Autonomous intelligent agents for the annotation of genomic databases

• US 5,966,711 A
• Filed: 04/15/1997
• Issued: 10/12/1999
• Est. Priority Date: 04/15/1997
• Status: Expired due to Fees

• Current Assignee: Hanger Solutions, LLC (IP Investments Group LLC)
• Original Assignee: Alpha Gene, Inc.
• Inventors: Adams, R. Mark
• Primary Examiner(s): Choules, Jack M.
• Application Number:
  US08/837,963
• Time in Patent Office: 910 Days
• Field of Search: 707/104, 707/10, 707/6, 707/200
• US Class Current: 1/1
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing
• CPC Class Codes: Y10S 707/99948 Application of database or data structure, e.g. distributed, multimedia, or image

Abstract

A genomic database system that makes use of autonomous agents for providing access to the database. The autonomous agents, which are preferably implemented in a multitasking environment, each seek target data to be processed and then call a program to process the target data. The results of the program are then placed in the database. The autonomous agent model permits the sequence data and processing programs to be changed without the need to be concerned with data synchronization or heterogeneity. The agents may be implemented as object oriented programs that permit the extraction of generic software code in an agent code base. The agents may implement annotation functions, analysis algorithms, or may control the assembly of gene sequences.

Claims

1. A genetic database system comprising:

a database of gene sequence entries, the gene sequence entries containing gene sequence data;

a plurality of programs for processing the gene sequence data;

a database of results entries containing results records generated by the application of the programs to the gene sequence entries;

a plurality of autonomous agent programs, each agent program comprising;

(A) a sensor process that seeks target gene sequence data to be processed by at least one of the programs;

(B) an intelligence process that invokes the at least one program to process the target gene sequence data; and

(C) an effector process for revising the results records in response to the intelligence process.

2. A database system as in claim 1 wherein each autonomous agent records annotations in the results records in accordance with output produced by at least one program.

3. A database system as in claim 1 wherein each autonomous agent includes a sensor process that determines the availability of system resources.

4. A database system as in claim 1 wherein the sensor process additionally invokes the intelligence process.

5. A database system as in claim 1 wherein the effector process calls a sensor process for processing other target gene sequence data.

6. A database system as in claim 1 wherein the agents run as self-invoking processes in a multitasking data processing environment.

7. A database system as in claim 1 wherein the agents include an effector process which revises the results entries with a gene sequence annotation record.

8. A database system as in claim 1 wherein the results records include a flag record indicating that a particular version of the program has processed at least one of the gene sequence entries.

9. A database system as in claim 1 wherein the results record contains output produced by at least one program.

10. A database system as in claim 1 wherein the agents are implemented as object oriented programs.

11. A database system as in claim 1 wherein the sensor process selects a candidate gene sequence entry for processing by the agent.

12. A database system as in claim 1 wherein the results records comprise a sequence identification record that uniquely identifies the program which created the results entry.

13. A database system as in claim 1 wherein a least one of the agents is an expression database agent having an intelligence process that obtains gene expression data from an expression database external to the database of gene sequence records.

14. A database system as in claim 1 wherein at least one of the agents is a laboratory expression agent having an intelligence process that obtains gene expression data from a laboratory analyzer.

15. A database system as in claim 1 wherein the intelligence process compares gene sequence records.

16. A database system as in claim 1 wherein at least one of the agents is a sequence assembly agent.

17. A database system as in claim 16 wherein a group of the sequence entries comprise an expressed tag sequence database of partial gene sequences, and the sequence assembly agent is a set of agents comprising a chosen-for-finishing agent having an intelligence process which identifies expressed sequence tags that are in need of assembly.

18. A database system as in claim 17 wherein a group of the sequence entries comprise a finish database.

19. A database system as in claim 18 wherein the chosen-for-finishing agent includes an effector process that adds a results entry to indicate the sequence entry in the finish database is in need of sequence assembly.

20. A database system as in claim 18 wherein the sequence finishing agent includes a sequence walk agent which adds a results entry to indicate instructions for finishing assembly of a sequence entry in the finish database.

21. A database system as in claim 18 wherein a group of sequence entries comprise a full length sequence database and the sequence finishing agent includes a sequence assembly agent that creates a sequence entry in the full length sequence database from data in the finish database.

22. A method of storing data in a genetic database system comprising the steps of:

storing a database of gene sequence entries, the gene sequence entries containing gene sequence data;

storing a plurality of programs using the gene sequence data as input;

storing a database of results entries containing results data records generated by the running the programs with the gene sequence entries as input; and

executing a plurality of autonomous agent programs, each autonomous agent program comprising the steps of;

(A) invoking a sensor process that seeks target gene sequence data to be processed by at least one of the stored programs;

(B) invoking an intelligence process that applies at least one program to process the target data; and

(C) invoking an effector process for revising the results entries in response to invoking the intelligence process.

23. A method as in claim 22 wherein the step of invoking an effector process comprises a step of creating annotation entries in accordance with output produced by at least one program.

24. A database system as in claim 22 wherein the step of invoking a sensor process comprises a step of determining the availability of system resources.

25. A database system as in claim 22 wherein the step of invoking a sensor process comprises a step of autonomously invoking the intelligence process.

26. A database system as in claim 22 wherein the step of invoking an effector process comprises a step of autonomously invoking a sensor process for processing other target gene sequence data.

27. A method as in claim 22 wherein the step of executing the plurality of autonomous agent programs comprises a set of steps of executing self-invoking processes in a multitasking data processing environment.

28. A method as in claim 22 wherein the step of executing the plurality of autonomous agent programs comprises the step of invoking an effector process which revises the results records with annotation data.

29. A method as in claim 28 wherein the step of invoking an effector process comprises revising the results records with a flag record indicating that a particular version of the program has annotated at least one of the gene sequence entries.

30. A method as in claim 28 wherein the step of invoking an effector process comprises revising the results records with output data produced by the program.

31. A method as in claim 22 wherein the step of executing agent programs comprises executing agent programs that are implemented as object oriented programs.

32. A method as in claim 22 wherein the step of invoking a sensor process additionally includes the step of selecting a candidate gene sequence entry for processing by the autonomous agent program.

33. A method as in claim 22 wherein the step of invoking an effector process comprises the step of revising the results records to contain a sequence identification record that uniquely identifies the program which created the results entry.

34. A method as in claim 22 wherein a least one of the autonomous agents is an expression database agent and the step of invoking an intelligence process comprises the step of obtaining gene expression data from an expression database external to the database of gene sequence records.

35. A database system as in claim 22 wherein at least one of the agents is a laboratory expression agent and the step of invoking an intelligence process comprises obtaining gene expression data from by a laboratory analyzer.

36. A method as in claim 22 wherein the step of invoking an intelligence process comprises the step of comparing gene sequence records.

37. A method as in claim 22 wherein the step of executing a plurality of autonomous agent programs executes a sequence assembly agent program.

38. A method as in claim 37 wherein a group of the sequence entries comprise an expressed tag sequence database of partial gene sequences, and the step of executing a sequence assembly agent includes a step of executing a chosen-for-finishing agent which invokes an intelligence process which identifies expressed sequence tags that are in need of assembly.

39. A method as in claim 38 wherein the step of storing a database of gene sequence entries comprises a step of storing gene sequence entries comprising a finish database.

40. A method as in claim 39 wherein the step of executing a chosen-for-finishing agent additionally comprises the step of invoking an effector process that adds an annotation entry to the result record to indicate the sequence entry in the finish database is in need of sequence assembly.

41. A method as in claim 39 wherein the step of executing a sequence assembly agent additionally comprises the step of invoking a sequence walk agent adds a results entry to indicate instructions for finishing assembly of a sequence entry in the finish database.

42. A database system as in claim 39 wherein a group of sequence entries comprise a full length sequence database and the step of executing a sequence assembly agent comprises creating a sequence entry in the full length sequence database from data in the finish database.