Medical Concept Representation: From Classification to

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Transcript Medical Concept Representation: From Classification to

Biomedical Informatics

Standards for interoperable EHR

Narrowing the Research-Practice Divide in Evidence-Based Medicine with the Adoption of EHRs NIDA

Christopher G Chute MD DrPH Professor, Biomedical Informatics Mayo Clinic College of Medicine July 13, 2009

Biomedical Informatics

Health Care Is An Information Intensive Industry

• • • • Control of Health Care Costs ...

Improved Quality of Care ...

Improved Health Outcomes ...

• Appropriate Use of Health Technology...

Compassionate Resource Management...

 ... depend upon information  … Ultimately Patient Data

Biomedical Informatics

Information Beyond Practice Secondary Re-use as Primary A Interest

• • Data Collected for Clinical Care Forms the Basis for Patient Experience Repositories The Importance of a Well Characterized, High Quality Patient Experience Repository May Exceed the Value of the Primary Information Many Fold

Biomedical Informatics

Repositories of Patient Information

• • • • • Disease Natural History Treatment Response (non-RCT) Basis for Guidelines, Clinical Paths, Best Practice “Just in Time” Source for Decision Support • Have we seen a patient just like this…

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Medical Concepts Events, Observations, Interventions

• • How should we represent it? Language: • • • • Nuance, detail, unfettered combination Timely, current, never obsolete Natural, friendly, established [Ambiguous, imprecise, unpredictable] Codes: • • • • Concise, precise Structured, consistent, well formed Analyzable, manipulable [Rigid, tedious, high maintenance]

Biomedical Informatics

Mayo: A Century-Long Tradition of Studying Patient Outcomes

Demographics Diagnoses Procedures Narratives Laboratories Pathology…

High-Volume Data Storage

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From Practice-based Evidence to Evidence-based Practice

Data Patient Encounters

Decision support

Clinical Databases Registries et al.

Shared Semantics

Inference Standards

Medical Knowledge Vocabularies & Terminologies Expert Systems Clinical Guidelines Knowledge Management

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Value Proposition

“Those with more detailed, reliable and comparable data for cost and outcome studies, identification of best practices, guidelines development, and management will be more successful in the marketplace.” SP Cohn; Kaiser Permanente

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Standards as the Basis for Scientific Data Representation and Interchange

• • • • • Without Standards...

Health Data is non-comparable Health Systems cannot Interchange Data Secondary Uses (Research, Efficiency) are not possible Linkage to Decision Support Resources not Possible Translational research is hobbled

• • • • • • • • • • Biomedical Informatics

US Health Standards Initiatives

1986 Laboratory transport message – ASTM 1987 HL7 founded 1991 Coalition for HISPP within ANSI • Health Information Standards Planning Panel 1992 HISPP formed 1995 HISB formed (Board) 1996 HIPAA passed; NCVHS rechartered 1998 ISO TC 215 formed 2005 Office of the National Coordinator formed 2005 HITSP formed (supersedes HISB) 2009 HIT Policy and Standards Committees

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2009– ARRA Requirements and Tiger Teams HITSP Process EHR Centric IS

• Capitalize on existing

specifications

• Organize according to EHR

Information Exchanges

• Establish Capability Concept

Security, Privacy, and Infrastructure

• Define Infrastructure Service

Collaborations

• Integrate Security and Privacy

functions

[adopted from HITSP Panel]

Quality IS

• Ability to interoperably specify

Measure

• Ability to extract patient-specific

data from EHR and other sources for a measure

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ARRA / HITECH Eight Priority Areas HITSP Tasks for ARRA EHR-Centric IS Eight Priority Areas for HIT in ARRA Security + HIT Infrastr Privacy ucture Certifi ed EHR Discl osure Audit Quality

n n

IIHI* Unus able Demog raphic Data Vulner able Pop

n n

Security and Privacy Service Collab Quality Measures

n n n n n n n n n

Supporting Deliverables Harmonization framework Data Architecture

n n n [adopted from HITSP Panel] n n n n n n

* Individually Identifiable Health Information (IIHI) Unusable

Biomedical Informatics

ARRA / HITECH Meaningful Use HITSP Tasks for ARRA EHR-Centric IS ARRA Title IV (Division B) – Section 401 – Medicare Incentives e Prescribing Info Exchange to Report Quality Improve Quality Measures Certified EHR

n n n n

Security and Privacy Service Collab Quality Measures

n n

Supporting Deliverables Harmonization framework

Data

Architecture

[adopted from HITSP Panel] n n n n n n n n

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Clinical Research in EHRs

• • • Proposed presentation to AHIC – early 2007 Discussed at CTSA/caBIG meeting w/ ONC • • AHIC approves as “alternative path” June 2008 • Funding to coordinate from research community ANSI convenes EHR Clinical Research Value Case Workgroup – fall 2008 • CCHIT adds Clinical Research to roadmap for EHR certification, January, 2009 HITSP Tiger Team for Research, May 2009

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HL7 Reality

• • • • • • ANSI accredited standards organization Peer international organization with ISO and CEN Roughly 5000 person members Working Group meetings three times per year • Roughly 500 attendees for one week De facto think tank and forum for state of the art issues in Health care record, messages, and

content

Recognized by CHI, HITSP, and ONC in US

Biomedical Informatics

So we are all using HL7, what is the problem?

OBX|1|CE| ABO ^ ABO GROUP | | O ^ Type O | OBX|1|CE| BLDTYP ^ ABO GROUP | | TYPEO ^ Type O | OBX|1|CE| ABOTYPE ^ ABO GROUP | | OPOS ^ Type O | Equivalence not obvious to computer 

OBX|1|CE| 883-9 ^ ABO GROUP | | F-D1250 ^ Group O |

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Core Abstractions of the RIM

Entity Role Participant Act

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Is that all?

• • • • The RIM adheres to a high-level abstract model Most of the “detail” exists within the vocabulary extensions of the RIM The Model goes much deeper than the boxes The surface boxes are the veneer

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Message structure from RMIM

ObservationOrder class_cd : CS mood_cd : CS id : SET cd : CD activity_time : GTS

0...

performer

Author

observationOrder author

type_cd : CS signature_cd : CS signature_txt : ED

subject observationOrder 8

Subject type_cd : CS

patient observationOrder 5 2

Performer type_cd : CS

3 origination certifiedEntity

CertifiedEntity class_cd : CS id : SET telecom : BAG

Patient

subjectOf

class_cd : CS id : SET addr : BAG

6 patient 4 certificate subjectPerson

PersonPractitioner class_cd : CS determiner_cd : CS id : SET nm : BAG telecom : BAG

10 healthCareProvider

Person class_cd : CS determiner_cd : CS id : SET nm : BAG telecom : BAG administrative_gender_cd : CE birth_time : TS

healthCareProvider performance

HealthCareProvider class_cd : CS id : SET telecom : BAG

healthCareOrganization

Organization class_cd : CS

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Specialization by restriction (constraint)

Act Observation class_cd <= ACT class_cd <=

OBS

ObservationOrder mood <= ActMood class_cd <=OBS mood <= ActMood code <= ActCode mood <=

ORD

code <=

ObservationType

code <= ObservationType LabOrder class_cd <=OBS mood <= ORD code <=

LabObservation

LabOrder (US) class_cd <=OBS mood <= ORD code <=

LOINC

LabOrder (UK) class_cd <=OBS mood <= ORD code <=

Biomedical Informatics

HL7 V2 vs V3

• • • V2 – bar delimited ASCII • • • No semantic interoperability Vocabulary binding – underspecified

Everybody is using it.

V3 – model driven architecture • • • • XML syntax (option) Well-defined semantic interoperability Elegant vocabulary binding

Nobody is using it.

ISO OSI vs. TCP/IP parable…

Biomedical Informatics • • • Clinical Data Interchange Standards Consortium – a global, open non-profit standards development organization (SDO) Standards openly available ( www.cdisc.org

) Initiated as volunteer group 1997; incorporated 2000 • • • now > 230 organizational members biopharmaceutical companies, technology providers, contract research organizations and academia active committees in U.S., Europe, Japan, China 24

Biomedical Informatics

Clinical Data Interchange Standards Consortium – CDISC (2)

• CDISC has established global standards for collection, exchange, regulatory submission and archive of medical research data.

• Charter Agreement with HL7 since 2002; commitment to harmonize standards • Liaison A status to ISO TC 215 (Healthcare

)

•

Newest member of JIC (Joint Initiative Council) [HL7/CEN/ISO/CDISC]

Standard SDTM, SEND ODM Define.xml

LAB ADaM Protocol Representation Terminology Codelists CDASH Description

Ready for regulatory submission of CRT Over 12,000 downloads as of Apr 08 CDISC Transport Standard for acquisition, exchange, submission (define.xml) archive Case Report Tabulation Data Definition Specification (CRTDDS) Content standard – available for transfer of clinical lab data to sponsors General Considerations document and examples of datasets for submission Collaborative effort to develop machine readable standard protocol with data layer Developing standard terminology to support all CDISC standards Data acquisition (CRF) standards

Implementation Version Release Date

2004* 2001* 2005* 2002 2004 In progress due in 2008 2006 (Pkg1 & 2A) Pkg 2B in progress In progress due in 2008

Biomedical Informatics

The BRIDG Model*

A clinical research domain analysis model (UML) initiated by CDISC, BRIDGing

•

Organizations (CDISC, HL7, FDA, NCI)

•

Standards - all CDISC standards harmonized into BRIDG

•

Research and Healthcare Towards semantic interoperability; a Portal to Healthcare Represents clinical research in the context of the HL7 RIM Open source ; Collaborative Project

•

See BRIDG Model on CDISC website or www.bridgmodel.org

* Biomedical Research Integrated Domain Group (BRIDG) Model

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The Revised, 2-layered (2-views) BRIDG Model Understandable to Domain Experts (DaM) Consistent levels of abstraction and explicitness in multiple sub Sub-Domain 1 Sub-Domain 2 domain ‘Requirements Models’ Sub-Domain 3 Sub-Domain 4 Sub-Domain 5 Unambiguously mappable to HL7 RIM (DAM) Consistent levels of RIM-compliance and explicitness in a single ‘Analysis Model’

NOTE: Sub-domains may or may not intersect semantically

Biomedical Informatics

ISO TC215 Health Informatics

• • Created in 1998 • Heritage of national standards organizations • Many countries REQUIRE use of ISO standards if they exist (not USA) • Organized by Core Infrastructure and Use Cases Coordinates with other standards development organizations through Joint Initiative Council

Biomedical Informatics

[IOM testimony] Urgent Need for US Health Terminology Authority

• • Model after HL7 “US Realm” notion Forum for adjudicating “value set” contents • Prototyped within HITSP Foundations Committee • Must also identify National Terminology Service • • • • Distribution point for USHTA Content Download whole code systems, values sets Synchronizing master for “local” terminology services • Built along standard for common terminology services May provide direct terminology services to small installations

Biomedical Informatics

HL7 Codes and Values – this week…

• • • • 364 Concept Domains • Kinds of things, Dx, Px, Appt, drug,… 251 code systems • • 155 internally maintained 96 managed by reference (ICD, CPT, SNOMED…) 1579 Value sets (hierarchical) • • • Lists of things used in messages or applications Drawn from coding systems Used to represent Concept Domains Tooling and maintenance done at Mayo

Biomedical Informatics

Proliferation of Content “Have it your way” Vocabulary Models

• • • • • • • Major ontologies • SNOMED CT; Gene Ontology; LOINC; NDF-RT UMLS Metathesaurus; NCI Thesaurus HL7 RIM and Vocabulary; DICOM RadLex CDC bioterrorism PHIN standards caBIG DSR / CDEs (Common Data Elements) All created with differing formats and models Mechanisms for content sharing • Research Area

Biomedical Informatics • • • •

Mayo LexGrid Project Ontology Services

HL7 ANSI Standard ISO Standard Open specification

Provide consistency and standardization required to support large-scale vocabulary adoption and use

• Common model, tools, formats, and interfaces • • Standard terminology model (Excel to OWL) Grid-nodal architecture • http://informatics.mayo.edu

Biomedical Informatics RRF OWL OBO XML Text

LexGrid Conceptual Architecture

LexGrid Registry Service Index

Components

Editors Browsers

Import Browse and Edit

Query Tools

Export

Text XML Protégé OBO LexGrid Node Data Index

S e r v i c e s

L e x B I G CTS

Web Clients Java .NET

...

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cd codingSchemes LexGrid Model

describable

codingScheme

Concepts Properties

+concepts

0..1

concepts::concepts +relations 0..*

describable

relations::relations +concept 1..* versionableAndDescribable concepts::codedEntry +association 1..*

describable

relations::association +property 0..* concepts::property +sourceConcept 0..*

relations::

associationInstance concepts:: presentation concepts::comment +targetConcept 0..*

associatableElement

relations:: associationTarget concepts::definition

Biomedical Informatics

Examples and Proof of Concept

• • • HL7 Vocabulary Model • Common Terminology Services NIH RoadMap: Nat. Center Biomedical Ontologies • • Mayo LexGrid project Clinical and basic science ( Gene Ontology ) communities NCI caBIG – Bioinformatics Grid • • LexEVS (Enterprise Vocabulary Services) NIH CTSA – Translational science

Biomedical Informatics

Mayo Enterprise Vocabulary Organization

Reference Vocabularies Mayo Thesauri Value Sets Cross Mapping Tables External SNOMED LOINC GO ICDs CPTs … ~200 Mayo Internal Table 22 Table 61 SNOMED mods Mayo CPTs WARS … ~50 External UMLS WHO FIC … ~3 Mayo Internal Drugs Disease Symptoms Pt Functioning

EDT Aggregation

… ~8 External JACHO NACCR Ca NIH/NCI … ~1000 Mayo Internal Flow sheets MICS apps/screens Dept systems Registry screens Form questions Inf. for your Phys.

… ~10,000 External SNOMED↔ICD CPT↔ICD LOINC↔SNOMED FDB↔NDC … ~500 Mayo Internal

All thesauri All value sets

Tab 22↔ICD FDB↔Fomulary … … >10,000 LexGrid: Data Model, Data Store and Machinery

Biomedical Informatics

Proposed Process

draft versioning not shown

ICD in LexGrid

Export and Load OWL RDF dump

OWL DL editor Protégé

HL7/ISO format Change Sets

Review and select

Biomedical Informatics

Biomedical Informatics • • • •

Where is This Going?

Standards and interopreabilty are emerging as a first-rank US health priority • The boundary between “clinical” and “research” standards in biology and medicine is eroding Information models and vocabulary exist along a continuum, that must integrate.

Information standards, especially vocabularies, are the foundation for scientific synergies.

Unprecedented consolidation has emerged across the health standards community

Medical Concept Representation: From Classification to

Transcript Medical Concept Representation: From Classification to

Standards for interoperable EHR

Decision support

Inference Standards

OBX|1|CE| 883-9 ^ ABO GROUP | | F-D1250 ^ Group O |

)

Newest member of JIC (Joint Initiative Council) [HL7/CEN/ISO/CDISC]

LexGrid Conceptual Architecture

Components

ICD in LexGrid

OWL DL editor Protégé

Directory