Slide 1OverviewGoalOntologySlide 5Advantages of OntologyDevelopment of OntologyExample of OntologyDisease OntologySlide 10Implemented Ontology in OWL FormatBio-Medical OntologiesSlide 13Slide 14Slide 15Slide 16Slide 17Need for IntegrationSlide 19Slide 20Slide 21Applications of OntologyRandomized Clinical Trials (RCT)Life Cycle of Clinical TrialsSlide 25RCT SchemaMatching Patient Records to Clinical TrialsTechnical ChallengesSlide 29ArchitectureSolutions to the ChallengesSlide 32Slide 33Clinical Decision Support SystemSlide 35Nursing COmputer Decision SupportSlide 37Slide 38SummarySlide 40Current status of Ontologies in Biomedical and Clinical Informatics.ByRishi Kanth SaripalleBiomedical Informatics, University of Connecticut, Storrs1OverviewAim of the Presentation.Ontology•Definition and Description.•Example.Present Biomedical OntologyNeed for IntegrationApplication of Biomedical Ontology•Clinical Trials•OASIS: Integration Technique•Clinical Decision Support SystemSummary2BioMedical InformaticsGoalTo study about ontologies, their advantages and applications in the field of Biomedical and Clinical informatics. 3BioMedical InformaticsOntologyDefinition (From Philosophy) :According to Philosophy, Ontology is study of being or existence and forms the basic subject matter of metaphysics. It seeks to describe the basic categories and relationships of being or existence to define entities and types of entities within its framework.4BioMedical InformaticsOntologyIn Computer science , Ontology means “specification of a conceptualization” .It means “A data model that represents a set of concepts within a domain and the relationships between those concepts”. Definition (From Computer Science) :5BioMedical InformaticsAdvantages of Ontology To Share the common structure of information. To reuse the similar domain Ontology. Intelligent system can provide reasoning Systems to make inferences within the Ontology. Semantic way of representing knowledge of the domain.6BioMedical Informatics Determine the domain and Scope ( Range ) of the knowledge. Look for already existing ontology in the similar domain Listing all the terminologies or Concepts of the domain List all the classes and instances to be created in the ontology. Create the properties which will relate these concepts in the ontology.Development of Ontology7BioMedical InformaticsWineAustralian Yellow TailColorFlavorMakerGrapeYellowDelicate AustraliaGermanClassIndividualProperty ValuesProperties 8Example of OntologyBioMedical InformaticsDisease OntologySub-Classes of Cardiology DiseasesInstances of Mitral_Valve_DisordersHierarchical organization of Cardiology Diseases 9BioMedical InformaticsDisease OntologyProperty DefinedRepresentation of “Mitral_Valve_Prolapse” knowledge using properties and instances10BioMedical InformaticsImplemented Ontology in OWL Format…………..<Congenital_Heart_Disease rdf:ID="Atrial_septal_defect"> <Complications> <Cardiac_Arrhythmias rdf:ID="Arrhythmia"> <Has_Intervention rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >defibrillation</Has_Intervention> <Have_Symptoms> <Cardiology_Symptoms rdf:ID="Dyspnea"/> </Have_Symptoms> <Has_Diagnosis_Test> <Cardiology_Diagnosis_Test rdf:ID="Coronary_Angiography"> <Has_Synonyms rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >coronary catheterization </Has_Synonyms> ………………..11BioMedical InformaticsBio-Medical OntologiesOpenCycWordNetGalenUMLSSNOMED – CTFMAGene Ontology12BioMedical InformaticsOpen CycOpen Cyc is an Upper level ontology developed by Cycorp Inc.  Open Cyc has 60,000 hand coded assertions that capture “common sense language”, so that AI algorithms can perform human like reasoning and contains 6,000 concepts13BioMedical InformaticsWord Net WordNet is an electronic lexical database developed at Princeton University that serves as a resource for applications in natural language processing and information retrieval. cancer, malignant neoplastic disease: any malignant growth or tumor caused by abnormal and uncontrolled cell division; it may spread to other parts of the body through the lymphatic system or the blood streamCancer, Crab: (astrology) a person who is born while the sun is in CancerCancer: a small zodiacal constellation in the northern hemisphere; between Leo and GeminiCancer, Cancer the Crab, Crab: the fourth sign of the zodiac; the sun is in this sign from about June 21 to July 22Cancer, genus Cancer: type genus of the family Cancridae14BioMedical InformaticsGalen GALEN stands for Generalised Architecture for Languages, Encyclopedia and Nomenclature in Medicine. It is a European project developed for reuse of terminology in clinical systems. 15BioMedical InformaticsUMLS UMLS acronym for Unifies Medical Language System was developed for National Library of Medicine.Disease is semantic type with around 392 relations (109 semantic relations and 22 other relations). Pneumonia categorized under one semantic type Disease, but has hundreds of relations.16BioMedical InformaticsSNOMED-CT SNOMED stands for Systemized Nomenclature Of Medicine Clinical Terms. SNOMED-CT is the result of merging two ontologies: SNOMED-RT and Clinical Terms.17BioMedical InformaticsNeed for Integration All the ontologies developed have a common aim, describing the domain knowledge Integration of ontologies is becoming very critical as applications tend to use multiple ontologies and concepts in the various ontology overlap or same concept is described in multiple ways. For example, the concept “Blood” is described differently in above discussed ontologies. One describes it as “Fluid”, another as “substance” and another as “semi- solid substance” etc. 18BioMedical InformaticsOntology AOntology B Semantics vs Structural Integration ? Difficulties of integration arise with similar, same and complementary ontology integration.19BioMedical InformaticsOASIS: Ontology Mapping and Integration frameworkOASIS20BioMedical Informatics Terms in the OBO ( Open Biomedical Ontology) are arranged in Directed Acyclic Graph. This allows each