Systems, methods and computer program products for integrating biological/chemical databases to create an ontology network

• US 20020194201A1
• Filed: 05/13/2002
• Published: 12/19/2002
• Est. Priority Date: 06/05/2001
• Status: Abandoned Application

• Current Assignee: Selventa, Inc.
• Original Assignee: Selventa, Inc.
• Inventors: Gardner, Richard N., Segaran, Suresh Toby, Levy, Joshua Lerner, Wilbanks, John Thompson
• Application Number:
  US10/145,521
• Publication Number:
  US 20020194201A1
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/30 Unsupervised data analysis
• 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 50/20 Heterogeneous data integration
• CPC Class Codes: G16C 20/90 Programming languages; Computing architectures; Database systems; Data warehousing

Abstract

Biological/chemical databases are integrated by obtaining an entity-relationship model for each of the biological/chemical databases, and identifying related entities in the entity-relationship models of at least two of the biological/chemical databases. At least two of the related entities that are identified are linked, to thereby create an entity-relationship model that integrates the plurality of biological/chemical databases. The entity-relationship model that integrates the biological/chemical databases provides an ontology network that integrates the diverse ontologies that are represented by the independent biological/chemical databases. By navigating the entity-relationship model in response to queries, discovery may be obtained that may not be obtainable from any one of the independent biological/chemical databases.

Claims

1. A method of integrating a plurality of biological/chemical databases, comprising:

obtaining an entity-relationship model for each of the plurality of biological/chemical databases;

identifying related entities in the entity-relationship models of at least two of the biological/chemical databases; and

linking at least two of the related entities that are identified, to thereby create an entity-relationship model that integrates the plurality of biological/chemical databases.

2. A method according to claim 1 wherein at least one of the plurality of databases represents an ontology and wherein the entity-relationship model that integrates the plurality of biological/chemical databases creates an ontology network.

3. A method according to claim 1 wherein the related entities are identical entities and wherein linking comprises merging the at least two of the identical entities that are identified into a single entity in the entity-relationship model that integrates the plurality of biological/chemical databases.

4. A method according to claim 3 wherein the merging further comprises establishing a plurality of aliases for the single entity in the entity-relationship model that integrates the plurality of biological/chemical databases, a respective alias of which refers to a respective one of the at least two of the identical entities that are identified.

5. A method according to claim 1 further comprising:

traversing the entity-relationship model that integrates the plurality of biological/chemical databases in response to a query to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases.

6. A method according to claim 5 wherein the traversing comprises:

traversing the entity-relationship model that integrates the plurality of biological/chemical databases from a starting entity to an ending entity in response to a query that specifies the starting entity and the ending entity to thereby identify relationships between the starting entity and the ending entity that are based on the entity-relationship model that integrates the plurality of biological/chemical databases.

7. A method according to claim 5 wherein the traversing comprises:

traversing the entity-relationship model that integrates the plurality of biological/chemical databases from a starting entity to a plurality of ending entities in response to a query that specifies the starting entity to thereby identify relationships between the starting entity and the plurality of ending entities that are based on the entity-relationship model that integrates the plurality of biological/chemical databases.

8. A method according to claim 5 wherein the traversing comprises:

traversing the entity-relationship model that integrates the plurality of biological/chemical databases in response to a query and in response to at least one path rule to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases.

9. A method according to claim 8 wherein the at least one path rule specifies a type of path to use in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases, a type of path not to use in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases, a type of ending entity that can be included in the query results, a type of ending entity that is not to be included in the query results, a type or class of relationship to be used in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases, a type or class of relationship that is not to be used in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases and/or a confidence level to be achieved in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases.

10. A method according to claim 8 further comprising storing the query and the path rule for reuse.

11. A method according to claim 5 further comprising:

storing the query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases as at least one new relationship in the entity-relationship model that integrates the plurality of biological/chemical databases to thereby store knowledge that was derived from the query in the entity-relationship model that integrates the plurality of biological/chemical databases.

12. A method according to claim 5 further comprising:

assigning a confidence level to at least one of the relationships in the entity-relationship model that integrates the plurality of biological/chemical databases.

13. A method according to claim 12 further comprising:

traversing the entity-relationship model that integrates the plurality of biological/chemical databases in response to a query to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases including the at least one confidence level that is assigned.

15. A method according to claim 14 wherein the entity-relationship model of the plurality of biological/chemical databases that links at least some related entities in the at least two of the biological/chemical databases provides an ontology network and wherein the entity-relationship model for the new biological/chemical database represents an ontology.

16. A method according to claim 14 wherein the related entities are identical entities and wherein the linking comprises merging the at least two of the identical entities that are identified into a single entity in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

17. A method according to claim 16 wherein the merging further comprises establishing a plurality of aliases for the single entity in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database, a respective alias of which refers to a respective one of the at last two of the identical entities that are identified.

18. A method according to claim 17 wherein the new biological/chemical database is an updated version of one of the plurality of biological/chemical databases, the method further comprising:

identifying at least one entity in the one of the plurality of biological/chemical databases that has been deleted from the updated version of the one of the plurality of biological/chemical databases; and

removing an alias that is associated with the at least one entity that has been removed.

19. A method according to claim 18 further comprising:

splitting at least one entity in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database based upon the alias that was removed.

20. A method according to claim 14 further comprising:

identifying entities in the new biological/chemical database that do not correspond to at least one of the entities in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database; and

adding at least one new entity to the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database that corresponds to the entities in the new biological/chemical database that do not correspond to at least one of the entities in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

21. A method according to claim 14 further comprising:

traversing the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database in response to a query to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

22. A method according to claim 14 further comprising:

traversing the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database in response to a query and in response to at least one path rule to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

23. A method according to claim 21 further comprising:

storing the query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database as at least one new relationship in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database to thereby store knowledge that was derived from the query in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

24. A method according to claim 14 further comprising:

maintaining an image of the entity-relationship model of the plurality of biological/chemical databases prior to the linking.

25. A method according to claim 24 further comprising:

comparing the image of the entity-relationship model of the plurality of biological/chemical databases prior to the linking and the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

26. A method according to claim 14 wherein the entity-relationship model of the new biological/chemical database does not include relationships therein.

28. A method according to claim 27 wherein the traversing comprises:

traversing the integrated entity-relationship model of the plurality of biological/chemical databases from a starting entity to an ending entity in response to a query that specifies the starting entity and the ending entity to thereby identify relationships between the starting entity and the ending entity that are based on the integrated entity-relationship model of the plurality of biological/chemical databases.

29. A method according to claim 27 wherein the traversing comprises:

traversing the integrated entity-relationship model of the plurality of biological/chemical databases from a starting entity to a plurality of ending entities in response to a query that specifies the starting entity to thereby identify relationships between the starting entity and the plurality of ending entities that are based on the integrated entity-relationship model of the plurality of biological/chemical databases.

30. A method according to claim 27 wherein the traversing comprises:

traversing the integrated entity-relationship model of the plurality of biological/chemical databases in response to a query and in response to at least one path rule to thereby obtain query results that are based on the integrated entity-relationship model of the plurality of biological/chemical databases.

31. A method according to claim 30 wherein the at least one path rule specifies a type of path to use in traversing through the plurality of entities, a type of path not to use in traversing through the plurality of entities, a type of ending entity that can be included in the query results, a type or class of ending entity that is not to be included in the query results, a type or class of relationship that is to be used in traversing through the plurality of entities, a type of relationship not to be used in traversing through the plurality of entities and/or a confidence level to be achieved in traversing through the plurality of entities.

32. A method according to claim 30 further comprising storing the query and the path rule for reuse.

33. A method according to claim 27 further comprising:

storing the query results that are based on the integrated entity-relationship model of the plurality of biological/chemical databases as at least one new relationship in the integrated entity-relationship model of the plurality of biological/chemical databases to thereby store knowledge that was derived from the query in the integrated entity-relationship model of the plurality of biological/chemical databases.

34. A method according to claim 27 further comprising:

assigning a confidence level to at least one of the relationships in the integrated entity-relationship model of the plurality of biological/chemical databases.

35. A method according to claim 34 further comprising:

traversing the integrated entity-relationship model of the plurality of biological/chemical databases in response to a query to thereby obtain query results that are based on the integrated entity-relationship model of the plurality of biological/chemical databases including the at least one confidence level that is assigned.

37. A system according to claim 36 wherein at least one of the plurality of databases represents an ontology and wherein the entity-relationship model that integrates the plurality of biological/chemical databases creates an ontology network.

38. A system according to claim 36 wherein the related entities are identical entities and wherein the means for linking comprises means for merging the at least two of the identical entities that are identified into a single entity in the entity-relationship model that integrates the plurality of biological/chemical databases.

39. A system according to claim 38 wherein the means for merging further comprises means for establishing a plurality of aliases for the single entity in the entity-relationship model that integrates the plurality of biological/chemical databases, a respective alias of which refers to a respective one of the at least two of the identical entities that are identified.

40. A system according to claim 36 further comprising:

means for traversing the entity-relationship model that integrates the plurality of biological/chemical databases in response to a query to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases.

41. A system according to claim 40 wherein the means for traversing comprises:

means for traversing the entity-relationship model that integrates the plurality of biological/chemical databases from a starting entity to an ending entity in response to a query that specifies the starting entity and the ending entity to thereby identify relationships between the starting entity and the ending entity that are based on the entity-relationship model that integrates the plurality of biological/chemical databases.

42. A system according to claim 40 wherein the means for traversing comprises:

means for traversing the entity-relationship model that integrates the plurality of biological/chemical databases from a starting entity to a plurality of ending entities in response to a query that specifies the starting entity to thereby identify relationships between the starting entity and the plurality of ending entities that are based on the entity-relationship model that integrates the plurality of biological/chemical databases.

43. A system according to claim 40 wherein the means for traversing comprises:

means for traversing the entity-relationship model that integrates the plurality of biological/chemical databases in response to a query and in response to at least one path rule to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases.

44. A system according to claim 43 wherein the at least one path rule specifies a type of path to use in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases, a type of path not to use in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases, a type of ending entity that can be included in the query results, a type of ending entity that is not to be included in the query results, a type or class of relationship to be used in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases, a type or class of relationship that is not to be used in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases and/or a confidence level to be achieved in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases.

45. A system according to claim 43 further comprising means for storing the query and the path rule for reuse.

46. A system according to claim 40 further comprising:

means for storing the query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases as at least one new relationship in the entity-relationship model that integrates the plurality of biological/chemical databases to thereby store knowledge that was derived from the query in the entity-relationship model that integrates the plurality of biological/chemical databases.

47. A system according to claim 40 further comprising:

means for assigning a confidence level to at least one of the relationships in the entity-relationship model that integrates the plurality of biological/chemical databases.

48. A system according to claim 47 further comprising:

means for traversing the entity-relationship model that integrates the plurality of biological/chemical databases in response to a query to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases including the at least one confidence level that is assigned.

50. A system according to claim 49 wherein the entity-relationship model of the plurality of biological/chemical databases that links at least some related entities in the at least two of the biological/chemical databases provides an ontology network and wherein the entity-relationship model for the new biological/chemical database represents an ontology.

51. A system according to claim 49 wherein the related entities are identical entities and wherein the means for linking comprises means for merging the at least two of the identical entities that are identified into a single entity in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

52. A system according to claim 51 wherein the means for merging further comprises means for establishing a plurality of aliases for the single entity in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database, a respective alias of which refers to a respective one of the at last two of the identical entities that are identified.

53. A system according to claim 52 wherein the new biological/chemical database is an updated version of one of the plurality of biological/chemical databases, the system further comprising:

means for identifying at least one entity in the one of the plurality of biological/chemical databases that has been deleted from the updated version of the one of the plurality of biological/chemical databases; and

means for removing an alias that is associated with the at least one entity that has been removed.

54. A system according to claim 53 further comprising:

means for splitting at least one entity in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database based upon the alias that was removed.

55. A system according to claim 49 further comprising:

means for identifying entities in the new biological/chemical database that do not correspond to at least one of the entities in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database; and

means for adding at least one new entity to the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database that corresponds to the entities in the new biological/chemical database that do not correspond to at least one of the entities in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

56. A system according to claim 49 further comprising:

means for traversing the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database in response to a query to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

57. A system according to claim 49 further comprising:

means for traversing the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database in response to a query and in response to at least one path rule to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

58. A system according to claim 56 further comprising:

means for storing the query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database as at least one new relationship in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database to thereby store knowledge that was derived from the query in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

59. A system according to claim 49 further comprising:

means for maintaining an image of the entity-relationship model of the plurality of biological/chemical databases before the at least two of the related entities are linked.

60. A system according to claim 54 further comprising:

means for comparing the image of the entity-relationship model of the plurality of biological/chemical databases before the at least two of the related entities are linked and the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

61. A system according to claim 49 wherein the entity-relationship model of the new biological/chemical database does not include relationships therein.

14. A method of integrating a new biological/chemical database with a plurality of biological/chemical databases, comprising:

providing an entity-relationship model of the plurality of biological/chemical databases that links at least some related entities in at least two of the biological/chemical databases;

obtaining an entity-relationship model of the new biological/chemical database;

identifying related entities in the entity-relationship model of the new biological/chemical database and the entity-relationship model of the plurality of biological/chemical databases; and

linking at least two of the related entities that are identified, to thereby create an entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

27. A method of querying a plurality of biological/chemical databases, each of which includes records for a plurality of biological/chemical entities, the method comprising:

providing an integrated entity-relationship model of the plurality of biological/chemical databases that links at least some related entities in at least two of the biological/chemical databases; and

traversing the integrated entity-relationship model of the plurality of biological/chemical databases in response to a query to thereby obtain query results that are based on the integrated entity-relationship model of the plurality of biological/chemical databases.

36. A system for integrating a plurality of biological/chemical databases, comprising:

an entity-relationship model for each of the plurality of biological/chemical databases;

means for identifying related entities in the entity-relationship models of at least two of the biological/chemical databases; and

means for linking at least two of the related entities that are identified, to thereby create an entity-relationship model that integrates the plurality of biological/chemical databases.

49. A system for integrating a new biological/chemical database with a plurality of biological/chemical databases, comprising:

an entity-relationship model of the plurality of biological/chemical databases that links at least some related entities in at least two of the biological/chemical databases;

an entity-relationship model of the new biological/chemical database;

means for identifying related entities in the entity-relationship model of the new biological/chemical database and the entity-relationship model of the plurality of biological/chemical databases; and

means for linking at least two of the related entities that are identified, to thereby create an entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

62. A system for querying a plurality of biological/chemical databases, each of which includes records for a plurality of biological/chemical entities, the system comprising:

an integrated entity-relationship model of the plurality of biological/chemical databases that links at least some related entities in at least two of the biological/chemical databases; and

means for traversing the integrated entity-relationship model of the plurality of biological/chemical databases in response to a query to thereby obtain query results that are based on the integrated entity-relationship model of the plurality of biological/chemical databases.

63. A system according to claim 62 wherein the means for traversing comprises:

means for traversing the integrated entity-relationship model of the plurality of biological/chemical databases from a starting entity to an ending entity in response to a query that specifies the starting entity and the ending entity to thereby identify relationships between the starting entity and the ending entity that are based on the integrated entity-relationship model of the plurality of biological/chemical databases.

64. A system according to claim 62 wherein the means for traversing comprises:

means for traversing the integrated entity-relationship model of the plurality of biological/chemical databases from a starting entity to a plurality of ending entities in response to a query that specifies the starting entity to thereby identify relationships between the starting entity and the plurality of ending entities that are based on the integrated entity-relationship model of the plurality of biological/chemical databases.

65. A system according to claim 62 wherein the means for traversing comprises:

means for traversing the integrated entity-relationship model of the plurality of biological/chemical databases in response to a query and in response to at least one path rule to thereby obtain query results that are based on the integrated entity-relationship model of the plurality of biological/chemical databases.

66. A system according to claim 65 wherein the at least one path rule specifies a type of path to use in traversing through the plurality of entities, a type of path not to use in traversing through the plurality of entities, a type of ending entity that can be included in the query results, a type of ending entity that is not to be included in the query results, a type or class of relationship that is to be used in traversing through the plurality of entities, a type or class of relationship not to be used in traversing through the plurality of entities and/or a confidence level to be achieved in traversing through the plurality of entities.

67. A system according to claim 65 further comprising storing the query and the path rule for reuse.

68. A system according to claim 62 further comprising:

means for storing the query results that are based on the integrated entity-relationship model of the plurality of biological/chemical databases as at least one new relationship in the integrated entity-relationship model of the plurality of biological/chemical databases to thereby store knowledge that was derived from the query in the integrated entity-relationship model of the plurality of biological/chemical databases.

69. A system according to claim 62 further comprising:

means for assigning a confidence level to at least one of the relationships in the integrated entity-relationship model of the plurality of biological/chemical databases.

70. A system according to claim 69 further comprising:

means for traversing the integrated entity-relationship model of the plurality of biological/chemical databases in response to a query to thereby obtain query results that are based on the integrated entity-relationship model of the plurality of biological/chemical databases including the at least one confidence level that is assigned.

71. A computer program product that is configured to integrate a plurality of biological/chemical databases, the computer program product comprising a computer usable storage medium having computer-readable program code embodied in the medium, the computer-readable program code comprising:

computer-readable program code that is configured to obtain an entity-relationship model for each of the plurality of biological/chemical databases;

computer-readable program code that is configured to identify related entities in the entity-relationship models of at least two of the biological/chemical databases; and

computer-readable program code that is configured to link at least two of the related entities that are identified, to thereby create an entity-relationship model that integrates the plurality of biological/chemical databases.

72. A computer program product according to claim 71 wherein at least one of the plurality of databases represents an ontology and wherein the entity-relationship model that integrates the plurality of biological/chemical databases creates an ontology network.

73. A computer program product according to claim 71 wherein the related entities are identical entities and wherein the computer-readable program code that is configured to link comprises computer-readable program code that is configured to merge the at least two of the identical entities that are identified into a single entity in the entity-relationship model that integrates the plurality of biological/chemical databases.

74. A computer program product according to claim 73 wherein the computer-readable program code that is configured to merge further comprises computer-readable program code that is configured to establish a plurality of aliases for the single entity in the entity-relationship model that integrates the plurality of biological/chemical databases, a respective alias of which refers to a respective one of the at least two of the identical entities that are identified.

75. A computer program product according to claim 71 further comprising:

computer-readable program code that is configured to traverse the entity-relationship model that integrates the plurality of biological/chemical databases in response to a query to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases.

76. A computer program product according to claim 75 wherein the computer-readable program code that is configured to traverse comprises:

computer-readable program code that is configured to traverse the entity-relationship model that integrates the plurality of biological/chemical databases from a starting entity to an ending entity in response to a query that specifies the starting entity and the ending entity to thereby identify relationships between the starting entity and the ending entity that are based on the entity-relationship model that integrates the plurality of biological/chemical databases.

77. A computer program product according to claim 75 wherein the computer-readable program code that is configured to traverse comprises:

computer-readable program code that is configured to traverse the entity-relationship model that integrates the plurality of biological/chemical databases from a starting entity to a plurality of ending entities in response to a query that specifies the starting entity to thereby identify relationships between the starting entity and the plurality of ending entities that are based on the entity-relationship model that integrates the plurality of biological/chemical databases.

78. A computer program product according to claim 75 wherein the computer-readable program code that is configured to traverse comprises:

computer-readable program code that is configured to traverse the entity-relationship model that integrates the plurality of biological/chemical databases in response to a query and in response to at least one path rule to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases.

79. A computer program product according to claim 78 wherein the at least one path rule specifies a type of path to use in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases, a type of path not to use in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases, a type of ending entity that can be included in the query results, a type of ending entity that is not to be included in the query results, a type or class of relationship to be used in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases, a type or class of relationship that is not to be used in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases and/or a confidence level to be achieved in traversing through the entity-relationship model that integrates the plurality of biological/chemical databases.

80. A computer program product according to claim 78 further comprising computer-readable program code that is configured to store the query and the path rule for reuse.

81. A computer program product according to claim 75 further comprising:

computer-readable program code that is configured to store the query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases as at least one new relationship in the entity-relationship model that integrates the plurality of biological/chemical databases to thereby store knowledge that was derived from the query in the entity-relationship model that integrates the plurality of biological/chemical databases.

82. A computer program product according to claim 75 further comprising:

computer-readable program code that is configured to assign a confidence level to at least one of the relationships in the entity-relationship model that integrates the plurality of biological/chemical databases.

83. A computer program product according to claim 82 further comprising:

computer-readable program code that is configured to traverse the entity-relationship model that integrates the plurality of biological/chemical databases in response to a query to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases including the at least one confidence level that is assigned.

84. A computer program product that is configured to integrate a new biological/chemical database with a plurality of biological/chemical databases, the computer program product comprising a computer usable storage medium having computer-readable program code embodied in the medium, the computer-readable program code comprising:

an entity-relationship model of the plurality of biological/chemical databases that links at least some related entities in at least two of the biological/chemical databases;

an entity-relationship model of the new biological/chemical database;

computer-readable program code that is configured to identify related entities in the entity-relationship model of the new biological/chemical database and the entity-relationship model of the plurality of biological/chemical databases; and

computer-readable program code that is configured to link at least two of the related entities that are identified, to thereby create an entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

85. A computer program product according to claim 84 wherein the entity-relationship model of the plurality of biological/chemical databases that links at least some related entities in the at least two of the biological/chemical databases provides an ontology network and wherein the entity-relationship model for the new biological/chemical database represents an ontology.

86. A computer program product according to claim 84 wherein the related entities are identical entities and wherein the computer-readable program code that is configured to link comprises computer-readable program code that is configured to merge the at least two of the identical entities that are identified into a single entity in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

87. A computer program product according to claim 86 wherein the computer-readable program code that is configured to merge further comprises computer-readable program code that is configured to establish a plurality of aliases for the single entity in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database, a respective alias of which refers to a respective one of the at last two of the identical entities that are identified.

88. A computer program product according to claim 87 wherein the new biological/chemical database is an updated version of one of the plurality of biological/chemical databases, the computer program product further comprising:

computer-readable program code that is configured to identify at least one entity in the one of the plurality of biological/chemical databases that has been deleted from the updated version of the one of the plurality of biological/chemical databases; and

computer-readable program code that is configured to remove an alias that is associated with the at least one entity that has been removed.

89. A computer program product according to claim 88 further comprising:

computer-readable program code that is configured to split at least one entity in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database based upon the alias that was removed.

90. A computer program product according to claim 84 further comprising:

computer-readable program code that is configured to identify entities in the new biological/chemical database that do not correspond to at least one of the entities in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database; and

computer-readable program code that is configured to add at least one new entity to the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database that corresponds to the entities in the new biological/chemical database that do not correspond to at least one of the entities in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

91. A computer program product according to claim 84 further comprising:

computer-readable program code that is configured to traverse the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database in response to a query to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

92. A computer program product according to claim 84 further comprising:

computer-readable program code that is configured to traverse the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database in response to a query and in response to at least one path rule to thereby obtain query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

93. A computer program product according to claim 91 further comprising:

computer-readable program code that is configured to store the query results that are based on the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database as at least one new relationship in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database to thereby store knowledge that was derived from the query in the entity-relationship model that integrates the plurality of biological/chemical databases and the new biological/chemical database.

94. A computer program products according to claim 84 further comprising:

computer-readable program code that is configured to maintain an image of the entity-relationship model of the plurality of biological/chemical databases before the at least two of the related entities are linked.

95. A computer program product according to claim 94 further comprising:

computer-readable program code that is configured to compare the image of the entity-relationship model of the plurality of biological/chemical databases before the at least two of the related entities are linked and the entity relationship mode that integrates the plurality of biological chemical databases and the new biological/chemical database.

96. A computer program product according to claim 84 wherein the entity-relationship model of the new biological/chemical database does not include relationships therein.

97. A computer program product that is configured to query a plurality of biological/chemical databases, each of which includes records for a plurality of biological/chemical entities, the computer program product comprising a computer usable storage medium having computer-readable program code embodied in the medium, the computer-readable program code comprising:

an integrated entity-relationship model of the plurality of biological/chemical databases that links at least some related entities in at least two of the biological/chemical databases; and

computer-readable program code that is configured to traverse the integrated entity-relationship model of the plurality of biological/chemical databases in response to a query to thereby obtain query results that are based on the integrated entity-relationship model of the plurality of biological/chemical databases.

98. A computer program product according to claim 97 wherein the computer-readable program code that is configured to traverse comprises:

computer-readable program code that is configured to traverse the integrated entity-relationship model of the plurality of biological/chemical databases from a starting entity to an ending entity in response to a query that specifies the starting entity and the ending entity to thereby identify relationships between the starting entity and the ending entity that are based on the integrated entity-relationship model of the plurality of biological/chemical databases.

99. A computer program product according to claim 97 wherein the computer-readable program code that is configured to traverse comprises:

computer-readable program code that is configured to traverse the integrated entity-relationship model of the plurality of biological/chemical databases from a starting entity to a plurality of ending entities in response to a query that specifies the starting entity to thereby identify relationships between the starting entity and the plurality of ending entities that are based on the integrated entity-relationship model of the plurality of biological/chemical databases.

100. A computer program product according to claim 97 wherein the computer-readable program code that is configured to traverse comprises:

computer-readable program code that is configured to traverse the integrated entity-relationship model of the plurality of biological/chemical databases in response to a query and in response to at least one path rule to thereby obtain query results that are based on the integrated entity-relationship model of the plurality of biological/chemical databases.

101. A computer program product according to claim 100 wherein the at least one path rule specifies a type of path to use in traversing through the plurality of entities, a type of path not to use in traversing through the plurality of entities, a type of ending entity that can be included in the query results, a type of ending entity that is not to be included in the query results, a type or class of relationship that is to be used in traversing through the plurality of entities, a type or class of relationship not to be used in traversing through the plurality of entities and/or a confidence level to be achieved in traversing through the plurality of entities.

102. A computer program products according to claim 100 further comprising computer-readable program code that is configured to store the query and the path rule for reuse.

103. A computer program product according to claim 97 further comprising:

computer-readable program code that is configured to store the query results that are based on the integrated entity-relationship model of the plurality of biological/chemical databases as at least one new relationship in the integrated entity-relationship model of the plurality of biological/chemical databases to thereby store knowledge that was derived from the query in the integrated entity-relationship model of the plurality of biological/chemical databases.

104. A computer program product according to claim 97 further comprising:

computer-readable program code that is configured to assign a confidence level to at least one of the relationships in the integrated entity-relationship model of the plurality of biological/chemical databases.

105. A computer program product according to claim 104 further comprising:

computer-readable program code that is configured to traverse the integrated entity-relationship model of the plurality of biological/chemical databases in response to a query to thereby obtain query results that are based on the integrated entity-relationship model of the plurality of biological/chemical databases including the at least one confidence level that is assigned.

106. A bioinformatics data processing system comprising:

an ontology network engine that is configured to build an integrated entity-relationship model of a plurality of independent biological/chemical databases, each of which includes records for a plurality of biological/chemical objects, the integrated entity-relationship model comprising;

a plurality of entities, a respective one of which corresponds to a single biological/chemical object, at least some of the entities including a plurality of links, a respective one of which directly or indirectly refers to at least one record in a respective one of the plurality of biological/chemical databases that relates to the single biological/chemical object; and

a plurality of relationships that link the plurality of entities in the entity-relationship model based upon relationships therebetween.

107. A system according to claim 106 further comprising:

a metadata database that is configured to store therein the integrated entity-relationship model of the plurality of independent biological/chemical databases.

108. A system according to claim 106 further comprising:

a loader that is configured to load an independent entity-relationship model of each of the independent biological/chemical databases into the ontology network engine.

109. A system according to claim 108 wherein the loader is configured to load an independent entity-relationship model of each of the independent biological/chemical databases into the ontology network engine in a typeless format.

110. A system according to claim 108 in combination with the plurality of independent biological/chemical databases.

111. A system according to claim 106 further comprising:

a query tool that is configured to traverse the integrated entity-relationship model in response to a query to thereby obtain query results that are based on the integrated entity-relationship model.

112. A system according to claim 111 wherein the query tool is a Web-based query tool.

113. A system according to claim 106 further comprising:

a virtual experiment tool that is configured to conduct virtual experiments on the integrated entity-relationship model.

114. A system according to claim 106 further comprising:

a discovery tool that is configured to discover biological/chemical knowledge from the integrated entity-relationship model.

115. A system according to claim 106 wherein the ontology network engine runs on a plurality of data processing systems that are configured in a peer-to-peer configuration.

117. A data structure according to claim 116 further comprising:

an independent entity-relationship model of each of the independent biological/chemical databases.

116. A bioinformatics data structure comprising:

an integrated entity-relationship model of a plurality of independent biological/chemical databases, each of which includes records for a plurality of biological/chemical objects, the integrated entity-relationship model comprising;

a plurality of entities, a respective entity of which corresponds to a single biological/chemical object, at least some of the entities including a plurality of links, a respective one of which directly or indirectly refers to at least one record in a respective one of the plurality of biological/chemical databases that relates to the single biological/chemical object; and

a plurality of relationships that link the plurality of entities in the entity-relationship model based upon relationships therebetween.