurality of individual assertions is a concept in at least a second assertion of the plurality of individual assertions, wherein one or more relationships in the plurality of individual assertions comprise relationships unconstrained by any hierarchical arrangement of concepts, and wherein each of the individual assertions of the one or more master multi-relational ontologies is associated with a confidence weight that is an indication of the confidence in the truth of the assertion;

applying one or more path-finding constraints to the two or more concepts to produce a subset of individual assertions from the plurality of individual assertions of the one or more master multi-relational ontologies, wherein the path finding constraints identify one or more individual assertions from the plurality of individual assertions of the one or more master multi-relational ontologies that connect, directly or indirectly, the two or more concepts; and

selecting a starting concept from the subset of individual assertions;

applying one or more expansion parameters to the starting concept to yield a redacted subset of individual assertions from the subset of individual assertions, wherein the one or more expansion parameters include one or more selectable characteristics of the subset of individual assertions, and wherein the redacted subset of individual assertions includes at least one assertion that includes the starting concept;

outputting the redacted subset of individual assertions to a predetermined location in a predetermined format.

24. The method of claim 23, wherein one or more of the path-finding constraints or expansion parameters include a user profile associated with a specific user, wherein the user profile identifies one or more characteristics of assertions to be included in one or more of the subset of individual assertions or the redacted subset of individual assertions.

25. The method of claim 24, wherein the user profile includes information regarding access rights of the specific user, such that at least one of the one or more characteristics of the assertions to be included in one of the subset of individual assertions or the redacted subset of individual assertions is the specific user'"'"'s right to access any given assertion.

26. The method of claim 24, wherein the user profile includes information regarding one or more personal themes of the specific user, wherein a personal theme defines the one or more characteristics of the assertions to be included in one of the subset of assertions or the redacted subset of individual assertions according to a specific goal defined by the user.

27. The method of claim 23, wherein one or more of the path-finding constraints or the expansion parameters include information regarding one or more of identified concepts or identified relationships from the plurality of individual assertions of the master multi-relational ontologies.

28. The method of claim 23, wherein one or more of the path-finding constraints or the expansion parameters include information regarding one or more of:

concept types of one or more concepts from the plurality of individual assertions of the one or more master multi-relational ontologies or relationship types of one or more relationships from the plurality of individual assertions of the one or more master multi-relational ontologies.

29. The method of claim 23, wherein one or more of the path-finding constraints or the expansion parameters include information regarding one or more data sources from which one or more of the plurality of individual assertions of the one or more master multi-relational ontologies were derived.

30. The method of claim 23, wherein one or more of the path-finding constraints or the expansion parameters include information regarding one or more data source types from which one or more of the plurality of individual assertions of the one or more master multi-relational ontologies were derived.

31. The method of claim 23, wherein each of the assertions of the plurality of individual assertions of the one or more master multi-relational ontologies is associated with a curator that is a person or routine that operated on each assertion prior to inclusion into the one or more master multi-relational ontologies, wherein one or more of the path-finding constraints or the expansion parameters specify at least one curator, such that one or more of the assertions of one of the subset of individual assertions or the redacted subset of individual assertions are associated with the at least one curator.

32. The method of claim 31, wherein curator operation on an assertion includes approval of inclusion of the assertion in the one or more master multi-relational ontologies.

33. The method of claim 23, wherein one or more of the path-finding constraints or the expansion parameters include information regarding confidence weights, such that one or more assertions in one or more of the subset of individual assertions or the redacted subset of individual assertions is selected based at least in part on its associated confidence weight.

34. The method of claim 23, wherein the path-finding constraints include assertions from the plurality of individual assertions of the one or more master multi-relational ontologies that form a predetermined number of best paths between the two or more selected concepts.

35. The method of claim 23, wherein one or more of the path-finding constraints or the expansion parameters include user access rights, such that one or more of the subset of individual assertions or the redacted subset of individual assertions include only assertions to which a particular user is permitted access.

36. The method of claim 35, wherein the user access rights include the particular user'"'"'s data source permissions, such that one or more of the subset of individual assertions or the redacted subset of individual assertions include only assertions derived from data sources to which the particular user is permitted access.

37. The method of claim 23, wherein outputting the redacted subset of individual assertions includes outputting evidence information underlying each assertion of the redacted subset of individual assertions along with the redacted subset of individual assertions.

38. The method of claim 37, wherein the evidence information includes one or more documents containing information supporting the validity of each assertion of the redacted subset of individual assertions.

39. The method of claim 23, wherein outputting the redacted subset of individual assertions further comprises outputting the redacted subset of individual assertions to a remote database.

40. The method of claim 23, wherein outputting the redacted subset of individual assertions further comprises outputting the redacted subset of individual assertions to one or more computer applications.

41. The method of claim 23, wherein outputting the redacted subset of individual assertions further comprises outputting the redacted subset of individual assertions to one or more computer applications, and wherein a user interacts with the redacted subset of individual assertions through the one or more computer applications.

42. The method of claim 41, wherein the one or more computer applications bi-directionally link the user to an ontology navigation application.

43. The method of claim 23, wherein each of the assertions of the plurality of individual assertions of the one or more master multi-relational ontologies is associated with one or more pieces of evidence underlying the plurality of assertions, each piece of evidence being associated with a data source from a plurality of data sources, wherein each of one or more users are associated with access rights to the plurality of data sources, and wherein one or more of the path finding constraints or the expansion parameters include the access rights of at least one of the one or more users, such that one or more of the subset of individual assertions or the redacted subset of individual assertions includes only assertions supported by evidence associated with data sources to which the at least one of the one or more users has access rights.

44. The method of claim 43, wherein outputting the redacted subset of individual assertions further comprises outputting at least one of the one or more pieces of evidence associated with the redacted subset of individual assertions, wherein only the pieces of evidence associated with the data sources to which the user has access rights is output.

45. A computer-implemented system for parsing and exporting data from one or more multi-relational ontologies, the system comprising:

one or more master multi-relational ontologies including a plurality of individual assertions, wherein an individual assertion comprises a first concept, a second concept, and a relationship between the first concept and the second concept, wherein at least one concept in a first of the plurality of individual assertions is a concept in at least a second assertion of the plurality of individual assertions, wherein one or more relationships in the plurality of individual assertions comprise relationships unconstrained by any hierarchical arrangement of concepts, and wherein each of the individual assertions of the one or more master multi-relational ontologies is associated with a confidence weight that is an indication of the confidence in the truth of the assertion;

means for selecting two or more concepts from the plurality of assertions of the one of the one or more master multi-relational ontologies;

means for applying one or more path-finding constraints to the two or more concepts to yield a subset of individual assertions from the plurality of individual assertions, wherein the path finding constraints identify one or more individual assertions from the plurality of individual assertions of the one or more master multi-relational ontologies that connect, directly or indirectly, the two or more concepts;

means for selecting a starting concept from the subset of individual assertions;

means for applying one or more expansion parameters to the starting concept to yield a redacted subset of assertions from the subset of individual assertions, wherein the one or more expansion parameters include one or more selectable characteristics of the subset of individual assertions, and wherein the redacted subset of assertions includes at least one assertion that includes the starting concept;

means for storing the redacted subset of assertions as individual assertions; and

means for outputting the redacted subset of individually stored assertions to a predetermined location in a predetermined format.