Method of storing fast throughput experimentation information in a database

• US 20050182775A1
• Filed: 11/24/2004
• Published: 08/18/2005
• Est. Priority Date: 12/01/2003
• Status: Abandoned Application

• Current Assignee: Accelrys Software, Inc. (Dassault Systemes SA)
• Original Assignee: Accelrys Software, Inc. (Dassault Systemes SA)
• Inventors: Fitzgerald, George, Tucker, Joseph B., Hill, Jorg-Rudiger
• Application Number:
  US10/997,778
• Publication Number:
  US 20050182775A1
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: G06F 16/282 Hierarchical databases, e.g. IMS, LDAP data stores or Lotus Notes
• CPC Class Codes: G16C 20/90 Programming languages; Computing architectures; Database systems; Data warehousing

Abstract

A database is disclosed for storing fast throughput experimentation information. The database is organized in a hierarchical structure such that various database objects have a parent-child relationship. The hierarchical structure facilitates control over user access to various parts of the database. A method is disclosed for automatically populating the database with sample definitions. The sample information is provided in an arbitrary electronic format, which is imported into the database. A method is also disclosed for tracking sample events. Whenever a user takes an action in the database that affects a sample, a sample event is recorded. Finally, a method for automatically importing experimental data resulting from fast throughput experimentation on samples is disclosed. The data is automatically associated with information already stored in the database, such as the test conditions that held during the experimentation and the sample recipes of the samples tested.

Claims

1. A hierarchical data structure stored on a machine readable medium, comprising:

a plurality of sample data objects, each sample data object corresponding to a sample that comprises a chemical or composition of chemicals, each said sample data object comprising data fields populated with one or more chemical ingredients used to synthesize the corresponding sample; and

a library data object comprising a data field populated with a name of the library data object and a plurality of fields populated with references to at least a subset of said plurality of sample data objects.

2. The data structure of claim 1, wherein said chemical comprises a chemical compound.

3. The data structure of claim 1, wherein said composition of chemicals comprises a mixture of chemical compounds.

4. The data structure of claim 1, wherein said composition of chemicals comprises a mixture of metals.

5. The data structure of claim 4, wherein said chemical ingredients comprise metals making up said mixture of metals.

6. The data structure of claim 1, wherein said references comprise names of said plurality of sample data objects.

7. The data structure of claim 1, wherein each said sample data object further comprises data fields populated with one or more process steps used to synthesize the corresponding sample.

8. The data structure of claim 7, wherein said process steps comprise a step of adding one of said ingredients.

9. The data structure of claim 1, wherein each said sample data object further comprises data fields populated with one or more results from experiments performed on the corresponding sample.

10. The data structure of claim 1, wherein each said sample data object further comprises a data field populated with a status indicator that indicates a status of the corresponding sample.

11. The data structure of claim 1, wherein the library data object further comprises data fields populated with one or more identifiers of plates to which said samples have been assigned.

12. The data structure of claim 1, wherein the library data object further comprises data fields populated with one or more process steps that have been applied to all of said samples after synthesis of said samples.

13. A graphical user interface that allows a user to view, create, or modify the hierarchical data structure of claim 1.

14. The graphical user interface of claim 13, comprising settings that determines whether a user is permitted to view the library data object or the sample data objects.

15. The graphical user interface of claim 13, comprising settings that determines whether a user is permitted to create the library data object or the sample data objects.

16. The graphical user interface of claim 13, comprising settings that determines whether a user is permitted to modify the library data object or the sample data objects.

17. The graphical user interface of claim 13, wherein a user that is permitted to view, create, or modify the library data object is automatically permitted to correspondingly view, create, or modify the sample data objects.

18. The graphical user interface of claim 15, wherein if a user created the library data object or sample data object, then the user-creator is automatically permitted to modify the corresponding library data object or sample data object.

19. A method of storing information regarding a plurality of samples that each comprise a chemical or composition of chemicals, the method comprising:

creating a library data object;

populating a data field in said library data object with a name of the library data object;

populating a plurality of data fields in said library data object with references to a plurality of sample data objects;

creating said plurality of sample data objects, each sample data object corresponding to one of said samples; and

populating data fields in each said sample data object with one or more chemical ingredients used to synthesize the corresponding sample.

20. The method of claim 19, wherein said chemical comprises a chemical compound.

21. The method of claim 19, wherein said composition of chemicals comprises a mixture of chemical compounds.

22. The method of claim 19, wherein said composition of chemicals comprises a mixture of metals.

23. The method of claim 22, wherein said chemical ingredients comprise metals making up said mixture of metals.

24. The method of claim 19, wherein said references comprise names of said plurality of sample data objects.

25. The method of claim 19, further comprising populating data fields of each sample data object with one or more process steps used to synthesize the corresponding sample.

26. The method of claim 25, wherein said process steps comprise a step of adding one of said ingredients.

27. The method of claim 19, further comprising populating data fields in each said sample data object with one or more results from experiments performed on the corresponding sample.

28. The method of claim 19, further comprising populating data fields in each said sample data object with a status indicator that indicates a status of the corresponding sample.

29. The method of claim 19, further comprising populating data fields in the library data object with one or more identifiers of plates to which said samples have been assigned.

30. The method of claim 19, further comprising populating data fields in the library data object with one or more process steps that have been applied to all of said samples after synthesis of said samples.

31. The method of claim 19, wherein said step of creating a library data object comprises copying another library data object.

32. The method of claim 31, wherein said copying automatically populates the plurality of data fields with references to sample data objects.

33. The method of claim 32, further comprising editing at least one of the references to sample data objects.

34. The method of claim 32, further comprising adding an additional reference to a sample data object.

35. A graphical user interface that is adapted to receive input from a user and use said input to perform the method of claim 19.

36. The graphical user interface of claim 35, wherein at least one of said populating steps is performed by reading data from a data file identified by the user.

37. A hierarchical data structure stored on a machine readable medium, comprising:

at least one test data object corresponding to analytical tests that can be performed on samples, each sample comprising a chemical or composition of chemicals;

at least one plate data object corresponding to a multi-well sample plate, each said plate data object comprising data fields populated with references to a plurality of samples located on said plate; and

at least one experiment data object corresponding to tests performed on said plurality of samples, said experiment data object comprising a data field populated with a reference to a test data object or a data object that itself references a test data object and a data field populated with a reference to a plate data object, the references to test data object and plate data object indicating that tests corresponding to said test data object are performed on said plurality of samples.

38. The data structure of claim 37, wherein said test data object comprises information regarding format of data obtained when the corresponding test is performed.

39. The data structure of claim 38, wherein said information includes at least one data parameter, each said data parameter indicating a type of laboratory variable.

40. The data structure of claim 38, wherein said information includes at least one data unit.

41. The data structure of claim 37, wherein said plate data object comprises information relating each sample of said plurality of samples to a particular well on said plate.

42. The data structure of claim 37, wherein said plate data object further comprises data fields populated with processes that are applied to all of said plurality of samples.

43. The data structure of claim 37, wherein said experiment data object further comprises data fields or references to data fields that comprise experimental results of said tests performed on said plurality of samples.

44. The data structure of claim 37, wherein said data object that references a test data object is an equipment data object corresponding to a piece of laboratory equipment adapted to perform said tests.

45. A graphical user interface that allows a user to view, create, or modify the hierarchical data structure of claim 37.

46. The graphical user interface of claim 45, comprising settings that determines whether a user is permitted to view the test data object, the plate data object, or the experiment data object.

47. The graphical user interface of claim 45, comprising settings that determines whether a user is permitted to create the test data object, the plate data object, or the experiment data object.

48. The graphical user interface of claim 45, comprising settings that determines whether a user is permitted to modify the test data object, the plate data object, or the experiment data object.

49. The graphical user interface of claim 47, wherein if a user created the test data object, plate data object, or experiment data object, then the user-creator is automatically permitted to correspondingly modify the test data object, plate data object, or experiment data object.

50. A method of storing information regarding experiments performed on a plurality of samples that each comprise a chemical or composition of chemicals, the method comprising:

creating a test data object corresponding to analytical tests that can be performed on said samples;

creating a plate data object corresponding to a multi-well sample plate;

populating data fields in the plate data object with references to a plurality of samples located on said plate;

creating an experiment data object corresponding to tests performed on said plurality of samples;

populating a data field in said experiment data object with a reference to the test data object or a data object that itself references the test data object; and

populating a data field in said experiment data object with a reference to a plate data object, wherein the references to test data object and plate data object indicate that tests corresponding to said test data object are performed on said plurality of samples.

51. The method of claim 50, wherein said test data object comprises information regarding format of data obtained when the corresponding test is performed.

52. The method of claim 51, wherein said information includes at least one data parameter, each said data parameter indicating a type laboratory variable.

53. The method of claim 51, wherein said information includes at least one data unit.

54. The method of claim 50, wherein said plate data object comprises information relating each sample of said plurality of samples to a particular well on said plate.

55. The method of claim 50, further comprising populating data fields in said plate data object with processes that are applied to all of said plurality of samples.

56. The method of claim 50, wherein said experiment data object further comprises data fields or references to data fields that comprise experimental results of said tests performed on said plurality of samples.

57. The method of claim 50, wherein said populating data fields in the plate data object with references to a plurality of samples located on said plate comprises:

providing a graphical display representative of said plate; and

receiving input from a user that identifies a well depicted on said graphical display and that identifies a sample assigned to said identified well.

58. A graphical user interface that is adapted to receive input from a user and use said input to perform the method of claim 50.

59. The graphical user interface of claim 58, wherein at least one of said populating steps is performed by reading data from a data file identified by the user.

60. A data structure for recording a history of a sample, the data structure stored on a machine readable medium, the data structure comprising:

at least one sample data object, each sample data object corresponding to a sample that comprises a chemical or composition of chemicals; and

a plurality of data fields populated with sample events occurring to said samples and the date said sample events occurred.

61. The data structure of claim 60, further comprising data fields populated with the location of said samples when said sample events occur.

62. The data structure of claim 61, wherein said location comprises an identification of a plate on which the sample is located.

63. The data structure of claim 60, wherein said sample events includes at least one event selected from the group consisting of creating a sample data object, copying a sample data object, copying a library data object that comprises a reference to a sample data object, assigning a sample data object to a plate data object, changing a status indicator in a plate data object that comprises a reference to a sample data object, changing a status indicator in a library data object that comprises a reference to a sample data object, changing a status indicator in a sample data object, creating an experiment data object that is associated with a plate data object comprising a reference to a sample data object, importing into a computer database results of an experiment conducted on a sample, changing or adding ingredients or processing steps in a sample database object, adding process steps to a library data object or plate data object that comprise references to a sample data object, and changing a location data field in a plate data object that comprises a reference to a sample data object.

64. A graphical user interface that allows a user to view at least one sample event stored in the data structure of claim 60.

65. The graphical user interface of claim 64, wherein the interface allows a user to view all of said sample events stored for a given sample.

66. The graphical user interface of claim 64, wherein the interface allows a user to select which sample events are displayed.

67. The graphical user interface of claim 64, wherein the interface allows a user to view the location of a sample when each displayed sample event occurred.

68. The graphical user interface of claim 64, further allowing a user to manually populate said data fields.

69. A graphical user interface that allows a user to view a current location of a sample comprising a chemical or composition of chemicals, said interface adapted to display the location stored in the data structure of claim 61 corresponding to the sample event stored last.

70. A method of recording a history of a sample, the sample comprising a chemical or composition of chemicals, said method comprising, for an occurrence of a sample event:

storing on a machine readable medium an identification of said sample event; and

storing on a machine readable medium the date said sample event occurred.

71. The method of claim 70, wherein said storing steps are performed for each occurrence of a sample event.

72. The method of claim 70, wherein said storing steps are performed automatically when said sample event occurs.

73. The method of claim 70, wherein said storing steps are performed manually by a user.

74. The method of claim 70, further comprising storing on a machine readable medium the location of said sample when said sample event occurs.

75. The method of claim 74, wherein said location comprises an identification of a plate on which the sample is located.

76. The method of claim 70, wherein said sample event is selected from the group consisting of creating a sample data object, copying a sample data object, copying a library data object that comprises a reference to a sample data object, assigning a sample data object to a plate data object, changing a status indicator in a plate data object that comprises a reference to a sample data object, changing a status indicator in a library data object that comprises a reference to a sample data object, changing a status indicator in a sample data object, creating an experiment data object that is associated with a plate data object comprising a reference to a sample data object, importing into a computer database results of an experiment conducted on a sample, changing or adding ingredients or processing steps in a sample database object, adding process steps to a library data object or plate data object that comprise references to a sample data object, and changing a location data field in a plate data object that comprises a reference to a sample data object.

77. A graphical user interface that allows a user to define types of sample events stored according to the method of claim 70.

78-86. -86. (canceled)