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  • 1. Dec. 14, 2009 Shanghai Jiao Tong University Medical School, 21 Century Forum OntologyOntology--based Medical Imagingbased Medical Imaging and Radiology Informaticsand Radiology Informatics —— Domain Mapping and DataDomain Mapping and Data ModelingModeling Dr. Jun Ni, Associate Professor, DirectorDr. Jun Ni, Associate Professor, Director Medical Imaging HPC and Informatics LabMedical Imaging HPC and Informatics Lab Department of RadiologyDepartment of Radiology Carver College of MedicineCarver College of Medicine The University of Iowa, Iowa City, Iowa, USAThe University of Iowa, Iowa City, Iowa, USA
  • 2. OutlineOutline Ontological Considerations of Medical ResearchOntological Considerations of Medical Research DomainDomain Emphasizing on the medical domain mapping and its role inEmphasizing on the medical domain mapping and its role in todaytoday’’s medical multidisciplinary researchs medical multidisciplinary research Medical Imaging Informatics Domain Scope and ModelMedical Imaging Informatics Domain Scope and Model ConsiderationsConsiderations Focusing on domain and data model distinctions andFocusing on domain and data model distinctions and challengeschallenges Projects in MHHI Lab at the University of IowaProjects in MHHI Lab at the University of Iowa Spotlighting some of relevant projects which reflects ourSpotlighting some of relevant projects which reflects our vision and task actionsvision and task actions
  • 3. Ontology vs. Medical ResearchOntology vs. Medical Research What is ontology?What is ontology? PhilologyPhilology’’s Subs Sub--specialtyspecialty (theoretical and practical)(theoretical and practical) Existing, Entity (naming, definition, catalog) and RelationshipsExisting, Entity (naming, definition, catalog) and Relationships Domain?Domain? Area with a scope or boundaryArea with a scope or boundary Special academic discipline or fieldSpecial academic discipline or field Interdisciplinary or multidisciplineInterdisciplinary or multidiscipline It has belongings (e.g., medical physics vs. physical medicine)It has belongings (e.g., medical physics vs. physical medicine) Domain ontology?Domain ontology? Domain entity, domain model, scope, boundary, crossing, object aDomain entity, domain model, scope, boundary, crossing, object andnd service model, class, object, services, process,service model, class, object, services, process, …… Each entityEach entity Medical domain and medical research domainMedical domain and medical research domain
  • 4. Medical and Medical ResearchMedical and Medical Research DomainsDomains Medical DomainMedical Domain Medical (Clinic) service domain (Healthcare)Medical (Clinic) service domain (Healthcare) PatientPatient--oriented service operations (hospital or clinicoriented service operations (hospital or clinic services)services) Business operationsBusiness operations Healthcare industrials (modality) interactionsHealthcare industrials (modality) interactions Social and government policy making and implementationSocial and government policy making and implementation Healthcare information system (HIS)Healthcare information system (HIS)
  • 5. Medical and Medical ResearchMedical and Medical Research DomainDomain Medical DomainMedical Domain Medical research domain (Science)Medical research domain (Science) ““MedicalMedical”” as theas the leadingleading entityentity Interaction with scientific research (including biological scienInteraction with scientific research (including biological science,ce, biochemistry,biochemistry, biophysiologybiophysiology, biophysics, computer science, and, biophysics, computer science, and engineering fieldsengineering fields Biomedical research domain (biomedical science and biomedicalBiomedical research domain (biomedical science and biomedical engineering)engineering) Biomedical research and biomedical engineeringBiomedical research and biomedical engineering Difference between sciences (explorations and discoveries) andDifference between sciences (explorations and discoveries) and engineering areas (implementation and integral efforts)engineering areas (implementation and integral efforts) Clinical translational or transformative efforts (linking to medClinical translational or transformative efforts (linking to medicalical service domain)service domain) CTSACTSA’’ss roadmaproadmap
  • 6. Medical Domain Medical Clinic Service Domain (Healthcare services, …) Medical Research Domain Clinical Translational Experiments and Science (CTSA in USA) Clinical Transformative
  • 7. MedicalMedical DomainDomain Clinic ServiceClinic Service DomainDomain ClinicalClinical TranslationalTranslational Medical ResearchMedical Research DomainDomain Internal MedicineInternal Medicine SurgerySurgery RadiologyRadiology NeurologyNeurology OncologyOncology CardiologyCardiology GastroenterologyGastroenterology DermatologyDermatology Obstetrics andObstetrics and GynecologyGynecology PathologyPathology CT, MRI, PET,CT, MRI, PET, XX--rayray Mammon graph,Mammon graph, Interventional,Interventional, Breast imaging,Breast imaging, Whole bodyWhole body imaging,imaging, NeuoradiologyNeuoradiology,, …… Chemotherapy,Chemotherapy, radiation therapy,radiation therapy, thermotherapy, genethermotherapy, gene therapytherapy InnovativeInnovative modality,modality, Diagnostics,Diagnostics, CAD,CAD, ImagingImaging informatics,informatics, PhysiologicalPhysiological AnatomicAnatomic analysis,analysis, …… Anatomical science,Anatomical science, medical physics,medical physics, medical imaging,medical imaging, image processing,image processing, image storage, ITimage storage, IT-- based healthcarebased healthcare systems,systems, medicalmedical imaging informaticsimaging informatics,, diagnostic analysis,diagnostic analysis, medical physics,medical physics, …… Nanotechnology,Nanotechnology, biotransport,biotransport, thermothermo--science,science, physiologicalphysiological analysis;analysis; NanoNano-- thermotherapythermotherapy …
  • 8. Medical Imaging InformaticsMedical Imaging Informatics DomainDomain What is Medical Imaging Informatics (MII)?What is Medical Imaging Informatics (MII)? Medical Imaging Informatics (MII) == Radiology Informatics?Medical Imaging Informatics (MII) == Radiology Informatics? SubSub--specialty of radiologyspecialty of radiology One of medical informatics disciplinesOne of medical informatics disciplines Domain Boundary ExtensionDomain Boundary Extension Medical imaging data management, processing, and displayingMedical imaging data management, processing, and displaying ------ >> medical image data mining?medical image data mining? Demand: patient healthcare system andDemand: patient healthcare system and teleradiologyteleradiology/telemedicine/telemedicine Job market: 70,000 on demand, education challengesJob market: 70,000 on demand, education challenges Hawkeye Radiology Informatics (HRI)Hawkeye Radiology Informatics (HRI)
  • 9. MII DomainMII Domain Medical Imaging Informatics (MII) ==Medical Imaging Informatics (MII) == Radiology Informatics (RI)?Radiology Informatics (RI)? One ofOne of medical informaticsmedical informatics SubSub--specialty of radiologyspecialty of radiology Domain BoundaryDomain Boundary ------ > medical image data> medical image data mining?mining? Technical driven:Technical driven: teleradiologyteleradiology/telemedicine/telemedicine Job market: 70,000 on demand, education challengesJob market: 70,000 on demand, education challenges Hawkeye Radiology Informatics (HRI)Hawkeye Radiology Informatics (HRI)
  • 10. MII Naming IdentityMII Naming Identity Imaging Informatics in Medicine (IIM), alsoImaging Informatics in Medicine (IIM), also known as Radiology Informatics (RI) orknown as Radiology Informatics (RI) or Medical Imaging Informatics (MII)Medical Imaging Informatics (MII) A subspecialty of radiology that aims to improveA subspecialty of radiology that aims to improve EfficiencyEfficiency AccuracyAccuracy UsabilityUsability Reliability of medical imaging services within theReliability of medical imaging services within the healthcare enterprisehealthcare enterprise
  • 11. MII Naming IdentityMII Naming Identity The fundamental issues in MII includeThe fundamental issues in MII include Standards for image exchangeStandards for image exchange Communication protocols, underlying computerCommunication protocols, underlying computer data and knowledge representationsdata and knowledge representations CodeCode Terminologies and vocabularies to be portable toTerminologies and vocabularies to be portable to electronic medical record, relation to digitalizedelectronic medical record, relation to digitalized healthcarehealthcare NetworkedNetworked teletele--radiologyradiology other IT issues (other IT issues (KulikowskiKulikowski, 2002), 2002)
  • 12. MII Naming IdentityMII Naming Identity MII is technically devoted to the study of howMII is technically devoted to the study of how information about and contained within medicalinformation about and contained within medical images is retrieved, analyzed, enhanced, andimages is retrieved, analyzed, enhanced, and exchanged within radiology and throughout theexchanged within radiology and throughout the medical enterprisemedical enterprise
  • 13. MII DomainMII Domain Radiology is an inherently metadataRadiology is an inherently metadata--intensive and multiintensive and multi-- technologytechnology--driven specialty of medicinedriven specialty of medicine Radiologists lead research and development in medical imagingRadiologists lead research and development in medical imaging informaticsinformatics With the proliferation of digitized images across the practice oWith the proliferation of digitized images across the practice off medicine to include fields such asmedicine to include fields such as CardiologyCardiology DermatologyDermatology SurgerySurgery GastroenterologyGastroenterology Obstetrics, gynecologyObstetrics, gynecology PathologyPathology ……
  • 14. MII WorkforcesMII Workforces Various industry playersVarious industry players Vendors involved with medical imagingVendors involved with medical imaging IT expertsIT experts Other biomedical informatics professionalsOther biomedical informatics professionals
  • 15. MII DomainMII Domain This domain interacts with broad disciplines:This domain interacts with broad disciplines: Biological scienceBiological science -- includes bench sciencesincludes bench sciences Biochemistry, microbiologyBiochemistry, microbiology Physiology and geneticsPhysiology and genetics Clinical servicesClinical services Practice of medicinePractice of medicine Bedside researchBedside research Outcomes and costOutcomes and cost--effectiveness studieseffectiveness studies Public health policyPublic health policy Information scienceInformation science Acquisition, retrieval and manipulation of dataAcquisition, retrieval and manipulation of data Medical physics / engineeringMedical physics / engineering Use of equipment and technology for a medical purposeUse of equipment and technology for a medical purpose
  • 16. MII DomainMII Domain Traditionally, MII deals with PACS, imageTraditionally, MII deals with PACS, image processing and analysis.processing and analysis. Now it moves towards the direction ofNow it moves towards the direction of knowledgeknowledge--based,based, ““realreal”” informaticsinformatics Deals with not only data formatting and theirDeals with not only data formatting and their integrations but also with processing entitiesintegrations but also with processing entities ((SinihaSiniha, 2002), 2002)
  • 17. MII DomainMII Domain Due to its overlapping, it has many challengesDue to its overlapping, it has many challenges DefiningDefining MIIMII’’ss entities (entities (KulikowskiKulikowski, 1997), 1997) Classifying domain spacesClassifying domain spaces Terminology and data integration (Terminology and data integration (UmitUmit, 2009), 2009) Interoperation in todayInteroperation in today’’s in medical imaging informaticss in medical imaging informatics systems.systems. In todayIn today’’s digital radiology, the ontological standardss digital radiology, the ontological standards must be encoded into an Entiremust be encoded into an Entire--PatientPatient--Entity (EPE)Entity (EPE) Collaborative team of radiologists and IT professionalsCollaborative team of radiologists and IT professionals ((GeisGeis, 2007)s, 2007)s
  • 18. Cloud of Medical Informatics andCloud of Medical Informatics and Computational MedicineComputational Medicine Computer Applications in Healthcare SystemComputer Applications in Healthcare System Knowledge Management and Data MiningKnowledge Management and Data Mining
  • 19. Computational medicineMedical Sociology Biostatistics Bioinformatics (computational genomics, computational genetics) Health informatics Pathology informatics Medical imaging informatics Nursing informatics Cloud of Medical Informatics DomainsCloud of Medical Informatics Domains
  • 20. MII ConnectionsMII Connections MII: medical image data and data processingMII: medical image data and data processing Radiology Informatics: Frontier in cancerRadiology Informatics: Frontier in cancer diagnostics and imagediagnostics and image workflowworkflow Proliferated applications:Proliferated applications: Oncology, cardiology, dermatology, surgery,Oncology, cardiology, dermatology, surgery, gastroenterology, obstetrics, gynecology andgastroenterology, obstetrics, gynecology and pathology, and other medical fieldspathology, and other medical fields Strong digital requirement and IT engagementStrong digital requirement and IT engagement
  • 21. Medical Imaging Informatics Interactions between MII and other medical informatics (Cloud) DermatologyDermatology SurgerySurgery GastroenterologyGastroenterology Obstetrics & gynecologyObstetrics & gynecology CardiologyCardiology RadiologyRadiology NeurologyNeurology PathologyPathology OncologyOncology External Domain Connections
  • 22. Medical Imaging Informatics (MII)Medical Imaging Informatics (MII) ScopeScope What is current scope of MII?What is current scope of MII? A subspecialty of radiology that aims to improveA subspecialty of radiology that aims to improve medicalmedical imaging relatedimaging related discovery and technical services within thediscovery and technical services within the healthcare enterprisehealthcare enterprise Accuracy (methodology)Accuracy (methodology) Efficiency (workflow)Efficiency (workflow) Usability (feasibility or applicability)Usability (feasibility or applicability) Reliability (accessibility)Reliability (accessibility) SustainabilitySustainability Cost/performanceCost/performance Its ultimate goal toIts ultimate goal to improve health care systemsimprove health care systems
  • 23. Medical Imaging Digital Radiology
  • 24. Digitization In Medical SciencesDigitization In Medical Sciences and Data Issueand Data Issue Source: UC Berkeley, School of Information Management and Systems. 0 C.E. 2003 40,000 BCE cave paintings bone tools 3500 writing paper 105 1450 printing 1870 electricity, telephone transistor 1947 computing 1950 1993 The Web Digital Cardiology Electronic Medical Record E-Health Initiatives/Linkages Digital Radiology 1999 Late 1960s Internet Petabytes Digital Pathology
  • 25. NM (128, 128) MRI (256, 256) CT (512, 512) DSA (1024, 1024) CR (2048, 2048) Mammogram (4096, 4096) From H. K Huang, 2004
  • 26. Medical Imaging Informatics Infrastructure -- Crossing Medical Imaging and IT Medical Imaging Software Resources Medical Imaging Hardware Facility
  • 27. Medical Imaging Informatics Infrastructure -- Crossing Medical Imaging and IT Medical Imaging Workforce Knowledge based computer-aided detection (diagnostics), CAD Clinic experience IT knowledge
  • 28. Previous Paradigm:Previous Paradigm: MIIMII’’ss DataData Oriented RoadmapOriented Roadmap Study how medical images (within radiology andStudy how medical images (within radiology and throughout medical enterprise) are processed bythroughout medical enterprise) are processed by AcquisitionAcquisition ArchivingArchiving Retrieving/recoveringRetrieving/recovering Image ProcessingImage Processing AnalyzedAnalyzed EnhancedEnhanced VisualizedVisualized Data format conversionData format conversion ……
  • 29. Current Paradigm: CrossingCurrent Paradigm: Crossing A multidiscipline and interdisciplinaryA multidiscipline and interdisciplinary Intersection with other fields:Intersection with other fields: Medical science (radiology, internal medicine,Medical science (radiology, internal medicine, neuroscience,neuroscience, ……)) Computer and information scienceComputer and information science Biomedical engineeringBiomedical engineering Electrical engineering (signal and data processing)Electrical engineering (signal and data processing) Biological and physiological sciencesBiological and physiological sciences Medical physicsMedical physics ……
  • 30. Hospital Registration Order exam Waiting room Exam operation Modality preparation Paperwork film packageRadiologist previewFetch report to HIS radiologist review final report on RIS Workflow
  • 31. MII Challenges (1)MII Challenges (1) PACS (Picture Archiving and CommunicationPACS (Picture Archiving and Communication System)System) Different regional and industrial interpretation,Different regional and industrial interpretation, configuration, and implementationconfiguration, and implementation Different interfaces and prototypesDifferent interfaces and prototypes Different standardizationDifferent standardization DICOM, HL7, Other IT standardsDICOM, HL7, Other IT standards Different image digitalization of modalitiesDifferent image digitalization of modalities Different scopesDifferent scopes
  • 32. MII Challenges (1)MII Challenges (1) Technical ComponentsTechnical Components Image acquisition and management technologyImage acquisition and management technology Data visualization or image displayData visualization or image display Network and communicationsNetwork and communications Computer application softwareComputer application software
  • 33. MII Challenges (1)MII Challenges (1) PACS Technical ConcernsPACS Technical Concerns Data MigrationData Migration BackBack--up archiveup archive FaultFault--tolerancetolerance Integration with legacy systemsIntegration with legacy systems Fast wideFast wide--area networksarea networks SecuritySecurity
  • 34. PACS Distributed ComputingPACS Distributed Computing ArchitectureArchitecture Large scale (multipleLarge scale (multiple modulemodule--based):based): Module 1 Module 2 Module 3 Distributed multiple- modules within multiple services units; but with single health organization Local networked
  • 35. PACS ClassificationPACS Classification Super scale (enterpriseSuper scale (enterprise--,, cyberinfrastructurecyberinfrastructure--, heterogeneous,, heterogeneous, distributed griddistributed grid--based, cross organization, or even globally):based, cross organization, or even globally): Module 1 of site A Module 2 of site A Module 1 of Site B Module 2 of site B High speed network
  • 36. MII Challenges (2)MII Challenges (2) Lack generic MII ontology (Lack generic MII ontology (Philological IssuePhilological Issue)) Systematic identification and classification of domainSystematic identification and classification of domain entities and existences, and entity relations (e.g.,entities and existences, and entity relations (e.g., communication)communication) No semantic languages for communications orNo semantic languages for communications or workflowsworkflows LooselyLoosely--defined terminologydefined terminology No linkage and leverage to knowledge, artificialNo linkage and leverage to knowledge, artificial intelligent (AI), decision makingintelligent (AI), decision making
  • 37. Ontology Wisdom Philology Knowledge Decision MakingCAD Cognitive Sciences Information Science Data Data Data Data Data Metadata MetadataMetadata Information Management Domain Entity Relations Artificial Intelligence
  • 38. MII Challenges (2)MII Challenges (2) Ontological data model (terminologyOntological data model (terminology classification, entity definition, and relationsclassification, entity definition, and relations establishing) (Methodology issue)establishing) (Methodology issue) KnowledgeKnowledge--drivendriven Artificial intelligenceArtificial intelligence--drivendriven Unprecedented capacity for handling massiveUnprecedented capacity for handling massive datadata System integration and interoperation amongSystem integration and interoperation among various hospital/clinic systemsvarious hospital/clinic systems
  • 39. MII Challenges (2)MII Challenges (2) No standard protocols (No standard protocols (Technical issuesTechnical issues)) To facilitate the interoperation and communicationTo facilitate the interoperation and communication among globallyamong globally--distributed MII resourcesdistributed MII resources To deploy concurrent hardware and softwareTo deploy concurrent hardware and software solutionssolutions To utilize cyberTo utilize cyber--enabled highenabled high--speed networksspeed networks Short of education/training programs (Short of education/training programs (BusinessBusiness issueissue)) To foster the next generation in digital health careTo foster the next generation in digital health care systems.systems.
  • 40. MII Challenges (4)MII Challenges (4) Software DevelopmentSoftware Development ComputerComputer--Aided Detection and Diagnosis (CAD)Aided Detection and Diagnosis (CAD) ComputerComputer--aided interventional radiologyaided interventional radiology Metrics and computing performanceMetrics and computing performance Medical imaging facility and infrastructureMedical imaging facility and infrastructure developmentdevelopment Fundamental research and developmentFundamental research and development Medical Imaging Service Pack (MISP)Medical Imaging Service Pack (MISP) Medical Imaging Informatics Knowledge IntegrationMedical Imaging Informatics Knowledge Integration Toolkit (M2KIT)Toolkit (M2KIT)
  • 41. Basic OntologyBasic Ontology Ontology is a major field in philosophyOntology is a major field in philosophy metaphysics.metaphysics. It is principal ofIt is principal of entitiesentities (objects) and their(objects) and their tiesties.. Ontology methodOntology method Intuitive study of the fundamental properties,Intuitive study of the fundamental properties, modes, and aspects of being, or of entities in generalmodes, and aspects of being, or of entities in general (Raul(Raul CorazzonCorazzon, 2009)., 2009). Ontology deals with the entities that are defined inOntology deals with the entities that are defined in philosophy as distinctions, or separate existences.philosophy as distinctions, or separate existences.
  • 42. Basic OntologyBasic Ontology OntologiesOntologies Ontologically defined entitiesOntologically defined entities Used in system developmental models that better displayUsed in system developmental models that better display communications and internal processing of communicationcommunications and internal processing of communication medium such as medical datamedium such as medical data Study the nature of entity, reality, and basic categories of theStudy the nature of entity, reality, and basic categories of theirir relationshipsrelationships OntologyOntology‘‘s main themes main theme Determine the categories of abstract beingDetermine the categories of abstract being Deals with abstract objectsDeals with abstract objects that are considered as a set that containsthat are considered as a set that contains subsetssubsets Development of external and internal connectionsDevelopment of external and internal connections (relationships)(relationships)
  • 43. Basic OntologyBasic Ontology In a technical perspective, a set of entities can beIn a technical perspective, a set of entities can be referred to a specialreferred to a special collectioncollection ofof abstractabstract objectsobjects Shared characteristics and similar, intellectual activities orShared characteristics and similar, intellectual activities or eventsevents Each object is depicted byEach object is depicted by AttributesAttributes Properties and characteristicsProperties and characteristics EventsEvents Process of activities such as behaviors or functionsProcess of activities such as behaviors or functions
  • 44. Significances of Basic OntologySignificances of Basic Ontology Successfully used in the foundation of semantics, especially inSuccessfully used in the foundation of semantics, especially in objectobject--oriented programming (OOP) languages in computer andoriented programming (OOP) languages in computer and information sciencesinformation sciences Ontological concepts have been intensively employed into the semOntological concepts have been intensively employed into the semanticsantics of objectof object--oriented programming languages, such as C++/C# or Javaoriented programming languages, such as C++/C# or Java Abstraction, Inheritance, and InterfaceAbstraction, Inheritance, and Interface Common ontological approach to a cognitive and integrativeCommon ontological approach to a cognitive and integrative systemsystem Needs to identify the extant entity and their categories with apNeeds to identify the extant entity and their categories with appropriatepropriate grouping or sorting schemesgrouping or sorting schemes In science, the ontology of scientific systems relates to manyIn science, the ontology of scientific systems relates to many principles and rules defined in theology, library science, andprinciples and rules defined in theology, library science, and artificial intelligenceartificial intelligence
  • 45. Basic Ontology: Attributes andBasic Ontology: Attributes and ClassificationClassification In ontological approach, quintessential ontological concepts canIn ontological approach, quintessential ontological concepts can be applied tobe applied to system designsystem design Universals and particularsUniversals and particulars Substance and accidentSubstance and accident Abstract and concrete objectsAbstract and concrete objects Essence and existenceEssence and existence Before one starts to develop a biomedical system architectureBefore one starts to develop a biomedical system architecture and design, he/she should consider the basic questions aboutand design, he/she should consider the basic questions about how to create abstract classes of special entities, and identifyhow to create abstract classes of special entities, and identify the fundamentals and specific properties or attributes of thethe fundamentals and specific properties or attributes of the entities, as well as relations with other classes (sets).entities, as well as relations with other classes (sets). Common question in the design circle of healthcare informationCommon question in the design circle of healthcare information systems.systems. DICOM standard is a perfect exam for this paradigmDICOM standard is a perfect exam for this paradigm
  • 46. Basic Ontology: RelationshipBasic Ontology: Relationship Once the consideration of class is initiated, one shouldOnce the consideration of class is initiated, one should establish system subject, object, and theirestablish system subject, object, and their relationshipsrelationships within the system under consideration.within the system under consideration. This practical ontology paradigm hasThis practical ontology paradigm has not only been applied to semantic descriptions innot only been applied to semantic descriptions in mathematics, computer science, and other physical sciencesmathematics, computer science, and other physical sciences (Heller, 1990)(Heller, 1990) but also been employed in social, religious, linguistics, andbut also been employed in social, religious, linguistics, and other communication related domains (John Symons, 2009).other communication related domains (John Symons, 2009).
  • 47. Ontological EnvironmentsOntological Environments Such philosophy of scientific domain is necessary toSuch philosophy of scientific domain is necessary to explore theexplore the domain knowledgedomain knowledge aboutabout beingbeing, as well as, as well as thethe interactionsinteractions with the subjects and objects of otherwith the subjects and objects of other domains of interdisciplinary and multidisciplinarydomains of interdisciplinary and multidisciplinary sciencessciences TheThe interaction and connectioninteraction and connection with other domainswith other domains must be seriously considered through ontologicalmust be seriously considered through ontological concepts in terms of body and environment.concepts in terms of body and environment. It deals with eitherIt deals with either ““isis--”” oror ““hashas”” relationships.relationships.
  • 48. Ontological EnvironmentsOntological Environments The body takes some special actions in an environmentThe body takes some special actions in an environment Relied to a great degree on insights derived from scientificRelied to a great degree on insights derived from scientific research into biomedical beings taking instinctive action inresearch into biomedical beings taking instinctive action in natural and artificial settings in biomedical sciences.natural and artificial settings in biomedical sciences. The processes by which bodies related to environmentsThe processes by which bodies related to environments became of great concernbecame of great concern Idea of being itself became really difficult to defineIdea of being itself became really difficult to define
  • 49. Ontological EnvironmentsOntological Environments The establishment of body and environment is basedThe establishment of body and environment is based on theon the ontological assumptionsontological assumptions embedded within theembedded within the semantic descriptivesemantic descriptive medium tools for communications,medium tools for communications, such assuch as semantic languagessemantic languages Context for communication: a horizon of unspokenContext for communication: a horizon of unspoken background meanings.background meanings. Because these assumptions both generate and areBecause these assumptions both generate and are regenerated in our everyday interactions,regenerated in our everyday interactions, the locus ofthe locus of our way of being is the communicative event ofour way of being is the communicative event of language in use, especially in biomedical research andlanguage in use, especially in biomedical research and medical services.medical services.
  • 50. Systematic Engineering RenovationSystematic Engineering Renovation System designSystem design’’s paradigm, vision, and envisionings paradigm, vision, and envisioning SubjectSubject--object relationsobject relations Body and environmental relationsBody and environmental relations Different ontological approaches (such as realism, empiricism,Different ontological approaches (such as realism, empiricism, positivism, and postpositivism, and post--modernism)modernism) Extremely important in todayExtremely important in today’’s medical imagings medical imaging informatics, like PACS and radiology Information (RIS)informatics, like PACS and radiology Information (RIS) or enterprise health information (or enterprise health information (eHISeHIS) systems.) systems.
  • 51. Systematic Engineering RenovationSystematic Engineering Renovation OntologyOntology--guided system approach becomes the superguided system approach becomes the super key to provide strategic, scalable and sustainablekey to provide strategic, scalable and sustainable solutions to many integrated informationsolutions to many integrated information--drivendriven systems.systems. In the design of an enterprise healthIn the design of an enterprise health--care system, onecare system, one needs to ensure that the system operates in an effective,needs to ensure that the system operates in an effective, efficient, consistent and reliable way, even process ofefficient, consistent and reliable way, even process of medical data and tasks and their communication ismedical data and tasks and their communication is complex.complex. Such system design needs an ontological vision in termsSuch system design needs an ontological vision in terms of clear entity classification, subject/object relations,of clear entity classification, subject/object relations, semantics in workflow and identitysemantics in workflow and identity
  • 52. Ontology for Computer andOntology for Computer and Information SciencesInformation Sciences The practicalities of achieving cohesion in anThe practicalities of achieving cohesion in an informationinformation--basedbased societysociety Is highly demandedIs highly demanded Is paid attention to ontology, especially in informationIs paid attention to ontology, especially in information science.science. Computer CommunityComputer Community Computer theory, artificial intelligence, formal andComputer theory, artificial intelligence, formal and computational linguistics, biomedical informatics, conceptualcomputational linguistics, biomedical informatics, conceptual modeling, knowledge engineering and informationmodeling, knowledge engineering and information retrievaretrieva Realize that a solid foundation for their research calls forRealize that a solid foundation for their research calls for serious work in ontology, a general theory of the types ofserious work in ontology, a general theory of the types of entities and relations that make up their respective domainsentities and relations that make up their respective domains of inquiryof inquiry
  • 53. Ontology for Computer andOntology for Computer and Information SciencesInformation Sciences Attention is now being focused on the content ofAttention is now being focused on the content of informationinformation rather than on just the formats andrather than on just the formats and languages used to represent information.languages used to represent information. The clearest example of this development is providedThe clearest example of this development is provided by the numerous initiatives powdered byby the numerous initiatives powdered by Semantic WebSemantic Web (W3C).(W3C). Need for integrating research in these different fieldsNeed for integrating research in these different fields arises, so does the realization that strong principles forarises, so does the realization that strong principles for building wellbuilding well--founded ontologies might providefounded ontologies might provide significant advantages over ad hoc, casesignificant advantages over ad hoc, case--based solutions.based solutions.
  • 54. Ontology for Computer andOntology for Computer and Information SciencesInformation Sciences Tools of formal ontology address precisely theseTools of formal ontology address precisely these needs, but a real effort is required in order toneeds, but a real effort is required in order to apply such philosophical tools to the domain ofapply such philosophical tools to the domain of information systemsinformation systems Reciprocally, research in the informationReciprocally, research in the information sciences raises specific ontological questionssciences raises specific ontological questions which call for further philosophicalwhich call for further philosophical investigations.investigations.
  • 55. Ontology for Computer andOntology for Computer and Information SciencesInformation Sciences Many efforts have been made in establishingMany efforts have been made in establishing communities in theoretical and practicalcommunities in theoretical and practical ontology for information science, as well as inontology for information science, as well as in other domain of ontologies.other domain of ontologies.
  • 56. Ontology for Computer andOntology for Computer and Information SciencesInformation Sciences Formal Ontology in Information Science (FOIS) holdsFormal Ontology in Information Science (FOIS) holds sequential conferences on many fundamental andsequential conferences on many fundamental and practical issues of theorems and concrete applications,practical issues of theorems and concrete applications, includingincluding Concepts, theorems, and usagesConcepts, theorems, and usages:: kinds of entitykinds of entity particulars vs. universalsparticulars vs. universals continuants vs. occurrencecontinuants vs. occurrence abstract vs. concreteabstract vs. concrete dependent vs. independentdependent vs. independent natural vs. artificial;natural vs. artificial;
  • 57. Ontology for Computer andOntology for Computer and Information SciencesInformation Sciences Formal relationsFormal relations vagueness and granularityvagueness and granularity identity and changeidentity and change formal comparison among domain ontologiesformal comparison among domain ontologies ontology of physical realityontology of physical reality ontology of mental realityontology of mental reality ontology of social realityontology of social reality ontology of the information societyontology of the information society ontology and natural and artificial language semanticsontology and natural and artificial language semantics ontology and cognitionontology and cognition ontology and medical domains, semioticsontology and medical domains, semiotics
  • 58. Ontology for Computer andOntology for Computer and Information SciencesInformation Sciences Methodologies and ApplicationsMethodologies and Applications TopTop--level vs. application ontologieslevel vs. application ontologies Role of reference ontologiesRole of reference ontologies Ontology integration and alignmentOntology integration and alignment OntologyOntology--driven information systems design requirementsdriven information systems design requirements engineering, knowledge engineeringengineering, knowledge engineering Knowledge management and organizationKnowledge management and organization Knowledge representationKnowledge representation Qualitative modeling, computational lexicaQualitative modeling, computational lexica Terminology information retrievalTerminology information retrieval QuestionQuestion--answering, semantic Webanswering, semantic Web Web services; cloud and Grid computing, domainWeb services; cloud and Grid computing, domain--specific ontologiesspecific ontologies (linguistics, geography, law, library science, biomedical scienc(linguistics, geography, law, library science, biomedical science, ee, e-- business, enterprise integration).business, enterprise integration).
  • 59. Promises of Ontology for BiomedicalPromises of Ontology for Biomedical InformaticsInformatics Information science forwards to the gateway ofInformation science forwards to the gateway of knowledgeknowledge--driven, biomedical data baseddriven, biomedical data based scientific and health care discoveries, andscientific and health care discoveries, and decision making mechanisms withdecision making mechanisms with highlyhighly intelligent communication protocolsintelligent communication protocols.. Such roadmap strongly requires largeSuch roadmap strongly requires large--scale systemscale system’’ss integration and high interoperability, and highlyintegration and high interoperability, and highly-- efficient communication workflow of data and tasks.efficient communication workflow of data and tasks.
  • 60. Promises of Ontology for BiomedicalPromises of Ontology for Biomedical InformaticsInformatics The methodology and conceptual rigor of aThe methodology and conceptual rigor of a philosophically inspired formal ontology can bringphilosophically inspired formal ontology can bring significant benefits in the development andsignificant benefits in the development and maintenance of application ontologies (maintenance of application ontologies (FlettFlett et al, 2003).et al, 2003). Such promise can be inspirited by many testaments in theSuch promise can be inspirited by many testaments in the collaboration between biomedical methodologies andcollaboration between biomedical methodologies and terminologies with semantic languages and computingterminologies with semantic languages and computing technologies for supporting natural language processing,technologies for supporting natural language processing, especially in the medical fields.especially in the medical fields. Barry Smith from the Institute forBarry Smith from the Institute for Formal OntologyFormal Ontology and Medical Information Science (IFOMIS)and Medical Information Science (IFOMIS) clearlyclearly addressed the theoretical foundations of ontologyaddressed the theoretical foundations of ontology (Barry Smith, 2009).(Barry Smith, 2009).
  • 61. Medical Industrials NeedsMedical Industrials Needs To transform a large terminologyTo transform a large terminology--basedbased ontology into one special domain to supportontology into one special domain to support practical applications becomes an urgentpractical applications becomes an urgent demand in healthcare industrials.demand in healthcare industrials. For example, a general procedure has been theFor example, a general procedure has been the implementation of a metaimplementation of a meta--ontological definitionontological definition space in which the definitions of all the conceptsspace in which the definitions of all the concepts and relations can be defined inand relations can be defined in LinkBaseLinkBase ((MontayneMontayne and Flanagan, 2003).and Flanagan, 2003).
  • 62. Natural Language Processing (NLP)Natural Language Processing (NLP) Language and Computing (Language and Computing (L&C)L&C)’’ss advancedadvanced TeSSITeSSI®® technologytechnology suite is developed to meet the needs of a broad range ofsuite is developed to meet the needs of a broad range of industries: healthcare providers, pharmaceutical and R&Dindustries: healthcare providers, pharmaceutical and R&D companies, Government, HIT vendors and software developers.companies, Government, HIT vendors and software developers. L&C offers advanced solutions to those sectors where our toolsL&C offers advanced solutions to those sectors where our tools and technology can offer a significant benefit in natural languaand technology can offer a significant benefit in natural languagege processing (NLP) solution,processing (NLP) solution, terminology/ontologyterminology/ontology andand knowledge management (content management, search andknowledge management (content management, search and retrieval, information extraction, text mining, Semantic Web).retrieval, information extraction, text mining, Semantic Web). Its solutions allow L&C customers and partners to leverageIts solutions allow L&C customers and partners to leverage NLPNLP technology to address a variety of healthcare and business needstechnology to address a variety of healthcare and business needs..
  • 63. Medical Education NeedsMedical Education Needs In education, many schools, including medical schools,In education, many schools, including medical schools, start to teach or provide workshops in ontologicalstart to teach or provide workshops in ontological approaches.approaches. Such education programs commonly introduce a newSuch education programs commonly introduce a new approach to the development of ontologies applicableapproach to the development of ontologies applicable to the medical domain.to the medical domain. The programs highlight the need for a rich reference onThe programs highlight the need for a rich reference on practical ontology for healthcare phenomena andpractical ontology for healthcare phenomena and services, and consider issues or challenges arising in theservices, and consider issues or challenges arising in the medical applications of such a theoretically groundedmedical applications of such a theoretically grounded ontology in improving working applications in theontology in improving working applications in the domain of electronic patient records (EPR).domain of electronic patient records (EPR).
  • 64. Medical Education NeedsMedical Education Needs Many institutions gradually begin to crystallize inMany institutions gradually begin to crystallize in the domain of information systems ontology.the domain of information systems ontology. Some education programs focus primarily on theSome education programs focus primarily on the realism or adequacy of an underlying ontologicalrealism or adequacy of an underlying ontological theory, leaving for others the task of transformingtheory, leaving for others the task of transforming this reference ontology into biomedical workingthis reference ontology into biomedical working applications.applications. They present recent developments in the field ofThey present recent developments in the field of realist ontology, focusing especially on biomedicalrealist ontology, focusing especially on biomedical information science.information science.
  • 65. Medical Education NeedsMedical Education Needs Others focus primarily on the construction of workingOthers focus primarily on the construction of working applications at the expense of ontological realism to practicalapplications at the expense of ontological realism to practical biomedical informatics, with an emphasis on the applicability ofbiomedical informatics, with an emphasis on the applicability of medical natural language understanding applications to detectmedical natural language understanding applications to detect inconsistencies and medical errors in patient reportsinconsistencies and medical errors in patient reports Specific systems in healthcare, and to foster new workforce in lSpecific systems in healthcare, and to foster new workforce in learningearning advanced technologies or toolsadvanced technologies or tools High dimensional ontologies (substances, qualities, functions anHigh dimensional ontologies (substances, qualities, functions andd processes; space and time; niches, contexts, environments) unifyprocesses; space and time; niches, contexts, environments) unifyinging ontologies of medicine at different levels of granularity, problontologies of medicine at different levels of granularity, problematicematic issues: absences, norms, reference to individual patients in cliissues: absences, norms, reference to individual patients in clinicalnical histories, conflicting clinical guidelines, computational tractahistories, conflicting clinical guidelines, computational tractability vs.bility vs. ontological adequacy.ontological adequacy.
  • 66. Medical Education NeedsMedical Education Needs However, there still remains many challengeHowever, there still remains many challenge issues, fundamentally.issues, fundamentally. For example, in biomedical terminology or ontologyFor example, in biomedical terminology or ontology development, one should consider how to identifydevelopment, one should consider how to identify relevant shortcomings in existing systems and howrelevant shortcomings in existing systems and how to properly describe niches/contexts of healthcare.to properly describe niches/contexts of healthcare.
  • 67. Medical Education NeedsMedical Education Needs FutureFuture electronic patient record (EPR) systemelectronic patient record (EPR) system developers must integrate their special domaindevelopers must integrate their special domain applications to largeapplications to large--scale systemsscale systems How to cooperatively and collaboratively develop generalHow to cooperatively and collaboratively develop general robotic, dynamic, and interoperable standards of datarobotic, dynamic, and interoperable standards of data ontology model, repository, standard expression andontology model, repository, standard expression and formation, and utility tools becomes a common task.formation, and utility tools becomes a common task. Current biomedical ontology research and developmentCurrent biomedical ontology research and development promoted and supported by NIH programs and NCIpromoted and supported by NIH programs and NCI’’s ands and caBiGcaBiG in USA built significant foundations for futurein USA built significant foundations for future developmentdevelopment
  • 68. caBIGcaBIG AA collection of imaging informaticscollection of imaging informatics tools developed under thetools developed under the umbrella of the National Cancer Institutesumbrella of the National Cancer Institutes caBIGcaBIG ((cancercancer Biomedical Informatics GridBiomedical Informatics Grid) demonstrates the potential for) demonstrates the potential for collecting, analyzing, integrating, and disseminating informatiocollecting, analyzing, integrating, and disseminating informationn associated with cancer research and care.associated with cancer research and care. TheThe caBIGcaBIG is an information networkis an information network enabling all constituenciesenabling all constituencies in the cancer community to share data and knowledge toin the cancer community to share data and knowledge to accelerate the discovery of new diagnostics and therapeutics, anaccelerate the discovery of new diagnostics and therapeutics, andd to improve patient outcomes.to improve patient outcomes. TheThe caBIGcaBIG imaging workspaceimaging workspace was created as a nationalwas created as a national multidisciplinary expert advisory board for the identification amultidisciplinary expert advisory board for the identification andnd prioritization of imaging informatics projects.prioritization of imaging informatics projects.
  • 69. Biomedical Ontology ResearchBiomedical Ontology Research DevelopmentDevelopment Over the past decades, ontologies have become keyOver the past decades, ontologies have become key components of information systems (Gruber, 1993;components of information systems (Gruber, 1993; GuarinoGuarino, N., 1998), N., 1998) Various applicationsVarious applications Natural language processing (NLP) (Natural language processing (NLP) (NirenburgNirenburg andand RaskinRaskin,, 2004)2004) Software engineering (Software engineering (CaleroCalero, et. al 2006), et. al 2006) Knowledge management in the semantic Web (Knowledge management in the semantic Web (KashyapKashyap,, 2008).2008). The use of ontologies also spans many domainsThe use of ontologies also spans many domains including biomedicine, geography and eincluding biomedicine, geography and e--commerce.commerce.
  • 70. Biomedical Ontology ResearchBiomedical Ontology Research DevelopmentDevelopment In the biomedical domain, ontologies play an importantIn the biomedical domain, ontologies play an important role in research (Blake androle in research (Blake and BultBult, 2006), healthcare, 2006), healthcare ((GardeGarde et al., 2007) and translational biomedicineet al., 2007) and translational biomedicine ((RuttenbergRuttenberg, 2008), supporting tasks, 2008), supporting tasks including knowledge management, data integration andincluding knowledge management, data integration and decision support (decision support (BodenreiderBodenreider, 2008)., 2008). A large number of biomedical ontologies have beenA large number of biomedical ontologies have been created by individual researchers, academic consortia,created by individual researchers, academic consortia, institutions and companies.institutions and companies.
  • 71. Biomedical Ontology ResearchBiomedical Ontology Research DevelopmentDevelopment Most ontologies are created for a given purpose (e.g., toMost ontologies are created for a given purpose (e.g., to annotate gene products) and independently of existingannotate gene products) and independently of existing ontologies.ontologies. As a consequence, although ontologies are ideallyAs a consequence, although ontologies are ideally created for sharing and reusing knowledge (created for sharing and reusing knowledge (MusenMusen,, 1992), its impact is still limited to small groups in a1992), its impact is still limited to small groups in a special field.special field. The abundance of ontologies should account for greatThe abundance of ontologies should account for great resources to biomedical researchers in their biomedicalresources to biomedical researchers in their biomedical applications.applications.
  • 72. Biomedical Ontology ResearchBiomedical Ontology Research DevelopmentDevelopment In practice, however, there is no comprehensiveIn practice, however, there is no comprehensive registry of biomedical ontologiesregistry of biomedical ontologies Few existing collections of ontologies do notFew existing collections of ontologies do not provide enough information about theprovide enough information about the ontologies to support effective discoverability.ontologies to support effective discoverability.
  • 73. Biomedical Ontology ResearchBiomedical Ontology Research DevelopmentDevelopment UMLSUMLS Unified Medical Language System (UMLS)Unified Medical Language System (UMLS) ((BodenreiderBodenreider, 2004), 2004) Developed at the National Library of Medicine,Developed at the National Library of Medicine, which integrates many biomedical terminologies andwhich integrates many biomedical terminologies and ontologies.ontologies.
  • 74. Biomedical Ontology ResearchBiomedical Ontology Research DevelopmentDevelopment BioPortalBioPortal National Center for Biomedical Ontologies (NCBO), funded by NIHNational Center for Biomedical Ontologies (NCBO), funded by NIH RoadmapRoadmap WebWeb--based application providing access to a large number of ontologibased application providing access to a large number of ontologieses in the biomedical domains (in the biomedical domains (BodenreiderBodenreider, O., 2004)., O., 2004). NCBONCBO’’ss BioPortalBioPortal ““defines relationships among those ontologies anddefines relationships among those ontologies and between the ontologies and online data resourcesbetween the ontologies and online data resources”” and supportsand supports ““communitycommunity--based participation in the evaluation and evolution ofbased participation in the evaluation and evolution of ontology contentontology content”” ((MusenMusen, 2008)., 2008). BioPortalBioPortal enables biomedical ontology users to discover, visualize,enables biomedical ontology users to discover, visualize, download and evaluate existing resources and their interrelationdownload and evaluate existing resources and their interrelations.s. BioPortalBioPortal will host the ontologies from thewill host the ontologies from the MetaOntologyMetaOntology issue and theirissue and their associated metadataassociated metadata Analogously, theAnalogously, the Ontology Lookup ServiceOntology Lookup Service (Cote, 2008) developed by the(Cote, 2008) developed by the European Bioinformatics Institute supports queries against ontolEuropean Bioinformatics Institute supports queries against ontologiesogies from the Open Biomedical Ontology (OBO) family.from the Open Biomedical Ontology (OBO) family.
  • 75. Biomedical Ontology ResearchBiomedical Ontology Research DevelopmentDevelopment Resources pros and consResources pros and cons Offer online lookup services, i.e., support theOffer online lookup services, i.e., support the discovery of individual entities through their namesdiscovery of individual entities through their names and identifiers.and identifiers. Although these ontologies are generally useful toAlthough these ontologies are generally useful to researchers, none of these resources isresearchers, none of these resources is comprehensive enoughcomprehensive enough The interfaces to ontologies are no substitute for aThe interfaces to ontologies are no substitute for a rich description of their content and characteristics.rich description of their content and characteristics.
  • 76. Ontology for Medical ImagingOntology for Medical Imaging InformaticsInformatics Although the XML technology has been successful for softwareAlthough the XML technology has been successful for software in a heterogeneous environment to establish consistency of ITin a heterogeneous environment to establish consistency of IT data format and expression, currently,data format and expression, currently, there is no easy way tothere is no easy way to map the knowledge contained in different domain sets.map the knowledge contained in different domain sets. This is due to the different domain structure, culture, andThis is due to the different domain structure, culture, and expression in languages.expression in languages. For example, in radiology community, a radiologist uses medicalFor example, in radiology community, a radiologist uses medical imagingimaging in their daily diagnostics.in their daily diagnostics. A standard terminology and anthologies are extremely importantA standard terminology and anthologies are extremely important in order to improve the clarity of report and efficientin order to improve the clarity of report and efficient communication; and to enhance their clinical and healthcarecommunication; and to enhance their clinical and healthcare services.services.
  • 77. Ontology for Medical ImagingOntology for Medical Imaging InformaticsInformatics RadLextRadLext a Lexicon for Uniform Indexing and Retrieval ofa Lexicon for Uniform Indexing and Retrieval of Radiology Information ResourcesRadiology Information Resources RadLextRadLext is supported both by theis supported both by the National InstituteNational Institute of Biomedical Imaging and Bioengineeringof Biomedical Imaging and Bioengineering (NIBIB)(NIBIB) and by the cancer Biomedical Informatics Gridand by the cancer Biomedical Informatics Grid ((caBIGcaBIG) project.) project. One of the challenges is how to better translateOne of the challenges is how to better translate thethe RadLextRadLext terminology to an ontologyterminology to an ontology representation in MII systemsrepresentation in MII systems
  • 78. Ontology for Medical ImagingOntology for Medical Imaging InformaticsInformatics Rubin (2008) recently reports their successfulRubin (2008) recently reports their successful translation of terminology form thetranslation of terminology form the RadLextRadLext format to the one offormat to the one of ProtProtééggéé, an open source, an open source ontology management tool.ontology management tool. There still needs to establish a standard,There still needs to establish a standard, ontologyontology--based knowledge bank of medicalbased knowledge bank of medical imaging informatics using ontologicalimaging informatics using ontological expressions, rather than redundantexpressions, rather than redundant representations and translationsrepresentations and translations
  • 79. Ontology for Medical ImagingOntology for Medical Imaging InformaticsInformatics It is of urgent need to develop an efficientIt is of urgent need to develop an efficient mechanismmechanism allows to map the terminology from one domain set,allows to map the terminology from one domain set, say radiology, to another domain set, say,say radiology, to another domain set, say, neuroneuro-- imaging when they deal with brain MRI data.imaging when they deal with brain MRI data. The data ontology model becomes the firstThe data ontology model becomes the first phase to establish integrated ontological domainphase to establish integrated ontological domain models.models.
  • 80. Ontology for Medical ImagingOntology for Medical Imaging InformaticsInformatics In the DICOM ontology, among other projects,In the DICOM ontology, among other projects, cerates a single common reference informationcerates a single common reference information model for allmodel for all caBIGcaBIG projects that need to referprojects that need to refer to imaging and other DICOMto imaging and other DICOM--relatedrelated information in their individual information.information in their individual information. Most of the current MII tools in PACS or RISMost of the current MII tools in PACS or RIS systems are websystems are web--application based software forapplication based software for diagnostics or reporting (Corey et al, 2007).diagnostics or reporting (Corey et al, 2007).
  • 81. Ontology for Medical ImagingOntology for Medical Imaging InformaticsInformatics Due to the recentlyDue to the recently--developed Webdeveloped Web--services for onlineservices for online image reading and reporting inimage reading and reporting in teletele--radiology, theradiology, the WSDL, Semantic Web, Web Ontology language (OWL),WSDL, Semantic Web, Web Ontology language (OWL), XML and other W3C protocols, with Hl7 and DICOMXML and other W3C protocols, with Hl7 and DICOM standards, are the fundamental components instandards, are the fundamental components in ontological approach in MII.ontological approach in MII. The ontologicallyThe ontologically--defined service objects should bedefined service objects should be applicable to RIS and HIS systems and associated tools.applicable to RIS and HIS systems and associated tools. They should have high compatibility and portability,They should have high compatibility and portability, and should appropriately be used in EHP systemsand should appropriately be used in EHP systems (Smith and(Smith and CeustersCeusters, 2006)., 2006).
  • 82. Ontology for Medical ImagingOntology for Medical Imaging InformaticsInformatics The National Center of Biomedical OntologyThe National Center of Biomedical Ontology (NCBO) provides many fundamental tools and(NCBO) provides many fundamental tools and ontology templatesontology templates allow researchers and investigators to conduct a newallow researchers and investigators to conduct a new ontology set under the roadmap of NIH, compatibleontology set under the roadmap of NIH, compatible withwith caGridcaGrid terminology server interminology server in caBIGcaBIG..
  • 83. MIIO ProjectMIIO Project We initiated aWe initiated a ““Medical Imaging InformaticsMedical Imaging Informatics OntologyOntology””, or MIIO, which maps two domains:, or MIIO, which maps two domains: medical imaging and information technology.medical imaging and information technology.
  • 84. MIIO ProjectMIIO Project The project collects 3800 technical terms (entities)The project collects 3800 technical terms (entities) MIIO project team starts to define each of the terms inMIIO project team starts to define each of the terms in ontology expressionontology expression Domain space definition, domain entity definition, spaceDomain space definition, domain entity definition, space belongs (is relationship), embedding attributes (hasbelongs (is relationship), embedding attributes (has relationships), inner relationships among the other entitiesrelationships), inner relationships among the other entities within the domain space, outer relationships to communicatewithin the domain space, outer relationships to communicate with other entities defined in other domain space, entitywith other entities defined in other domain space, entity attributes, characteristics, feature, and properties, entityattributes, characteristics, feature, and properties, entity information acquisition and achieving, and retrievinginformation acquisition and achieving, and retrieving methods, entity (object) declaration and construction, andmethods, entity (object) declaration and construction, and entity abstraction and inheritance, etc.entity abstraction and inheritance, etc.
  • 85. MIIO ProjectMIIO Project The domain space currently only covers medicalThe domain space currently only covers medical imaging and information technology.imaging and information technology. MIIOMIIO’’ss infrastructure is designed to be highlyinfrastructure is designed to be highly scalable to extend to other domain space andscalable to extend to other domain space and portable and compatible to other standards inportable and compatible to other standards in ontology expressions.ontology expressions.
  • 86. MIIO Project Strategic Task ActionsMIIO Project Strategic Task Actions Multiple expressionsMultiple expressions in multiple ontological formats or expressions, mainly inin multiple ontological formats or expressions, mainly in OWL, OBO, UMLS RRF,OWL, OBO, UMLS RRF, ProgeteProgete, and, and ProgeteProgete--OWLOWL respectively.respectively. A dynamic search engineA dynamic search engine For the uses of special domain ontologiesFor the uses of special domain ontologies By a Java search code through Google search engine.By a Java search code through Google search engine. Statistical data miningStatistical data mining The entities were found by decoding the words using stringThe entities were found by decoding the words using string token and by a statistical analysis to see the appearing withtoken and by a statistical analysis to see the appearing with each articles or online pageseach articles or online pages HPCHPC--enabledenabled
  • 87. MIIOMIIO--TK ModulesTK Modules The MIIOThe MIIO--TK has several components orTK has several components or modulesmodules File moduleFile module ---- allows users to open file and projectallows users to open file and project Search ModuleSearch Module ––a search enginea search engine Definition moduleDefinition module ------ for input, modify, and expressfor input, modify, and express modulemodule Format conversion moduleFormat conversion module ------ allows users toallows users to convert one expression format to anotherconvert one expression format to another Visualization moduleVisualization module ------ allows users to visualizeallows users to visualize different formatted enmity expression.different formatted enmity expression.
  • 88. Spotlight of MIIOSpotlight of MIIO ToolKitToolKit
  • 89. Lab MissionLab Mission Establishment of a nationally and globallyEstablishment of a nationally and globally-- recognized research lab in medical imagingrecognized research lab in medical imaging informatics or radiology informaticsinformatics or radiology informatics
  • 90. Short Term Action TasksShort Term Action Tasks Learning any subjects and shaping knowledgeLearning any subjects and shaping knowledge Develop infrastructure of unprecedented computingDevelop infrastructure of unprecedented computing facility in medical imaging informaticsfacility in medical imaging informatics Collaborating with enterprise IT and health careCollaborating with enterprise IT and health care industrialsindustrials Working with external and internal professionalsWorking with external and internal professionals Seeking for fundsSeeking for funds Develop software solutions for future health careDevelop software solutions for future health care systemssystems Attract more people including you.Attract more people including you.
  • 91. LongLong--Term GoalTerm Goal Computation (future projects)Computation (future projects) Infrastructure and algorithm developments for dataInfrastructure and algorithm developments for data mining in medical imagemining in medical image Artificial Intelligence in medical imagingArtificial Intelligence in medical imaging LargeLarge--scale image processing and associatedscale image processing and associated modeling and simulationsmodeling and simulations Digitalization of human body (massDigitalization of human body (mass--phantomphantom system)system) Computational radiologyComputational radiology System radiologySystem radiology
  • 92. MIHI Lab ProjectsMIHI Lab Projects Medical Imaging & Radiology Informatics (MIRI)Medical Imaging & Radiology Informatics (MIRI) Hawkeye Radiology Informatics (HRI)Hawkeye Radiology Informatics (HRI) http://http://www.uiowa.edu/~hriwww.uiowa.edu/~hri// Radiology Informatics Domain Ontology (RIDO)Radiology Informatics Domain Ontology (RIDO) Medical Imaging Informatics Ontology (MIIO)Medical Imaging Informatics Ontology (MIIO) Medical Imaging Informatics Terminology (MIIT)Medical Imaging Informatics Terminology (MIIT) CyberinfrastructureCyberinfrastructure--enabled Radiology Informatics (CIRI)enabled Radiology Informatics (CIRI) Medical Imaging Information System (MIIS)Medical Imaging Information System (MIIS) http://http://www.uiowa.edu/mihpclab/projects_miis.htmlwww.uiowa.edu/mihpclab/projects_miis.html Radiology Informatics Education and Training (RIET)Radiology Informatics Education and Training (RIET) http://http://www.uiowa.edu/~hri/education.htmlwww.uiowa.edu/~hri/education.html
  • 93. ProjectsProjects Parallel Computing in Medical Imaging (PCMI)Parallel Computing in Medical Imaging (PCMI) http://http://www.uiowa.edu/mihpclab/projects_pcmi.htmlwww.uiowa.edu/mihpclab/projects_pcmi.html Parallelism of Medical Imaging ProcessingParallelism of Medical Imaging Processing CT ReconstructionCT Reconstruction SegregationSegregation RegistrationRegistration Texturing and classificationTexturing and classification EnhancementEnhancement Image compressionImage compression Image data miningImage data mining ……
  • 94. ProjectsProjects Modeling Biotransport in Biophysical System (MBBS)Modeling Biotransport in Biophysical System (MBBS) http://http://www.uiowa.edu/mihpclab/projects_mbbs.htmlwww.uiowa.edu/mihpclab/projects_mbbs.html NanothermotheropyNanothermotheropy ((nanoHyperthmiananoHyperthmia)) http://http://www.uiowa.edu/mihpclab/projects_nmni.htmlwww.uiowa.edu/mihpclab/projects_nmni.html Tumor growth and dynamics (computational oncology)Tumor growth and dynamics (computational oncology) Optical Imaging Tomography and Applications (OITA)Optical Imaging Tomography and Applications (OITA) http://http://www.uiowa.edu/mihpclab/projects_oita.htmlwww.uiowa.edu/mihpclab/projects_oita.html
  • 95. ProjectsProjects Stereological Analysis and Tumor VolumeStereological Analysis and Tumor Volume Metrics (SATVM)Metrics (SATVM) voluMeasurevoluMeasure Software Development Project (RSNA'05)Software Development Project (RSNA'05) The Effect of the Shape and Orientation of a Mass on the AccuracThe Effect of the Shape and Orientation of a Mass on the Accuracyy Estimating Its Size Using RECIST (RSNA'09)Estimating Its Size Using RECIST (RSNA'09) Tumor volume measurement in MRI breast imagingTumor volume measurement in MRI breast imaging http://http://www.uiowa.edu/mihpclab/projects_isca.htmlwww.uiowa.edu/mihpclab/projects_isca.html Stereotactic Atlas for the Anatomic TopologyStereotactic Atlas for the Anatomic Topology (SAAT)(SAAT) http://http://www.uiowa.edu/mihpclab/projects_saat.htmlwww.uiowa.edu/mihpclab/projects_saat.html Couple Diffusions for Image Enhancement (DDIE)Couple Diffusions for Image Enhancement (DDIE) http://http://www.uiowa.edu/mihpclab/projects_cdie.htmlwww.uiowa.edu/mihpclab/projects_cdie.html
  • 96. ProjectsProjects KnowledgeKnowledge--based CAD for Breast Imagingbased CAD for Breast Imaging (KCBI)(KCBI) architectural distortionarchitectural distortion calcificationcalcification DeformationDeformation http://http://www.uiowa.edu/mihpclab/projects_kcbi.htmlwww.uiowa.edu/mihpclab/projects_kcbi.html New projectsNew projects Tomosynthesis and Molecular Breast ImagingTomosynthesis and Molecular Breast Imaging US Medical ImagingUS Medical Imaging 3D Volume Rendering3D Volume Rendering
  • 97. Sponsorships and CollaborationsSponsorships and Collaborations Current sponsorsCurrent sponsors NIH (NIBIBNIH (NIBIB--medical imaging)medical imaging) NSF (CISENSF (CISE--computer information science and engineering)computer information science and engineering) Intel (High performance computing)Intel (High performance computing) Microsoft (Window computing server, technical specificationMicrosoft (Window computing server, technical specification and software development)and software development) Collaborators:Collaborators: Siemens (Medical modality and software resources)Siemens (Medical modality and software resources) IBM (Cell/BE/IBM (Cell/BE/OpenCLOpenCL--based medical imaging)based medical imaging) NavidaNavida (GPU/CUDA(GPU/CUDA--based medical imaging)based medical imaging) Mayo Clinic (Cloud computingMayo Clinic (Cloud computing--based medical imaging)based medical imaging)
  • 98. Institutional CollaborationsInstitutional Collaborations UIUI--Medical SchoolMedical School –– SJTUSJTU--Medical SchoolMedical School
  • 99. Thanks!Thanks! Q & AQ & A