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

• US 20050273475A1
• Filed: 08/02/2005
• Published: 12/08/2005
• 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: Oi, Vernon T., Herzenberg, Leonore A., Herzenberg, Leonard A., Parks, David Rhodes, Moore, Wayne A.
• Granted Patent: US 7,650,351 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• 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 for an experimental or clinical laboratory using a lightweight directory access protocol for identifying and storing information with said database, said method comprising the steps of:

(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 for at least one of experimental and clinical data; and

(c) transforming said standardized data for mapping onto said plurality of nodes, wherein said standardized data includes reagent data.

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 extensions, elements selected from 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 standardized data.

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

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

(a) studies;

‘

(b) experiments;

(c) data; and

(d) analysis.

39. The method of claim 1, wherein the standardized data further includes measurement data.

8-16. -16. (canceled)

17. A method for interactively creating experimental protocols for an experimental or clinical laboratory comprising:

(a) selecting, by a user from a plurality of experimental options generated by a computer including reagents available in an inventory;

(b) storing said selected experimental options in a computer; and

(c) outputting, by said computer, an experimental protocol including reagents used in the experimental protocol.

18. The method of claim 17, further including coupling the experimental protocol to analysis software to analyze data created while performing the experimental protocol.

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, further including providing a user additional options for creating an experimental protocol based on the current inventory of laboratory supplies.

22. The method of claim 17, wherein outputting the experimental protocol further comprises:

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

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

(c) providing 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 database.

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

(a) applying a 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.

37. The method of claim 17, wherein the reagents include reagents from data inputted by a user that are not in the database of the computer.

25. A method for interactively creating study protocols on a computer for an experimental or clinical laboratory comprising:

(a) inserting research criteria to be followed into a computer;

(b) inserting research parameters to be followed into a computer; and

(c) outputting a study protocol based on the inserted research criteria and the inserted research parameters,

wherein said study protocol includes reagents used in the study protocol.

26. (canceled)

27. A method for interactively collecting data on a computer for an experimental or clinical laboratory comprising:

(a) creating an experimental protocol interactively on a computer including reagents and amounts of reagents;

(b) conducting experimental steps according to the reagents and amount of reagents listed in the created experimental protocol, including collecting data from an instrument based on reagents from the experimental protocol; and

(c) outputting the collected data of an experiment including data associated with reagents, amounts of reagents and the experimental protocol to at least one of a database and a user after the data is collected while conducting the experimental steps.

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

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

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

32. The method of claim 28, wherein said storing data to the 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.

33. The method of claim 27, further including the steps of:

(a) accessing experimental data from a database;

(b) running an analysis program to analyze the experimental data by a computer capable of analyzing said experimental data, after the completion of an experiment.

35. The method of claim 33, wherein storing said data to said database comprises:

(a) applying a 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.

38. The method of claim 27, wherein files for storing results of an experimental protocol are formatted to allow a particular instrument to use the experimental protocol and are then reformatted back to an original format after the instrument completes writing experimental data into a storage device.

40. The method of claim 27, wherein the data collected from an instrument is stored in the database.

41. The method of claim 27, wherein the creating step includes sending a file to an instrument delineated in the created experimental protocol.

42. The method of claim 41, wherein the file includes parameters for the experiment.

43. The method of claim 27, wherein the reagents are stored in at least one of a local computer and a database.

44. The method of claim 27, wherein the amount of reagent in a database is reduced after the creation of the experimental protocol.

45. The method of claim 27, wherein the amount of reagent in a database is reduced after the conducting of an experiment.

31. (canceled)

34. (canceled)

36. (canceled)