System and method for data deposition and annotation

• US 20020169565A1
• Filed: 04/24/2002
• Published: 11/14/2002
• Est. Priority Date: 04/25/2001
• Status: Abandoned Application

• Current Assignee: Helen M. Berman, John D. Westbrook
• Original Assignee: Helen M. Berman, John D. Westbrook
• Inventors: Berman, Helen M., Westbrook, John D.
• Application Number:
  US10/132,627
• Publication Number:
  US 20020169565A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 15/20 Protein or domain folding
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics

Abstract

The present invention provides an integrated data system for processing deposition and annotation of data such as three dimensional macromolecular structure data. The system is based on a new community data standard referred to as meta data. The meta data structure provides data or information about other data. Unlike the previous PDB data format, in the present invention PDB both the syntax and semantics of the PDB data standard are rigorously defined and encoded in meta data dictionaries which are fully software accessible. The data processing system of the present invention uses meta data at every functional step beginning with data collection.

Claims

1. A method for processing data comprising the steps of:

receiving input data related to macromolecular structure data;

converting said received input data into a data specification of a persistent data dictionary defining crystallography and macromolecular structure using meta data;

depositing said data specification into an archival data file; and

archiving said archival data file.

2. The method of claim 1 further comprising viewing items of said data specification from said archival data file.

3. The method of claim 1 further comprising the steps of:

annotating said received input data to form annotated output data, said step of annotating said received input data being performed in parallel with said step of converting said received input data; and

storing said annotated output data.

4. The method of claim 3 wherein said annotated output data is stored in a relational database.

5. The method of claim 1 wherein said step of receiving input data comprises a user interface including one or more HTML forms for each category of said input data.

6. The method of claim 1 wherein said input data is a data file.

7. The method of claim 1 wherein said input data is selected from the group consisting of atomic coordination data, genome information and structure determination information.

8. The method of claim 1 wherein said persistent data dictionary is defined in a dictionary description language.

9. The method of claim 1 wherein said persistent data dictionary is a macromolecular crystallographic information file (mmCIF) data dictionary represented by meta data.

10. The method of claim 1 further comprising the step of loading one or more data dictionaries into said persistent data dictionary, said one or more data dictionaries being defined in meta data.

11. The method of claim 1 wherein said data specification describes an attribute of a crystallographic cell constant.

12. The method of claim 1 wherein said persistent data dictionary is represented by a database schema including meta data corresponding to a data dictionary.

13. The method of claim 12 further comprising a mapping between said database schema and said data dictionary.

15. The system of claim 14 further comprising:

means for viewing items of said data specification from said archival data file.

16. The system of claim 14 further comprising:

means for annotating said received input data to form annotated output data; and

means for storing said annotated output data.

17. The system of claim 16 wherein said annotated output data is stored in a relational database.

18. The system of claim 14 wherein said means for receiving input data comprises a user interface including one or more HTML forms for each category of said input data.

19. The system of claim 14 wherein said input data is a data file.

20. The system of claim 14 wherein said input data is selected from the group consisting of atomic coordination data, genome information and structure determination information.

21. The system of claim 14 wherein said persistent data dictionary is defined in a dictionary description language.

22. The system of claim 14 wherein said persistent data dictionary is a macromolecular crystallographic information file (mmCIF) data dictionary represented by meta data.

23. The system of claim 14 further comprising a dictionary loader which loads one or more data dictionaries into said persistent data dictionary, said one or more data dictionaries being defined in meta data.

24. The system of claim 14 wherein said data specification describes an attribute of a crystallographic cell constant.

25. The system of claim 14 wherein said persistent data dictionary is represented by a database schema including meta data corresponding to a data dictionary.

26. The system of claim 25 further comprising a mapping between said database schema and said data dictionary.

28. The method of claim 27 further comprising viewing items of said data specification from said archival data file.

29. The method of claim 27 further comprising the steps of:

annotating said received input data to form annotated output data, said step of annotating said received input data being performed in parallel with said step of converting said received input data; and

storing said annotated output data.

30. The method of claim 29 wherein said annotated output data is stored in a relational database.

31. The method of claim 27 wherein said step of receiving input data comprises a user interface including one or more HTML forms for each category of said input data.

32. The method of claim 27 wherein said persistent data dictionary is defined in a dictionary description language.

33. The method of claim 27 further comprising the step of loading one or more data dictionaries into said persistent data dictionary, said one or more data dictionaries being defined in meta data.

34. The method of claim 27 wherein said persistent data dictionary is represented by a database schema including meta data corresponding to a data dictionary.

36. The system of claim 35 further comprising means for viewing items of said data specification from said archival data file.

37. The system of claim 35 further comprising:

means for annotating said received input data to form annotated output data, said step of annotating said received input data being performed in parallel with said step of converting said received input data; and

means for storing said annotated output data.

38. The system of claim 37 wherein said annotated output data is stored in a relational database.

39. The system of claim 35 wherein said means for receiving input data comprises a user interface including one or more HTML forms for each category of said input data.

40. The system of claim 35 wherein said persistent data dictionary is defined in a dictionary description language.

41. The system of claim 38 further comprising a dictionary loader which loads one or more data dictionaries into said persistent data dictionary, said one or more data dictionaries being defined in meta data.

42. The system of claim 35 wherein said persistent data dictionary is represented by a database schema including meta data corresponding to a data dictionary.

43. The system of claim 42 further comprising a mapping between said database schema and said data dictionary.

14. A system for processing data comprising the steps of:

means for receiving input data related to macromolecular structure data;

means for converting said received input data into a data specification of a persistent data dictionary defining crystallography and macromolecular structure using meta data;

means for depositing said data specification into an archival data file; and

means for archiving said archival data file.

27. A method for processing data comprising the steps of:

receiving input data;

converting said received input data into a data specification of a persistent data dictionary using meta data;

depositing said data specification into an archival data file; and

archiving said archival data file.

35. The method of claim 34 further comprising a mapping between said database schema and said data dictionary.

35-1. A system for processing data comprising the steps of:

means for receiving input data;

means for converting said received input data into a data specification of a persistent data using meta data;

means for depositing said data specification into an archival data file; and

means for archiving said archival data file.