Laboratory database system and methods for combinatorial materials research

• US 7,085,773 B2
• Filed: 01/07/2002
• Issued: 08/01/2006
• Est. Priority Date: 01/05/2001
• Status: Expired due to Term

• Current Assignee: Symyx Solutions, Inc.
• Original Assignee: Symyx Technologies Incorporated (Dassault Systemes SA)
• Inventors: Dorsett, David R. Jr.
• Primary Examiner(s): Shah, Sanjiv
• Application Number:
  US10/250,618
• Publication Number:
  US 20040088117A1
• Time in Patent Office: 1,667 Days
• Field of Search: 707/104, 707/1, 707/100, 707/103, 382/282, 717/103, 717/108, 703/17
• US Class Current: 707/755
• 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;

associating the received data with 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;

parsing the representation to map data from the representation to one or more tables in a relational database; and

storing the data from the representation in the relational database according to the mapping.

2. The method of claim 1, wherein:

parsing the representation includes extracting object information from the representation, and mapping one or more object properties to one or more database tables based on the extracted object information.

3. The method of claim 2, wherein:

the extracted object information includes for each object in the representation an object class and one or more object properties; and

parsing the representation includes mapping different classes of objects to different database tables, with each row in a given database table representing an object instantiated from the corresponding class and each column corresponding to one of a set of properties defined for objects instantiated from the class.

4. The method of claim 1, wherein:

the chemical experiment has an experiment type corresponding to one of a set of one or more experiment types;

the chemical experiment is represented by a generic experiment object and a derived experiment object, the generic experiment object having a classname property and a library ID property, the classname property associated with the experiment type of the chemical experiment and the library ID property identifying the library of materials, the derived experiment object having a plurality of derived experiment class properties derived from the associated experiment type; and

parsing the representation includes mapping the generic experiment object to a database table including data for experiments having a plurality of different experiment types in the set of experiment types arid mapping the derived experiment object to a database table including data only for experiments having the experiment type of the chemical experiment.

5. 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;

associate the received data with 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;

parse the representation to map data from the representation to one or more tables in a relational database; and

store the data from the representation in the relational database according to the mapping.

6. The computer program product of claim 5, wherein:

the instructions operable to cause a programmable processor to parse the representation include instructions operable to cause a programmable processor to extract object information from the representation and map one or more object properties to one or more database tables based on the extracted object information.

7. The computer program product of claim 6, wherein:

the extracted object information includes for each object in the representation an object class and one or more object properties; and

the instructions operable to cause a programmable processor to parse the representation include instructions operable to cause a programmable processor to map different classes of objects to different database tables, with each row in a given database table representing an object instantiated from the corresponding class and each column corresponding to one of a set of properties defined for objects instantiated from the class.

8. The computer program product of claim 5, wherein:

the chemical experiment has an experiment type corresponding to one of a set of one or more experiment types;

the chemical experiment is represented by a generic experiment object and a derived experiment object, the generic experiment object having a classname property and a library ID property, the classname property associated with the experiment type of the chemical experiment and the library ID property identifying the library of materials, the derived experiment object having a plurality of derived experiment class properties derived from the associated experiment type; and

the instructions operable to cause a programmable processor to parse the representation include instructions operable to cause a programmable processor to map the generic experiment object to a database table including data for experiments having a plurality of different experiment types in the set of experiment types and map the derived experiment object to a database table including data only for experiments having the experiment type of the chemical experiment.

9. 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 associate the received data with 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.

10. 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;

associating the received data with 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

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.

11. The method of claim 10, 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.

12. The method of claim 11, wherein:

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

13. 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;

associating the received data with 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

parsing the representation to map 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.

14. 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;

associate the received data with 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

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.

15. The computer program product of claim 14, 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.

16. The computer program product of claim 15, wherein:

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

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;

associate the received data with 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

parse the representation to map 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.

18. 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 associate the received data with 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 a subset of the data from the representation to tables in a relational database based on the experiment object properties.

19. The laboratory data management system of claim 18, 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.

20. The laboratory data management system of claim 19, wherein:

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

21. 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 associate the received data with 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 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.

22. A laboratory data management system for processing data from 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, 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; 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.

23. A computer-implemented method for processing data from experiments performed on libraries of materials, comprising:

receiving data from a chemical experiment on a library of materials having a plurality of members, the chemical experiment having an experiment type from a set of experiment types; and

associating the received data with a representation of the chemical experiment, the representation including data defining a first experiment object and a second experiment object, the first experiment object being associated with the library of materials, the second experiment object having a plurality of properties derived from the experiment type of the chemical experiment and being associated with one or more element objects representing members of the library of materials, each of the one or more element objects being associated in the representation with data from the received data for the corresponding library member.

24. The method of claim 23, further comprising:

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

generating the representation of the chemical experiment, the first experiment object being instantiated from the experiment base class, the first experiment object having a library ID value identifying the library of materials and a derived experiment class value identifying the experiment type of the chemical experiment, the second experiment object being instantiated from the derived experiment class corresponding to the experiment type of the chemical experiment and including the one or more element objects representing members of the library of materials.

25. The method of claim 23, wherein:

the second experiment object references the one or more element objects representing the library of materials as children in an object hierarchy.

26. The method of claim 23, further comprising:

generating a representation of a second chemical experiment performed on the library of materials, the representation of the second chemical experiment including one or more additional experiment objects associated with the library of materials.

27. The method of claim 23, further comprising:

parsing the representation to map the received data to one or more tables in a relational database; and

storing the received data in the relational database according to the mapping.

28. 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, the chemical experiment having an experiment type from a set of experiment types; and

associate the received data with a representation of the chemical experiment, the representation including data defining a first experiment object and a second experiment object, the first experiment object being associated with the library of materials, the second experiment object having a plurality of properties derived from the experiment type of the chemical experiment and being associated with one or more element objects representing members of the library of materials, each of the one or more element objects being associated in the representation with data from the received data for the corresponding library member.

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

provide an experiment base class and one or more derived experiment classes, the experiment base class having a set of class properties including a library ID property for identifying a library of materials and a derived experiment class property for identifying an experiment type from the set of experiment types, each derived experiment class being associated with one of a set of predetermined experiment types and having a plurality of derived experiment class properties derived from the associated experiment type; and

generate the representation of the chemical experiment, the first experiment object being instantiated from the experiment base class, the first experiment object having a library ID value identifying the library of materials and a derived experiment class value identifying the experiment type of the chemical experiment, the second experiment object being instantiated from the derived experiment class corresponding to the experiment type of the chemical experiment and including the one or more element objects representing members of the library of materials.

30. The computer program product of claim 28, wherein:

the second experiment object references the one or more element objects representing the library of materials as children in an object hierarchy.

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

generate a representation of a second chemical experiment performed on the library of materials, the representation of the second chemical experiment including one or more additional experiment objects associated with the library of materials.

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

parse the representation to map the received data to one or more tables in a relational database; and

store the received data in the relational database according to the mapping.