Dec. 14, 2009Shanghai Jiao Tong University Medical

School, 21 Century Forum

OntologyOntology--based Medical Imaging based Medical Imaging and Radiology Informatics and Radiology Informatics

—— Domain Mapping and Data Domain Mapping and Data ModelingModeling

Dr. Jun Ni, Associate Professor, DirectorDr. Jun Ni, Associate Professor, DirectorMedical Imaging HPC and Informatics LabMedical Imaging HPC and Informatics Lab

Department of RadiologyDepartment of RadiologyCarver College of MedicineCarver College of Medicine

The University of Iowa, Iowa City, Iowa, USAThe University of Iowa, Iowa City, Iowa, USA

OutlineOutline

Ontological Considerations of Medical Research Ontological Considerations of Medical Research DomainDomain

Emphasizing on the medical domain mapping and its role in Emphasizing on the medical domain mapping and its role in todaytoday’’s medical multidisciplinary researchs medical multidisciplinary research

Medical Imaging Informatics Domain Scope and Model Medical Imaging Informatics Domain Scope and Model ConsiderationsConsiderations

Focusing on domain and data model distinctions and Focusing on domain and data model distinctions and challengeschallenges

Projects in MHHI Lab at the University of IowaProjects in MHHI Lab at the University of IowaSpotlighting some of relevant projects which reflects our Spotlighting some of relevant projects which reflects our vision and task actionsvision and task actions

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 boundarySpecial academic discipline or fieldSpecial academic discipline or field

Interdisciplinary or multidisciplineInterdisciplinary or multidisciplineIt 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 and nd 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

Medical and Medical Research Medical and Medical Research DomainsDomains

Medical DomainMedical DomainMedical (Clinic) service domain (Healthcare)Medical (Clinic) service domain (Healthcare)

PatientPatient--oriented service operations (hospital or clinic oriented service operations (hospital or clinic services)services)Business operationsBusiness operationsHealthcare industrials (modality) interactionsHealthcare industrials (modality) interactionsSocial and government policy making and implementationSocial and government policy making and implementationHealthcare information system (HIS)Healthcare information system (HIS)

Medical and Medical Research Medical and Medical Research DomainDomain

Medical DomainMedical DomainMedical research domain (Science)Medical research domain (Science)

““MedicalMedical”” as the as the leadingleading entityentityInteraction 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 fieldsBiomedical research domain (biomedical science and biomedical Biomedical research domain (biomedical science and biomedical engineering)engineering)Biomedical research and biomedical engineeringBiomedical research and biomedical engineering

Difference between sciences (explorations and discoveries) and Difference 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 medical ical service domain)service domain)

CTSACTSA’’ss roadmaproadmap

Medical Domain

Medical Clinic Service Domain(Healthcare services, …)

Medical ResearchDomain

Clinical Translational Experiments and Science(CTSA in USA)

Clinical Transformative

Medical Medical DomainDomain

Clinic Service Clinic Service DomainDomain

Clinical Clinical TranslationalTranslational

Medical Research Medical Research DomainDomain

Internal MedicineInternal Medicine

SurgerySurgery

RadiologyRadiology

NeurologyNeurology

OncologyOncology

CardiologyCardiology

GastroenterologyGastroenterology

DermatologyDermatology

Obstetrics and Obstetrics and GynecologyGynecology

PathologyPathology

CT, MRI, PET, CT, MRI, PET, XX--rayray

Mammon graph, Mammon graph, Interventional, Interventional, Breast imaging, Breast imaging, Whole body Whole body imaging, imaging, NeuoradiologyNeuoradiology,,……

Chemotherapy, Chemotherapy, radiation therapy, radiation therapy, thermotherapy, gene thermotherapy, gene therapytherapy

Innovative Innovative modality, modality, Diagnostics, Diagnostics, CAD, CAD, Imaging Imaging informatics,informatics,Physiological Physiological Anatomic Anatomic analysis,analysis,……

Anatomical science, Anatomical science, medical physics, medical physics, medical imaging, medical imaging, image processing, image processing, image storage, ITimage storage, IT--

based healthcare based healthcare systems, systems, medical medical imaging informaticsimaging informatics, , diagnostic analysis, diagnostic analysis, medical physics, medical physics, ……

Nanotechnology, Nanotechnology, biotransport, biotransport, thermothermo--science, science, physiological physiological analysis;analysis;

NanoNano--thermotherapythermotherapy

…

Medical Imaging Informatics Medical 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 radiologyOne of medical informatics disciplinesOne of medical informatics disciplines

Domain Boundary ExtensionDomain Boundary ExtensionMedical imaging data management, processing, and displaying Medical imaging data management, processing, and displaying ------ > > medical image data mining?medical image data mining?

Demand: patient healthcare system and Demand: patient healthcare system and teleradiologyteleradiology/telemedicine/telemedicine

Job market: 70,000 on demand, education challengesJob market: 70,000 on demand, education challengesHawkeye Radiology Informatics (HRI)Hawkeye Radiology Informatics (HRI)

MII DomainMII Domain

Medical Imaging Informatics (MII) == Medical Imaging Informatics (MII) == Radiology Informatics (RI)?Radiology Informatics (RI)?

One of One of medical informaticsmedical informaticsSubSub--specialty of radiologyspecialty of radiology

Domain Boundary Domain 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 challengesHawkeye Radiology Informatics (HRI)Hawkeye Radiology Informatics (HRI)

MII Naming IdentityMII Naming Identity

Imaging Informatics in Medicine (IIM), also Imaging Informatics in Medicine (IIM), also known as Radiology Informatics (RI) or known 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

EfficiencyEfficiencyAccuracyAccuracyUsabilityUsabilityReliability of medical imaging services within the Reliability of medical imaging services within the healthcare enterprisehealthcare enterprise

MII Naming IdentityMII Naming Identity

The fundamental issues in MII include The fundamental issues in MII include Standards for image exchangeStandards for image exchangeCommunication protocols, underlying computer Communication protocols, underlying computer data and knowledge representationsdata and knowledge representationsCodeCodeTerminologies and vocabularies to be portable to Terminologies and vocabularies to be portable to electronic medical record, relation to digitalized electronic medical record, relation to digitalized healthcarehealthcareNetworked Networked teletele--radiologyradiologyother IT issues (other IT issues (KulikowskiKulikowski, 2002), 2002)

MII Naming IdentityMII Naming Identity

MII is technically devoted to the study of how MII is technically devoted to the study of how information about and contained within medical information about and contained within medical images is retrieved, analyzed, enhanced, and images is retrieved, analyzed, enhanced, and exchanged within radiology and throughout the exchanged within radiology and throughout the medical enterprisemedical enterprise

MII DomainMII Domain

Radiology is an inherently metadataRadiology is an inherently metadata--intensive and multiintensive and multi--technologytechnology--driven specialty of medicinedriven specialty of medicineRadiologists lead research and development in medical imaging Radiologists lead research and development in medical imaging informaticsinformaticsWith the proliferation of digitized images across the practice oWith the proliferation of digitized images across the practice of f medicine to include fields such as medicine to include fields such as

CardiologyCardiologyDermatologyDermatologySurgerySurgeryGastroenterologyGastroenterologyObstetrics, gynecologyObstetrics, gynecologyPathologyPathology……

MII WorkforcesMII Workforces

Various industry playersVarious industry playersVendors involved with medical imagingVendors involved with medical imagingIT expertsIT expertsOther biomedical informatics professionalsOther biomedical informatics professionals

MII DomainMII Domain

This domain interacts with broad disciplines: This domain interacts with broad disciplines: Biological science Biological science -- includes bench sciencesincludes bench sciences

Biochemistry, microbiologyBiochemistry, microbiologyPhysiology and geneticsPhysiology and genetics

Clinical servicesClinical servicesPractice of medicinePractice of medicine

Bedside researchBedside researchOutcomes and costOutcomes and cost--effectiveness studieseffectiveness studiesPublic health policyPublic health policy

Information scienceInformation scienceAcquisition, retrieval and manipulation of dataAcquisition, retrieval and manipulation of data

Medical physics / engineeringMedical physics / engineeringUse of equipment and technology for a medical purposeUse of equipment and technology for a medical purpose

MII DomainMII Domain

Traditionally, MII deals with PACS, image Traditionally, MII deals with PACS, image processing and analysis. processing and analysis. Now it moves towards the direction of Now it moves towards the direction of knowledgeknowledge--based, based, ““realreal”” informaticsinformaticsDeals with not only data formatting and their Deals with not only data formatting and their integrations but also with processing entities integrations but also with processing entities ((SinihaSiniha, 2002), 2002)

MII DomainMII Domain

Due to its overlapping, it has many challengesDue to its overlapping, it has many challengesDefining Defining MIIMII’’ss entities (entities (KulikowskiKulikowski, 1997), 1997)Classifying domain spacesClassifying domain spacesTerminology and data integration (Terminology and data integration (UmitUmit, 2009), 2009)Interoperation in todayInteroperation in today’’s in medical imaging informatics s in medical imaging informatics systems. systems.

In todayIn today’’s digital radiology, the ontological standards s 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 professionals Collaborative team of radiologists and IT professionals ((GeisGeis, 2007)s, 2007)s

Cloud of Medical Informatics and Cloud of Medical Informatics and Computational MedicineComputational Medicine

Computer Applications in Healthcare SystemComputer Applications in Healthcare SystemKnowledge Management and Data MiningKnowledge Management and Data Mining

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

MII ConnectionsMII Connections

MII: medical image data and data processingMII: medical image data and data processingRadiology Informatics: Frontier in cancer Radiology Informatics: Frontier in cancer diagnostics and image diagnostics and image workflowworkflowProliferated applications:Proliferated applications:

Oncology, cardiology, dermatology, surgery, Oncology, cardiology, dermatology, surgery, gastroenterology, obstetrics, gynecology and gastroenterology, obstetrics, gynecology and pathology, and other medical fieldspathology, and other medical fields

Strong digital requirement and IT engagementStrong digital requirement and IT engagement

Medical Imaging Informatics

Interactions between MII and other medical informatics (Cloud)

DermatologyDermatology

SurgerySurgery

GastroenterologyGastroenterology

Obstetrics & gynecologyObstetrics & gynecology

CardiologyCardiologyRadiologyRadiology

NeurologyNeurologyPathologyPathologyOncologyOncology

External Domain Connections

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 improve A subspecialty of radiology that aims to improve medical medical imaging relatedimaging related discovery and technical services within the discovery 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)SustainabilitySustainabilityCost/performanceCost/performance

Its ultimate goal to Its ultimate goal to improve health care systemsimprove health care systems

Medical Imaging Digital

Radiology

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 1051450

printing1870

electricity, telephonetransistor 1947

computing 1950

1993The Web

Digital Cardiology

Electronic Medical Record

E-Health Initiatives/Linkages

Digital Radiology

1999

Late 1960sInternet

P e t a b y t e s

Digital Pathology

NM (128, 128)

MRI (256, 256)

CT (512, 512)

DSA (1024, 1024)

CR (2048, 2048)

Mammogram (4096, 4096)

From H. K Huang, 2004

Medical Imaging Informatics Infrastructure

--

Crossing Medical Imaging and IT

Medical Imaging Software Resources

Medical Imaging Hardware Facility

Medical Imaging Informatics Infrastructure --

Crossing Medical Imaging and IT

Medical Imaging WorkforceKnowledge based computer-aided detection (diagnostics), CAD Clinic experienceIT knowledge

Previous Paradigm: Previous Paradigm: MIIMII’’ss

Data Data Oriented RoadmapOriented Roadmap

Study how medical images (within radiology and Study how medical images (within radiology and throughout medical enterprise) are processed by throughout medical enterprise) are processed by

AcquisitionAcquisitionArchivingArchivingRetrieving/recoveringRetrieving/recoveringImage ProcessingImage Processing

AnalyzedAnalyzedEnhancedEnhancedVisualizedVisualizedData format conversionData format conversion……

Current Paradigm: CrossingCurrent Paradigm: Crossing

A multidiscipline and interdisciplinaryA multidiscipline and interdisciplinaryIntersection 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 scienceBiomedical engineeringBiomedical engineeringElectrical engineering (signal and data processing)Electrical engineering (signal and data processing)Biological and physiological sciences Biological and physiological sciences Medical physicsMedical physics……

Hospital Registration Order exam Waiting room

Exam operation

Modality preparation

Paperwork film packageRadiologist previewFetch report to HIS

radiologist review final report on RIS

Workflow

MII Challenges (1)MII Challenges (1)

PACS (Picture Archiving and Communication PACS (Picture Archiving and Communication System)System)

Different regional and industrial interpretation, Different regional and industrial interpretation, configuration, and implementationconfiguration, and implementationDifferent interfaces and prototypesDifferent interfaces and prototypesDifferent standardization Different standardization

DICOM, HL7, Other IT standardsDICOM, HL7, Other IT standards

Different image digitalization of modalitiesDifferent image digitalization of modalitiesDifferent scopesDifferent scopes

MII Challenges (1)MII Challenges (1)

Technical ComponentsTechnical ComponentsImage acquisition and management technologyImage acquisition and management technologyData visualization or image displayData visualization or image displayNetwork and communicationsNetwork and communicationsComputer application softwareComputer application software

MII Challenges (1)MII Challenges (1)

PACS Technical Concerns PACS Technical Concerns Data MigrationData MigrationBackBack--up archiveup archiveFaultFault--tolerancetoleranceIntegration with legacy systemsIntegration with legacy systemsFast wideFast wide--area networksarea networksSecuritySecurity

PACS Distributed Computing PACS Distributed Computing ArchitectureArchitecture

Large scale (multiple Large 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

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

MII Challenges (2)MII Challenges (2)

Lack generic MII ontology (Lack generic MII ontology (Philological IssuePhilological Issue))Systematic identification and classification of domain Systematic 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 or No semantic languages for communications or workflowsworkflowsLooselyLoosely--defined terminologydefined terminologyNo linkage and leverage to knowledge, artificial No linkage and leverage to knowledge, artificial intelligent (AI), decision makingintelligent (AI), decision making

Ontology Wisdom

Philology

Knowledge Decision MakingCAD

Cognitive Sciences

Information Science

Data Data Data Data Data

Metadata MetadataMetadata

Information Management

Domain

Entity Relations

Artificial Intelligence

MII Challenges (2)MII Challenges (2)

Ontological data model (terminology Ontological data model (terminology classification, entity definition, and relations classification, entity definition, and relations establishing) (Methodology issue)establishing) (Methodology issue)KnowledgeKnowledge--drivendrivenArtificial intelligenceArtificial intelligence--driven driven Unprecedented capacity for handling massive Unprecedented capacity for handling massive datadataSystem integration and interoperation among System integration and interoperation among various hospital/clinic systemsvarious hospital/clinic systems

MII Challenges (2)MII Challenges (2)

No standard protocols (No standard protocols (Technical issuesTechnical issues))To facilitate the interoperation and communication To facilitate the interoperation and communication among globallyamong globally--distributed MII resources distributed MII resources To deploy concurrent hardware and software To deploy concurrent hardware and software solutions solutions To utilize cyberTo utilize cyber--enabled highenabled high--speed networksspeed networks

Short of education/training programs (Short of education/training programs (Business Business issueissue))

To foster the next generation in digital health care To foster the next generation in digital health care systems.systems.

MII Challenges (4)MII Challenges (4)

Software DevelopmentSoftware DevelopmentComputerComputer--Aided Detection and Diagnosis (CAD)Aided Detection and Diagnosis (CAD)ComputerComputer--aided interventional radiologyaided interventional radiologyMetrics and computing performanceMetrics and computing performanceMedical imaging facility and infrastructure Medical imaging facility and infrastructure developmentdevelopmentFundamental research and developmentFundamental research and development

Medical Imaging Service Pack (MISP)Medical Imaging Service Pack (MISP)Medical Imaging Informatics Knowledge Integration Medical Imaging Informatics Knowledge Integration Toolkit (M2KIT)Toolkit (M2KIT)

Basic OntologyBasic Ontology

Ontology is a major field in philosophy Ontology is a major field in philosophy metaphysics.metaphysics.

It is principal of It is principal of entitiesentities (objects) and their (objects) and their tiesties. .

Ontology methodOntology methodIntuitive study of the fundamental properties, Intuitive study of the fundamental properties, modes, and aspects of being, or of entities in general modes, and aspects of being, or of entities in general (Raul (Raul CorazzonCorazzon, 2009). , 2009). Ontology deals with the entities that are defined in Ontology deals with the entities that are defined in philosophy as distinctions, or separate existences. philosophy as distinctions, or separate existences.

Basic OntologyBasic Ontology

OntologiesOntologiesOntologically defined entitiesOntologically defined entitiesUsed in system developmental models that better display Used in system developmental models that better display communications and internal processing of communication communications and internal processing of communication medium such as medical datamedium such as medical dataStudy the nature of entity, reality, and basic categories of theStudy the nature of entity, reality, and basic categories of their ir relationshipsrelationships

OntologyOntology‘‘s main themes main themeDetermine the categories of abstract beingDetermine the categories of abstract being

Deals with abstract objectsDeals with abstract objects that are considered as a set that contains that are considered as a set that contains subsetssubsets

Development of external and internal connections Development of external and internal connections (relationships)(relationships)

Basic OntologyBasic Ontology

In a technical perspective, a set of entities can be In a technical perspective, a set of entities can be referred to a special referred to a special collectioncollection of of abstractabstract objectsobjects

Shared characteristics and similar, intellectual activities or Shared characteristics and similar, intellectual activities or events events

Each object is depicted by Each object is depicted by AttributesAttributes

Properties and characteristicsProperties and characteristics

EventsEventsProcess of activities such as behaviors or functions Process of activities such as behaviors or functions

Significances of Basic OntologySignificances of Basic Ontology

Successfully used in the foundation of semantics, especially in Successfully used in the foundation of semantics, especially in objectobject--oriented programming (OOP) languages in computer and oriented programming (OOP) languages in computer and information sciences information sciences

Ontological concepts have been intensively employed into the semOntological concepts have been intensively employed into the semantics antics of objectof object--oriented programming languages, such as C++/C# or Javaoriented programming languages, such as C++/C# or JavaAbstraction, Inheritance, and InterfaceAbstraction, Inheritance, and Interface

Common ontological approach to a cognitive and integrative Common 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 appropriate propriate grouping or sorting schemesgrouping or sorting schemes

In science, the ontology of scientific systems relates to many In science, the ontology of scientific systems relates to many principles and rules defined in theology, library science, and principles and rules defined in theology, library science, and artificial intelligenceartificial intelligence

Basic Ontology: Attributes and Basic Ontology: Attributes and ClassificationClassification

In ontological approach, quintessential ontological concepts canIn ontological approach, quintessential ontological concepts canbe applied to be applied to system designsystem design

Universals and particularsUniversals and particularsSubstance and accidentSubstance and accidentAbstract and concrete objectsAbstract and concrete objectsEssence and existence Essence and existence

Before one starts to develop a biomedical system architecture Before one starts to develop a biomedical system architecture and design, he/she should consider the basic questions about and 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 identifythe fundamentals and specific properties or attributes of the the 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 information Common 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

Basic Ontology: RelationshipBasic Ontology: Relationship

Once the consideration of class is initiated, one should Once the consideration of class is initiated, one should establish system subject, object, and their establish system subject, object, and their relationshipsrelationshipswithin the system under consideration. within the system under consideration. This practical ontology paradigm has This practical ontology paradigm has

not only been applied to semantic descriptions in not only been applied to semantic descriptions in mathematics, computer science, and other physical sciences mathematics, computer science, and other physical sciences (Heller, 1990)(Heller, 1990)but also been employed in social, religious, linguistics, and but also been employed in social, religious, linguistics, and other communication related domains (John Symons, 2009). other communication related domains (John Symons, 2009).

Ontological EnvironmentsOntological Environments

Such philosophy of scientific domain is necessary to Such philosophy of scientific domain is necessary to explore the explore the domain knowledgedomain knowledge about about beingbeing, as well as , as well as the the interactionsinteractions with the subjects and objects of other with the subjects and objects of other domains of interdisciplinary and multidisciplinary domains of interdisciplinary and multidisciplinary sciencessciencesThe The interaction and connectioninteraction and connection with other domains with other domains must be seriously considered through ontological must be seriously considered through ontological concepts in terms of body and environment. concepts in terms of body and environment. It deals with either It deals with either ““isis--”” or or ““hashas”” relationships. relationships.

Ontological EnvironmentsOntological Environments

The body takes some special actions in an environment The body takes some special actions in an environment Relied to a great degree on insights derived from scientific Relied to a great degree on insights derived from scientific research into biomedical beings taking instinctive action in research 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 environments The processes by which bodies related to environments became of great concernbecame of great concernIdea of being itself became really difficult to define Idea of being itself became really difficult to define

Ontological EnvironmentsOntological Environments

The establishment of body and environment is based The establishment of body and environment is based on the on the ontological assumptionsontological assumptions embedded within the embedded within the semantic descriptivesemantic descriptive medium tools for communications, medium tools for communications, such as such as semantic languagessemantic languages

Context for communication: a horizon of unspoken Context for communication: a horizon of unspoken background meanings. background meanings.

Because these assumptions both generate and are Because these assumptions both generate and are regenerated in our everyday interactions, regenerated in our everyday interactions, the locus of the locus of our way of being is the communicative event of our way of being is the communicative event of language in use, especially in biomedical research and language in use, especially in biomedical research and medical services.medical services.

Systematic Engineering RenovationSystematic Engineering Renovation

System designSystem design’’s paradigm, vision, and envisionings paradigm, vision, and envisioningSubjectSubject--object relationsobject relationsBody and environmental relationsBody and environmental relationsDifferent 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 imaging s 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.

Systematic Engineering RenovationSystematic Engineering Renovation

OntologyOntology--guided system approach becomes the super guided system approach becomes the super key to provide strategic, scalable and sustainable key to provide strategic, scalable and sustainable solutions to many integrated informationsolutions to many integrated information--driven driven systems. systems. In the design of an enterprise healthIn the design of an enterprise health--care system, one care 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 of efficient, consistent and reliable way, even process of medical data and tasks and their communication is medical data and tasks and their communication is complex. complex. Such system design needs an ontological vision in terms Such 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

Ontology for Computer and Ontology for Computer and Information Sciences Information Sciences

The practicalities of achieving cohesion in an The practicalities of achieving cohesion in an informationinformation--based based societysociety

Is highly demandedIs highly demandedIs paid attention to ontology, especially in information Is paid attention to ontology, especially in information science. science.

Computer Community Computer Community Computer theory, artificial intelligence, formal and Computer theory, artificial intelligence, formal and computational linguistics, biomedical informatics, conceptual computational linguistics, biomedical informatics, conceptual modeling, knowledge engineering and information modeling, knowledge engineering and information retrievaretrievaRealize that a solid foundation for their research calls for Realize that a solid foundation for their research calls for serious work in ontology, a general theory of the types of serious work in ontology, a general theory of the types of entities and relations that make up their respective domains entities and relations that make up their respective domains of inquiryof inquiry

Ontology for Computer and Ontology for Computer and Information Sciences Information Sciences

Attention is now being focused on the content of Attention is now being focused on the content of informationinformation rather than on just the formats and rather than on just the formats and languages used to represent information. languages used to represent information. The clearest example of this development is provided The clearest example of this development is provided by the numerous initiatives powdered by by the numerous initiatives powdered by Semantic Web Semantic Web (W3C). (W3C). Need for integrating research in these different fields Need for integrating research in these different fields arises, so does the realization that strong principles for arises, so does the realization that strong principles for building wellbuilding well--founded ontologies might provide founded ontologies might provide significant advantages over ad hoc, casesignificant advantages over ad hoc, case--based solutions. based solutions.

Ontology for Computer and Ontology for Computer and Information Sciences Information Sciences

Tools of formal ontology address precisely these Tools of formal ontology address precisely these needs, but a real effort is required in order to needs, but a real effort is required in order to apply such philosophical tools to the domain of apply such philosophical tools to the domain of information systemsinformation systemsReciprocally, research in the information Reciprocally, research in the information sciences raises specific ontological questions sciences raises specific ontological questions which call for further philosophical which call for further philosophical investigations. investigations.

Ontology for Computer and Ontology for Computer and Information Sciences Information Sciences

Many efforts have been made in establishing Many efforts have been made in establishing communities in theoretical and practical communities in theoretical and practical ontology for information science, as well as in ontology for information science, as well as in other domain of ontologies. other domain of ontologies.

Ontology for Computer and Ontology for Computer and Information Sciences Information Sciences

Formal Ontology in Information Science (FOIS) holds Formal Ontology in Information Science (FOIS) holds sequential conferences on many fundamental and sequential conferences on many fundamental and practical issues of theorems and concrete applications, practical issues of theorems and concrete applications, including including

Concepts, theorems, and usagesConcepts, theorems, and usages: : kinds of entitykinds of entityparticulars vs. universalsparticulars vs. universalscontinuants vs. occurrencecontinuants vs. occurrenceabstract vs. concreteabstract vs. concretedependent vs. independentdependent vs. independentnatural vs. artificial; natural vs. artificial;

Ontology for Computer and Ontology for Computer and Information Sciences Information Sciences

Formal relationsFormal relationsvagueness and granularityvagueness and granularityidentity and changeidentity and changeformal comparison among domain ontologiesformal comparison among domain ontologiesontology of physical reality ontology of physical reality ontology of mental realityontology of mental realityontology of social realityontology of social realityontology of the information societyontology of the information societyontology and natural and artificial language semanticsontology and natural and artificial language semanticsontology and cognitionontology and cognitionontology and medical domains, semioticsontology and medical domains, semiotics

Ontology for Computer and Ontology for Computer and Information Sciences Information Sciences

Methodologies and ApplicationsMethodologies and ApplicationsTopTop--level vs. application ontologieslevel vs. application ontologiesRole of reference ontologiesRole of reference ontologiesOntology integration and alignmentOntology integration and alignmentOntologyOntology--driven information systems design requirements driven information systems design requirements engineering, knowledge engineeringengineering, knowledge engineeringKnowledge management and organizationKnowledge management and organizationKnowledge representationKnowledge representationQualitative modeling, computational lexicaQualitative modeling, computational lexicaTerminology information retrievalTerminology information retrievalQuestionQuestion--answering, semantic Webanswering, semantic WebWeb services; cloud and Grid computing, domainWeb services; cloud and Grid computing, domain--specific ontologies specific ontologies (linguistics, geography, law, library science, biomedical scienc(linguistics, geography, law, library science, biomedical science, ee, e--business, enterprise integration). business, enterprise integration).

Promises of Ontology for Biomedical Promises of Ontology for Biomedical Informatics Informatics

Information science forwards to the gateway of Information science forwards to the gateway of knowledgeknowledge--driven, biomedical data based driven, biomedical data based scientific and health care discoveries, and scientific and health care discoveries, and decision making mechanisms with decision making mechanisms with highly highly intelligent communication protocolsintelligent communication protocols. .

Such roadmap strongly requires largeSuch roadmap strongly requires large--scale systemscale system’’s s 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.

Promises of Ontology for Biomedical Promises of Ontology for Biomedical Informatics Informatics

The methodology and conceptual rigor of a The methodology and conceptual rigor of a philosophically inspired formal ontology can bring philosophically inspired formal ontology can bring significant benefits in the development and significant 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 the Such promise can be inspirited by many testaments in the collaboration between biomedical methodologies and collaboration between biomedical methodologies and terminologies with semantic languages and computing terminologies 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 for Barry Smith from the Institute for Formal Ontology Formal Ontology and Medical Information Science (IFOMIS)and Medical Information Science (IFOMIS) clearly clearly addressed the theoretical foundations of ontology addressed the theoretical foundations of ontology (Barry Smith, 2009). (Barry Smith, 2009).

Medical Industrials Needs Medical Industrials Needs

To transform a large terminologyTo transform a large terminology--based based ontology into one special domain to support ontology into one special domain to support practical applications becomes an urgent practical applications becomes an urgent demand in healthcare industrials. demand in healthcare industrials. For example, a general procedure has been the For example, a general procedure has been the implementation of a metaimplementation of a meta--ontological definition ontological definition space in which the definitions of all the concepts space in which the definitions of all the concepts and relations can be defined in and relations can be defined in LinkBaseLinkBase((MontayneMontayne and Flanagan, 2003).and Flanagan, 2003).

Natural Language Processing (NLP)Natural Language Processing (NLP)

Language and Computing (Language and Computing (L&C)L&C)’’ss advanced advanced TeSSITeSSI®® technology technology suite is developed to meet the needs of a broad range of suite is developed to meet the needs of a broad range of industries: healthcare providers, pharmaceutical and R&D industries: 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 tools L&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 language ge processing (NLP) solution, processing (NLP) solution, terminology/ontologyterminology/ontology and and knowledge management (content management, search and knowledge 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 leverage Its solutions allow L&C customers and partners to leverage NLP NLP technology to address a variety of healthcare and business needstechnology to address a variety of healthcare and business needs..

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 ontological start to teach or provide workshops in ontological approaches. approaches. Such education programs commonly introduce a new Such education programs commonly introduce a new approach to the development of ontologies applicable approach to the development of ontologies applicable to the medical domain. to the medical domain. The programs highlight the need for a rich reference on The programs highlight the need for a rich reference on practical ontology for healthcare phenomena and practical ontology for healthcare phenomena and services, and consider issues or challenges arising in the services, and consider issues or challenges arising in the medical applications of such a theoretically grounded medical applications of such a theoretically grounded ontology in improving working applications in the ontology in improving working applications in the domain of electronic patient records (EPR). domain of electronic patient records (EPR).

Medical Education NeedsMedical Education Needs

Many institutions gradually begin to crystallize in Many institutions gradually begin to crystallize in the domain of information systems ontology. the domain of information systems ontology.

Some education programs focus primarily on the Some education programs focus primarily on the realism or adequacy of an underlying ontological realism or adequacy of an underlying ontological theory, leaving for others the task of transforming theory, leaving for others the task of transforming this reference ontology into biomedical working this reference ontology into biomedical working applications. applications. They present recent developments in the field of They present recent developments in the field of realist ontology, focusing especially on biomedical realist ontology, focusing especially on biomedical information science. information science.

Medical Education NeedsMedical Education Needs

Others focus primarily on the construction of working Others focus primarily on the construction of working applications at the expense of ontological realism to practical applications at the expense of ontological realism to practical biomedical informatics, with an emphasis on the applicability ofbiomedical informatics, with an emphasis on the applicability ofmedical natural language understanding applications to detect medical 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 learning earning advanced technologies or toolsadvanced technologies or toolsHigh dimensional ontologies (substances, qualities, functions anHigh dimensional ontologies (substances, qualities, functions and d processes; space and time; niches, contexts, environments) unifyprocesses; space and time; niches, contexts, environments) unifying ing ontologies of medicine at different levels of granularity, problontologies of medicine at different levels of granularity, problematic ematic issues: absences, norms, reference to individual patients in cliissues: absences, norms, reference to individual patients in clinical nical histories, conflicting clinical guidelines, computational tractahistories, conflicting clinical guidelines, computational tractability vs. bility vs. ontological adequacy.ontological adequacy.

Medical Education NeedsMedical Education Needs

However, there still remains many challenge However, there still remains many challenge issues, fundamentally. issues, fundamentally.

For example, in biomedical terminology or ontology For example, in biomedical terminology or ontology development, one should consider how to identify development, one should consider how to identify relevant shortcomings in existing systems and how relevant shortcomings in existing systems and how to properly describe niches/contexts of healthcare. to properly describe niches/contexts of healthcare.

Medical Education NeedsMedical Education Needs

FutureFuture electronic patient record (EPR) system electronic patient record (EPR) system developers must integrate their special domain developers must integrate their special domain applications to largeapplications to large--scale systemsscale systems

How to cooperatively and collaboratively develop general How to cooperatively and collaboratively develop general robotic, dynamic, and interoperable standards of data robotic, dynamic, and interoperable standards of data ontology model, repository, standard expression and ontology 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 development Current biomedical ontology research and development promoted and supported by NIH programs and NCIpromoted and supported by NIH programs and NCI’’s and s and caBiGcaBiG in USA built significant foundations for future in USA built significant foundations for future developmentdevelopment

caBIGcaBIG

A A collection of imaging informaticscollection of imaging informatics tools developed under the tools developed under the umbrella of the National Cancer Institutes umbrella of the National Cancer Institutes caBIGcaBIG ((cancer cancer Biomedical Informatics GridBiomedical Informatics Grid) demonstrates the potential for ) demonstrates the potential for collecting, analyzing, integrating, and disseminating informatiocollecting, analyzing, integrating, and disseminating information n associated with cancer research and care. associated with cancer research and care. The The caBIGcaBIG is an information networkis an information network enabling all constituencies enabling all constituencies in the cancer community to share data and knowledge to in 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, and d to improve patient outcomes. to improve patient outcomes. The The caBIGcaBIG imaging workspaceimaging workspace was created as a national was created as a national multidisciplinary expert advisory board for the identification amultidisciplinary expert advisory board for the identification and nd prioritization of imaging informatics projects. prioritization of imaging informatics projects.

Biomedical Ontology Research Biomedical Ontology Research Development Development

Over the past decades, ontologies have become key Over 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 applications Various applications

Natural language processing (NLP) (Natural language processing (NLP) (NirenburgNirenburg and and 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 domains The use of ontologies also spans many domains including biomedicine, geography and eincluding biomedicine, geography and e--commerce. commerce.

Biomedical Ontology Research Biomedical Ontology Research Development Development

In the biomedical domain, ontologies play an important In the biomedical domain, ontologies play an important role in research (Blake and role in research (Blake and BultBult, 2006), healthcare , 2006), healthcare ((GardeGarde et al., 2007) and translational biomedicine et al., 2007) and translational biomedicine ((RuttenbergRuttenberg, 2008), supporting tasks , 2008), supporting tasks

including knowledge management, data integration and including knowledge management, data integration and decision support (decision support (BodenreiderBodenreider, 2008). , 2008).

A large number of biomedical ontologies have been A 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.

Biomedical Ontology Research Biomedical Ontology Research Development Development

Most ontologies are created for a given purpose (e.g., to Most ontologies are created for a given purpose (e.g., to annotate gene products) and independently of existing annotate gene products) and independently of existing ontologies. ontologies. As a consequence, although ontologies are ideally As 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 a 1992), its impact is still limited to small groups in a special field. special field. The abundance of ontologies should account for great The abundance of ontologies should account for great resources to biomedical researchers in their biomedical resources to biomedical researchers in their biomedical applications. applications.

Biomedical Ontology Research Biomedical Ontology Research Development Development

In practice, however, there is no comprehensive In practice, however, there is no comprehensive registry of biomedical ontologiesregistry of biomedical ontologiesFew existing collections of ontologies do not Few existing collections of ontologies do not provide enough information about the provide enough information about the ontologies to support effective discoverability.ontologies to support effective discoverability.

Biomedical Ontology Research Biomedical Ontology Research Development Development

UMLSUMLSUnified 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 and which integrates many biomedical terminologies and ontologies. ontologies.

Biomedical Ontology Research Biomedical Ontology Research Development Development

BioPortalBioPortalNational Center for Biomedical Ontologies (NCBO), funded by NIH National Center for Biomedical Ontologies (NCBO), funded by NIH RoadmapRoadmapWebWeb--based application providing access to a large number of ontologibased application providing access to a large number of ontologies es in the biomedical domains (in the biomedical domains (BodenreiderBodenreider, O., 2004). , O., 2004). NCBONCBO’’ss BioPortalBioPortal ““defines relationships among those ontologies and defines relationships among those ontologies and between the ontologies and online data resourcesbetween the ontologies and online data resources”” and supports and supports ““communitycommunity--based participation in the evaluation and evolution of based 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 the will host the ontologies from the MetaOntologyMetaOntology issue and their issue and their associated metadata associated metadata Analogously, the Analogously, 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 ontologies ogies from the Open Biomedical Ontology (OBO) family. from the Open Biomedical Ontology (OBO) family.

Biomedical Ontology Research Biomedical Ontology Research Development Development

Resources pros and consResources pros and consOffer online lookup services, i.e., support the Offer online lookup services, i.e., support the

discovery of individual entities through their names discovery of individual entities through their names and identifiers. and identifiers. Although these ontologies are generally useful to Although these ontologies are generally useful to researchers, none of these resources is researchers, none of these resources is comprehensive enoughcomprehensive enoughThe interfaces to ontologies are no substitute for a The interfaces to ontologies are no substitute for a rich description of their content and characteristics.rich description of their content and characteristics.

Ontology for Medical Imaging Ontology for Medical Imaging Informatics Informatics

Although the XML technology has been successful for software Although the XML technology has been successful for software in a heterogeneous environment to establish consistency of IT in a heterogeneous environment to establish consistency of IT data format and expression, currently, data format and expression, currently, there is no easy way to there 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, and This is due to the different domain structure, culture, and expression in languages. expression in languages.

For example, in radiology community, a radiologist uses medical For example, in radiology community, a radiologist uses medical imaging imaging in their daily diagnostics. in their daily diagnostics.

A standard terminology and anthologies are extremely important A standard terminology and anthologies are extremely important in order to improve the clarity of report and efficient in order to improve the clarity of report and efficient communication; and to enhance their clinical and healthcare communication; and to enhance their clinical and healthcare services. services.

Ontology for Medical Imaging Ontology for Medical Imaging Informatics Informatics

RadLextRadLexta Lexicon for Uniform Indexing and Retrieval of a Lexicon for Uniform Indexing and Retrieval of Radiology Information ResourcesRadiology Information ResourcesRadLextRadLext is supported both by the is supported both by the National Institute National Institute of Biomedical Imaging and Bioengineeringof Biomedical Imaging and Bioengineering (NIBIB) (NIBIB) and by the cancer Biomedical Informatics Grid and by the cancer Biomedical Informatics Grid ((caBIGcaBIG) project. ) project.

One of the challenges is how to better translate One of the challenges is how to better translate the the RadLextRadLext terminology to an ontology terminology to an ontology representation in MII systemsrepresentation in MII systems

Ontology for Medical Imaging Ontology for Medical Imaging Informatics Informatics

Rubin (2008) recently reports their successful Rubin (2008) recently reports their successful translation of terminology form the translation of terminology form the RadLextRadLextformat to the one of format 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 medical based knowledge bank of medical imaging informatics using ontological imaging informatics using ontological expressions, rather than redundant expressions, rather than redundant representations and translationsrepresentations and translations

Ontology for Medical Imaging Ontology for Medical Imaging Informatics Informatics

It is of urgent need to develop an efficient It 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 first The data ontology model becomes the first phase to establish integrated ontological domain phase to establish integrated ontological domain models. models.

Ontology for Medical Imaging Ontology for Medical Imaging Informatics Informatics

In the DICOM ontology, among other projects, In the DICOM ontology, among other projects, cerates a single common reference information cerates a single common reference information model for all model for all caBIGcaBIG projects that need to refer projects that need to refer to imaging and other DICOMto imaging and other DICOM--related related information in their individual information. information in their individual information. Most of the current MII tools in PACS or RIS Most of the current MII tools in PACS or RIS systems are websystems are web--application based software for application based software for diagnostics or reporting (Corey et al, 2007). diagnostics or reporting (Corey et al, 2007).

Ontology for Medical Imaging Ontology for Medical Imaging Informatics Informatics

Due to the recentlyDue to the recently--developed Webdeveloped Web--services for online services for online image reading and reporting in image reading and reporting in teletele--radiology, the radiology, the WSDL, Semantic Web, Web Ontology language (OWL), WSDL, Semantic Web, Web Ontology language (OWL), XML and other W3C protocols, with Hl7 and DICOM XML and other W3C protocols, with Hl7 and DICOM standards, are the fundamental components in standards, are the fundamental components in ontological approach in MII. ontological approach in MII. The ontologicallyThe ontologically--defined service objects should be defined 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 systems and should appropriately be used in EHP systems (Smith and (Smith and CeustersCeusters, 2006). , 2006).

Ontology for Medical Imaging Ontology for Medical Imaging Informatics Informatics

The National Center of Biomedical Ontology The 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 new allow researchers and investigators to conduct a new ontology set under the roadmap of NIH, compatible ontology set under the roadmap of NIH, compatible with with caGridcaGrid terminology server in terminology server in caBIGcaBIG..

MIIO Project MIIO Project

We initiated a We initiated a ““Medical Imaging Informatics Medical 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.

MIIO Project MIIO 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 in MIIO project team starts to define each of the terms in ontology expressionontology expression

Domain space definition, domain entity definition, space Domain space definition, domain entity definition, space belongs (is relationship), embedding attributes (has belongs (is relationship), embedding attributes (has relationships), inner relationships among the other entities relationships), inner relationships among the other entities within the domain space, outer relationships to communicate within the domain space, outer relationships to communicate with other entities defined in other domain space, entity with other entities defined in other domain space, entity attributes, characteristics, feature, and properties, entity attributes, characteristics, feature, and properties, entity information acquisition and achieving, and retrieving information acquisition and achieving, and retrieving methods, entity (object) declaration and construction, and methods, entity (object) declaration and construction, and entity abstraction and inheritance, etc. entity abstraction and inheritance, etc.

MIIO Project MIIO Project

The domain space currently only covers medical The domain space currently only covers medical imaging and information technology. imaging and information technology. MIIOMIIO’’ss infrastructure is designed to be highly infrastructure is designed to be highly scalable to extend to other domain space and scalable to extend to other domain space and portable and compatible to other standards in portable and compatible to other standards in ontology expressions.ontology expressions.

MIIO Project Strategic Task ActionsMIIO Project Strategic Task Actions

Multiple expressionsMultiple expressionsin multiple ontological formats or expressions, mainly in in multiple ontological formats or expressions, mainly in OWL, OBO, UMLS RRF, OWL, OBO, UMLS RRF, ProgeteProgete, and , and ProgeteProgete--OWL OWL respectively.respectively.

A dynamic search engineA dynamic search engineFor the uses of special domain ontologiesFor the uses of special domain ontologiesBy a Java search code through Google search engine. By a Java search code through Google search engine.

Statistical data miningStatistical data miningThe entities were found by decoding the words using string The entities were found by decoding the words using string token and by a statistical analysis to see the appearing with token and by a statistical analysis to see the appearing with each articles or online pageseach articles or online pages

HPCHPC--enabledenabled

MIIOMIIO--TK ModulesTK Modules

The MIIOThe MIIO--TK has several components or TK has several components or modulesmodules

File module File module ---- allows users to open file and projectallows users to open file and projectSearch Module Search Module ––a search enginea search engineDefinition module Definition module ------ for input, modify, and express for input, modify, and express modulemoduleFormat conversion module Format conversion module ------ allows users to allows users to convert one expression format to anotherconvert one expression format to anotherVisualization module Visualization module ------ allows users to visualize allows users to visualize different formatted enmity expression. different formatted enmity expression.

Spotlight of MIIO Spotlight of MIIO ToolKitToolKit

Lab MissionLab Mission

Establishment of a nationally and globallyEstablishment of a nationally and globally--recognized research lab in medical imaging recognized research lab in medical imaging informatics or radiology informaticsinformatics or radiology informatics

Short Term Action TasksShort Term Action Tasks

Learning any subjects and shaping knowledgeLearning any subjects and shaping knowledgeDevelop infrastructure of unprecedented computing Develop infrastructure of unprecedented computing facility in medical imaging informaticsfacility in medical imaging informaticsCollaborating with enterprise IT and health care Collaborating with enterprise IT and health care industrialsindustrialsWorking with external and internal professionalsWorking with external and internal professionalsSeeking for fundsSeeking for fundsDevelop software solutions for future health care Develop software solutions for future health care systemssystemsAttract more people including you.Attract more people including you.

LongLong--Term GoalTerm Goal

Computation (future projects)Computation (future projects)Infrastructure and algorithm developments for data Infrastructure and algorithm developments for data mining in medical imagemining in medical imageArtificial Intelligence in medical imagingArtificial Intelligence in medical imagingLargeLarge--scale image processing and associated scale image processing and associated modeling and simulationsmodeling and simulationsDigitalization of human body (massDigitalization of human body (mass--phantom phantom system)system)Computational radiologyComputational radiologySystem radiologySystem radiology

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

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 ProcessingCT ReconstructionCT ReconstructionSegregationSegregationRegistrationRegistrationTexturing and classificationTexturing and classificationEnhancementEnhancementImage compressionImage compressionImage data miningImage data mining……

ProjectsProjectsModeling 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

ProjectsProjects

Stereological Analysis and Tumor Volume Stereological 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 Accuracy y 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 Topology Stereotactic 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

ProjectsProjectsKnowledgeKnowledge--based CAD for Breast Imaging based CAD for Breast Imaging (KCBI) (KCBI)

architectural distortionarchitectural distortioncalcification calcification DeformationDeformation

http://http://www.uiowa.edu/mihpclab/projects_kcbi.htmlwww.uiowa.edu/mihpclab/projects_kcbi.html

New projectsNew projectsTomosynthesis and Molecular Breast ImagingTomosynthesis and Molecular Breast ImagingUS Medical ImagingUS Medical Imaging3D Volume Rendering3D Volume Rendering

Sponsorships and CollaborationsSponsorships and Collaborations

Current sponsorsCurrent sponsorsNIH (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 specification Microsoft (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)

Institutional CollaborationsInstitutional Collaborations

UIUI--Medical School Medical School –– SJTUSJTU--Medical SchoolMedical School

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