SOA In Health Care - july9 - OMG...Party o Core Data Types, i.e. for “Amount, Code, Measure, Name,...

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SOA In Health CareUsage of Standard based Ontology

Pavithra KenjigePK TechnologiesJuly 12th, 2010


Usage of Standard Based ontology

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


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.


Overview

What is OntologyTypes of Ontologies, and methodologies Ontology Representation languagesExample of Medical OntologiesEnterprise Architecture and Ontology developmentStandards based OntologyIntegration and Interoperability of Medical systems

ProblemOntology as solution

Ontology usage for SOA & Semantic WebBenefits of OntologyReferences


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 existenceAn ontology is a specification of a conceptualization. - Tom Gruber


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 interestThe relationships between those thingsThe properties (and property values) of those thingsThe functions and processes involving those thingsConstraints on and rules about those things


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 humansData � Information � Knowledge � Wisdom


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


Types of Ontologies

upper-level Ontologies DOLCE : Domain Ontology for Linguistic and Cognitive EngineeringSUMO :Suggested Upper Merged OntologyBFO : Basic Formal Ontology

mid-level, domain-spanning Ontologies PSL : Patterns to Specify Processes – by NIST

Domain Ontologlies Geospacial Ontologies. Medical Ontologies ..etc.


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 integrationEtc…


Medical Ontologies using BFO

BioTop: A Biomedical Top-Domain OntologyCommon Anatomy Reference Ontology (CARO)Foundational Model of Anatomy (FMA)Gene Ontology (GO)Infectious Disease OntologyOntology for Biomedical Investigations (OBIOntology for Clinical Investigations (OCI)Phenotypic Quality Ontology (PaTO)Protein Ontology (PRO)RNA Ontology (RnaO)Senselab OntologySequence Ontology (SO)Subcellular Anatomy Ontology (SAO)Vaccine Ontology (VO)


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-dimensionalEtc

Independent vs Dependant


Example of relations in OBO - Bio medical Ontology

Foundational : is_a, part_ofadult human is_a human

Spatial : located_in contained_in, contained_adjacent_toTemporal : transformation_of,derives_from

preceded_by- larva transformation_of pupaParticipation: has_participant


Ontology Representation languages

RDF, OWL, OWL2, Common Logic ..SWRL, RIF, SKOS; OBO; UML; E-R, IKL, ...)

Tools:Protégé, OntoEdit, WebODE … etc


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 terminologieshttp://bioportal.bioontology.org

Ontolog Forum has Open Ontology repositoryOOR sandbox – http://oor-01.cim3.net

http://bioportal.bioontology.org/


BioPortal.org


BioPortal search results


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


Protégé OWL class view


Protégé – View OWLViz graphically


Standards Provide

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


Ontology Based Standards

ISO 15926 in modeling business informationISO 15926 Realtime Interoperability Network Grid

-used for Content collaboration, referece datapublication and collaborative generation of reference data – Mathew West

ISO 11179 standard - EPA….etc


Ontology Based Standards

ISO 15000- Supports data modelingCreates 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


Medical Ontology Based Standards

SNOMEDUnified Medical Language SystemNational Cancer Institute ThesaurusHL7 Reference Information ModelInternational Classification of Functioning,Disability and Health


Inventory of Relevant Standards for EHRSystems

• Architecture standards- HL7 versions 2.x/3, CORBA, MDA, HISA• Modelling standards- UML, CEN 15300: “CEN Report: Framework for formal modelling of healthcaresecurity policies”• Communication standards- CEN 13608: “Security for healthcare communication”, CEN 13606: “Electronichealthcare record communication”• Infrastructure standards- ISO 17090: “Public key infrastructure”, ETSI TS 101733: “Electronic SignatureFormats”• Privacy standards- ASTM E1987-98: “Standard guide for individual rights regarding healthinformation”, CEN 13729: “Secure user identification - Strong authenticationusing microprocessor cards”; ISO/IEC PDTS Pseudonymisation Practices for theProtection of Personal Health Information and Health Related Services• Safety standards- CEN 13694: “CEN Report: Safety and security related software quality standardsfor healthcare”; ISO/DTS 25238 Classification of Safety Risks• Quality standards- ISO 9000:• Terminology and ontology standards- UMLS, SNOMED• Identifier and identification schemes- LOINC, ASTM E1714-00: “Standard guide for properties of a UniversalHealthcare Identifier”

By European Commission – DG Information Society


Enterprise Architecture & Ontology

Enterprise Architecture provides the blueprint of the organization. Frameworks are used to develop enterprise architecture

- Ex: Zachman, FIAF, DODAF, TOGAF etc


Example, Zachman framework


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 diagramsSupports ER diagrams

FEAF supports semantic modeling like Zackman.. DoDAF, on has to develop Ontologies as part of Information Veiw..


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 systemInteroperability 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.


What problems does Ontology help to solve..

Enterprise wide, domain wide interoperabilityCurrently: system-of-systems, vertical stovepipesAnthologies act as conceptual model representing enterprise consensus semantics

Heterogeneous Data ProblemDifferent organizational units, Service Needers/Providers have radically different databaseswhat’s the format? - Syntactichow are they structured? - Structurewhat do they mean ? – SemanticThey all speak different languages (access, description, schemas, meaning)


Ontology as Knowledge base


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, http://www.cis.hut.fi/AKRR08/papers/nirenburg.pdf


Usage of Ontologies in SOA

Ref: An Ontology-Driven Service-Oriented Approach by Saïd Izza, Lucien Vincent, Patrick Burlat


Desirable candidate services for NHIN

Future SOA Components (NHIN and beyond)As presneted by :Steve Steffensen, MD. TATRC on NHIN interoperability show case

UniversalClient

MedicalDeviceInterop

FullHITSP

DocSupport

ClinicalDecisionSupport

PatientEducation

DataMapping

(CAL)

HIESupport

MobileDeviceSupport

InpatientCharting

PHRInterface

Future SOA services can be

developed to support additional use cases for both the NHIN and the

MHS. These components plug

into the standards-based enterprise

service bus to rapidly provide

new functionality.


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.. ??


Semantic Web

Tim Berners-Lee’s vision, 1999I 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

http://en.wikipedia.org/wiki/Intelligent_agent


Semantic Web Layers:


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 servicesSOA to provide semantic servicesSemantic WebTherefore serve and harness the power of computing and new technologies to enhance human wisdom and decision making


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.


References

Bio-ontologies: current trends and future directions,by Olivier Bodenreider and Robert StevensIntroduction to Bio medical Ontologies by Barry Smith http://www.bioontology.org/seminar-seriesSemantic Interoperability and Strategies for the Standardization of Medical Information: epSOS project : By Barry SmithNational center for Biomedical Ontology : http://www.bioontology.org/Ontologies for Intelligence Community, by Dr.Leo Obrst, MITREOntology Forum : http://ontolog.cim3.net/cgibin/wiki.pl?WikiHomePageIntegrating Semantic Systems, Expressing, sharing, and using knowledge, Dr John Sowa http://www.jfsowa.com/talks/iss.pdf Standford’s Protégé, Ontology development tool : http://protege.stanford.edu/Cost Benefits of Ontology – Tim Menzies, NISTZachman framework – zifa.com FEAF framework- http://www.cio.gov/documents/fedarch1.pdf

http://www.bioontology.org/seminar-series

http://www.bioontology.org/seminar-series

http://www.bioontology.org/

http://ontolog.cim3.net/cgibin/wiki.pl?WikiHomePage

http://www.jfsowa.com/talks/iss.pdf

http://protege.stanford.edu/

http://www.cio.gov/documents/fedarch1.pdf

SOA In Health Care - july9 - OMG...Party o Core Data Types, i.e. for “Amount, Code, Measure, Name,...

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