System, method and computer program product for managing genomic data

• US 20050108197A1
• Filed: 10/12/2004
• Published: 05/19/2005
• Est. Priority Date: 03/12/2001
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Bernhart, Derek, Sheppy, Conrad G., Jevons, Luis
• Application Number:
  US10/962,973
• Publication Number:
  US 20050108197A1
• Time in Patent Office: Days
• 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

1-33. -33. (canceled)

34. A data manager for publishing probe array results to a selected database, comprising:

a database generator that receives a selection of a database for publishing probe array results, wherein the selection includes an existing or a new database;

a results-for-publication identifier to identify at least one set of probe array results for publishing in the selected database; and

a publisher to publish the at least one set of probe array results as a first set of data in the selected database, wherein the at least one set of probe array results is in a first format and the first set of data is in a second format.

35. The data manager of claim 34, wherein:

the selection includes a user selection.

36. The data manager of claim 34, wherein:

the selected database is represented by information stored in a data structure.

37. The data manager of claim 34, wherein:

the second format includes a database schema.

38. The data manager of claim 37, wherein:

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

39. The data manager of claim 34, wherein:

the selected database is a relational database.

40. The data manager of claim 34, wherein:

the selected 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.

41. A method for publishing probe array results to a selected database, comprising:

receiving a selection of a database for publishing probe array results, wherein the selection includes an existing or a new database;

identifying at least one set of probe array results for publishing in the selected database; and

publishing the at least one set of probe array results as a first set of data in the selected database, wherein the at least one set of probe array results is in a first format and the first set of data is in a second format.

42. The method of claim 41, wherein:

the selection includes a user selection.

43. The method of claim 41, wherein:

the selected database is represented by information stored in a data structure.

44. The method of claim 41, wherein:

the second format includes an integrated database schema.

45. The method of claim 44, wherein:

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

46. The method of claim 41, wherein:

the selected database is a relational database.

47. 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:

receiving a selection of a database for publishing probe array results, wherein the selection includes an existing or a new database;

identifying at least one set of probe array results for publishing in the selected database; and

publishing the at least one set of probe array results as a first set of data in the selected database, wherein the at least one set of probe array results is in a first format and the first set of data is in a second format.

48. The computer program product of claim 47, wherein:

the selection includes a user selection.

49. The computer program product of claim 47, wherein:

the selected database is represented by information stored in a data structure.

50. The computer program product of claim 47, wherein:

the second format includes an integrated database schema.

51. The computer program product of claim 50, wherein:

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

52. The computer program product of claim 47, wherein:

the selected database is a relational database