System and method for biotechnology information access and data analysis

• US 20040068514A1
• Filed: 10/04/2002
• Published: 04/08/2004
• Est. Priority Date: 10/04/2002
• Status: Abandoned Application

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Graham, Simon, Collins, Patricia, Vailaya, Aditya, Chundi, Parvathi
• Application Number:
  US10/264,598
• Publication Number:
  US 20040068514A1
• Time in Patent Office: Days
• US Class Current: 707/102
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/30 Unsupervised data analysis
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 Ontologies; Annotations
• CPC Class Codes: G16B 50/20 Heterogeneous data integration

Abstract

Systems and methods for database searching and data analysis with simultaneous, unified access to multiple heterogeneous data sources with effective reuse of user search session information for data analysis. The systems comprise a data source containing at least a partial copy of at least two public databases, at least one search program module operatively coupled to the data source and configured to carry out a search of the databases in the data source according to a user query, a data mining module operatively coupled to the data source and configured to provide for clustering of search results or documents from the user query and a user interface program module operatively coupled to the search program module and the data mining module, the user interface program module configured provide a visual interface for creating the user query and viewing the search results.

Claims

1. A data access and analysis system, comprising:

(a) a data source containing at least a partial copy of at least two public databases;

(b) at least one search program module operatively coupled to the data source and configured to carry out a search of said databases in said data source according to a user query;

(c) a data mining module operatively coupled to the data source and configured to provide for clustering of search results from said user query; and

(d) a user interface program module operatively coupled to said search program module and said data mining module, said user interface program module configured provide a visual interface for creating said user query and viewing said search results.

2. The system of claim 1, further comprising a reuse program module operatively coupled to said search program module, said data mining module and said user interface program module, said reuse module configured to store user action information in a user data source.

3. The system of claim 1, further comprising a request broker program element operatively coupled to said search program module, said data mining module and said user interface program module, said request broker program element configured to direct at least a portion of said user query to said search program module.

4. The system of claim 1, wherein said at least one search program module comprises a keyword search program module and a structured query search program module.

5. The system of claim 1, wherein said at least one search program module comprises an ontology mapping program module configured to search said data source according to annotation of a selectable ontology.

6. The system of claim 1, further comprising a flexible automation program module configured to allow users to define re-usable search scripts.

7. The system of claim 1, wherein said user interface module is configured to recognize repetitions of user tasks and provide predictions, based on said repetitions, to a user via said visual interface.

8. The system of claim 1, wherein said data mining module is further configured to identify search results according to a selected reference.

9. The system of claim 1, wherein said data mining module is further configured to form clusters of related search results according to an unsupervised clustering procedure.

10. The system of claim 9, wherein said data mining module is capable of preparing a single list of all search results retrieved independently of said unsupervised clustering procedure.

11. The system of claim 1, wherein said data mining module is further configured to assign a relevance score to said search results based upon a frequency of terms from said query that appear within each said search result.

12. The system of claim 9, wherein the unsupervised clustering procedure performed by said data mining module employs a group-average-linkage technique to determine relative distances between said search results.

13. The method of claim 12, wherein said group-average-linkage technique employs an algorithm for determining a proximity score that defines relative distances between said search results, said algorithm comprising

S_ij=2×

(1/2−

N(T_i,T_j)/(N(T_i)+N(T_j))

wherein T₁ is a term in a search result I, T_j is a term in a search result J, N(T₁,T_j) is the number of co-occurring terms that said search results I and J have in common, N(T_i) is the number of terms in search result I, and N(T_j) is the number of terms in search result J.

14. A method for data access and data analysis, comprising

(a) providing a data store containing at least partial copies of at least two public databases;

(b) formulating a query by a user;

(c) submitting said query uniformly to each said database in said data store;

(d) fetching search results based on said query; and

(e) forming clusters of related said search results by a data mining module according to an unsupervised clustering procedure.

15. The method of claim 14, further comprising displaying said clusters of said related search results on a user interface.

16. The method of claim 14, further comprising storing said clusters of said related search results in a user data store.

17. The method of claim 16, further comprising storing at least one user action, associated with said submitting said query, in said user data store.

18. The method of claim 16, further comprising defining a reusable query script and storing said query script in said user data store.

19. The method of claim 16, further comprising identifying a repetitive user action and storing said repetitive user action in said user data store.

20. The method of claim 14, further comprising identifying search results, by said data mining module, according to a selected reference.

21. The method of claim 14, further comprising preparing, by said data mining module, a single list of all search results independently of said unsupervised clustering procedure.

22. The method of claim 14, further comprising assigning a relevance score, by said data mining module, to said search results based upon a frequency of terms from the query that appear within each said search result.

23. The method of claim 14, wherein said forming said clusters of said search results comprises employing, by said data mining module, a group-average-linkage technique to determine relative distances between said search results.

24. The method of claim 23, wherein said employing said group-average-linkage technique comprises employing an algorithm for determining a proximity score that defines relative distances between said search results, said algorithm comprising

S_ij=2×

(1/2−

N(T_i,T_j)/(N(T₁)+N(T_j))

wherein T₁ is a term in a search result I, T_j is a term in a search result J, N(T_i,T_j) is the number of co-occurring terms that said search results I and J have in common, N(T_i) is the number of terms in search result I, and N(T_j) is the number of terms in search result J.

25. A data access and analysis system, comprising:

(a) data source means for providing at least a partial copy of each of a plurality of public databases;

(b) means for searching said data bases in said data source according to user queries;

(c) data mining means for clustering of documents resulting from said user queries; and

(d) user interface means for providing a visual interface for creating said user queries and viewing said resulting documents.

26. The system of claim 25, further comprising reuse program means for storing user action information associated with said user interface program means in a user data source.

27. The system of claim 25, further comprising request broker means for directing at least a portion of each said user queries to said searching means.

28. The system of claim 25, wherein said searching means comprises keyword search means for querying said data source according to at least one keyword.

29. The system of claim 25, wherein said searching means comprises structured query search means for extraction of structured information from said data source according to said user queries.

30. The system of claim 25, wherein said searching means comprises ontology mapping means for searching said data source according to annotation using a selectable ontology.

31. The system of claim 25, further comprising flexible automation means for defining re-usable user search scripts.

32. The system of claim 25, wherein said user interface means comprises means for recognizing repetitions of user tasks and providing predictions, based on said repetitions, to a user via said visual interface.

33. The system of claim 25, wherein said data mining means further comprises means for identifying said according to a selected reference document.

34. The system of claim 25, wherein said data mining means further comprises means for forming clusters of related said documents according to an unsupervised clustering procedure.

35. The system of claim 34, wherein said data mining means further comprises means for preparing a single list of all said documents retrieved independently of said unsupervised clustering procedure.

36. The system of claim 25, wherein said data mining means further comprises means for assigning a relevance score to said documents resulting from said user queries, based upon a frequency of terms from said query that appear within each said search result.

37. The system of claim 34, wherein said unsupervised clustering procedure employs a group-average-linkage technique to determine relative distances between said search results.

38. The system of claim 37, wherein said group-average-linkage technique employs an algorithm for determining a proximity score that defines relative distances between said search results, said algorithm comprising

S_ij=2×

(½

−

N(T_i,T_j)/(N(T₁)+N(T_j))

wherein T₁ is a term in a search result I, T_j is a term in a search result J, N(T₁,T_j) is the number of co-occurring terms that said search results I and J have in common, N(T_i) is the number of terms in search result I, and N(T_j) is the number of terms in search result J.