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Ontologies
Appendix 6 Ontologies
Definition According to Studer [STU 98], an ontology is an explicit specification of a shared conceptualization that consists of a set of basic category definitions (objects, relationships, properties). These make it possible to describe the objects of the field of interest, their properties and their mutual relationships. Let us return to the terms used by Struder in his definition: – The representation provided is shared: the concepts described are understood and accepted by ontology users. – Conceptualization consists of identifying objects, entities and concepts that exist in the real field described as well as the relationships that link them. It is a simplified view of the world to be represented. – The formalization must be explicit, which requires language to describe these concepts and their relationships. This language must be interpreted by the machine. Ontologies are more complex description structures than classifications, taxonomies and thesauri. They offer opportunities to develop reasoning through inference. It is necessary to distinguish between the semantic model (ontology) and the information model (the model expressing how the data is structured (in an XML message or in the database of a healthcare application)). Why ontologies? The purpose of an ontology is to share common knowledge between people and between components of information systems. They play a central role in ensuring
288
Health Data Processing
the interoperability of systems between organizations, as well as on the semantic web. As a result, from a practical point of view, the knowledge expressed in the ontologies can help us to verify the validity of the statements contained in the messages. The semantic consistency of a message is assessed by referring to the ontology which it is supposed to respect. Broadly speaking, we can distinguish three main functions and contributions of ontologies in healthcare information systems: – Knowledge management. The terminological vocabularies that are used in ontologies are an important resource in any semantic processing, in natural language processing, for example. – Data integration. Their function in service interoperability devices is widely emphasized. – Decision support. The ability of ontologies to develop inferences through the definition of concepts, the explicit expression of their properties and the relationships that bind them is the basis of the possibilities of these tools in decision support. The formalism of the ontologies used to represent knowledge is suited well for modeling the medical knowledge contained in Good Clinical Practice Guidelines. This allows the automated reasoning and implementation of guides using the patient’s data in routine clinical settings. Characteristic
Use
The use of standard identifiers for classes and relationships in Classes and relationships ontologies makes it possible to integrate data across multiple databases
Vocabulary in the field
Labels associated with classes and relationships provide a domain vocabulary that can be used for different applications (natural language processing, user interfaces, etc.)
Metadata and descriptions
The textual definitions, descriptions and additional metadata associated with the classes make it possible to understand the precise meaning of the class in ontology
Axioms and formal definitions
Formal definitions and axioms allow automated and computational access to the semantics of a class or relationship
Table A6.1. The use of the main characteristics of ontologies
Appendix 6
289
Despite their obvious interest in the development of healthcare information systems, it is regrettable that ontologies are not sufficiently integrated into the tools proposed by software publishers. They remain in the field of research, which has developed considerably in recent years. How do ontologies work? A state of the art of classifications and ontologies used in the field of health has been developed by the partners in the CRYSTAL1 (Critical System Engineering Acceleration) project.
1 http://www.crystal-artemis.eu/fileadmin/user_upload/Deliverables/CRYSTAL_D_407_010 _v1.0.pdf.
Definition According to Studer [STU 98], an ontology is an explicit specification of a shared conceptualization that consists of a set of basic category definitions (objects, relationships, properties). These make it possible to describe the objects of the field of interest, their properties and their mutual relationships. Let us return to the terms used by Struder in his definition: – The representation provided is shared: the concepts described are understood and accepted by ontology users. – Conceptualization consists of identifying objects, entities and concepts that exist in the real field described as well as the relationships that link them. It is a simplified view of the world to be represented. – The formalization must be explicit, which requires language to describe these concepts and their relationships. This language must be interpreted by the machine. Ontologies are more complex description structures than classifications, taxonomies and thesauri. They offer opportunities to develop reasoning through inference. It is necessary to distinguish between the semantic model (ontology) and the information model (the model expressing how the data is structured (in an XML message or in the database of a healthcare application)). Why ontologies? The purpose of an ontology is to share common knowledge between people and between components of information systems. They play a central role in ensuring
288
Health Data Processing
the interoperability of systems between organizations, as well as on the semantic web. As a result, from a practical point of view, the knowledge expressed in the ontologies can help us to verify the validity of the statements contained in the messages. The semantic consistency of a message is assessed by referring to the ontology which it is supposed to respect. Broadly speaking, we can distinguish three main functions and contributions of ontologies in healthcare information systems: – Knowledge management. The terminological vocabularies that are used in ontologies are an important resource in any semantic processing, in natural language processing, for example. – Data integration. Their function in service interoperability devices is widely emphasized. – Decision support. The ability of ontologies to develop inferences through the definition of concepts, the explicit expression of their properties and the relationships that bind them is the basis of the possibilities of these tools in decision support. The formalism of the ontologies used to represent knowledge is suited well for modeling the medical knowledge contained in Good Clinical Practice Guidelines. This allows the automated reasoning and implementation of guides using the patient’s data in routine clinical settings. Characteristic
Use
The use of standard identifiers for classes and relationships in Classes and relationships ontologies makes it possible to integrate data across multiple databases
Vocabulary in the field
Labels associated with classes and relationships provide a domain vocabulary that can be used for different applications (natural language processing, user interfaces, etc.)
Metadata and descriptions
The textual definitions, descriptions and additional metadata associated with the classes make it possible to understand the precise meaning of the class in ontology
Axioms and formal definitions
Formal definitions and axioms allow automated and computational access to the semantics of a class or relationship
Table A6.1. The use of the main characteristics of ontologies
Appendix 6
289
Despite their obvious interest in the development of healthcare information systems, it is regrettable that ontologies are not sufficiently integrated into the tools proposed by software publishers. They remain in the field of research, which has developed considerably in recent years. How do ontologies work? A state of the art of classifications and ontologies used in the field of health has been developed by the partners in the CRYSTAL1 (Critical System Engineering Acceleration) project.
1 http://www.crystal-artemis.eu/fileadmin/user_upload/Deliverables/CRYSTAL_D_407_010 _v1.0.pdf.