Managing Medical Ontologies, OWL using an

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15 Νοε 2013 (πριν από 3 χρόνια και 8 μήνες)

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XML 2004

Medical Ontology, OWL, 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


Clinical Metadata : Communities of Interests


Ontology Management : Controlled Vocabularies


Choice Points : Contextual Validation


Semantic Specifications : Concept URI Collaboration


Deep Dive

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

21
st

Century : e
-
Knowledge Economy

Human Capital

Competitive Capability

Co
-
opetition

Skills Capacity


Productivity & Efficiency

Communities of Interest

Community Trust

Communities of Practice

e
-
Ology


e
-
Business e
-
Population

Co
-
operating Registries

Peer to Peer Repositories

Service Architecture &
Networking Infrastructure

Standards for Business
Process Workflow & Quality
of Service Agreements


Best Practice
Collaboration
Protocols & Policies

Knowledge & IP

Semantic Information Grids

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

e
-
Society : Freely Exchanged Knowledge

e
-
Health

e
-
Learning

e
-
Research

e
-
Government

e
-
Community of Interest

e
-
Community of Practice

e
-
Business

e
-
Science

Knowledge
Mediation &
Interoperation

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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"



XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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 Agencies

to create service processes that support
internationally agreed business process definitions, trust mechanisms and
process control methods

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

e
-
Prescribing Knowledge Application : Appropriate,
Alternate, Approve

Source: Electronic Prescribing: Toward Maximum Value and
Rapid Adoption
-

eHealth Initiative

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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 Architecture

artifacts and constraints
while achieving semantic
interoperability


XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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


XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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
.


XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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

Registry
D

Registry
E

Registry
B

Registry
A

Registry
C

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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

Registration
Business Process and Information Models
(Compliant to the ebXML Meta Model)
Model to XML Conversion
Internal
Business
Application
Implementers
Retrieval of Profiles &
new/updated ebXML Models
Retrieval of Profiles &
new/updated ebXML Models
Register
Collaboration
Protocol Profile
(CPP)
Retrieval of ebXML
Models and Profiles
Build
Build
Collaboration
Protocol
Agreement (CPA)
Payload
CPA
Governs
CPP
Derives
Business Service
Interface
Internal
Business
Application
Business Service
Interface
Registry Service
Interface
Registries
Register
Collaboration
Protocol Profile
(CPP)
XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

ebXML Registry Information Model (RIM)
-

Knowledge
Classification

RegistryObject

ClassificationNode

Classification

RegistryPackage

ExtrinsicObject

Service

Association

RegistryEntry

ClassificationScheme

The structure of the classification scheme may be defined internal or external to the registry


A Classification instance identifies a ClassificationScheme instance and
taxonomy value defined within the classification scheme

Classification

trees
constructed with
ClassificationNodes are
used to define the structure
of Classification schemes or
ontologies

Person

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

Semantic Spectrum of e
-
Business Knowledge

Business Usage Semantics

Data Usage Semantics

System Interoperability

Service Quality

Data Dictionary

Info Engineering Model

Object Oriented Model / Thesaurus

DTD / XML Schema / Dublin Core

RDFS / UML / Topic Map / UNSPSC

OWL
-
S Ontology + Templates + SKOS + Archetypes

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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 .


XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

WC3 Semantic Web : RDF (Resource
Description Framework) Knowledge Graphs



Uniform Resource
Identifiers
e.g.
http://www.w3.org/peopl
e/em/


Application
Statements


individual label #me


genus #person


property #fullname
value ‘Eric Miller’


property #mailbox value
‘mailto:em@w3.org’


XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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>


XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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.

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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)

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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


XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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.


XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

LOINC 10,000 + Archetype Material


Logical Observation Identifiers Names and Codes developed for
use as observation identifiers in standardized

messages
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





XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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.



XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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 aids

for presentation of base classes,
attributes, relationships, and constraints.


OWL
-
related template artifacts submitted by HL7 participants active in the
Templates technical committee

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

Linking OWL to ebXMLRegistry Objects

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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)



XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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.

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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 …

XML 2004

Medical Ontology, OWL, e
-
Business
Registry & Repository

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