Method, system, and computer software for providing a genomic web portal

• US 20050004768A1
• Filed: 07/30/2004
• Published: 01/06/2005
• Est. Priority Date: 01/25/2000
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Norviel, Vernon A., Craford, David M.
• Application Number:
  US10/903,641
• Publication Number:
  US 20050004768A1
• Time in Patent Office: Days
• US Class Current: 702/20
• 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 50/00 ICT programming tools or database systems specially adapted for bioinformatics

Abstract

Systems, methods, and computer program products are described that process inquiries or orders regarding purchase of biological devices, substances, or related reagents. In some implementations, a user selects probe-set identifiers that identify microarray probe sets capable of enabling detection of biological molecules. Corresponding genes or EST'"'"'s are identified and are correlated with related product data, which is provided to the user. Further, the user may select products for purchase based on the product data. If so, the user'"'"'s account may be adjusted based on the purchase order. In the same or other implementations, a local genomic database is periodically updated. In response to a user selection of probe-set identifiers, data related to corresponding genes or EST'"'"'s is provided to the user from the local genomic database.

Claims

1. A system for providing data related to one or more genes or EST'"'"'s, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of a biological molecule, comprising:

an input manager constructed and arranged to receive from a user a selection of a first set of one or more of the probe-set identifiers;

a gene determiner constructed and arranged to identify a first set of one or more genes or EST'"'"'s corresponding to the probe sets identified by the first set of probe-set identifiers;

a correlator constructed and arranged to correlate the first set of genes or EST'"'"'s with a first set of one or more data; and

an output manager constructed and arranged to provide the first set of data to the user.

2. The system of claim 1, wherein:

the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.

3. The system of claim 1, wherein:

the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.

4. The system of claim 1, wherein:

the first set of probe-set identifiers comprises all or part of a second set of one or more probe-set identifiers of probe sets that have enabled detection of the expression or differential expression of their corresponding genes or EST'"'"'s.

5. The system of claim 4, wherein:

the probe sets identified by the second set of probe-set identifiers are disposed on one or more probe arrays.

6. The system of claim 5, wherein:

the probe sets identified by the second set of probe-set identifiers include in situ synthesized oligonucleotides.

7. The system of claim 6, wherein:

the probe arrays include a GeneChip®

probe array.

8. The system of claim 5, wherein:

at least one of the probe sets identified by the second set of probe-set identifiers consists of a single spot on a spotted probe array.

9. The system of claim 5, wherein:

the probe arrays include a spotted array.

10. The system of claim 9, wherein:

at least one spot of the spotted array comprises an oligonucleotide.

11. The system of claim 1, wherein:

the user includes a remote user, and

the input manager receives the remote user'"'"'s selection over a network.

12. The system of claim 11, wherein:

the network includes the Internet.

13. The system of claim 1, wherein:

at least a first probe-set identifier of the first set of probe-set identifiers comprises a gene identifier of the gene corresponding to the first probe-set identifier.

14. The system of claim 13, wherein:

the gene identifier comprises an accession number.

15. The system of claim 1, wherein:

the user selects the first set of probe-set identifiers based, at least in part, on an indication of a degree of expression or differential expression of the genes or EST'"'"'s corresponding to the probe sets identified by the first set of probe-set identifiers.

16. The system of claim 1, wherein:

the first set of one or more data includes one or any combination of product data related to availability, pricing, composition, suitability, or ordering.

17. The system of claim 16, wherein:

the first set of one or more data includes product data regarding a biological device or substance, or a reagent that may be used with a biological device or substance.

18. The system of claim 17, wherein:

the device, substance, or reagent includes one or any combination of an oligonucleotide, probe array, clone, antibody, or protein.

19. The system of claim 1, wherein:

the first set of one or more data includes data stored, at least in part, in a local products database.

20. The system of claim 19, wherein:

the first set of one or more data includes at least one link to remote data representing a vendor of biological products.

21. The system of claim 20, wherein:

the link includes an Internet URL.

22. The system of claim 20, wherein:

the remote data include an HTML or XML document.

23. The system of claim 1, wherein:

the user includes a remote user, and

the output manager provides the first set of product data to the user over a network.

24. The system of claim 23, wherein:

the network includes the Internet.

25. A method for providing data related to one or more genes or EST'"'"'s, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of a biological molecule, comprising the steps of:

receiving from a user a selection of a first set of one or more of the probe-set identifiers;

identifying a first set of one or more genes or EST'"'"'s corresponding to the probe sets identified by the first set of probe-set identifiers;

correlating the first set of genes or EST'"'"'s with a first set of one or more data; and

providing the first set of data to the user.

26. The method of claim 25, wherein:

the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.

27. The method of claim 25, wherein:

the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.

28. A computer program product for providing data related to one or more genes or EST'"'"'s, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of a biological molecule, wherein the computer program product, when executed on a computer system, performs a method comprising the steps of:

receiving from a user a selection of a first set of one or more of the probe-set identifiers;

identifying a first set of one or more genes or EST'"'"'s corresponding to the probe sets identified by the first set of probe-set identifiers;

correlating the first set of genes or EST'"'"'s with a first set of one or more data; and

providing the first set of data to the user.

29. The computer program product of claim 28, wherein:

the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.

30. The computer program product of claim 28, wherein:

the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.

31-102. -102. Cancelled