Indexing scheme for formulation workflows

• US 20050130229A1
• Filed: 12/16/2004
• Published: 06/16/2005
• Est. Priority Date: 12/16/2003
• Status: Abandoned Application

• Current Assignee: Freeslate Inc. (Unchained Labs Inc.)
• Original Assignee: Symyx Technologies Incorporated (Dassault Systemes SA)
• Inventors: Dorsett, David R. Jr.
• Application Number:
  US11/016,145
• Publication Number:
  US 20050130229A1
• Time in Patent Office: Days
• US Class Current: 435/7.100
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry
• CPC Class Codes: G16C 20/64 Screening of libraries
• CPC Class Codes: G16C 20/90 Programming languages; Computing architectures; Database systems; Data warehousing

Abstract

Methods and computer program products for managing data associated with members of related libraries of materials that include a recipient library and first and second source libraries. The members of the recipient library comprise materials derived from the first and second source libraries. An experiment object representing an experiment performed on members of the recipient library, and having a plurality of associated elements, each representing member(s) of the recipient library, is defined. A source identifier identifying a source from which the material of the corresponding recipient library member was derived is stored in association with each of the plurality of elements.

Claims

1. A computer-implemented method for managing data associated with members of related libraries of materials including a recipient library, a first source library, and a second source library, the members of the recipient library comprising one or more materials derived from one or more members of the first source library and one or more materials derived from one or more members of the second source library, the method comprising:

defining an experiment object representing an experiment performed on members of the recipient library of materials, the experiment object having a plurality of associated elements, each of the plurality of elements representing one or more members of the recipient library; and

storing at least one source identifier in association with each of the plurality of elements, the source identifier associated with a given element identifying a source from which the material of the corresponding recipient library member was derived, a first source identifier identifying a member in the first source library and a second source identifier identifying a member in the second source library.

2. The method of claim 1, wherein:

the recipient library is a daughter library derived from at least one of the first and second source libraries in a daughtering operation.

3. The method of claim 1, wherein:

at least one of the first and second source libraries is related to the recipient library by at least two degrees of relationship.

4. The method of claim 1, wherein:

at least one of the first and second source libraries is related to the recipient library by at least three degrees of relationship.

5. The method of claim 1, wherein:

the first source library, the second source library and the recipient library are related libraries in a defined workflow having N degrees of relationship between an original source library and the most distantly related recipient library for the defined workflow, N being at least three.

6. The method of claim 5, wherein:

N is at least five.

7. The method of claim 1, wherein:

storing a source identifier in association with an element includes, for an element representing one of the one or more members, determining the member in the first or second source library from which the material of the member of the recipient library corresponding to the element was derived by;

querying a library map object based on a recipient library identifier and a recipient library element identifier identifying the element in the recipient library, and

receiving a source library identifier and a source library element identifier for the element in response to the query.

8. The method of claim 7, wherein:

the recipient library element identifier identifies a position of the corresponding member in the recipient library and the source library element identifier identifies a position in the source library from which the material of the corresponding member was derived.

9. The method of claim 7, wherein:

the library map object includes a plurality of library map elements, each library map element mapping from an element of the recipient library to an element of a source library from which the material of the corresponding recipient library member was derived.

10. The method of claim 1, further comprising:

receiving a request for experimental data associated with an element of the first or second source library;

querying a database of experiments based on the source library identifier of the source library and the source library element identifier of the element; and

retrieving one or more data values corresponding to recipient library elements satisfying the query.

11. A computer-implemented method for managing experiment data associated with one or more recipient libraries of materials, each library including two or more members, the recipient library members comprising materials derived directly or indirectly from two or more source libraries, the method comprising:

receiving a request for experimental data associated with a member of a source library represented by an object in a database of experiment objects, each experiment object representing an experiment involving a library of materials, each experiment object having one or more associated elements representing members of the corresponding library, the source library being indicated by a source library identifier and a member of the source library being indicated by a source identifier;

searching the database of experiment objects based on a search query derived from the request and using the source library identifier and the source identifier; and

returning one or more elements from one or more experiment objects representing experiments involving the recipient libraries, the returned elements having element identifiers satisfying the search query.

12. A computer-implemented method for managing experiment data associated with one or more families of related libraries of materials, each family including three or more related libraries of materials, the three or more related libraries including a recipient library and two or more source libraries, each library including one or more members, at least one member of the recipient library comprising materials derived directly or indirectly from members of the two or more source libraries, the method comprising:

receiving data specifying a first recipient library, the first recipient library having members derived directly or indirectly from materials in at least a first source library and a second source library in a first family of related libraries of materials, the family of related libraries having a first library family structure defined by the relationships of at least the first recipient library, the first source library and the second source library;

defining a plurality of elements of a first library map, the plurality of elements including a library map element identifying each member of the first recipient library, each library map element also identifying a member of a source library from which a material was transferred to the corresponding recipient library member in one or more daughtering operations; and

generating a first experiment object according to a data model representing an experiment on members of the first recipient library, the experiment object having a plurality of associated elements representing members of the first recipient library, the generating including assigning to each experiment element an element identifier based on the source library member identified in the library map element for the recipient library member.

13. The computer-implemented method of claim 12, wherein:

the first recipient library is a daughter library derived from at least one of the first and second source libraries in a daughtering operation.

14. The computer-implemented method of claim 12, wherein:

within the first family, at least one of the first and second source libraries is related to the first recipient library by at least three degrees of relationship.

15. The computer-implemented method of claim 13, wherein:

within the first family, the first source library, the second source library and the first recipient library are related libraries in a defined workflow comprising N degrees of relationship between an original source library and the farthest related recipient library for the defined workflow, N being at least three, and

at least one of the first and second source libraries is related to the first recipient library by at least n degrees of relationship, where n ranges from 1 to N.

16. The computer-implemented method of claim 15, wherein:

N is at least five.

17. The computer-implemented method of claim 12, further comprising:

receiving data specifying a second recipient library, the second recipient library having members being derived from materials in two or more source libraries in a second family of library family structure defined by the relationships of the three or more related libraries in the second family, the second library family structure being different than the first library family structure;

defining a plurality of elements of a second library map, the plurality of elements including a library map element identifying each member of the second recipient library, each library map element also identifying a member of the source library from which a material was transferred to the corresponding recipient library member in one or more daughtering operations; and

generating a second experiment object according to the data model representing an experiment on the second recipient library, the second experiment object having a plurality of associated elements representing members of the second recipient library, the generating including assigning to each experiment element of the second experiment object an element identifier based on the source library member identified in the library map element for the recipient library member.

18. The computer-implemented method of claim 12, further comprising:

associating one or more experimental data values with one or more elements of the first experiment object, each experimental data value representing an observation associated with the corresponding member of the first recipient library.

19. A computer program product, tangibly embodied in an information carrier, for managing data associated with members of related libraries of materials including a recipient library, a first source library, and a second source library, the members of the recipient library comprising one or more materials derived from one or more members of the first source library and one or more materials derived from one or more members of the second source library, the computer program comprising instructions to:

define an experiment object representing an experiment performed on members of the recipient library of materials, the experiment object having a plurality of associated elements, each of the plurality of elements representing one or more members of the recipient library; and

store at least one source identifier in association with each of the plurality of elements, the source identifier associated with a given element identifying a source from which the material of the corresponding recipient library member was derived, a first source identifier identifying a member in the first source library and a second source identifier identifying a member in the second source library.

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

the recipient library is a daughter library derived from at least one of the first and second source libraries in a daughtering operation.

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

at least one of the first and second source libraries is related to the recipient library by at least two degrees of relationship.

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

at least one of the first and second source libraries is related to the recipient library by at least three degrees of relationship.

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

the first source library, the second source library and the recipient library are related libraries in a defined workflow having N degrees of relationship between an original source library and the most distantly related recipient library for the defined workflow, N being at least three.

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

N is at least five.

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

storing a source identifier in association with an element includes, for an element representing one of the one or more members, determining the member in the first or second source library from which the material of the member of the recipient library corresponding to the element was derived by;

querying a library map object based on a recipient library identifier and a recipient library element identifier identifying the element in the recipient library, and

receiving a source library identifier and a source library element identifier for the element in response to the query.

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

the recipient library element identifier identifies a position of the corresponding member in the recipient library and the source library element identifier identifies a position in the source library from which the material of the corresponding member was derived.

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

the library map object includes a plurality of library map elements, each library map element mapping from an element of the recipient library to an element of a source library from which the material of the corresponding recipient library member was derived.

28. The computer program product of claim 19, further comprising:

receiving a request for experimental data associated with an element of the first or second source library;

querying a database of experiments based on the source library identifier of the source library and the source library element identifier of the element; and

retrieving one or more data values corresponding to recipient library elements satisfying the query.