System, method, and user interfaces for managing genomic data

• US 6,804,679 B2
• Filed: 03/08/2002
• Issued: 10/12/2004
• 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.
• Primary Examiner(s): Coby, Frantz
• Application Number:
  US09/683,982
• Publication Number:
  US 20020128993A1
• Time in Patent Office: 949 Days
• Field of Search: 700/90, 250/458.1, 250/559.06, 356/318, 435/6, 705/14, 705/500, 707/4, 707/10, 707/1, 707/102, 707/3, 707/2, 600/407, 600/316
• US Class Current: 1/1
• 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 to identify at least one set of probe array results for publishing; and

a publisher to publish the at least one set of probe array results and the at least one set of spotted probe array results as a first set of data in a publish database, said publish database is in a format or organized in accordance with a schema to facilitate access by data analysis applications, data mining applications, data reporting applications, other data processing applications or any combination thereof;

wherein the at least one set of probe array results is in a first format and the publisher is constructed and arranged to publish the first set of data in a second format.

2. The data manager of claim 1, wherein:

the results-for-publication identifier identifies the at least one set of 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 publisher stores 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.

7. The data manager of claim 1, wherein:

the publisher stores the publish database in a memory unit of a computer as one or more related files.

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

an experimental results registration processor to register for publishing the at least one set of probe array results.

9. The data manager of claim 8, wherein:

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

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

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

publishing the at least one set of probe array results as a first set of data in a publish database, said publish database is in a format or organized in accordance with a schema to facilitate access by data analysis applications, data mining applications, data reporting applications, other data processing applications or any combination thereof;

wherein the at least one set of probe array results is in a first format and the publishing step includes publishing the first set of data in a second format.

11. The method of claim 10, wherein:

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

12. The method of claim 10, wherein:

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

13. The method of claim 10, wherein:

the publish database is a relational database.

14. The method of claim 10, 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.

15. The method of claim 10, wherein:

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

16. The method of claim 10, further comprising the step of:

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

17. The method of claim 16, wherein:

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

18. 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 probe array results;

receiving a user, said publish database is in a format or organized in accordance with a schema to facilitate access by data analysis applications, data mining applications, data reporting applications, other data processing applications or any combination thereof;

wherein the at least one set of probe array results is in a first format and the publisher is constructed and arranged to publish the first set of data in a second format selection of one or more of the first or second sets set of graphical elements for publication in a publish database;

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

19. The method of claim 18, wherein:

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

20. The method of claim 19, wherein:

the first set of graphical elements is arranged in a branch of the first tree structure.

21. The method of claim 18, wherein:

the first set of graphical elements corresponds to a probe array result file.

22. The method of claim 18, wherein:

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

23. The method of claim 18, further comprising:

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

24. The method of claim 23, wherein:

the step of receiving a user activation includes the steps of

receiving a user selection of one or more of the third set of graphical elements, and

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

25. 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 probe array results;

a second frame including a second set of graphical elements corresponding to a publish database and, in relation thereto, a third set of one or more graphical elements corresponding to those of the first set of graphical elements selected by a user, said publish database is in a format or organized in accordance with a schema to facilitate access by data analysis applications, data mining applications, data reporting applications, other data processing applications or any combination thereof;

wherein the at least one set of probe array results is in a first format and the publisher is constructed and arranged to publish the first set of data in a second format.

26. The GUI of claim 25, wherein:

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

27. The GUI of claim 26, wherein:

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

28. The GUI of claim 25, wherein:

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

29. The GUI of claim 25, wherein:

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

30. 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 probe array results for publishing; and

publishing the at least one set of probe array results as a first set of data in a publish database, said publish database is in a format or organized in accordance with a schema to facilitate access by data analysis applications, data mining applications, data reporting applications, other data processing applications or any combination thereof;

wherein the at least one set of probe array results is in a first format and the publisher is constructed and arranged to publish the first set of data in a second format.

31. 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 probe array for publishing, and publishing the at least one set of probe array results as a first set of data in a publish database, said publish database is in a format or organized in accordance with a schema to facilitate access by data analysis applications, data mining applications, data reporting applications, other data processing applications or any combination thereof;

wherein the at least one set of probe array results is in a first format and the publisher is constructed and arranged to publish the first set of data in a second format.