System and method for creating customized ontologies

• US 7,505,989 B2
• Filed: 05/05/2005
• Issued: 03/17/2009
• Est. Priority Date: 09/03/2004
• Status: Expired due to Fees

• Current Assignee: BioWisdom Ltd. (Instem Plc)
• Original Assignee: BioWisdom Ltd. (Instem Plc)
• Inventors: Davis, Benjamin, Blue, Neil Andrew Miller, Eldridge, Matthew David, Chambers, Jonathan Kim, Gardner, Stephen Philip, Hill, Robin Duncan, McMenamin, Conor
• Primary Examiner(s): Vital; Pierre M
• Assistant Examiner(s): Nofal; Christopher P
• Application Number:
  US11/122,007
• Publication Number:
  US 20060053098A1
• Time in Patent Office: 1,412 Days
• Field of Search: 707/1, 707/3, 707/9, 707/10, 707/101, 707/102, 707/103.R, 707/104.1, 709/202, 709/217, 709/224, 715/502, 715/513, 715/514, 715/768, 715/804, 715/835, 715/866, 717/106, 717/120, 717/146, 704/4, 704/9, 706/45, 702/19
• US Class Current: 1/1
• CPC Class Codes: G06F 16/367 Ontology
• CPC Class Codes: Y10S 707/99943 Generating database or data structure, e.g. via user interface
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing

Abstract

The invention relates generally to a system and method for creating custom multi-relational ontologies. The invention includes a system and method for creating a master ontology and the application of one or more customizing constraints to the master ontology. Also provided are methods for creating custom ontologies using path-finding and creation of custom ontologies by applying customizing constraints to extraction, assembly, curation, and publication processes.

Claims

1. A computer-implemented system for creating one or more customized ontologies from a master ontology, the system comprising:

a master ontology including a plurality of individual assertions, wherein an assertion comprises a first concept, a second concept, and a relationship between the first concept and the second concept, wherein at least one concept in a first assertion of the plurality of individual assertions is a concept in at least a second assertion of the plurality of individual assertions, and wherein one or more relationships in the plurality of individual assertions comprise relationships unconstrained by any hierarchical arrangement of concepts;

a set of master data sources from which the plurality of individual assertions of the master ontology are derived, each master data source associated with an origin tag indicating its origin; and

at least one processor and a memory, the memory including instructions that cause the processor to;

apply one or more customizing constraints to the plurality of individual assertions of the master ontology to produce a customized set of individual assertions from the plurality of assertions of the master ontology, wherein the one or more customizing constraints include;

(i) an exclusion list of master data sources that are selected for exclusion from the customized set of individual assertions such that none of the individual assertions in the customized set include assertions from the plurality of individual assertions of the master ontology derived from the master data sources on the exclusion list, wherein each master data source in the exclusion list is listed along with its origin tag, and

(ii) a list of additional data sources not in the set of master data sources to be utilized in the custom ontology, wherein one or more individual assertions derived from the list of additional data sources are included in the customized set of individual assertions,

remove individual assertions derived from the excluded master data sources from a copy of the plurality of individual assertions of the master ontology,

extract additional individual assertions from the additional data sources,

confirm the validity of the information contained in additional assertions,

add the additional individual assertions to the copy of the plurality of individual assertions after the individual assertions derived from the excluded master data sources have been removed, to form the customized set of individual assertions, and

store the customized set of individual assertions in a data storage device as a custom ontology.

2. The system of claim 1, wherein the exclusion list of master data sources includes a subset of data sources from the set of master data sources.

3. The system of claim 1, wherein the one or more customizing constraints further include one or more properties of one or more concepts that are to be used in the custom ontology such that one or more of the assertions in the customized set of individual assertions includes concepts having at least one of the one or more properties.

4. The system of claim 1, wherein the one or more customizing constraints further include one or more of:

one or more concepts that are to be used in the custom ontology such that one or more of the assertions in the customized set of assertions include at least one of the one or more concepts;

one or more concept types that are to be used in the custom ontology such that one or more of the assertions in the customized set of assertions include concepts of the one or more concept types;

one or more relationships that are to be used in the custom ontology such that one or more of the assertions in the customized set of assertions include at least one of the one or more relationships;

or

one or more relationship types that are to be used in the custom ontology such that one or more of the assertions in the customized set of assertions include relationships of the one or more relationship types.

5. A computer-implemented method for creating one or more customized ontologies from a master ontology, comprising:

providing a master ontology including a plurality of individual assertions, wherein an assertion comprises a first concept, a second concept, and a relationship between the first concept and the second concept, wherein at least one concept in a first assertion of the plurality of individual assertions is a concept in at least a second assertion of the plurality of individual assertions, and wherein one or more relationships in the plurality of individual assertions comprise relationships unconstrained by any hierarchical arrangement of concepts, wherein the master ontology is associated with a set of master data sources from which the plurality of individual assertions of the master ontology are derived, each master data source associated with an origin tag indicating its origin;

applying one or more customizing constraints to the plurality of individual assertions of the master ontology to produce a customized set of individual assertions from the plurality of individual assertions of the master ontology, wherein the one or more customizing constraints include;

(i) an exclusion list of master data sources that are selected for exclusion from the customized set of individual assertions such that none of the individual assertions in the customized set include assertions from the plurality of individual assertions of the master ontology derived from the master data sources on the exclusion list, wherein each master data source in the exclusion list is listed along with its origin tag, and

(ii) a list of additional data sources not in the set of master data sources to be utilized in the custom ontology, wherein one or more individual assertions derived from the list of additional data sources are included in the customized set of individual assertions;

removing individual assertions derived from the excluded master data sources from a copy of the plurality of individual assertions of the master ontology;

extracting additional individual assertions from the additional data sources;

confirming the validity of the information contained in additional assertions;

adding the additional individual assertions to the copy of the plurality of individual assertions after the individual assertions derived from the excluded master data sources have been removed, to form the customized set of individual assertions; and

storing the customized set of individual assertions as a custom ontology.

6. The method of claim 5, wherein the exclusion list of master data sources includes a subset of data sources from the set of master data sources.

7. The method of claim 5, wherein the one or more customizing constraints further include one or more properties of one or more concepts that are to be used in the custom ontology such that one or more of the assertions in the customized set of individual assertions includes concepts having at least one of the one or more properties.

8. The method of claim 5, wherein the one or more customizing constraints further include one or more of:

one or more concepts that are to be used in the custom ontology such that one or more of the assertions in the customized set of assertions include at least one of the one or more concepts;

one or more concept types that are to be used in the custom ontology such that one or more of the assertions in the customized set of assertions include concepts of the one or more concept types;

one or more relationships that are to be used in the custom ontology such that one or more of the assertions in the customized set of assertions include at least one of the one or more relationships;

or

one or more relationship types that are to be used in the custom ontology such that one or more of the assertions in the customized set of assertions include relationships of the one or more relationship types.