Method and system for an ontology, including a representation of unified medical language system (UMLS) using simple knowledge organization system (SKOS)
View Patent ↗Embodiments of an informatics platform where collected data can be normalized, integrated and mapped to a knowledge source, such as medical vocabulary systems are disclosed. One example of such a knowledge source is Unified Medical Language System (UMLS) which is a knowledge source for biomedical applications. Embodiments as depicted herein may provided a method to convert the desired information from UMLS into an ontology representation to allow for its use in conjunction with an informatics system.
1. A system for creating an ontology representation, comprising:
an informatics system comprising a processor and a non-transitory computer readable medium comprising instructions for:
creating a Simple Knowledge Organization System (SKOS) representation of the unified medical language system (UMLS), wherein the UMLS includes a UMLS-Semantic Network (UMLS-SN) and a UMLS-Metathesaurus (UMLS-MTH) comprised of one or more source vocabularies and the SKOS representation of the UMLS includes a SKOS representation of the UMLS-SN, a SKOS representation of the UMLS-MTH and a representation of one or more relationships between the UMLS-SN and the UMLS-MTH, wherein creating the SKOS representation of UMLS comprises converting the UMLS-SN to a SKOS representation, converting the UMLS-MTH to SKOS; populating the SKOS representation of the UMLS-MTH with concept unique identifiers (CUI) for concepts of the UMLS-MTH, creating one or more representations of the source vocabularies comprising UMLS-MTH, populating the representations of the one or more source vocabularies for the SKOS representation of UMLS and mapping the representations of the one or more source vocabularies in the SKOS representation of ULMS to the UMLS-MTH representation to assert correspondence of concepts and wherein the populated CUIs in the representation of the UMLS-MTH are used as a mapping point between concepts of the representations of the one or more source vocabularies.
2. The system of claim 1 , wherein converting the UMLS-SN to a SKOS representation comprises, creating a representation of each semantic type in UMLS, creating one property for each semantic relation in UMLS and representing a hierarchy for the semantic types and a hierarchy for the semantic relations.
3. The system of claim 2 , wherein the UMLS-SKOS domain ontology maps each UMLS Semantic Type into a corresponding owl:Class and each UMLS Semantic Relationship into an owl:ObjectProperty.
4. The system of claim 3 , wherein converting the UMLS-MTH comprises representing each source vocabulary of the UMLS.
5. The system of claim 4 , wherein each concept in each source vocabulary is represented as a skos:ConceptScheme concept.
6. The system of claim 5 , wherein the populating the SKOS representation of the UMLS-MTH with concept unique identifiers (CUI) comprises, for each CUI in UMLS creating a single skos:Concept and making that skos:Concept an rdf:type of a semantic type.
7. A method for creating an ontology representation, comprising:
creating a Simple Knowledge Organization System (SKOS) representation of the unified medical language system (UMLS), wherein the UMLS includes a UMLS-Semantic Network (UMLS-SN) and a UMLS-Metathesaurus (UMLS-MTH) comprised of one or more source vocabularies and the SKOS representation of the UMLS includes a SKOS representation of the UMLS-SN, a SKOS representation of the UMLS-MTH and a representation of one or more relationships between the UMLS-SN and the UMLS-MTH, wherein creating the SKOS representation of UMLS comprises converting the UMLS-SN to a SKOS representation, converting the UMLS-MTH to SKOS; populating the SKOS representation of the UMLS-MTH with concept unique identifiers (CUI) for concepts of the UMLS-MTH, creating one or more representations of the source vocabularies comprising UMLS-MTH, populating the representations of the one or more source vocabularies for the SKOS representation of UMLS and mapping the representations of the one or more source vocabularies in the SKOS representation of ULMS to the UMLS-MTH representation to assert correspondence of concepts and wherein the populated CUIs in the representation of the UMLS-MTH are used as a mapping point between concepts of the representations of the one or more source vocabularies.
8. The method of claim 7 , wherein converting the UMLS-SN to a SKOS representation comprises, creating a representation of each semantic type in UMLS, creating one property for each semantic relation in UMLS and representing a hierarchy for the semantic types and a hierarchy for the semantic relations.
9. The method of claim 8 , wherein the UMLS-SKOS domain ontology maps each UMLS Semantic Type into a corresponding owl:Class and each UMLS Semantic Relationship into an owl:ObjectProperty.
10. The method of claim 9 , wherein converting the UMLS-MTH comprises representing each source vocabulary of the UMLS.
11. The method of claim 10 , wherein each concept in each source vocabulary is represented as a skos:ConceptScheme concept.
12. The method of claim 11 , wherein the populating the SKOS representation of the UMLS-MTH with concept unique identifiers (CUI) comprises, for each CUI in UMLS creating a single skos:Concept and making that skos:Concept an rdf:type of a semantic type.
13. A non-transitory computer readable medium comprising instructions for:
creating a Simple Knowledge Organization System (SKOS) representation of the unified medical language system (UMLS), wherein the UMLS includes a UMLS-Semantic Network (UMLS-SN) and a UMLS-Metathesaurus (UMLS-MTH) comprised of one or more source vocabularies and the SKOS representation of the UMLS includes a SKOS representation of the UMLS-SN, a SKOS representation of the UMLS-MTH and a representation of one or more relationships between the UMLS-SN and the UMLS-MTH, wherein creating the SKOS representation of UMLS comprises converting the UMLS-SN to a SKOS representation, converting the UMLS-MTH to SKOS; populating the SKOS representation of the UMLS-MTH with concept unique identifiers (CUI) for concepts of the UMLS-MTH, creating one or more representations of the source vocabularies comprising UMLS-MTH, populating the representations of the one or more source vocabularies for the SKOS representation of UMLS and mapping the representations of the one or more source vocabularies in the SKOS representation of ULMS to the UMLS-MTH representation to assert correspondence of concepts and wherein the populated CUls in the representation of the UMLS-MTH are used as a mapping point between concepts of the representations of the one or more source vocabularies.
14. The computer readable medium of claim 13 , wherein
converting the UMLS-SN to a SKOS representation comprises, creating a representation of each semantic type in UMLS, creating one property for each semantic relation in UMLS and representing a hierarchy for the semantic types and a hierarchy for the semantic relations.
15. The computer readable medium of claim 14 , wherein the UMLS-SKOS domain ontology maps each UMLS Semantic Type into a corresponding owl:Class and each UMLS Semantic Relationship into an owl:ObjectProperty.
16. The computer readable medium of claim 15 , wherein converting the UMLS-MTH comprises representing each source vocabulary of the UMLS.
17. The computer readable medium of claim 16 , wherein each concept in each source vocabulary is represented as a skos:ConceptScheme concept.
18. The computer readable medium of claim 17 , wherein the populating the SKOS representation of the UMLS-MTH with concept unique identifiers (CUI) comprises, for each CUI in UMLS creating a single skos:Concept and making that skos:Concept an rdf:type of a semantic type.