Internet-linked system for directory protocol based data storage, retrieval and analysis

• US 20020049782A1
• Filed: 05/18/2001
• Published: 04/25/2002
• Est. Priority Date: 11/05/1999
• Status: Active Grant

• Current Assignee: David Rhodes Parks, Leonard A. Herzenberg, Leonore A. Herzenberg, Vernon T. Oi, Wayne A. Moore
• Original Assignee: David Rhodes Parks, Leonard A. Herzenberg, Leonore A. Herzenberg, Vernon T. Oi, Wayne A. Moore
• Inventors: Herzenberg, Leonore A., Herzenberg, Leonard A., Parks, David Rhodes, Moore, Wayne A., Oi, Vernon T.
• Granted Patent: US 6,947,953 B2
• Time in Patent Office: Days
• US Class Current: 715/500.1
• CPC Class Codes: G06F 16/25 Integrating or interfacing systems involving database management systems
• CPC Class Codes: G06F 16/258 Data format conversion from or to a database
• CPC Class Codes: G06Q 10/10 Office automation; Time management
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures
• CPC Class Codes: G16B 50/40 Encryption of genetic data
• CPC Class Codes: G16H 10/60 for patient-specific data, e.g. for electronic patient records
• CPC Class Codes: G16H 70/00 ICT specially adapted for the handling or processing of medical references
• CPC Class Codes: Y10S 707/99942 Manipulating data structure, e.g. compression, compaction, compilation
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing
• CPC Class Codes: Y10S 707/99948 Application of database or data structure, e.g. distributed, multimedia, or image

Abstract

The present invention is related to databases and the exchange of scientific information. Specifically the invention disclosed a unified scientific database that allows researchers to easily share their data with other researches. The present invention also allows for the ease of data collection, annotation, storage, management, retrieval and analysis of scientific data through and into the database. In addition, it allows for archival storage and retrieval of data collected directly from laboratory instruments to ensure data consistency for patent and other purposes. It also allows for ease of sharing data between laboratories in remote locations. The present invention also supports the automated creation of experimental protocols.

Claims

1. A method for managing a database using a lightweight directory access protocol for identifying and storing information with said database, said method comprising:

(a) applying said light directory access protocol to create a directory structure for said database, said directory structure having a plurality of nodes with distinguished names;

(b) defining standardized data; and

(c) transforming said standardized data for mapping onto said plurality of nodes.

2. The method of claim 1, wherein said step of defining comprises annotating said standardized data.

3. The method of claim 1, wherein said transformation step further comprises:

(a) developing extensions with XML; and

(b) mapping said extensions to said plurality of nodes.

4. The method of claim 3, wherein said developing step further comprises adding to said extension elements selected for the group consisting of cross-references, external pointers and links.

5. The method of claim 1, further comprising a centralized Internet-accessible archive for storing, analyzing, retrieving, and sharing said data.

6. The method of claim 1, further comprising a security means for user-controlled sharing of the data.

7. The method of claim 1, further comprising a structured hierarchy, said structured hierarchy comprising, in order:

(a) studies;

(b) experiments;

(c) data; and

(d) analysis.

8. A method for managing supplies of a laboratory using a computer comprising:

(a) Recording supplies used in said laboratory on a computer readable medium;

(b) Recording amount of said supplies in said laboratory on a computer on said computer readable medium; and

(c) Notifying laboratory personnel of said amount of said supplies.

9. The method of claim 8, further comprising sending automatic notifications when said amount of supplies is low.

10. The method of claim 9, wherein said automatic notification is performed through electronic mail.

11. The method of claim 8, wherein amount of said supplies is automatically updated.

12. The method of claim 11, wherein:

(a) said computer is coupled to an experiment protocol tracker;

(b) said automatic updating of said supplies occurs when an experimental protocol on said experimental protocol tracker is completed.

13. The method of claim 12 wherein, said automatic updating further comprises an estimation of supplies wasted.

14. The method of claim 13, wherein said estimation of wasted supplies comprises estimating supplies wasted during an experimental protocol.

15. The method of claim 8 wherein said computer readable medium comprises a database using a directory access protocol for identifying and storing information with said database.

16. The method of claim 15,wherein said database comprises:

(a) applying said directory access protocol to create a directory structure for said database, said directory structure having a plurality of nodes with distinguished names;

(b) defining standardized data; and

(c) transforming said standardized data for mapping onto said plurality of nodes.

18. The method of claim 17, wherein said interactive protocol maker is coupled to analysis software.

19. The method of claim 18, wherein said analysis software is further used to provide said experimental options to the user.

20. The method of claim 19, wherein proper units are automatically transferred to the analysis software.

21. The method of claim 17, wherein said additional options are based on the current inventory of laboratory supplies.

22. The method of claim 17, wherein an output comprises an experimental protocol comprising:

(a) instructions detailing the steps of the experiment to be performed;

(b) supplies to be used in the experiment; and

(c) instructions detailing which of said supplies and which subparts of said supplies are to be used during each of said steps in said experiment.

23. The method of claim 17 wherein said created experimental protocols are recorded on a computer readable medium comprising a database using a directory access protocol for identifying and storing information with said database.

24. The method of claim 23, wherein said database comprises:

(a) applying said directory access protocol to create a directory structure for said database, said directory structure having a plurality of nodes with distinguished names;

(b) defining standardized data; and

(c) transforming said standardized data for mapping onto said plurality of nodes.

26. The method of claim 25 wherein said created experimental protocols are recorded on a computer readable medium comprising a database using a directory access protocol for identifying and storing information with said database.

28. The method of claim 27, further comprising storing data created from said experimental steps onto a computer readable medium.

29. The method of claim 28, wherein said computer readable medium is accessible over an interconnection network.

30. The method of claim 29, wherein said interconnection network is the Internet.

31. The method of claim 28 wherein the computer readable medium comprises a database using a directory access protocol for identifying and storing information with said database.

32. The method of claim 31 ,wherein said database comprises:

(a) applying said directory access protocol to create a directory structure for said database, said directory structure having a plurality of nodes with distinguished names;

(b) defining standardized data; and

(a) transforming said standardized data for mapping onto said plurality of nodes.

17. A method for interactively creating experimental protocols comprising:

(a) a user selecting options from a plurality of experimental options;

(b) said experimental options being stored in a computer;

(c) said computer provides additional options to the user based on said user selected options.

25. A method for interactively creating study protocols comprising:

(a) inserting a hypothesis to be tested;

(b) inserting research criteria to be followed; and

(c) inserting research parameters to be followed.

27. A method for interactively collecting data comprising:

(a) creating an interactive experimental protocol; and

(b) conducting experimental steps from said protocol.

33. A method for analyzing data comprising:

(a) accessing experimental data from a computer readable medium;

(b) accessing an analysis program from a computer readable medium capable of analyzing said experimental data.

34. The method of claim 33, wherein the computer readable medium comprises a database using a directory access protocol for identifying and storing information with said database.

35. The method of claim 34, wherein said database comprises:

(a) applying said directory access protocol to create a directory structure for said database, said directory structure having a plurality of nodes with distinguished names;

(b) defining standardized data; and

(c) transforming said standardized data for mapping onto said plurality of nodes.