Laboratory database system and methods for combinatorial materials research

• US 20040088117A1
• Filed: 12/29/2003
• Published: 05/06/2004
• Est. Priority Date: 01/05/2001
• Status: Active Grant

• Current Assignee: Symyx Solutions, Inc.
• Original Assignee: Symyx Technologies Incorporated (Dassault Systemes SA)
• Inventors: Dorsett, David R. Jr.
• Granted Patent: US 7,085,773 B2
• Time in Patent Office: Days
• US Class Current: 702/22
• CPC Class Codes: B01J 2219/007 Simulation or vitual synthesis
• CPC Class Codes: G16C 20/10 Analysis or design of chemical reactions, syntheses or processes
• CPC Class Codes: Y10S 707/954 Relational
• CPC Class Codes: Y10S 707/99931 Database or file accessing
• 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

Systems, methods, and apparatus, including computer program apparatus, are described for implementing techniques for processing data from a combinatorial experiment. The techniques include receiving data from a chemical experiment on a library of materials having a plurality of members and generating a representation of the chemical experiment. The representation includes data defining an experiment object having a plurality of properties derived from the chemical experiment. The experiment object is associated with the library of materials. The representation also includes data defining one more element objects. Each element object is associated with one or more members of the library of materials. A data model and corresponding data structures for describing such experiments are also disclosed.

Claims

1. A computer-implemented method for processing data from a chemical experiment on a library of materials, the method comprising:

receiving data from a chemical experiment on a library of materials having a plurality of members; and

generating a representation of the chemical experiment, the representation including data defining an experiment object having a plurality of properties derived from the chemical experiment, the experiment object being associated with the library of materials, the representation also including data defining one or more element objects, each element object being associated with one or more members of the library of materials.

2. The method of claim 1, wherein:

the chemical experiment has a type that is one of a pre-defined set of one or more experiment types;

the representation implements a data model describing the one or more experiment types, the data model including an experiment base class having a set of experiment base class properties including a classname property for identifying a derived experiment class and a library ID property for identifying a library of materials, the data model also including one or more derived experiment classes, each derived experiment class being associated with one of the experiment types and having a plurality of derived experiment class properties derived from the associated experiment type; and

the chemical experiment is represented in the representation by a first experiment object instantiated from the derived experiment class associated with the type of the chemical experiment, and by a second experiment object instantiated from the experiment base class, the classname property of the second experiment object having a value identifying the derived experiment class associated with the experiment type of the chemical experiment, and the library ID property of the second experiment object having a value identifying the library of materials.

3. The method of claim 2, wherein:

the representation includes data defining one or more data set objects, each data set object including data defining a set of values derived from the chemical experiment, each value of the set of values being associated with one or more of the plurality of members of the library of materials, each data set object being associated with a property of the first experiment object.

4. The method of claim 2, wherein:

the representation includes data defining one or more image objects, each image object including data representing a state of at least a subset of the plurality of members of the library of materials at a time during the chemical experiment, each image object being associated with a property of the first experiment object.

5. The method of claim 2, wherein:

the representation includes a self-describing representation of the chemical experiment.

6. The method of claim 2, wherein:

the representation includes an XML stream, a Java object, a COM IDL interface or a CORBA IDL interface describing the chemical experiment.

7. The method of claim 2, further comprising:

parsing the representation to map the data from the chemical experiment to tables in a relational database based on the properties of at least the first experiment object.

8. The method of claim 7, wherein:

the representation includes an XML stream describing the chemical experiment; and

parsing the representation includes identifying each of a plurality of XML entities in the XML stream, each entity having associated content;

mapping each XML entity into a corresponding object property; and

assigning the content associated with an XML entity to a database table based on the corresponding object property.

9. The method of claim 2, wherein:

the derived experiment class properties include one or more properties derived from one or more parameters of the associated experiment type.

10. The method of claim 3, wherein:

at least one data set object includes data defining a set of values derived from a parameter of the chemical experiment; and

the at least one data set object is associated with a property of the first experiment object derived from the parameter of the chemical experiment.

11. The method of claim 10, wherein:

the set of values is a set of values measured for the parameter of the chemical experiment.

12. The method of claim 8, further comprising:

storing the content in the assigned database table in the relational database.

13. The method of claim 12, further comprising:

receiving a query specifying search terms for one or more searchable data fields in the relational database;

searching the relational database according to the query; and

returning a search result including data identifying a set of one or more element objects satisfying the search terms of the query.

14. The method of claim 13, further comprising:

receiving an input specifying one or more displayable fields for display; and

displaying one or more values associated with the specified displayable fields for each of the set of element objects satisfying the search terms of the query.

15. The method of claim 13, further comprising:

storing the search result as a list of element objects satisfying the search terms of the query.

16. The method of claim 12, further comprising:

receiving a database access request including an object identifier specifying content to be retrieved from the relational database;

retrieving the specified content from a table in the relational database;

generating an object representation of the content based on a classname included in the specified content; and

mapping the object representation to an XML stream describing the content.

51. The method of claim 1, further comprising:

parsing the representation to map a subset of the data from the representation to tables in a relational database based on the properties of the experiment object.

52. The method of claim 51, wherein:

parsing the representation includes mapping a first subset of the data from the representation to a first set of database tables based on a first mapping schema and a second subset of the data from the chemical experiment to a second set of database tables based on a second mapping schema, the first mapping schema being different from the second mapping schema.

53. The method of claim 52, wherein:

the first subset of the data is different from the second subset of the data.

54. The method of claim 1, further comprising:

parsing the representation to map the data from the representation to a first set of database tables based on a first mapping schema and a second set of database tables based on a second mapping schema, the first set of database tables being different from the second set of database tables.

17. A computer program product on a computer-readable medium for processing data from a chemical experiment on a library of materials, the computer program product comprising instructions operable to cause a programmable processor to:

receive data from a chemical experiment on a library of materials having a plurality of members; and

generate a representation of the chemical experiment, the representation including data defining an experiment object having a plurality of properties derived from the chemical experiment, the experiment object being associated with the library of materials, the representation also including data defining one or more element objects, each element object being associated with one or more members of the library of materials.

18. The computer program product of claim 17, wherein:

the chemical experiment has a type that is one of a pre-defined set of one or more experiment types;

the representation implements a data model describing the one or more experiment types, the data model including an experiment base class having a set of experiment base class properties including a classname property for identifying a derived experiment class and a library ID property for identifying a library of materials, the data model also including one or more derived experiment classes, each derived experiment class being associated with one of the experiment types and having a plurality of derived experiment class properties derived from the associated experiment type; and

the chemical experiment is represented in the representation by a first experiment object instantiated from the derived experiment class associated with the type of the chemical experiment, and by a second experiment object instantiated from the experiment base class, the classname property of the second experiment object having a value identifying the derived experiment class associated with the experiment type of the chemical experiment, and the library ID property of the second experiment object having a value identifying the library of materials.

19. The computer program product of claim 18, wherein:

the representation includes data defining one or more data set objects, each data set object including data defining a set of values derived from the chemical experiment, each value of the set of values being associated with one or more of the plurality of members of the library of materials, each data set object being associated with a property of the experiment object.

20. The computer program product of claim 18, wherein:

the representation includes data defining one or more image objects, each image object including data representing a state of at least a subset of the plurality of members of the library of materials at a time during the chemical experiment, each image object being associated with a property of the experiment object.

21. The computer program product of claim 18, wherein:

the representation includes a self-describing representation of the chemical experiment.

22. The computer program product of claim 18, wherein:

the representation includes an XML stream, a Java object, a COM IDL interface or a CORBA IDL interface describing the chemical experiment.

23. The computer program product of claim 18, further comprising instructions operable to cause a programmable processor to:

parse the representation to map the data from the chemical experiment to tables in a relational database based on the properties of at least the first experiment object.

24. The computer program product of claim 23, wherein:

the representation includes an XML stream describing the chemical experiment; and

the instructions to parse the representation include instructions operable to cause a programmable processor to identify each of a plurality of XML entities in the XML stream, each entity having associated content;

map each XML entity into a corresponding object property; and

assign the content associated with an XML entity to a database table based on the corresponding object property.

25. The computer program product of claim 18, wherein:

the derived experiment class properties include one or more properties derived from one or more parameters of the associated experiment type.

26. The computer program product of claim 19, wherein:

at least one data set object includes data defining a set of values derived from a parameter of the chemical experiment; and

the at least one data set object is associated with a property of the first experiment object derived from the parameter of the chemical experiment.

27. The computer program product of claim 26, wherein:

the set of values is a set of values measured for the parameter of the chemical experiment.

28. The computer program product of claim 24, further comprising instructions operable to cause a programmable processor to:

store the content in the assigned database table in the relational database.

29. The computer program product of claim 28, further comprising instructions operable to cause a programmable processor to:

receive a query specifying search terms for one or more searchable data fields in the relational database;

search the relational database according to the query; and

return a search result including data identifying a set of one or more element objects satisfying the search terms of the query.

30. The computer program product of claim 29, further comprising instructions operable to cause a programmable processor to:

receive an input specifying one or more displayable fields for display; and

display one or more values associated with the specified displayable fields for each of the set of element objects satisfying the search terms of the query.

31. The computer program product of claim 29, further comprising instructions operable to cause a programmable processor to:

store the search result as a list of element objects satisfying the search terms of the query.

32. The computer program product of claim 28, further comprising instructions operable to cause a programmable processor to:

receive a database access request including an object identifier specifying content to be retrieved from the relational database;

retrieve the specified content from a table in the relational database;

generate an object representation of the content based on a classname included in the specified content; and

map the object representation to an XML stream describing the content.

55. The computer program product of claim 17, further comprising instructions operable to cause a programmable processor to:

parse the representation to map a subset of the data from the representation to tables in a relational database based on the properties of the experiment object.

56. The computer program product of claim 55, wherein:

the instructions operable to cause a programmable processor to parse the representation include instructions operable to cause a programmable processor to map a first subset of the data from the representation to a first set of database tables based on a first mapping schema and a second subset of the data from the chemical experiment to a second set of database tables based on a second mapping schema, the first mapping schema being different from the second mapping schema.

57. The computer program product of claim 56, wherein:

the first subset of the data is different from the second subset of the data.

58. The computer program product of claim 17, further comprising instructions operable to cause a programmable processor to:

parse the representation to map the data from the representation to a first set of database tables based on a first mapping schema and a second set of database tables based on a second mapping schema, the first set of database tables being different from the second set of database tables.

33. A computer-implemented laboratory data management system for processing data from a chemical experiment involving a library of materials, the system comprising:

one or more client processes running on one or more computers coupled to a network, at least one of the client processes being operable to receive data from a chemical experiment on a library of materials having a plurality of members and generate a representation of the chemical experiment, the representation including data defining an experiment object having a plurality of properties derived from the chemical experiment, the experiment object being associated with the library of materials, the representation also including data defining one or more element objects, each element object being associated with one or more members of the library of materials; and

a database server process running on a computer coupled to the network, the database server process being operable to receive the representation of the chemical experiment and to parse the representation to map the data from the chemical experiment to tables in a relational database stored in a memory coupled to the network based on the experiment object properties.

34. The laboratory data management system of claim 33, wherein:

the chemical experiment has a type that is one of a pre-defined set of one or more experiment types;

the database server process implements a data model describing the one or more experiment types, the data model including an experiment base class having a set of experiment base class properties including a classname property for identifying a derived experiment class and a library ID property for identifying a library of materials, the data model also including one or more derived experiment classes, each derived experiment class being associated with one of the experiment types and having a plurality of derived experiment class properties derived from the associated experiment type; and

the representation includes a first experiment object instantiated from the derived experiment class associated with the type of the chemical experiment, and a second experiment object instantiated from the experiment base class, the classname property of the second experiment object having a value identifying the derived experiment class associated with the experiment type of the chemical experiment, and the library ID property of the second experiment object having a value identifying the library of materials.

35. The laboratory data management system of claim 34, wherein:

the representation includes data defining one or more data set objects, each data set object including data defining a set of values derived from the chemical experiment, each value of the set of values being associated with one or more of the plurality of members of the library of materials, each data set object being associated with a property of the first experiment object.

36. The laboratory data management system of claim 34, wherein:

the representation includes data defining one or more image objects, each image object including data representing a state of at least a subset of the plurality of members of the library of materials at a time during the chemical experiment, each image object being associated with a property of the first experiment object.

37. The laboratory data management system of claim 34, wherein:

the representation includes a self-describing representation of the chemical experiment.

38. The laboratory data management system of claim 34, wherein:

the representation includes an XML data stream, a Java object, a COM IDL interface or a CORBA IDL interface describing the chemical experiment.

39. The laboratory data management system of claim 34, wherein:

the representation includes an XML stream describing the chemical experiment; and

the database server process is operable to identify each of a plurality of XML entities in the XML stream, each entity having associated content;

map each XML entity into a corresponding object property; and

assign the content associated with an XML entity to a database table based on the corresponding object property.

40. The laboratory data management system of claim 34, wherein:

the derived experiment class properties include one or more properties derived from one or more parameters of the associated experiment type.

41. The laboratory data management system of claim 35, wherein:

at least one data set object includes data defining a set of values derived from a parameter of the chemical experiment; and

the at least one data set object is associated with a property of the first experiment object derived from the parameter of the chemical experiment.

42. The laboratory data management system of claim 41, wherein:

the set of values is a set of values measured for the parameter of the chemical experiment.

43. The laboratory data management system of claim 39, wherein:

the database server process is operable to store the content in the assigned database table in the relational database.

44. The laboratory data management system of claim 43, wherein:

the database server process is operable to receive a query specifying search terms for one or more searchable data fields in the relational database;

search the relational database according to the query; and

return a search result including data identifying a set of one or more element objects satisfying the search terms of the query.

45. The laboratory data management system of claim 44, wherein:

the database server process is operable to store the search result as a list of element objects satisfying the search terms of the query.

46. The laboratory data management system of claim 39, wherein:

the database server process is operable to receive a database access request including an object identifier specifying content to be retrieved from the relational database;

retrieve the specified content from a table in the relational database;

generate an object representation of the content based on a classname included in the specified content; and

map the object representation to an XML stream describing the content.

59. The laboratory data management system of claim 33, wherein:

the database server process is operable to map a subset of the data from the representation to tables in a relational database based on the experiment object properties.

60. The laboratory data management system of claim 59, wherein:

the database server process is operable to map a first subset of the data from the representation to a first set of database tables based on a first mapping schema and a second subset of the data from the chemical experiment to a second set of database tables based on a second mapping schema, the first mapping schema being different from the second mapping schema.

61. The laboratory data management system of claim 60, wherein:

the first subset of the data is different from the second subset of the data.

62. The laboratory data management system of claim 33, wherein:

the database server process is operable to map the data from the representation to a first set of database tables based on a first mapping schema and a second set of database tables based on a second mapping schema, the first set of database tables being different from the second set of database tables.

47. A laboratory data management system for processing data from a chemical experiment involving a library of materials, the system comprising:

means for receiving data from a chemical experiment on a library of materials having a plurality of members, the chemical experiment having a type that is one of a pre-defined set of one or more experiment types;

means for generating a first representation of the chemical experiment, the first representation implementing a data model describing the one or more experiment types, the data model including an experiment base class having a set of experiment base class properties including a classname property for identifying a derived experiment class and a library ID property for identifying a library of materials, the data model also including one or more derived experiment classes, each derived experiment class being associated with one of the experiment types and having a plurality of derived experiment class properties derived from the associated experiment type, the first representation including data defining a first experiment object instantiated from the derived experiment class associated with the type of the chemical experiment, the first representation also including data defining a second experiment object instantiated from the experiment base class, the classname property of the second experiment object having a value identifying the derived experiment class associated with the experiment type of the chemical experiment, and the library ID property of the second experiment object having a value identifying the library of materials;

means for parsing the first representation to map the data from the chemical experiment to tables in a relational database based on the properties of at least the first experiment object; and

means for generating, in response to a database access request, a second representation of the chemical experiment from data stored in the relational database based solely on data stored in the relational database.

48. A laboratory data management system for processing data from a chemical experiment involving a library of materials, the system comprising:

one or more client processes running on one or more computers coupled to a network, each client process being operable to generate a data set including a value for each of a plurality of members of a library of materials and to generate an intermediate representation of the data set, the intermediate representation including data defining an experiment object having a plurality of properties derived from the chemical experiment, the plurality of properties including a data set object assigning each first data set value to one of a set of elements corresponding to a plurality of members of the library of materials;

a middle-tier server process running on a computer coupled to the network, the middle-tier server process being operable to receive the intermediate representation and to parse the intermediate representation to map the element values to database tables according to a predetermined database schema; and

a database process running on a computer coupled to the network, the database process being operable to store the element values in a memory coupled to the network.

63. The laboratory data management system of claim 48, wherein:

the middle-tier server process is operable to map the element values from the intermediate representation to a first set of database tables according to a first predetermined database schema and a second set of database tables according to a second predetermined database schema, the first set of database tables being different from the second set of database tables.

49. A computer-implemented data model for describing data from a set of pre-defined types of chemical experiments capable of being performed on a library of materials, the data model comprising:

an experiment base class having a plurality of experiment base class properties including a classname property for identifying a derived experiment class and a library ID property for identifying a library of materials;

one or more derived experiment classes, each derived experiment class being associated with one of the set of pre-defined types of chemical experiments capable of being performed on the library of materials and having a plurality of derived experiment class properties derived from the associated experiment type; and

an element class having a plurality of element class properties including a position property for identifying one or more members of a library of materials and a value property for storing a value derived from a chemical experiment for the members identified by the position property;

wherein;

a specific experiment in the set of pre-defined experiments is represented by a first experiment object instantiated from the derived experiment class associated with the type of the chemical experiment, and by a second experiment object instantiated from the experiment base class, the classname property of the second experiment object having a value identifying the derived experiment class associated with the experiment type of the chemical experiment, and the library ID property of the second experiment object having a value identifying the library of materials.

50. A data structure for processing data from a chemical experiment involving a library of materials, the chemical experiment having a type selected from a set of pre-defined experiment types, the data structure comprising:

a first experiment object representing the chemical experiment, the first experiment object being instantiated from an experiment base class and having a plurality of experiment base class properties including a classname property identifying a derived experiment class corresponding to the type of the chemical experiment, and a library ID property identifying the library of materials;

a second experiment object representing the chemical experiment, the second experiment object being instantiated from the derived experiment class corresponding to the type of the chemical experiment, the second experiment object having a plurality of derived experiment class properties derived from the corresponding experiment type;

one or more element objects, each element object being associated with one or more members of the library of materials; and

one or more data set objects, each data set object including a set of values derived from the chemical experiment, each value of the set of values being associated with one or more element objects, each data set object being associated with a derived experiment class property of the second experiment object.