System and method for managing gene expression data

• US 20030100999A1
• Filed: 05/23/2001
• Published: 05/29/2003
• Est. Priority Date: 05/23/2000
• Status: Abandoned Application

• Current Assignee: Gene Logic, Inc. (Steel Partners Holdings LP)
• Original Assignee: Gene Logic, Inc. (Steel Partners Holdings LP)
• Inventors: Markowitz, Victor M.
• Application Number:
  US09/862,424
• Publication Number:
  US 20030100999A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/30 Microarray design
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• 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

Abstract

The present invention pertains to a system and method for providing a common interface for multiple databases containing gene expression data, gene annotation data, and sample information in a relational format supporting efficient exploration and analysis.

Claims

1. A method of integrating multiple gene databases containing gene expression data, gene annotation data, and sample data, the method comprising:

defining new classes and associations for the gene expression data, gene annotation data, and sample data contained in at least one of the multiple gene databases;

grouping gene fragments into at least two groups; and

annotating gene fragments,

so as to permit a database analytical engine to analyze the gene expression data, gene annotation data contained in the multiple gene databases.

2. The method of integrating multiple gene databases containing gene expression data, gene annotation data, and sample data according to claim 1, wherein the at least two groups are known and not known.

3. The method of integrating multiple gene databases containing gene expression data, gene annotation data, and sample data according to claim 1, wherein the annotating if gene fragments comprises automatic annotation of predefined fields.

4. The method of integrating multiple gene databases containing gene expression data, gene annotation data, and sample data according to claim 1, wherein the annotating if gene fragments comprises manual annotation of individual gene fragments.

5. The method of integrating multiple gene databases containing gene expression data, gene annotation data, and sample data according to claim 2, wherein the grouping of gene fragments into at least two groups comprises name-based matching.

6. The method of integrating multiple gene databases containing gene expression data, gene annotation data, and sample data according to claim 2, wherein the grouping of gene fragments into at least two groups comprises sequence-based matching.

7. The method of integrating multiple gene databases containing gene expression data, gene annotation data, and sample data according to claim 2, wherein the grouping of gene fragments into at least two groups comprises manual data curation.

8. A computer program product comprising a computer-usable medium having computer-readable program code embodied thereon relating to multiple gene databases containing gene expression data, gene annotation data, and sample data, the computer program product comprising computer-readable program code for effecting the following steps within a computing system:

defining new classes and associations for the gene expression data, gene annotation data, and sample data contained in at least one of the multiple gene databases;

grouping gene fragments into at least two groups; and

annotating gene fragments,

so as to permit a database analytical engine to analyze the gene expression data, gene annotation data contained in the multiple gene databases.

9. The computer program product comprising a computer-usable medium having computer-readable program code embodied thereon relating to multiple gene databases containing gene expression data, gene annotation data, and sample data according to claim 8, wherein the at least two groups are known and not known.

10. The computer program product comprising a computer-usable medium having computer-readable program code embodied thereon relating to multiple gene databases containing gene expression data, gene annotation data, and sample data according to claim 8, wherein the annotating if gene fragments comprises automatic annotation of predefined fields.

11. The computer program product comprising a computer-usable medium having computer-readable program code embodied thereon relating to multiple gene databases containing gene expression data, gene annotation data, and sample data according to claim 8, wherein the annotating if gene fragments comprises manual annotation of individual gene fragments.

12. The computer program product comprising a computer-usable medium having computer-readable program code embodied thereon relating to multiple gene databases containing gene expression data, gene annotation data, and sample data according to claim 9, wherein the grouping of gene fragments into at least two groups comprises name-based matching.

13. The computer program product comprising a computer-usable medium having computer-readable program code embodied thereon relating to multiple gene databases containing gene expression data, gene annotation data, and sample data according to claim 9, wherein the grouping of gene fragments into at least two groups comprises sequence-based matching.

14. The computer program product comprising a computer-usable medium having computer-readable program code embodied thereon relating to multiple gene databases containing gene expression data, gene annotation data, and sample data according to claim 9, wherein the grouping of gene fragments into at least two groups comprises manual data curation.