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Managing Medical Ontologies, OWL using an e-Business Registry : Repository

Managing Medical Ontologies, OWL using an e-Business Registry : Repository. e-Health Service : Interoperate & Mediate BCM : Business Centric Guidelines e-Business : Co-operating Registry & Repository Semantic Web : Smarter Knowledge Tagging Medical Documents : Generic & Specific

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Managing Medical Ontologies, OWL using an e-Business Registry : Repository

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  1. Managing Medical Ontologies, OWL using an e-Business Registry : Repository • e-Health Service : Interoperate & Mediate • BCM : Business Centric Guidelines • e-Business : Co-operating Registry & Repository • Semantic Web : Smarter Knowledge Tagging • Medical Documents : Generic & Specific • Clinical Metadata : Communities of Interests • Ontology Management : Controlled Vocabularies • Choice Points : Contextual Validation • Semantic Specifications : Concept URI Collaboration Deep Dive Medical Ontology, OWL, e-Business Registry & Repository

  2. Carl Mattocks @ CHECKMi.com • Co-Chair (ISO/TS 15000) ebXMLRegistry Semantic Content SC • Co-Chair Business Centric Methodology TC • CEO CHECKMi • Multiple Agent Training Engine (MATE) binding 1000 databases • Federation of Vendor Repositories • Supporting Operational Metadata Information Needs at Metlife (CA AllFusion, Logidex, Unicorn, Tivoli) • Knowledge Compendium (.Net open source code) • Crosswalk UDDI / ebXML Registry / IMS Repository • Multiple Taxonomies, Z39.50 SRW Gateway, XACML Medical Ontology, OWL, e-Business Registry & Repository

  3. 21st Century : e-Knowledge Economy Knowledge & IP Competitive Capability Human Capital Co-opetition Productivity & Efficiency Skills Capacity Communities of Practice Communities of Interest Community Trust Standards for Business Process Workflow & Quality of Service Agreements Best Practice Collaboration Protocols & Policies Service Architecture & Networking Infrastructure Semantic Information Grids Co-operating Registries Peer to Peer Repositories e-Ology e-Business e-Population Medical Ontology, OWL, e-Business Registry & Repository

  4. e-Society : Freely Exchanged Knowledge e-Community of Practice e-Research e-Science Knowledge Mediation & Interoperation e-Government e-Learning e-Health e-Business e-Community of Interest Medical Ontology, OWL, e-Business Registry & Repository

  5. e-Health Service Objectives : Inform, Interoperate Involve, Improve • Bringing information tools to the point of care by the EHR (Electronic Health Record)systems used in physician offices and hospitals aka"Inform Clinical Practice" • Building an interoperable health information infrastructure, so that records follow the patient and clinicians have access to critical health care information when treatment decisions are being made aka"Interconnect Clinicians" • Using health information technology to give consumers more access and involvement in health decisions aka"Personalize Care" • Expanding capacity for public health monitoring, quality of care measurement, and bringing research advances more quickly into medical practice aka"Improve Population Health" Medical Ontology, OWL, e-Business Registry & Repository

  6. e-Health Care Knowledge Requirements : Observe, Experience, Expand • Publish Observations ‘whenever patient and professionals need it ‘ • Accurate - prevent errors originating with partial notes • Effective - eliminate duplicative care records, lowering administration costs • Compliant - with regulations, privacy laws, etc e.g. HIPAA • Disseminate Experience regarding Treatment Options • Speed the application of research findings; reducing (estimated 17 years) time it takes to be fully integrated into practice • access to specialty information; especially beneficial for medically under served areas • Expand Sharing of Public Health Alerts • Mercury Global Bio-Threat Monitoring exercise • http://www.checkmi.com/wpapers/MercBioDCheckmiScout.pdf Medical Ontology, OWL, e-Business Registry & Repository

  7. e-Health Knowledge Mediation Goals : Re-Use, Re-Usable, Re-Useful • Support Communities of Practice & Communities of Interest • Locally, regionally, nationally, internationally • Use Natural Knowledge models suitable for wide audience not just IT support specialists e.g. the Patient • Ability to mitigate business vocabularies and multi-lingual challenges • Automate sharing Semantically rich MetaData • provide discovery, understanding, and exchange of Electronic Health Record (EHR) information • Enable Providers, Pharmacy, Health Plans / PBM’s (pharmacy benefit management), and other Agenciesto create service processes that support internationally agreed business process definitions, trust mechanisms and process control methods Medical Ontology, OWL, e-Business Registry & Repository

  8. e-Prescribing Knowledge Application : Appropriate, Alternate, Approve Source: Electronic Prescribing: Toward Maximum Value and Rapid Adoption - eHealth Initiative Medical Ontology, OWL, e-Business Registry & Repository

  9. Business Centric Methodology : SOA Knowledge • Enables precise communication between business users and technical experts & enterprise applications and their respective business partner systems • Involves a layered approach for strategically managing Service Oriented Architectureartifacts and constraints while achieving semantic interoperability Medical Ontology, OWL, e-Business Registry & Repository

  10. BCM Conceptual Layer : Knowledge Semantics • Role - semantically connect facts and facets • Provide trace-ability from business vision to system implementation • Ensure alignment of business concepts with automated procedures • Facilitate faster information utilization between business parties • Enable accurate information discovery and synchronization • Integrate information by interest, perspective or requirement • Resource - Controlled Vocabularies, Thesauri, Ontologies, RDF, OWL • Leverage COP knowledge organization systems • SKOS Core http://www.w3.org/2004/02/skos/core/ • Classification schemes for Federated e-Health artifacts and constraints e.g. archetypes Medical Ontology, OWL, e-Business Registry & Repository

  11. Federated Knowledge Management Needs • A Federated Registry not only acts as an interface to a Repository of stored content, it formalises how information is to be registered and shared beyond a single enterprise or agency. • Specifically, a federated content management capability is required when there is a need for managing and accessing metadata across physical boundaries in a secure manner. Those physical boundaries might be the result of community-of-interest, line of business, system, department, or enterprise separation. • Irrespective of the boundary type, a Federated Registry must enable information users to seamlessly access, share and perform analysis on information, including : • map of the critical path of information flowing across a business value chain; • quality indicators such as statements of information integrity, authentication and certification; and • policies supporting security and privacy requirements. Medical Ontology, OWL, e-Business Registry & Repository

  12. Registry D Registry E Registry B Registry A Registry C Co-operating Knowledge Registry & Repository : Federated Content • Mappings for the critical path of information flowing across a business value chain e.g. ordering & payment of e-Prescription • Quality indicators such as statements of information integrity, authentication and certification e.g. electronic signature used for e-prescribing • Policies supporting security and privacy requirements e.g. HIPAA • e-Business XML (e.g. XSDs, Elements, Templates) and Semantics Medical Ontology, OWL, e-Business Registry & Repository

  13. Universal XML Schema Management Knowledge • Interacting entities need re-usable data items with known semantics • These items are required as XML Schema components • The Schema (document) and the Components must be shared within and often outside the organization • Components may use external components such as code lists • Domain Components must be managed cooperatively • Core components must be common • Data definition arbitration agreements are essential • Data types must be standardized Medical Ontology, OWL, e-Business Registry & Repository

  14. ISO/TS 15000 OASIS ebXML Registry One interface (HTTP, SwA, ebMS) to classified knowledge content : • Electronic Forms • Web Services WSDL / WSRP • Collaboration Agreements • Business Process Requirements, Objects, Data • Domain specific Semantics and Relationships between Assets & Artifacts • SQL queries and APIs Medical Ontology, OWL, e-Business Registry & Repository

  15. Web Service Knowledge Registration & Classification • WSDL is an XML format for describing network services as a set of endpoints operating on messages containing either document-oriented or procedure-oriented information. The operations and messages are described abstractly, and then bound to a concrete network protocol and message format to define an endpoint. Related concrete endpoints are combined into abstract endpoints (services). • Registration & Classification provides for a number of uses: • Find a single web service element from among many • Convey semantic content that may be incompletely specified by other attributes - such as names and definitions • Disambiguate between data elements of varying contextual classifications Medical Ontology, OWL, e-Business Registry & Repository

  16. ebXML Registry Information Model (RIM) - Knowledge Classification Classificationtrees constructed with ClassificationNodes are used to define the structure of Classification schemes or ontologies RegistryObject ClassificationNode Classification RegistryEntry Association A Classification instance identifies a ClassificationScheme instance and taxonomy value defined within the classification scheme ClassificationScheme RegistryPackage ExtrinsicObject Service The structure of the classification scheme may be defined internal or external to the registry Person Medical Ontology, OWL, e-Business Registry & Repository

  17. e-Business Knowledge : XML Registry Version 3 • Registration and classification of any type of object • Namespaces defined for certain types of content • Messages defined as XML Schemas • Taxonomy hosting, browsing and validation • Links to external content • Built-in security (SAML) • Event notification, Event-archiving (audit trail) • Life cycle management of objects • Federation for inter-registry relocation, replication, references • metadata is stored in one registry; a registry may cooperate with multiple federations for the purpose of federated queries Medical Ontology, OWL, e-Business Registry & Repository

  18. Semantic Spectrum of e-Business Knowledge Business Usage Semantics System Interoperability OWL-S Ontology + Templates + SKOS + Archetypes RDFS / UML / Topic Map / UNSPSC DTD / XML Schema / Dublin Core Object Oriented Model / Thesaurus Info Engineering Model Data Dictionary Data Usage Semantics Service Quality Medical Ontology, OWL, e-Business Registry & Repository

  19. WC3 Semantic Web : Smarter Knowledge Tagging • XML provides syntax for structured documents, but imposes no semantic constraints on the meaning of these documents. • XML Schema is a language for restricting the structure of XML documents and also extends XML with datatypes. • RDF is a datamodel for resources and relations between them. • RDF Schema is a vocabulary for describing properties and classes of RDF resources, with a semantics for generalization-hierarchies of such properties and classes. • OWL adds more vocabulary for describing properties and classes e.g. relations between classes, cardinality, equality. • SKOS-Core is an [RDF & OWL] schema for representing thesauri and similar types of Simple Knowledge Organization Systems . Medical Ontology, OWL, e-Business Registry & Repository

  20. WC3 Semantic Web : RDF (Resource Description Framework) Knowledge Graphs • Uniform Resource Identifiers e.g. http://www.w3.org/people/em/ • Application Statements • individual label #me • genus #person • property #fullname value ‘Eric Miller’ • property #mailbox value ‘mailto:em@w3.org’ Medical Ontology, OWL, e-Business Registry & Repository

  21. RDF / XML :RDF statement using XML-based syntax • Eric Miller Graph • <?xml version="1.0"?> • <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" • xmlns:contact="http://www.w3.org/2000/10/swap/pim/contact#"> • <contact:Person rdf:about="http://www.w3.org/People/EM/contact#me"> • <contact:fullName>Eric Miller</contact:fullName> • <contact:mailbox rdf:resource="mailto:em@w3.org"/> • <contact:personalTitle>Dr.</contact:personalTitle> • </contact:Person> • </rdf:RDF> Medical Ontology, OWL, e-Business Registry & Repository

  22. RDF Schema & OWL (Web Ontology Language) • RDF Schema is an extension to RDF framework used to describe application-specific classes and properties e.g. Dr. e-Prescribing. • Classes in RDF Schema allow resources to be defined as instances of classes, and subclasses of classes. • rdfs:subClassOf, rdfs:subPropertyOf • OWL describes the structure of a domain in terms of classes and properties • owl:sameClassAs, owl:samePropertyAs, owl:disjointWith, • owl:sameIndividualAs, owl:differentIndividualFrom, • owl:inverseOf, owl:transitiveProperty, • owl:functionalProperty, owl:inverseFunctionalProperty Medical Ontology, OWL, e-Business Registry & Repository

  23. OWL-S (OWL web Service) Service Profile • When registering and linking descriptors of a Web service, WSDL and OWL-S a key factor is the Service Profile which is used to concisely represent the service in terms of capabilities, provenance, and operational parameters • contact information that refers to the entity that provides the service • functional description of the service is expressed in terms of the transformation produced by the service • inputs required by the service and the outputs generated • the preconditions required by the service and the expected effects that result from the execution of the service • category of the service within a classification system • quality rating of the service • feature specific constraints e.g. geographic availability Medical Ontology, OWL, e-Business Registry & Repository

  24. e-Medical Service : HL7 Clinical Document Architecture • HL7 (Health Level) V3 Reference Information Model (RIM) • > domain information models (DIMs) > restricted message information models (RMIMs) > common message element types (CMETs) > hierarchical message definitions (HMDs) > message schemas in XML • e.g. e-prescription would reference multiple DMIM's (Domain Message Information Model) and payload “value sets” for Orders, Observations, Pharmacy, Medications, Patient Administration. • HL7 Clinical Document Architecture (CDA) a generic model for the communication of clinical documents • Document-level, section-level and entry-level Templates can be used to constrain the generic CDA Medical Ontology, OWL, e-Business Registry & Repository

  25. CEN ENV 13606-2 : Electronic Health Record • European Committee for Standardization Electronic Health Record employs four sub-categories: • Folder: High-level subdivisions of the entire EHR for a patient, usually grouping entries over long time-spans within one organization or department, or for a particular health problem. • Composition: A set of record entries relating to one time and place of care delivery; grouped contributions to an aspect of health care activity; composed reports and overviews of clinical progress. • Headed Section: Sub-divisions used to group entries with a common theme or derived through a common healthcare process. • Cluster: Low-level aggregations of elementary entries (Record Items) to represent a compound clinical concept. Medical Ontology, OWL, e-Business Registry & Repository

  26. Good European Health Record GEHR • Extensions on the GEHR approach uses a formal semantic model, known as the GEHR Object Model (GOM) which provides concepts at a number of levels: • EHR and Transaction level • Navigation level • Content (e.g. observation, subjective, instruction) level • Clinical models are expressed in the form of XML-Schema archetype constraint definitions • Transaction types, e.g. contact, summary, etc; • Navigational headings e.g. EPR workcards • Clinical content types e.g. lab-results, prescriptions, including their structure (list, table, series etc) Medical Ontology, OWL, e-Business Registry & Repository

  27. openEHR Container Classes • openEHR specifications separate generic features of any EHR from the domain-specific information about the patient or data subject • EHR Extract class contains all information that is to be transferred to another HER e.g. HL7 CDA. • EHR Folder class allows information within an EHR to be organized. • Composition class that contains information committed to the EHR by a clinician. • Section - this class allows information within a composition to be segmented • Entry - this class contains meaningful information that is to be processed by the machine and read by the clinician • Templates & Clinical Vocabulary Archetypes together frame clinical domain content e.g. valid values of e-Prescription XForm Medical Ontology, OWL, e-Business Registry & Repository

  28. Consolidated Health Informatics (CHI) portfolio of Clinical Vocabularies • National Council on Prescription Drug Programs (NCDCP) standards for ordering drugs from retail pharmacies. • The Institute of Electrical and Electronics Engineers 1073 (IEEE1073) series of standards that allow for health care providers to plug medical devices into information and computer systems • Digital Imaging Communications in Medicine® (DICOM®) standards that enable images and associated diagnostic information to be retrieved and transferred from various manufacturers' devices • Laboratory Logical Observation Identifier name Codes® (LOINC®) to standardize the electronic exchange of clinical laboratory results. Medical Ontology, OWL, e-Business Registry & Repository

  29. LOINC 10,000 + Archetype Material • Logical Observation Identifiers Names and Codes developed for use as observation identifiers in standardizedmessages exchanged between clinical computer systems • Includes entries for vital signs, hemodynamics, intake/output, EKG, obstetric ultrasound, cardiac echo, urologic imaging, gastroendoscopic procedures, pulmonary ventilator management, selected survey instruments, and other clinical observations Medical Ontology, OWL, e-Business Registry & Repository

  30. Integrating the Healthcare Enterprise (IHE) XDS • The IHE Integration XDS Profile for Cross Enterprise Clinical Documents Sharing is document-content neutral. • XDS documents contain simple text, formatted text, images or structured and vocabulary coded clinical information. • Based on the ebXML Registry specification (implemented with freebXML Registry) the XDS defines the (document) Registry as an actor that maintains metadata about each registered document in a document entry. • Enforces policies at the time of document registration • Registry meta data includes a link to the (document) Repository where the actual document is stored which in turn assigns and maintains a unique identifier for each document Medical Ontology, OWL, e-Business Registry & Repository

  31. Key XDS Concepts • A XDS Affinity Domain is made of a well-defined (federated) set of Document Repositories and Document Consumers that have agreed to share the clinical documents. • A shared clinical record is called an EHR-LR (Longitudinal Record) • The care delivery systems used within an enterprise for managing episodes of patient care are called the HER-CR (Care Delivery Record) • An XDS Document is a composition of clinical information that contains observations and services for the purpose of exchange with the following characteristics: Persistence, Stewardship, Potential for Authentication, and Wholeness (characteristics that are well defined in the HL7 CDA) • An XDS Folder provides a collaborative mechanism for several XDS Document Sources to group XDS Documents for a variety of reasons. XDS Documents may be placed into an existing Folder at any time, as long as they relate to the same patient. • A Document Source may only contribute documents with Document Codes and Health Facility Codes that draw from a Vocabulary Value Set that is approved by the Affinity Domain. Medical Ontology, OWL, e-Business Registry & Repository

  32. NIST HL7 Experimental freebXML Registry DMIMs, RMIMs, HMDs, and MessageTypes • HL7-specific classification schemes, especially the code hierarchies for the structural attributes in the RIM. • RMIM static models from technical domains, including finance, Patient Administration, Scheduling, Laboratory Orders, Research Trials, Pharmacy, Medical Records, Common Message Types, Message Control, Master File, and Clinical Documents • RMIM static models from the CMETs domain, each with a an association to the DMIM it is derived from (using external identifiers to the HL7 identification schemes) with external links to diagrams and descriptions, and a number of classifications by specific codes that are fixed by constraints on the RMIM. • RMIMs leads to one or more derived HMDs and MessageTypes. • Each registered artifact has ExternalLinks to its base UML diagrams, long html descriptions, and other visual display aidsfor presentation of base classes, attributes, relationships, and constraints. • OWL-related template artifacts submitted by HL7 participants active in the Templates technical committee Medical Ontology, OWL, e-Business Registry & Repository

  33. Ontology Annotated e-Health Services • e-Health service information can be managed by two different e-Health service entities using different message structures. • ARTEMIS project providing a standard way of accessing the data by registering & storing • ontologies based on existing healthcare standards, • the semantic mapping between these ontologies, • invoke each others web services by semantic mediation. • Discovery of Services stored in a Registry need semantic service registry query mechanisms that leverage previous research linking OWL to the Registry Information Model Medical Ontology, OWL, e-Business Registry & Repository

  34. Linking OWL to ebXMLRegistry Objects Medical Ontology, OWL, e-Business Registry & Repository

  35. Community of Interest : Multiple-levels of Ontologies • BCM COI & XDS Affinity Domain defined by formal or informal organizational structures • Upper level ontology is focused on the non-volatile language and principles of a domain • Lower ontology is focused on the knowledge specific to particular community of practice (as formulated by the recognized experts) Medical Ontology, OWL, e-Business Registry & Repository

  36. BCM Choice Points : XForm & Templates • Electronic PRocess (EPR) Web Service Portal Technology e-Health Service employs semantically rich XML templates • Mayo Clinic Template types • Constraint : operate on code combinations permitted in a code phrase • Style : allow the distribution of semantic details between name and value in name-value pairs • Pattern : defining specific class of items • Document : construct of particular data elements. • Profile : dataset of selected items that describes an existing entity • Extension : constrains or modifies a profile template • Meta : ordered aggregation of multiple other templates, such as an EHR template for the Electronic Health Record Medical Ontology, OWL, e-Business Registry & Repository

  37. BCM Choice Points : Templates & Archetypes • Template & Archetype Choice Points significantly aids to comprehensibility, alignment, while promoting tracing and accountability when : • archetype is a computable expression of a domain level (clinical) concept in the form of structured constraint statements, based on some reference model (RMIM) • archetypes are aligned with Affinity Domain concepts • archetypes all have the same formalism i.e. may be part of a COP ontology but belong to only one or other ontological level • template is used to narrow the choices of archetypes for local or specific purposes (DMIM). • archetype defines constraints on reference model instances which express valid structure (i.e. composition, cardinality). • archetype defines constraints on instances of a reference model which express valid types and values. Medical Ontology, OWL, e-Business Registry & Repository

  38. ebXML Registry Semantic Content Management • Providing support for semantic links based on RDF and OWL the check list of requirements includes : • Re-usable dictionaries of noun definitions for specific industry domains • Re-useful dictionaries of Business Process catalogues • Ontology searching and browsing • Collaborative (COP) ontology development • Classify content using OWL Ontology class hierarchies • Discover content using semantic queries • Attach semantic Objects to Stored Content • Semantic reasoning … Medical Ontology, OWL, e-Business Registry & Repository

  39. With thankful links to : Members of ebXMLRegistry Semantic Content SC http://www.oasis-open.org/committees/sc_home.php?wg_abbrev=regrep-semantic Members of Business Centric Methodology TC http://www.oasis-open.org/committees/download.php/5931/BCM%20Executive%20Brochure.pdf Contact: CarlMattocks@CHECKMi.com Medical Ontology, OWL, e-Business Registry & Repository

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