System and method for internet-accessible tools and knowledge base for protocol design, metadata capture and laboratory experiment management

• US 7,555,492 B2
• Filed: 04/26/2004
• Issued: 06/30/2009
• Est. Priority Date: 11/05/1999
• Status: Expired due to Term

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Inventors: Meehan, Stephen, Tung, James, Musen, Mark, Moore, Wayne, Parks, David, Herzenberg, Leonore
• Primary Examiner(s): Le; Debbie M
• Application Number:
  US10/833,164
• Publication Number:
  US 20050044110A1
• Time in Patent Office: 1,891 Days
• Field of Search: 707 1- 10, 707100-1041, 707/200, 707/201, 707203-205, 700/90, 700/266, 702/1, 702/19, 702/22, 705 1- 4, 705 26- 29, 706/10, 706/15, 706/16, 706/23, 706/25, 706/45, 706/903, 706/906, 709200-203, 709217-219, 128/920, 600/300
• US Class Current: 1/1
• 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 50/20 Heterogeneous data integration
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures
• CPC Class Codes: G16B 50/40 Encryption of genetic data
• CPC Class Codes: Y10S 707/99943 Generating database or data structure, e.g. via user interface
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing

Abstract

The present invention is related to databases and the exchange of scientific information. Specifically the invention discloses a laboratory data management system including a knowledge base that stores characteristics of laboratory reagents, experiment subjects, tissues and cells. The invention also includes an experiment input module that accepts input of parameters of an experiment and data from a knowledge base module. Further, the invention includes a protocol creator connected to the knowledge base module and the experiment input module that creates a laboratory protocol for an experiment based on data supplied from the knowledge base module and the experiment input module. The invention also includes methods to use the described system.

Claims

1. A laboratory data management and protocol creation system, used to create an experiment plan or protocol, including:

(a) an ontology knowledge module embedded in a server architecture that enables controlled simultaneous access by multiple users, wherein the server architecture comprises a computer processor, configured to store characteristics and controlled references for at least one of laboratory reagents, experiment subjects, tissues and cells as data in the ontology knowledge module;

(b) an experiment input module configured to accept input of at least one parameter of an experiment to be executed, wherein the at least one parameter of the experiment is selected from entries in the configured ontology knowledge module, and wherein the at least one parameter is annotated with data from the experiment input module; and

(c) an automated protocol creator module connected to the ontology knowledge module and the experiment input module, wherein the automated protocol creator module is configured to create and annotate a laboratory protocol for an experiment that then is executed based on inputs from the ontology knowledge module and the experiment input module.

2. The system of claim 1, wherein the system is programmed in an object oriented language.

3. The system of claim 1, further including a laboratory inventory module configured to store an inventory of laboratory materials and connected to the protocol creator module, wherein the protocol creator module is further configured to take input information from the laboratory inventory module when creating the laboratory protocol.

4. The system of claim 1, further including at least one laboratory data storage module configured to store results from at least one laboratory experiment, the at least one laboratory data storage module connected to the protocol creator module.

5. The system of claim 4, wherein the protocol creator module is further configured to take input information from the laboratory data storage module when creating a laboratory protocol.

6. The system of claim 5, further including a laboratory experiment analysis module configured to analyze data of at least one experiment, wherein the laboratory experiment analysis module is connected to the laboratory data storage module and the protocol creator module.

7. The system of claim 6, wherein the laboratory experiment analysis modules is configured to perform cluster analysis on data of at least one experiment.

8. The system of claim 4, wherein the system is configured to store at least one of the experiment, protocol and data in the laboratory data storage module.

9. The system of claim 8, wherein the system is configured to store the at least one of the experiment, protocol and data to a unique file location that is named and controlled by the laboratory data storage module.

10. The system of claim 9, wherein the unique file location is accessible through a Uniform Resource Locator (URL) reference.

11. The system of claim 4, wherein the laboratory data management system includes a searchable directory of items in the data storage module.

12. The system of claim 11, wherein the searchable directory includes information from at least one of the experiment, an analysis and the laboratory protocol stored as searchable metadata.

13. The system of claim 12, wherein the directory is configured to provide data annotated with metadata to the laboratory experiment analysis module.

14. The system of claim 11, wherein the knowledge module is configured to search the searchable directory.

15. The system of claim 3, wherein the protocol creator module is configured to determine and output feasible combinations of materials used for the laboratory protocol.

16. The system of claim 15, wherein the materials include at least two Fluorescent Activated Cell Sorting (FACS) machines, FACS machine configurations, Microarray machines, Microarray machine configurations, reagents and chemicals.

17. The system of claim 4, wherein the data management system is configured to take input from a user and provide output to a user though a graphical user interface.

18. The system of claim 17, wherein the graphical user interface outputs an interactive diagram of a layout for the laboratory protocol.

19. The system of claim 18, wherein the layout is a laboratory experiment organizational matrix including at least one of a well plate, a test tube rack, Enzyme-Linked Immunosorbent Assay (ELISA) array, and Microarray.

20. The system of claim 17, wherein the user is capable of interactively changing the laboratory protocol by changing information within the layout presented by the laboratory protocol.

21. The system of claim 17, wherein the graphical user interface is configured to present the user a tree structure configured to enable selection of a group of nodes including any two nodes.

22. The system of claim 21, wherein the system is configured to permit a noncontiguous selection, wherein;

a first child node is deselected after a first parent node is selected; and

a second child node is deselected after a second parent node is selected;

wherein the first parent node is not a parent of the second parent node; and

the second parent node is not a parent of the first parent node.

23. The system of claim 22, wherein the system is configured to determine if an edit made by the user in the graphical user interface is valid for all the selected nodes.

24. The system of claim 20, wherein the graphical user interface is configured to automatically update the laboratory protocol in the protocol creator module when the laboratory protocol is altered by a user within the graphical user interface.

25. The system of claim 17, wherein the graphical user interface is configured to automatically update the knowledge module when the knowledge base is altered by a user within the graphical user interface.

26. The system of claim 1, wherein the knowledge module is configured to be updated through a data import export Application Program Interface (API).

27. The system of claim 1, wherein the knowledge module is configured to be updated by an updating module, the updating module is connected to the knowledge module and the data storage module and reviews experimental data to determine if the knowledge module should be updated and upon such determination updates the knowledge module.

28. The system of claim 4, further including a scheduling module connected to the protocol creator module, wherein the schedule module is configured to schedule use times for experiments based on availability of usable laboratory instruments including at least one of a FACS machine and a Microarray reader.

29. The system of claim 4, further including a scheduling module connected to the protocol creator module and knowledge module module, wherein the scheduling module is configured to determine appropriate laboratory instruments to be used for experiments based on the characteristics and capabilities of the laboratory instruments including FACS machines and Microarray reader.

30. The system of claim 28, wherein an instrument control module connected to the knowledge module and the protocol creator module is configured to:

import information from the knowledge module and protocol creator module; and

export information, based on the imported information, to a laboratory instrument selected for a protocol, wherein the exported information is used to at least one of the following;

set up the instrument, standardize the instrument, set instrument parameters, name data files for the instrument output corresponding to the laboratory protocol, label instrument display parameters, and drive data collection based on the laboratory protocol.

31. The system of claim 17, wherein the graphical user interface is configured to allow users to search metadata to determine which past experiments stored in the at least one laboratory data storage module match a query by the user.

32. The system of claim 18, wherein the protocol creator module is configured to implement combinatories algorithms to determine feasible products.

33. The system of claim 32, wherein a check-in module is configured to receive information from at least one of the protocol maker module, an instrument, the knowledge module and the user and couples the information to data files connected to an experiment and is further configured to package and store the data files in the data storage module.

34. The system of claim 12, wherein the search is based on the input of a combination of metadata.

35. The system of claim 34, wherein the search module is configured to output a graphical user interface to a user to allow the user to retrieve results of a search;

and wherein the system further includes a hypothesis testing module connected to the system configured to test an inputted hypotheses based on inputted data and to output the result of a hypothesis test through the graphical user interface.

36. A method for creating a laboratory protocol to be used in conducting an experiment, the method including the steps of:

(a) storing characteristics and controlled references for at least one of laboratory reagents, experiment subjects, tissues and cells in an ontology knowledge module embedded in a server architecture that enables controlled simultaneous access by multiple users, wherein the server architecture comprises a computer processor, as data in the ontology knowledge module;

(b) accepting input through an experiment input module of at least one parameter of the experiment to be executed, wherein the at least one parameter of the experiment is selected from entries in the configured ontology knowledge module, and is annotated with data from the experiment input module; and

(c) automatically creating and annotating a laboratory protocol by an automatic protocol creator module for the experiment based on inputs from the ontology knowledge module and the experiment input modules.

37. The method of claim 36, wherein portions of the ontology knowledge module is written in an object oriented language.

38. The method of claim 36, further including the steps of storing an inventory of laboratory materials in a laboratory inventory module connected to the protocol creator module, and receiving input information from the laboratory inventory module when creating the laboratory protocol.

39. The method of claim 36, further including the step of storing results from at least one laboratory experiment in at least one laboratory data storage module, the at least one laboratory data storage module connected to the protocol creator module.

40. The method of claim 39, further including the step of taking input information by the protocol creator module from the laboratory data storage module when creating the laboratory protocol.

41. The method of claim 40, further including the step of analyzing a laboratory experiment by an experiment analysis module of at least one experiment, wherein the laboratory experiment analysis module analyzes data from the laboratory data storage module and the protocol creator module.

42. The method of claim 41, further including the step of performing cluster analysis on data of at least one experiment by the experiment analysis module.

43. The method of claim 39, further including the step of storing at least one of the experiment, protocol and data in the laboratory data storage module.

44. The method of claim 43, further including the step of storing the at least one of the experiment, protocol and data to a unique file location that is named and controlled by the laboratory data storage module.

45. The method of claim 44, wherein the unique file location is accessible through a URL reference.

46. The method of claim 39, further including the step of searching a directory of items in the data storage module.

47. The method of claim 46, wherein the directory includes information from at least one of an experiment, an analysis and the laboratory protocol stored as searchable metadata.

48. The method of claim 47, further including the step of providing data annotated with metadata to the laboratory experiment analysis module.

49. The method of claim 46, further including the step of searching by the knowledge module of the searchable directory.

50. The method of claim 38, further including the steps of determine and outputting by the protocol creator module feasible combinations of materials used for the laboratory protocol.

51. The method of claim 49, wherein the materials include at least two of FACS machines, FACS machine configurations, Microarray machines, Microarray machine configurations, reagents and chemicals.

52. The method of claim 39, further including the step of taking input from a user by the protocol maker module and providing output of a laboratory protocol to a user through a graphical user interface.

53. The method of claim 52, further including the step of outputting an interactive diagram of a graphical user interface layout for the laboratory protocol.

54. The method of claim 53, wherein the layout is a laboratory experiment organizational matrix including at least one of a well plate, a test tube rack, enzyme-linked immunosorbent array and microarray.

55. The method of claim 49, including the step of changing the laboratory protocol by the user by changing information within the layout presented by the laboratory protocol.

56. The method of claim 49, including the steps of presenting to a user the graphical tree structure, and selecting of a group of modes including any two nodes.

57. The method of claim 56, including the step of selecting a noncontiguous selection of a group of nodes, wherein:

a first child node is deselected after a first parent node is selected; and

a second child node is deselected after a second parent node is selected;

wherein the first parent node is not a parent of the second parent node; and

the second parent node is not a parent of the first parent node.

58. The method of claim 57, including the step of determining if an edit made by the user in the graphical user interface is valid for all the selected nodes.

59. The method of claim 55, including the step of updating by the graphical user interface the protocol in the protocol creator module when the protocol is altered by a user within the graphical user interface.

60. The method of claim 52, including the step of updating the knowledge module when the knowledge module is altered by a user within the graphical user interface.

61. The method of claim 36, including the step of updating the knowledge module through a data import export application program interface.

62. The method of claim 36, including the steps of:

receiving information by the updating module from the ontology knowledge module and the data storage modules;

reviewing experimental data by the updating module to determine if the knowledge module should be updated; and

updating the knowledge module.

63. The method of claim 39, including the step of scheduling use times for experiments based on availability of usable laboratory instruments including at least one of FACS machines and microarray reader.

64. The method of claim 39, further including determining appropriate laboratory instruments to be used for experiments based on the characteristics and capabilities of the laboratory instruments including at least one of a FACS machine and a microarray reader.

65. The method of claim 63, further including the steps of:

importing information by an instrument control module from the knowledge module and protocol creator module; and

exporting information, based on the imported information, to a laboratory instrument selected for a protocol, wherein the exported information is used to at least one of the following;

set up the instrument, standardize the instrument, set the instrument parameters, name data files for the instrument output corresponding to the protocol, label instrument display parameters, and drive data collection based on the protocol.

66. The method of claim 62, including the step of searching metadata to determine which past experiments stored in the at least one laboratory data storage module match a query by the user on a graphical user interface.

67. The method of claim 36, further including the step of configuring the protocol creator module to implement combinatories algorithms to determine feasible protocols.

68. The method of claim 67, including the steps of:

receiving by checking module information from at least one of the protocol maker module, an instrument, the ontology knowledge module and the user;

coupling the information by the checking module to data files connected to an experiment; and

packaging and storing the data files in the data storage module.