System, method, and user interfaces for managing genomic data

• US 20020128993A1
• Filed: 03/08/2002
• Published: 09/12/2002
• Est. Priority Date: 03/12/2001
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Jevons, Luis, Bernhart, Derek, Sheppy, Conrad G.
• Granted Patent: US 6,804,679 B2
• Time in Patent Office: Days
• US Class Current: 707/1
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/20 Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
• CPC Class Codes: G16B 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/20 Heterogeneous data integration
• CPC Class Codes: Y10S 707/99931 Database or file accessing
• CPC Class Codes: Y10S 707/99932 Access augmentation or optimizing
• CPC Class Codes: Y10S 707/99933 Query processing, i.e. searching
• CPC Class Codes: Y10S 707/99934 Query formulation, input preparation, or translation
• CPC Class Codes: Y10S 707/99943 Generating database or data structure, e.g. via user interface

Abstract

A data manager is described for providing a publish database for access by data mining tools and other data processing software applications. The data manager includes a results-for-publication identifier that identifies synthesized probe array results and spotted probe array results for publishing. This identification may be based, at least in part, on user selections. The data in the publish database is organized in accordance with an integrated database schema. The data manager may also include an experimental results registration processor that registers the synthesized probe array results and the spotted probe array results for publishing. This registration may be based, at least in part, on user selections. For example, a user may select certain probe array results from a graphical user interface displaying a tree of files containing probe array results from multiple experiments with synthesized and/or spotted probe arrays.

Claims

1. A data manager for providing a publish database, comprising:

a results-for-publication identifier constructed and arranged to identify at least one set of synthesized probe array results and at least one set of spotted probe array results for publishing; and

a publisher constructed and arranged to publish the at least one set of synthesized probe array results and the at least one set of spotted probe array results as a first set of data in a publish database.

2. The data manager of claim 1, wherein:

the results-for-publication identifier identifies the at least one set of synthesized probe array results and the at least one set of spotted probe array results based, at least in part, on one or more user selections.

3. The data manager of claim 1, wherein:

the first set of data is organized in accordance with an integrated database schema.

4. The data manager of claim 3, wherein:

the integrated database schema includes all or part of an AADM schema.

5. The data manager of claim 1, wherein:

the publish database is a relational database.

6. The data manager of claim 1, wherein:

the at least one set of synthesized probe array results is in a first format, the at least one set of spotted probe array results is in a second format; and

the publisher is constructed and arranged to publish the first set of data in a third format.

7. The data manager of claim 1, wherein:

the publisher is constructed and arranged to store the publish database in a memory unit of a computer; and

each of the first set of data in the publish database is addressable from a common reference address of the memory unit.

8. The data manager of claim 1, wherein:

the publisher is constructed and arranged to store the publish database in a memory unit of a computer as one or more related files.

9. The data manager of claim 1, further comprising:

an experimental results registration processor constructed and arranged to register for publishing the at least one set of synthesized probe array results and the at least one set of spotted probe array results.

10. The data manager of claim 9, wherein:

the experimental results registration processor registers for publishing the at least one set of synthesized probe array results and the at least one set of spotted probe array results based, at least in part, on one or more user selections.

11. A method for providing a publish database, comprising the steps of:

identifying at least one set of synthesized probe array results and at least one set of spotted probe array results for publishing; and

publishing the at least one set of synthesized probe array results and the at least one set of spotted probe array results as a first set of data in a publish database.

12. The method of claim 11, wherein:

the identifying step includes identifying the at least one set of synthesized probe array results and the at least one set of spotted probe array results based, at least in part, on one or more user selections.

13. The method of claim 11, wherein:

the first set of data is organized in accordance with an integrated database schema.

14. The method of claim 11, wherein:

the publish database is a relational database.

15. The method of claim 11, wherein:

the at least one set of synthesized probe array results is in a first format, the at least one set of spotted probe array results is in a second format; and

the publishing step includes publishing the first set of data in a third format.

16. The method of claim 11, wherein:

the publishing step includes storing the publish database in a memory unit of a computer; and

each of the first set of data in the publish database is addressable from a common reference address of the memory unit.

17. The method of claim 11, wherein:

the publishing step includes storing the publish database in a memory unit of a computer as one or more related files.

18. The method of claim 11, further comprising the step of:

registering for publishing the at least one set of synthesized probe array results and the at least one set of spotted probe array results.

19. The method of claim 18, wherein:

the registering for publishing step includes publishing the at least one set of synthesized probe array results and the at least one set of spotted probe array results based, at least in part, on one or more user selections.

20. In a computer display system having a processor coupled to a display device such that data is displayed on the display device in a graphical user interface (GUI), a method for displaying the GUI and operating upon data displayed in or received from the GUI, comprising the steps of:

displaying a first frame in the GUI including a first set of graphical elements corresponding to at least one set of synthesized probe array results, and a second set of graphical elements corresponding to at least one set of spotted probe array results;

receiving a user selection of one or more of the first or second sets of graphical elements for publication in a publish database;

displaying a second frame in the GUI including a third set of graphical elements corresponding to the publish database and, in relation thereto, a fourth set of one or more graphical elements corresponding to those of the first or second sets of graphical elements selected by the user.

21. The method of claim 20, wherein:

the first frame includes a data file view wherein the first and second sets of graphical elements are arranged in a first tree structure.

22. The method of claim 21, wherein:

the first set of graphical elements is arranged in one branch of the first tree structure and the second set of graphical elements is arranged in another branch of the first tree structure.

23. The method of claim 20, wherein:

at least one of the first set of graphical elements corresponds to a synthesized probe array result file; and

at least one of the second set of graphical elements corresponds to a spotted probe array result file.

24. The method of claim 20, wherein:

the second frame includes an active database view wherein the third set of graphical elements is associated with a root of a tree structure and the one or more graphical elements corresponding to those of the first or second sets of graphical elements selected by the user are associated with branches attached to the root.

25. The method of claim 20, further comprising:

receiving a user activation of a publishing operation to be applied to one or more of the set of synthesized probe array results and/or one or more of the set of spotted probe array results.

26. The method of claim 25, wherein:

the step of receiving a user activation includes the steps of receiving a user selection of one or more of the fourth set of graphical elements, and

causing the probe array results corresponding to the user-selected ones of the fourth set of graphical elements to be published to the publish database.

28. The GUI of claim 27, wherein:

the first frame includes a data file view wherein the first and second sets of graphical elements are arranged in a first tree structure.

29. The GUI of claim 28, wherein:

the first set of graphical elements is arranged in one branch of the first tree structure and the second set of graphical elements is arranged in another branch of the first tree structure.

30. The GUI of claim 27, wherein:

at least one of the first set of graphical elements corresponds to a synthesized probe array result file; and

at least one of the second set of graphical elements corresponds to a spotted probe array result file.

31. The GUI of claim 27, wherein:

the second frame includes an active database view wherein the third set of graphical elements is associated with a root of a tree structure and the one or more graphical elements corresponding to those of the first or second sets of graphical elements selected by the user are associated with branches attached to the root.

27. A graphical user interface (GUI) for use with a computer display system having a processor coupled to a display device such that data is displayed on the display device in the GUI, comprising:

a first frame including a first set of graphical elements corresponding to at least one set of synthesized probe array results, and a second set of graphical elements corresponding to at least one set of spotted probe array results;

a second frame including a third set of graphical elements corresponding to the publish database and, in relation thereto, a fourth set of one or more graphical elements corresponding to those of the first or second sets of graphical elements selected by a user.

32. A computer program product for providing a publish database comprising a computer usable medium storing control logic that, when executed on a computer system, performs a method comprising the steps of:

identifying at least one set of synthesized probe array results and at least one set of spotted probe array results for publishing; and

publishing the at least one set of synthesized probe array results and the at least one set of spotted probe array results as a first set of data in a publish database.

33. A computer system, comprising:

a processor; and

a memory unit having stored therein a set of data management instructions that, when executed by the processor, performs a method for providing a publish database comprising the steps of identifying at least one set of synthesized probe array results and at least one set of spotted probe array results for publishing, and publishing the at least one set of synthesized probe array results and the at least one set of spotted probe array results as a first set of data in a publish database.