Method and system for an ontology, including a representation of unified medical language system (UMLS) using simple knowledge organization system (SKOS)
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 wherein 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, and wherein creating the SKOS representation of UMLS comprises:
converting the UMLS-SN to the SKOS representation;
converting the UMLS-MTH to the SKOS representation;
populating the SKOS representation of the UMLS-MTH with concept unique identifiers (CUI) for concepts of the UMLS-MTH; and
mapping one or more source vocabularies in the SKOS representation of UMLS to the SKOS representation of UMLS-MTH to represent correspondence of concepts using the populated CUIs in the representation of the UMLS-MTH as mapping points between concepts 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 wherein 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, and wherein creating the SKOS representation of UMLS comprises:
converting the UMLS-SN to the SKOS representation;
converting the UMLS-MTH to the SKOS representation;
populating the SKOS representation of the UMLS-MTH with concept unique identifiers (CUI) for concepts of the UMLS-MTH; and
mapping one or more source vocabularies in the SKOS representation of UMLS to the SKOS representation of UMLS-MTH to represent correspondence of concepts using the populated CUls in the representation of the UMLS-MTH as mapping points between concepts 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 wherein 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, and wherein creating the SKOS representation of UMLS comprises:
converting the UMLS-SN to the SKOS representation;
converting the UMLS-MTH to the SKOS representation;
populating the SKOS representation of the UMLS-MTH with concept unique identifiers (CUI) for concepts of the UMLS-MTH; and
mapping one or more source vocabularies in the SKOS representation of UMLS to the SKOS representation of UMLS-MTH to represent correspondence of concepts using the populated CUls in the representation of the UMLS-MTH as mapping points between concepts 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.