Applied Semantic Knowledgebases and Applications Thereof

• US 20100223295A1
• Filed: 04/12/2010
• Published: 09/02/2010
• Est. Priority Date: 12/06/2000
• Status: Abandoned Application

• Current Assignee: IO Informatics, Inc. (Melissa Data Corp)
• Original Assignee: IO Informatics, Inc. (Melissa Data Corp)
• Inventors: Gombocz, Erich A., Stanley, Robert A.
• Application Number:
  US12/758,415
• Publication Number:
  US 20100223295A1
• Time in Patent Office: Days
• US Class Current: 707/794
• CPC Class Codes: G06F 16/284 Relational databases

Abstract

Novel tools and techniques for generating and/or implementing an applied semantic knowledgebase. Some tools allow for data integration into coherent, semantically connected networks and for generation of sets of query-based models describing complex functional relationships as sub-networks. In an aspect, an applied semantic knowledgebase may comprise collections of SPARQL network queries describing a specific set of sub-network relationships and their applicable ranges for each element in the query.

Claims

1. A method, comprising:

importing, into an informatics program, a plurality of sets of data from a plurality of sources;

synthesizing the plurality of sets of data to produce a coherent data set;

creating one or more semantic networks, the semantic networks expressing data relationships among data in the coherent data set;

obtaining a pattern characteristic for a biologically relevant function by reducing network complexity of the one or more semantic networks;

generating one or more SPARQL arrays from the pattern characteristic;

storing the one or more SPARQL arrays in a database; and

generating an applied semantic knowledgebase from the one or more SPARQL arrays.

2. The method of claim 1, further comprising:

screening an unknown data population with one or more of the SPARQL arrays;

identifying one or more relationships in the unknown data population, based on the screening; and

displaying an indication of the one or more relationships in a user interface.

3. An apparatus, comprising:

a computer readable medium having encoded thereon a set of instructions executable by one or more computers to perform one or more operations, the set of instructions comprising;

instructions for importing, into an informatics program a plurality of sets of data from a plurality of sources;

instructions for synthesizing the plurality of sets of data to produce a coherent data set;

instructions for creating one or more semantic networks, the semantic networks expressing data relationships among data in the coherent data set;

instructions for obtaining a pattern characteristic for a biologically relevant function by reducing network complexity of the one or more semantic networks;

instructions for generating one or more SPARQL arrays from the pattern characteristic;

instructions for storing the one or more SPARQL arrays in a database; and

instructions for generating an applied semantic knowledgebase from the one or more SPARQL arrays.

4. A computer system, comprising:

one or more processors; and

a computer readable medium in communication with the one or more processors, the computer readable medium having encoded thereon a set of instructions executable by the computer system to perform one or more operations, the set on instructions comprising;

instructions for importing, into an informatics program a plurality of sets of data from a plurality of sources;

instructions for synthesizing the plurality of sets of data to produce a coherent data set;

instructions for creating one or more semantic networks, the semantic networks expressing data relationships among data in the coherent data set;

instructions for obtaining a pattern characteristic for a biologically relevant function by reducing network complexity of the one or more semantic networks;

instructions for generating one or more SPARQL arrays from the pattern characteristic;

instructions for storing the one or more SPARQL arrays in a database; and

instructions for generating an applied semantic knowledgebase from the one or more SPARQL arrays.

5. A method, comprising,

generating an applied semantic knowledgebase from one or more SPARQL arrays;

screening an unknown data population with one or more of the SPARQL arrays;

identifying one or more relationships in the unknown data population, based on the screening; and

displaying an indication of the one or more relationships in a user interface.

6. The method of claim 5, wherein generating an applied semantic knowledgebase comprises merging a plurality of data sets under a common ontology to produce a unified semantic network.

7. The method of claim 6, wherein the unified semantic network is multidimensional.

8. The method of claim 6, wherein generating an applied semantic knowledgebase further comprises:

displaying a plurality of markers from within the semantic network;

receiving a selection of a set of markers from within the plurality of markers, the selected set of markers representing a sub-network of the semantic network; and

saving the sub-network as a SPARQL array.

9. The method of claim 5, wherein generating an applied semantic knowledgebase comprises generating an applied semantic knowledgebase based on patterns or profiles representing characteristics in datasets applicable to predictive modeling and screening.

10. The method of claim 9, wherein generating an applied semantic knowledgebase further comprises:

performing one or more SPARQL queries to identify said patterns or profiles; and

saving said patterns or profiles as one or more applied semantic knowledgebases.

11. The method of claim 10, wherein the one or more SPARQL queries comprises a textual query.

12. The method of claim 10, wherein the one or more SPARQL queries comprises a graphical query.

13. The method of claim 10, wherein the one or more SPARQL queries comprises a numeric query.

14. The method of claim 5, further comprising:

validating, with the applied semantic knowledgebase, a predictive modeling quality of one or more known reference datasets.

15. The method of claim 5, further comprising:

modeling, with the applied semantic knowledgebase, one or more unknown datasets.

16. The method of claim 5, further comprising:

providing decision support, with the applied semantic knowledgebase, for experimental result interpretation in translational research.

17. The method of claim 5, further comprising:

providing decision support, with the applied semantic knowledgebase, for experimental result interpretation in drug discovery or development.

18. The method of claim 17, wherein providing decision support comprises target validation.

19. The method of claim 17, wherein providing decision support comprises biomarker discovery.

20. The method of claim 17, wherein biomarker discovery comprises compound efficacy and toxicity screening.

21. The method of claim 5, further comprising:

performing predictive modeling, using the applied semantic knowledgebase, in a personalized medicine application.

22. The method of claim 21, wherein the personalized medicine application is selected from the group consisting of patient screening, disease characterization and patient stratification.

23. An apparatus, comprising:

a computer readable medium having encoded thereon a set of instructions executable by one or more computers to perform one or more operations, the set of instructions comprising;

instructions for generating an applied semantic knowledgebase from one or more SPARQL arrays;

instructions for identifying one or more relationships in the unknown data population, based on the screening; and

instructions for displaying an indication of the one or more relationships in a user interface.

24. A computer system, comprising:

one or more processors; and

a computer readable medium in communication with the one or more processors, the computer readable medium having encoded thereon a set of instructions executable by the computer system to perform one or more operations, the set on instructions comprising;

instructions for generating an applied semantic knowledgebase from one or more SPARQL arrays;

instructions for identifying one or more relationships in the unknown data population, based on the screening; and

instructions for displaying an indication of the one or more relationships in a user interface.