SOA In Health Care Usage of Standard based Ontology Pavithra Kenjige PK Technologies July 12th, 2010

Transcription

1 SOA In Health Care Usage of Standard based Ontology Pavithra Kenjige PK July 12th, 2010

2 Usage of Standard Based ontology Usage of Standard based Ontology to achieve interoperability and system integration and Enterprise Architecture in medical domain.

3 Usage of Standard Based Ontology Modern medical information management is a knowledge intensive activity requiring a high degree of interoperability across various health management entities and systems to provide consistent optimal services across. Usage of standard based ontology will help with interoperability, systems integration, and should be developed as part of conceptual information modeling (CIM) while developing Enterprise Architecture, for the organization. An ontology based approach which includes security policies and standards provide a framework for better interactions in a distributed medical systems environment without the limitation of the traditional approach. In addition to interoperability, this would also support SOA and semantic web architectural patterns.

4 Overview What is Ontology Types of Ontologies, and methodologies Ontology Representation languages Example of Medical Ontologies Enterprise Architecture and Ontology development Standards based Ontology Integration and Interoperability of Medical systems Problem Ontology as solution Ontology usage for SOA & Semantic Web Benefits of Ontology References

5 What is Ontology Is derived from the two Greek words (ontos) meaning to be and (logos) meaning word. Ontology is the science or study of being. In philosophy, ontology refers to the study of nature of being and existence An ontology is a specification of a conceptualization. - Tom Gruber

6 What is Ontology In computer science and information science, an ontology is a formal representation of the knowledge by a set of concepts within a domain and the relationships between those concepts. It is used to reason about the properties of that domain, and may be used to describe the domain. A well developed Ontology would include: Objects (things) in the many domains of interest The relationships between those things The properties (and property values) of those things The functions and processes involving those things Constraints on and rules about those things

7 Ontology Usage In Bio medical & Ontolog Forums an Ontology is described as a controlled vocabulary with well defined terms with specified relationships between them, capable of interpreted by both humans and computers.. Ontology is used to develop standardized, well defined terms and concepts and that support syntactic and semantic interoperability across domains For a given Enterprise, or a Domain & systems that support the domain Knowledge Information Data From Information Systems to humans Data Information Knowledge Wisdom

8 Ontology, Terminology & Lexical resources Ontology: The study of what exists and how it can be formally described and axiomatized. Terminology: A classification of the technical terms used in any branch of science, engineering, business, and the arts. Lexical resource: A dictionary, thesaurus, grammar, or other representation of the vocabulary, syntax, or semantics of some natural language. These are three related, but different kinds of representations. - John Sowa

9 Types of Ontologies upper-level Ontologies DOLCE : Domain Ontology for Linguistic and Cognitive Engineering SUMO :Suggested Upper Merged Ontology BFO : Basic Formal Ontology mid-level, domain-spanning Ontologies PSL : Patterns to Specify Processes by NIST Domain Ontologlies Geospacial Ontologies. Medical Ontologies..etc.

10 Bio medical Ontologies The Gene Ontology (GO), The Foundational Model of Anatomy (FMA) The Infectious Disease Ontology (IDO) The OBO Foundry: A suite of biomedical ontologies to support reasoning and data integration Etc

11 Medical Ontologies using BFO BioTop: A Biomedical Top-Domain Ontology Common Anatomy Reference Ontology (CARO) Foundational Model of Anatomy (FMA) Gene Ontology (GO) Infectious Disease Ontology Ontology for Biomedical Investigations (OBI Ontology for Clinical Investigations (OCI) Phenotypic Quality Ontology (PaTO) Protein Ontology (PRO) RNA Ontology (RnaO) Senselab Ontology Sequence Ontology (SO) Subcellular Anatomy Ontology (SAO) Vaccine Ontology (VO)

12 BFO concepts Examples of Basic Formal Ontology (BFO) concepts: - Universal vs instances - Continuant vs Occurrent Similar to Substance, ( objects, entities etc) and Process - You are a substance - Your life is a process - You are 3-dimensional - Your life is 4-dimensional Etc Independent vs Dependant

13 Example of relations in OBO - Bio medical Ontology Foundational : is_a, part_of adult human is_a human Spatial : located_in contained_in, contained_adjacent_to Temporal : transformation_of,derives_from preceded_by - larva transformation_of pupa Participation: has_participant

14 Ontology Representation languages RDF, OWL, OWL2, Common Logic.. SWRL, RIF, SKOS; OBO; UML; E-R, IKL,...) Tools: Protégé, OntoEdit, WebODE etc

15 Example of Medical Ontology Portal and tools The National Center for Biomedical Ontology has developed BioPortal 2.5, a Web-based platform for browsing, visualizing, mapping, and commenting on biomedical ontologies and terminologies Ontolog Forum has Open Ontology repository OOR sandbox

16 BioPortal.org

17 BioPortal search results

18 BioPortal Web accessible repository of ontologies for the biomedical community Archived locally - Anywhere in cyberspace Support for ontology Peer review Annotation (marginalia) Versioning Alignment Search

19 Protégé OWL class view

20 Protégé View OWLViz graphically

21 Standards Provide common structure and terminology single data source for review (less redundant data) Standards allow use of common tools and techniques, common training single validation of data Ontology = Good standard data Ontology = Semantic reasoning

22 Ontology Based Standards ISO in modeling business information ISO Realtime Interoperability Network Grid -used for Content collaboration, referece data publication and collaborative generation of reference data Mathew West ISO standard - EPA.etc

23 Ontology Based Standards ISO Supports data modeling Creates common re-usable building blocks o Template Data Constructs Core Components e.g. Party, Address, Organization o Reusable logical/physical Data Constructs called BIEs e.g. Buyer_ Party, Seller_ Party o Core Data Types, i.e. for Amount, Code, Measure, Name, and Quantity o Business Messages, e.g. Order, Invoice, Financial Reporting Based on Semantic Definitions o Clear rules on how to define semantics to explain what items mean Uses a Context Mechanism that controls how data constructs vary depending on the context o e.g. By business process, business process role, industry, country/region, etc. Syntax neutral o Can be used to define business documents OR business objects/databases Provides the heavy lifting for syntax specific representations o XML Naming and Design Rules define how to map to XML Schema o XMI Profile for future UML2XML o UML2EDIFACT for traditional EDI --David Connelly

24 Medical Ontology Based Standards SNOMED Unified Medical Language System National Cancer Institute Thesaurus HL7 Reference Information Model International Classification of Functioning, Disability and Health

25 Inventory of Relevant Standards for EHR Systems Architecture standards - HL7 versions 2.x/3, CORBA, MDA, HISA Modelling standards - UML, CEN 15300: CEN Report: Framework for formal modelling of healthcare security policies Communication standards - CEN 13608: Security for healthcare communication, CEN 13606: Electronic healthcare record communication Infrastructure standards - ISO 17090: Public key infrastructure, ETSI TS : Electronic Signature Formats Privacy standards - ASTM E : Standard guide for individual rights regarding health information, CEN 13729: Secure user identification - Strong authentication using microprocessor cards ; ISO/IEC PDTS Pseudonymisation Practices for the Protection of Personal Health Information and Health Related Services Safety standards - CEN 13694: CEN Report: Safety and security related software quality standards for healthcare ; ISO/DTS Classification of Safety Risks Quality standards - ISO 9000: Terminology and ontology standards - UMLS, SNOMED Identifier and identification schemes - LOINC, ASTM E : Standard guide for properties of a Universal Healthcare Identifier By European Commission DG Information Society

26 Enterprise Architecture & Ontology Enterprise Architecture provides the blueprint of the organization. Frameworks are used to develop enterprise architecture - Ex: Zachman, FIAF, DODAF, TOGAF etc

27 Example, Zachman framework

28 Where does Ontology fit into EA? As you can see Zachman framework the second row first column One needs to develop a semantic model.. In olden days we called it conceptual information model.. (CIM) Ontology can be developed as part of semantic model.. List of things that exist and their properties and relationships.. Etc.. At a system level these models can be based to develop data models depending on the methodology used.. Supports UML diagrams Object diagrams / Class diagrams / activity diagrams Supports ER diagrams FEAF supports semantic modeling like Zackman.. DoDAF, on has to develop Ontologies as part of Information Veiw..

29 Integration & Interoperability Integration is the arrangement of an organization s information systems in way that allows them to communicate efficiently and effectively and brings together related parts into a single system Interoperability is the ability of health information systems to work together within and across organizational boundaries in order to advance the effective delivery of healthcare for individuals and communities.

30 What problems does Ontology help to solve.. Enterprise wide, domain wide interoperability Currently: system-of-systems, vertical stovepipes Anthologies act as conceptual model representing enterprise consensus semantics Heterogeneous Data Problem Different organizational units, Service Needers/Providers have radically different databases what s the format? - Syntactic how are they structured? - Structure what do they mean? Semantic They all speak different languages (access, description, schemas, meaning)

31 Ontology as Knowledge base

32 Ontology as Knowledge base Students talk with a patient, tutor, consultant, or lab technician. All dialogs use the same ontology and knowledge base. Source: Adaptivity in a multi-agent clinical simulation system, by S. Nirenburg,M. McShane, S. Beale, & B. Jarrell,

33 Usage of Ontologies in SOA Ref: An Ontology-Driven Service-Oriented Approach by Saïd Izza, Lucien Vincent, Patrick Burlat

34 Future SOA Components (NHIN and beyond) As presneted by :Steve Steffensen, MD. TATRC on NHIN interoperability show case Desirable candidate services for NHIN Future SOA services can be developed to support additional use cases for both the NHIN and the MHS. These components plug into the standardsbased enterprise service bus to rapidly provide new functionality. Data Mapping (CAL) Clinical Decision Support Patient Education Medical Device Interop Universal Client Full HITSP Doc Support PHR Interface HIE Support Mobile Inpatient Device Charting PK

35 Usage of Ontologies in SOA In addition to traditional Service Oriented Architecture pattern, one could include semantic layers by including: - Ontology services - Ontology mediation services to resolve any differences in heterogeneous ontology descriptions in the federal SOA service proposition..??

36 Semantic Web Tim Berners-Lee s vision, 1999 I have a dream for the Web [in which computers] become capable of analyzing all the data on the Web the content, links, and transactions between people and computers. A Semantic Web, which should make this possible, has yet to emerge, but when it does, the day-to-day mechanisms of trade, bureaucracy and our daily lives will be handled by machines talking to machines. The intelligent agents people have touted for ages will finally materialize. - Wikipedia

37 Semantic Web Layers:

38 Benefits of Ontology For humans Ontology enables better access to information and promotes shared understanding of information, terms and concepts Data Information Knowledge Wisdom For computers Ontologies enable comprehension of Information and more extensive processing Knowledge Information Data & processing Systems that are developed, based on well developed ontologies would support Integration and syntactic and semantic interoperability Supports latest architecture patterns for web services SOA to provide semantic services Semantic Web Therefore serve and harness the power of computing and new technologies to enhance human wisdom and decision making

39 Benefits of Ontology Interoperability: When interfacing two components, access the ontology of each component to design a mapping between different concepts in different components. Browsing/searching: The meta-knowledge within an ontology can assist an intelligent search engine with processing your query. For example, if a query returns no results, then the ontology could be used to automatically generalize the query to find nearest partial matches. Reuse: Why waste time and money rebuilding component X when X already exists in someone else s library? Structuring: It may be faster to build new systems via ontological bootstrapping ; i.e. use the conceptualizations in ontologies to assist you with structuring the knowledge in a new domain.

40 References Bio-ontologies: current trends and future directions,by Olivier Bodenreider and Robert Stevens Introduction to Bio medical Ontologies by Barry Smith org/seminar-series Semantic Interoperability and Strategies for the Standardization of Medical Information: epsos project : By Barry Smith National center for Biomedical Ontology : Ontologies for Intelligence Community, by Dr.Leo Obrst, MITRE Ontology Forum : Integrating Semantic Systems, Expressing, sharing, and using knowledge, Dr John Sowa Standford s Protégé, Ontology development tool : Cost Benefits of Ontology Tim Menzies, NIST Zachman framework zifa.com FEAF framework-