Claims
- 1. A software platform for integrating, managing and analyzing gene expression data and associated information, the software platform comprising:
a gene expression module comprising a data warehouse comprising a gene expression database for storing quantitative gene expression measurements for tissues and cell lines; a sample database for storing information on bio-samples and donors associated with the tissues and cell lines; and process database for storing information about experiments performed on the tissue and cell lines; a gene index for storing information obtained from external sources about genes of interest, and an analysis engine for analyzing gene expression data in the data warehouse; a connection module in communication with the gene expression module and comprising a plurality of staging databases for customer-supplied gene expression data, sample data and process data and a migration manager for controlling migration of customer-supplied data into the data warehouse; and a user interface for entering and receiving a response to a query for analysis of data within the data warehouse and for uploading customer-supplied gene expression data, sample data and process data into the connection module for migration into the data warehouse.
- 2. The software platform of claim 1, the gene expression module further comprising a data manager for maintaining a partition between migrated customer-supplied data and data pre-existing within the data warehouse.
- 3. The software platform of claim 2, wherein the data manager updates the pre-existing data in data warehouse without modification of the customer-supplied data.
- 4. The software platform of claim 2, wherein the data manager further combines migrated customer-supplied data and pre-existing data for analysis by the analysis engine.
- 5. The software platform of claim 1, wherein the connection module permits registering of more than one source of customer-supplied gene expression and sample information and extraction of a list of experiments from the more than one source of gene expression and sample information.
- 6. The software platform of claim 5, wherein the connection module provides for refreshing of the list of experiments from the more than one source of gene expression and sample information.
- 7. The software platform of claim 5, wherein the connection module permits checking for consistency the more than one source of gene expression and sample information.
- 8. The software platform of claim 1, wherein the connection module includes a XML parser for entering customer sample data into a XML template.
- 9. The software platform of claim 8, wherein the connection module provides a download back-up for preserving customer-entered sample data.
- 10. The software platform of claim 1, wherein the connection module includes a sample data editor for manually entering new customer sample data
- 11. The software platform of claim 1, wherein the connection module includes a sample data editor for editing or updating customer sample data that was previously entered.
- 12. The software platform of claim 1, wherein the connection module includes a migration tool for linking customer-supplied experiment data to customer-supplied sample data.
- 13. The software platform of claim 1, wherein the connection module includes a migration tool for validating customer-supplied gene expression data prior to migration into the data warehouse.
- 14. The software platform of claim 1, further comprising a GenCarta module for accessing a transcriptome database for providing information about genes represented by the gene expression data, sample data and process data.
- 15. A software platform for integrating, managing and analyzing gene expression data and associated information, the software platform comprising:
a gene expression module comprising:
a data warehouse comprising a gene expression database for storing quantitative gene expression measurements for tissues and cell lines; a sample database for storing information on bio-samples and donors associated with the tissues and cell lines; and process database for storing information about experiments performed on the tissue and cell lines; a gene index for storing information obtained from external sources about genes of interest, and an analysis engine for analyzing gene expression data in the data warehouse; a connection module in communication with the gene expression module, the connection module comprising:
a plurality of staging databases for customer-supplied gene expression data, sample data and process data; and a migration manager for controlling migration of customer-supplied data into the data warehouse; a XML template for entry of sample data; and a sample data tool for uploading customer-supplied sample data, wherein the migration manager links customer-supplied experiment data to customer-supplied sample data; a user interface for entering and receiving a response to a query for analysis of data within the data warehouse and for uploading customer-supplied gene expression data, sample data and process data into the connection module for migration into the data warehouse.
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority to U.S. provisional application Serial No. 60/299,741, filed on Jun. 22, 2001 and is a continuation-in-part of each of application Ser. No. 09/862,424, filed May 23, 2001, which claims priority to U.S. provisional application Ser. No. 60/206,571, filed May 23, 2000, Ser. No. 10/090,144, filed Mar. 5, 2002, which claims priority to application Ser. No. 09/797,803, filed Mar. 5, 2001, and Ser. No. 10/096,645, filed Mar. 14, 2002, which claims priority to U.S. provisional application Ser. No. 60/275,465, filed Mar. 14, 2001. Each of the related applications is incorporated herein by reference in its entirety for all purposes.
PCT Information
Filing Document |
Filing Date |
Country |
Kind |
PCT/US02/19877 |
6/24/2002 |
WO |
|
Provisional Applications (1)
|
Number |
Date |
Country |
|
60299741 |
Jun 2001 |
US |