Method and apparatus for providing a bioinformatics database

• US 6,229,911 B1
• Filed: 07/24/1998
• Issued: 05/08/2001
• 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., Aggarwal, Arun
• Primary Examiner(s): Bella, Matthew C.
• Assistant Examiner(s): Mahmood, Choobin
• Application Number:
  US09/122,167
• Time in Patent Office: 1,019 Days
• Field of Search: 382/128, 382/129, 435/6, 422/68
• US Class Current: 382/128
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• 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 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

System and method for organizing information relating to polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information relating to sample preparation, chip layout, application of samples to chips, scanning of chips, expression analysis of chip results, etc. The model is readily translatable into database languages such as SQL. The database model scales to permit mass processing of probe array chips.

Claims

1. A computer-implemented method for managing information relating to processing of polymer probe arrays, said method comprising:

creating an electronically-stored experiment table, said experiment table storing a record for an experiment, said experiment record comprising a plurality of fields storing at least one of a plurality of data identifiers, including;

a first identifier identifying target sample applied to a polymer probe array chip in said experiment;

a second identifier identifying said polymer probe array chip to which said target sample was applied in said experiment; and

creating an electronically-stored chip table, said chip table storing a record for said polymer probe array chip, said chip record comprising a plurality of fields storing at least one of a plurality of data identifiers, including;

said second identifier identifying said polymer probe array chip, and

a third identifier specifying a layout of polymer probes on said polymer probe array chip.

2. The method of claim 1 further comprising:

performing an experiment wherein said target sample is applied to said polymer probe array chip.

3. The method of claim 1 further comprising:

creating an electronically-stored target table, said target table storing a record for said target sample, said target sample record comprising;

said first identifier identifying said target sample; and

a fourth identifier specifying parameters of preparation of said target sample.

4. The method of claim 1 wherein said polymer probe array chip comprises an oligonucleotide array chip.

5. A computer-implemented method for managing information relating to processing of polymer probe arrays, said method comprising:

storing in an electronically-stored experiment table having a plurality of fields holding at least one of a plurality of data identifiers, for each of a plurality of experiments, a first identifier identifying a target sample applied to an polymer probe array chip in a particular experiment;

storing in said electronically-stored experiment table for each of said plurality of experiments a second identifier identifying said polymer probe array chip to which said target sample was applied in said particular experiment;

storing in an electronically-stored chip table having a plurality of fields holding at least one of a plurality of data identifiers, for each of a plurality of polymer probe array chips, said second identifier identifying a particular polymer probe array chip; and

storing in said electronically-stored chip table for each of said plurality of polymer probe arrays chips a third identifier specifying a layout of polymer probes on said polymer probe array chip.

6. The method of claim 5 further comprising:

storing in an electronically-stored target table, for each of a plurality of target samples, said first identifier identifying a particular target sample; and

storing in said electronically-stored target table, for each of said plurality of target samples, a fourth identifier specifying parameters of preparation of said particular target sample.

7. The method of claim 5 wherein said polymer probe array chip comprises an oligonucleotide array chip.

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

code for creating an electronically-stored experiment table, said experiment table listing for each of a plurality of experiments a plurality of fields storing at least one of a plurality of data identifiers, including;

a first identifier identifying a target sample applied to an oligonucleotide array chip in a particular experiment;

a second identifier identifying said oligonucleotide array chip to which said target sample was applied in said particular experiment; and

code for creating an electronically-stored chip table, said chip table listing for each of a plurality of oligonucleotide array chips a plurality of fields storing at least one of a plurality of data identifiers, including;

said second identifier identifying said particular oligonucleotide array chip; and

a third identifier specifying a layout of oligonucleotide probes on said particular oligonucleotide array chip.

9. The computer-readable storage medium of claim 8 having further stored thereon:

code for creating an electronically-stored target table, said target table listing records comprising;

said first identifier identifying said target sample for one or more of said plurality of experiments; and

a fourth identifier specifying parameters of preparation of said target sample for one or more of said plurality of experiments.

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

an electronically-stored experiment table, said experiment table listing for each of a plurality of experiments a plurality of fields storing at least one of a plurality of data identifiers, including;

a first identifier identifying a target sample applied to an oligonucleotide array chip in a particular experiment;

a second identifier identifying said oligonucleotide array chip to which said target sample was applied in said particular experiment; and

an electronically-stored chip table, said chip table listing for each of a plurality of oligonucleotide array chips a plurality of fields storing at least one of a plurality of data identifiers, including;

said second identifier identifying a particular oligonucleotide array chip; and

a third identifier specifying a layout of oligonucleotide probes on said particular oligonucleotide array chip.

11. A database method for analyzing gene expression information, said method comprising:

providing a first database comprising a first plurality of records, one for each of a plurality of experiments, said records having at least one of a plurality of fields storing;

a first attribute identifying a target sample applied to a polymer probe array chip in said experiment;

a second attribute identifying said polymer probe array chip to which said target sample was applied in said experiment; and

providing a second database comprising a second plurality of records for said polymer probe array chip, said records having at least one of a plurality of fields storing;

said second attribute identifying said polymer probe array chip; and

a third attribute specifying a layout of polymer probes on said polymer probe array chip.

12. The database method for analyzing gene expression information of claim 11, wherein said first database and said second database are relational database tables.

13. The database method for analyzing gene expression information of claim 11, wherein at least one of said first attribute, said second attribute and said third attribute is searchable using a search key.

14. A computer system for analyzing gene expression information, said computer system comprising:

a server,

at least one of a plurality of workstations;

a network, interconnecting said server and said at least one of a plurality of workstations, wherein, operatively disposed at said server is a first database comprising a first plurality of records, one for each of a plurality of experiments, said records having at least one of a plurality of fields storing;

a first attribute identifying a target sample applied to a polymer probe array chip in said experiment;

a second attribute identifying said polymer probe array chip to which said target sample was applied in said experiment; and

a second database comprising a second plurality of records for said polymer probe array chip, said records having at least one of a plurality of fields storing;

said second attribute identifying said polymer probe array chip; and

a third attribute specifying a layout of polymer probes on said polymer probe array chip.