Method and system for providing a probe array chip design database

• US 6,826,296 B2
• Filed: 12/14/2000
• Issued: 11/30/2004
• Est. Priority Date: 07/25/1997
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Balaban, David J., Dai, Josie, Mittmann, Michael P., Cheung, Gloria, Hubbell, Earl
• Primary Examiner(s): Mehta, Bhavesh M.
• Assistant Examiner(s): Choobin, Barry
• Application Number:
  US09/737,838
• Publication Number:
  US 20010018642A1
• Time in Patent Office: 1,447 Days
• Field of Search: 382/129, 382/133, 435/6, 707/3, 707/104.1
• US Class Current: 382/129
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• 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
• CPC Class Codes: H04M 1/006 Call diverting means
• CPC Class Codes: H04M 1/724 User interfaces specially adapted for cordless or mobile telephones
• CPC Class Codes: H04M 2207/206 composed of PSTN and wireless network
• CPC Class Codes: H04M 3/46 Arrangements for calling a number of substations in a predetermined sequence until an answer is obtained
• CPC Class Codes: H04M 3/54 Arrangements for diverting calls for one subscriber to another predetermined subscriber based on the calling party profile H04M3/42059; based on location H04M3/42348; based on presence H04M3/42365; to voice mail H04M3/53308
• CPC Class Codes: Y10S 128/922 including image analysis
• CPC Class Codes: Y10S 707/925 Drafting an application
• CPC Class Codes: Y10S 707/955 Object-oriented
• 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 707/99945 Object-oriented database structure processing

Abstract

Systems and method for organizing information relating to the design of polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information interrelating probes on a chip, genomic items investigated by the chip, and sequence information relating to the design of the chip. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of chips having complex designs.

Claims

1. A computer-readable storage medium having stored thereon:

a relational database comprising;

a probe table including a plurality of probe records, each of said probe records specifying a polymer probe for use in one or more polymer probe arrays;

a sequence item table including a plurality of sequence item record, each of said sequence item records specifying a nucleotide sequence to be investigated in said one or more polymer probe arrays; and

a tiling item for representing a grouping of the probe records.

2. The medium of claim 1 wherein said relational database further comprises:

a tiling item table including a plurality of tiling item records, each of said tiling item records having an aggregation relationship with said probe records so that each tiling item record has many associated probe records.

3. The medium of claim 1 wherein said relational database further comprises:

a genomic item table including a plurality of genomic item records, each of said genomic item records specifying a genomic item to be investigated by said one or more polymer probe arrays; and

wherein there is a many to many relationship between genomic item records and sequence item records.

4. The medium of claim 1 wherein said relational database further comprises:

a chip design table including a plurality of chip design records, each of said chip design records specifying a design of a chip including a subset of said plurality of probe records.

5. A computer implemented method for operating a relational database comprising:

creating a probe table including a plurality of probe records, each of said probe records specifying a polymer probe for use in one or more polymer probe arrays;

creating a sequence item table including a plurality of sequence item records, each of said sequence item records specifying a nucleotide sequence to be investigated in said one or more polymer probe arrays;

storing data in said probe table and said sequence item table; and

creating a tiling item representing a grouping of the probe records.

6. The method of claim 5 further comprising the step of:

creating a tiling item table including a plurality of tiling item records, each of said tiling item records having an aggregation relationship with said probe records so that each tiling item record has many associated probe records.

7. The method of claim 5 further comprising the step of:

creating a genomic item table including a plurality of genomic item records, each of said genomic item records specifying a genomic item to be investigated by said one or more polymer probe arrays; and

wherein there is a many to many relationship between genomic item records and sequence item records.

8. The method of claim 5 further comprising the step of:

creating a chip design table including a plurality of chip design records, each of said chip design records specifying a design of a chip including a subset of said plurality of probe records.

9. A computer system comprising

a processor;

and

a storage medium storing a relational database accessible by said processor, said storage medium having stored thereon;

a relational database comprising;

a probe table including a plurality of probe records, each of said probe records specifying a polymer probe for use in one or more polymer probe arrays;

a sequence item table including a plurality of sequence item records, each of said sequence item records specifying a nucleotide sequence to be investigated in said one or more polymer probe arrays; and

a tiling item for representing a grouping of the probe records.