Relational database and system for storing information relating to biomolecular sequences and reagents

• US 6,553,317 B1
• Filed: 03/04/1998
• Issued: 04/22/2003
• Est. Priority Date: 03/05/1997
• Status: Expired due to Fees

• Current Assignee: Incyte Corporation
• Original Assignee: Incyte Pharmaceuticals, Inc.
• Inventors: Akerblom, Ingrid E., Klingler, Tod M., Lincoln, Stephen E., Hodgson, David M., Panzer, Scott R., McKelligon, Brian M., Ament, Andrew D., Wong, Landes C., Cathcart, Richard, Jolley, Helen E., Thanawala, Mayank K., Ito, Laura Y.
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): KIM, YOUNG J
• Application Number:
  US09/034,807
• Time in Patent Office: 1,875 Days
• Field of Search: 435/6, 707/104, 707/10, 702/19-20
• US Class Current: 702/20
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 Ontologies; Annotations
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing

Abstract

The present invention provides relational database systems for storing biomolecular sequence information together with biological annotations detailing the source of the sequence information, and associated reagent information. The acquisition, storage and access of reagent information associated with databased biomolecular sequence information is a particular advantage of the present invention. Such reagent information identifies genetic information and materials which may be made available to a user of the relational database system of the present invention for further application in research, therapeutic pharmaceutical development or other fields. The reagent information aspect of the present invention is preferably used in conjunction with a biomolecular sequence relational database system.

Claims

1. A computer system, comprising:

a relational database having

(i) records containing information identifying sequences of a plurality of reagent clones, wherein said reagent clones have been nominated based on specified priority criteria, and

(ii) records containing information identifying reagent information accumulated in sequencing and verification of said plurality of reagent clones, wherein verification comprises using laboratory processes to verify that said plurality of reagent clones is viable; and

a user interface allowing a user to selectively access the information contained in the records.

2. The computer system of claim 1, wherein said records are organized into a plurality of tables.

3. The computer system of claim 1, wherein the regent information includes physical data and ordering information for said clones.

4. The computer system of claim 3, wherein said physical data and ordering information for a clone includes the clone'"'"'s processing history, availability, and location.

5. The computer system of claim 1, wherein said clones are cDNA clones.

6. A computer system, comprising:

a relational database having

(i) records containing information identifying sequences with associated information from a relational gene sequence database,

(ii) records containing information identifying sequences of a plurality of reagent clones that have been nominated from said gene sequence database based on specified priority criteria, and

(iii) records containing information identifying reagent information accumulated in sequencing and verification of said reagent clones, wherein verification comprises using laboratory processes to verify that said plurality of reagent clones is viable; and

a user interface allowing a user to selectively access the information contained in the records.

7. The computer system of claim 6, wherein said records are organized into a plurality of tables.

8. The computer system of claim 6, wherein the information includes physical data and ordering information for said reagent clones.

9. The computer system of claim 8, wherein said physical data and ordering information for a clone includes the clone'"'"'s processing history, availability, and location.

10. The computer system of claim 6, wherein said clones are cDNA clones.

11. A method, implemented on a computer system, for accessing information relating to one or more reagent clones, comprising:

providing a relational database having

(i) records containing information identifying sequences of a plurality of reagent clones, wherein said reagent clones have been nominated based on specified priority criteria, and

(ii) records containing information identifying reagent information accumulated in sequencing and verification of said plurality of reagent clones, wherein verification comprises using laboratory processes to verify that said plurality of reagent clones is viable;

entering, in a graphical user interface, a query relating to the information contained in the records;

determining matches between said query entry and said information; and

displaying the results of said determination.

12. The method of claim 11, wherein the reagent information includes physical data and ordering information for said clones.

13. The method of claim 12, wherein said physical data and ordering information for a clone includes the clone'"'"'s processing history, availability, and location.

14. The method of claim 11, wherein said clones are cDNA clones.

15. A method, implemented on a computer system, for accessing information relating to one or more reagent clones, comprising:

providing a relational database having

(i) records containing information identifying sequences with associated information from a relational gene sequence database,

(ii) records containing information identifying sequences of a plurality of reagent clones that have been nominated from said relational gene sequence database based on specified priority criteria, and

(iii) records containing information identifying reagent information accumulated in sequencing and verification of said reagent clones, wherein verification comprises using laboratory processes to verify that said plurality of reagent clones is viable;

entering, in a graphical user interface, a query relating to the information contained in the records;

determining matches between said query entry and said information; and

displaying the results of said determination.

16. The method of claim 15, wherein the reagent information includes physical data and ordering information for said reagent clones.

17. The method of claim 16, wherein said physical data and ordering information for said reagent clones includes the clone'"'"'s processing history, availability, and location.

18. The method of claim 15, wherein said clones are cDNA clones.

19. A computer program product, comprising a computer-usable medium having computer-readable program code embodied thereon relating to a relational database

(i) records containing information identifying sequences of a plurality of reagent clones, wherein said reagent clones have been nominated based on specified priority criteria, and

(ii) records containing information identifying reagent information accumulated in sequencing and verification of said plurality of reagent clones, wherein verification comprises using laboratory processes to verify that said plurality of reagent clones is viable.

20. The computer program product of claim 19, wherein the reagent information includes physical data and ordering information for said clones.

21. The computer program product of claim 20, wherein said physical data and ordering information for a clone includes the clone'"'"'s processing history, availability, and location.

22. The computer program product of claim 19, wherein said clones are cDNA clones.

23. A computer program product, comprising a computer-usable medium having computer-readable program code embodied thereon relating to a relational database having

(i) records containing information identifying sequences with associated information from a relational gene sequence database,

(ii) records containing information identifying sequences of a plurality of reagent clones that have been nominated from said relational gene sequence database based on specified priority criteria, and

(iii) records containing information identifying reagent information accumulated in sequencing and verification of said reagent clones, wherein verification comprises using laboratory processes to verify that said plurality of reagent clones is viable.

24. The computer program product of claim 23, wherein the reagent information includes physical data and ordering information for said clones.

25. The computer program product of claim 24, wherein said physical data and ordering information for a clone includes the clone'"'"'s processing history, availability, and location.

26. The computer program product of claim 23, wherein said clones are cDNA clones.

27. A computer program product, comprising a computer-usable medium having computer-readable program code embodied thereon relating to a relational database having

(i) records containing information identifying sequences of a plurality of reagent clones, wherein said reagent clones have been nominated based on specified priority criteria, and

(ii) records containing information identifying reagent information accumulated in sequencing and verification of said plurality of reagent clones, wherein verification comprises using laboratory processes to verify that said plurality of reagent clones is viable;

the computer program product comprising computer-readable program code for effecting the following steps within a computing system;

providing an interface for receiving a query relating to the information contained in the records;

determining matches between said query entry and said information; and

displaying the results of said determination.

28. The computer program product of claim 27, wherein the reagent information includes physical data and ordering information for said clones.

29. The computer program product of claim 28, wherein said physical data and ordering information for a clone includes the clone'"'"'s processing history, availability, and location.

30. The computer program product of claim 27, wherein said clones are cDNA clones.

31. A computer program product, comprising a computer-usable medium having computer-readable program code embodied thereon relating to a relational database having

(i) records containing information identifying sequences with associated information from a relational gene sequence database,

(ii) records containing information identifying sequences of a plurality of reagent clones that have been nominated from said relational gene sequence database based on specified priority criteria, and

(iii) records containing information identifying reagent information accumulated in sequencing and verification of said reagent clones, wherein verification comprises using laboratory processes to verify that said plurality of reagent clones is viable;

the computer program product comprising computer-readable program code for effecting the following steps within a computing system;

providing an interface for receiving query relating to the information contained in the records;

determining matches between said query entry and said information; and

displaying the results of said determination.

32. The computer program product of claim 31, wherein the reagent information includes physical data and ordering information for said clones.

33. The computer program product of claim 32, wherein said physical data and ordering information for a clone includes the clone'"'"'s processing history, availability, and location.

34. The computer program product of claim 31, wherein said clones are cDNA clones.

35. A method, at least partially implemented on a computer system, for establishing a set of reagent clones, comprising:

grouping initial sequences of polynucleotide inserts in a plurality of clones into a master cluster;

assembling the initial sequences of the master cluster into one or more contiguous sequences, such that relationships of sequences to each other in the master cluster are elucidated;

nominating at least one clone represented by a master cluster as a reagent clone, according to specified priority criteria and verifying the quality of the reagent clone by laboratory processes, wherein said laboratory processes comprise verifying that the reagent clone is viable and can grow to amounts suitable for isolating the clone'"'"'s polynucleotide insert sequence; and

sequencing said clone'"'"'s polynucleotide insert sequence using 5′ and

3′

long read sequencing,

wherein said priority criteria comprise;

(1) a clone associated with a 5′

-most initial sequence in an assembly;

(2) a clone having an insert in a pINCY vector, such that if the 5′

-most clone in the assembly is not a pINCY clone, the 5′

-most pINCY clone is nominated if it is no more than 150 bases shorter than the 5′

-most clone; and

(3) if the polynucleotide sequences of a cluster do not assemble, then the most recently sequenced clone insert in a pINCY vector is nominated.

36. A reagent clone identified by a process, at least partially implemented on a computer system, for establishing a set of reagent clones, comprising:

grouping initial sequences of polynucleotide inserts in a plurality of clones into a master cluster;

assembling the initial sequences of the master cluster into one or more contiguous sequences, such that relationships or sequences to each other in the master cluster are elucidated; and

nominating at least one clone represented by a master cluster as a reagent clone, according to specified priority criteria wherein said priority criteria comprise;

(1) a clone associated with a 5′

-most initial sequence in an assembly;

(2) a clone having an insert in a pINCY vector, such that is the 5′

-most clone in the assembly is not a pINCY clone, the 5′

-most pINCY clone is nominated if it is no more than 150 bases shorter than the 5′

-most clone; and

(3) if the polynucleotide sequences of a cluster do not assemble, then the most recently sequenced clone insert in a pINCY vector is nominated.