Query Health Concept-to-Codes (C2C) SWG Meeting #3

Query Health Concept-to-Codes (C2C) SWGMeeting #3

December 20, 2011

1

Today’s Agenda

Topic Time Allotted

Review of Updated Timeline and Future Meeting Times

Questions for Consideration and Proposed outline of end deliverable

3:00 – 3:05

Presentation by Subject Matter ExpertsShawn Murphy – i2B2 (Cont.) 3:05 - 3:15Stan Huff – CMIO Intermountain Health 3:15 – 3:30Rick Biehl – DOQS 3:30 – 3:45Oliver Bodenreider - NLM 3:45 - 4:00

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Proposed Timeline

Meeting 1 – Dec 6 Meeting 2 – Dec 13 Meeting 3 – Dec 20 Meeting 4 – Jan 03 Meeting 5 – Jan 10 Meeting 6 – Jan 17th

Tasks •Review of presented concept mapping frameworks to develop a proposed approach•Presentation and review of Draft Deliverable with the SWG

Tasks •Presentation from 3-4 additional SMEs on Concept Mapping in their organizations (if needed)

Tasks •Presentation from 3-4 SMEs on Concept Mapping in their organizations


Tasks•Introductions •Scope•Proposed Approach•Identify SME and presentation timeline for next few meetings

TODAY

Coordinate offline activities to summarize approaches and develop draft deliverable from presenters

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Starting Jan 3rd, meeting times extended from 2:30-4:00pm

Link - http://wiki.siframework.org/C2C+SME+Presentation+Schedule

Questions for ConsiderationsFrameworks

(Ex. - i2B2, PMN, hQuery)Tools

(Ex. RxNav, RELMA, LexEVS)Standards

Overview and Current Status

•How do you define concept mapping within your system (e.g. are you mapping in between standards, or are you mapping from standards to your local data dictionary)?•Are there any internal mechanism?•Do you use any external tools?•Are you able to maintain the integrity of the original data in its native form (i.e. data as collected and not modified)?

•How does your tool function?•Are you able to maintain the integrity of the original data in its native form (i.e. data as collected and not modified)?

•How do your standards relate to concept mapping?•Are you able to maintain the integrity of the original data in its native form (i.e. data as collected and not modified)?

Integration and

Infrastructure

•How can you integrate with external tools for mapping? JavaScript library? Java? Web Services API?

•How can your tool be leveraged? Are there any external APIs or other interfaces?

•What infrastructure is necessary to implement / utilize your standard?

Alignment to Query Health

•Is your framework geared towards the Data Source? The Information Requestor? Or Both?

•Is your tool geared towards the Data Source? The Information Requestor? Or Both?

•Are the standards developed around concept mapping at the data source level? The Information Requestor level? Or Both?

Maintenance

•Who maintains your concept mapping tool?•Who maintains the mappings and how often are they released?•What is the associated cost with maintenance?

•Who maintains your concept mapping tool?•Who maintains the mappings and how often are they released?•What is the associated cost with maintenance ?

•Who maintains the development of standards?•Who maintains the mappings and how often are they released?•What is the associated cost with maintenance and periodic releases?

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Proposed Layout of Deliverable

The deliverable will be a Word document divided into the following sections.

• Abstract – Short summary of recommended concept mapping approach• Background

– Scope and Objectives• Discovery

– SMEs / Organization Scan– Distributed query systems– Concept mapping experts on standards/frameworks– Other relevant concept mapping tools

– Development and discussion of targeted questions– Review of short presentations by SME

• Discuss Summary of gathered information on concept mapping– General summary of the organization– Summary of the tool, framework, or standard presented– Key points from the presentation

• Conclusion– Recommendation on proposed framework for Concept Mapping

• Next Steps

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Shawn Murphy (Cont.)Distributed Query Framework - i2B2

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Use cases for i2b2 Ontology Services

1 - Mapping a Global to a Local Terminology for SHRINE queries2 - Merging one terminology into another to enable queries using two terminologies simultaneously

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Ontology Use Case in i2b2 for Shared Health Research Information Network (SHRINE)

Queries are created using ontology presented in web clientQueries are distributed to multiple sites using central ontology Central ontology is transformed to local ontology at each site

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Distributed Query System

Dark Blue = core i2b2 technologyLight Blue = SHRINE modules (“cells”)

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Example – Using BioPortal SNOMED_CT to populate i2b2 ontology

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Bioportal Clinical Finding view

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NCBO Extraction workflow

NCBORESTXML

Request to extract ontology

i2b2Metadata

ExtractionWorkflow

SNOMED view

ExtractedData

Process

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Extracted SNOMED terms

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Providing mappings using NCBO services

Mapping cell Need for mapping different site-specific ontologies in cross-institutional

settings. (SNOMED_CT ICD-9, RxNORM NDC) First look for locally mapped data Then seek mappings through NCBO services.

http://bioportal.bioontology.org/mappings/service/1101/

MapperCell

Request to map local code

ICD9 SNOMED_CT

NCBORESTXML

LocallyMapped data

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http://bioportal.bioontology.org/mappings/service/1101/

Integrating two i2b2 ontologies with NCBO services

Integrate ICD-9 into SNOMED For each SNOMED term, find a mapped ICD9 term:

Request to integrate

IntegrationWorkflow

ICD9 into SNOMED_CT

SNOMED with ICD9 Data

MapperCell

Add new terms with SNOMED hierarchy, ICD9 name, basecode

NCBORESTXML

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SNOMED folder with ICD9 terms

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ICD10 folder with ICD9 terms

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Stanley M. Huff, MD

Intermountain Healthcare

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Define concept mapping?Concept mapping is typically to

support data transformationConcept mapping is always

purpose specific◦Clinical care◦Public health reporting◦Billing◦Secondary use of data

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Information modelsSince mappings are typically for

data transformation or conversion, detailed clinical data models provide context

data 138 mmHg

quals

SystolicBPObs

data Right Arm

BodyLocation

data Sitting

PatientPosition

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Kinds of mappingsStructure changes and code

translations on storage◦Only normalized data in the EHR

Usually from local codes to standard codes◦Local lab test and result codes to

LOINC◦Local problems to SNOMED CT

Clinical problems (SNOMED CT) to billing codes (ICD-10)

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Mapping ToolsInternal tools

◦Lexical matching using Dice CoefficientExternal tools

◦RELMAPreservation of original data

◦Mostly – eventual deletion of log files◦Responsibility of sending system

Geared to data source or requestor?◦ I don’t understand the question

We can use terminology services◦Can also use Java, Java Script

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Maintenance of mappingsWe maintain our own mappingsCost

◦14 FTEs that create models, terminology, and mappings

◦1,200 HL7 interfaces◦3 million patients◦31,000 employees

No one else uses our mappings

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Rick Biehl, Ph.D Data Oriented Quality Solutions (DOQS)

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Query Health – Clinical WG, 2011-12-2025


CLINICAL

PHENOTYPE

GENOTYPE

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CLINICAL

PHENOTYPE

GENOTYPE

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All of the dimensions

are the same 6-table

implementation.

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Largely inspired by the

work of Ralph Kimball

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CATEGORY

HospitalPhysicianDrug

The categories represent the LOGICAL subdimensions of the data warehouse.31


ROLE

Admitting HospitalTransferring HospitalAttending PhysicianConsulting PhysicianAdmitting PhysicianOrdered DrugAdministered Drug

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PERSPECTIVE

TYPE : Network, Directed Acyclic Graph, or Hierarchy

ICD-9 384.6 decomposes ICD-9 384Acetaminophen is an AnalgesicTylenol brands AcetaminophenTylenol 350 Caps instantiates TylenolVesicle is an OrganelleLower jaw bone is synonym of Mandible

Ontologies

happen

here!

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How many analgesics were administered?

PERSPECTIVE

ROLE

CATEGORY

Query all facts where a drug (category) was administered (role) and Analgesic was

available in any higher perspective.

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Data that complies with the meta-model defined by the BFO will be able to behave in an integrated way across widely varying federated data structures.

Open Biomedical

Ontology (OBO) Group

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Who?What?Where?When?How?Why?

QUERY

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Spatiotemporal Region

SNAPContinuant

SPANOccurrent

SpatialRegion

IndependentContinuant

DependentContinuant

ProcessualEntity

TemporalRegion

SiteObjectObject AggregateFiat Part of ObjectBoundary of Object

3D, 2D, 1D, 0D

QualityRealizable Entity Function Role Disposition

Scattered Spatiotemporal RegionConnected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant

Processual ContextProcess AggregateProcessFiat Part of ProcessBoundary of Process

Scattered Temporal RegionConnected Temporal Region Temporal Interval Temporal Instant

Basic Formal Ontology (BFO)

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SNAPContinuant

SPANOccurrent

SpatialRegion


DependentContinuant

ProcessualEntity

TemporalRegion


3D, 2D, 1D, 0D






Calendar

Clock

Clinical Data Warehouse (CDW)

(a)

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SNAPContinuant

SPANOccurrent

SpatialRegion


DependentContinuant

ProcessualEntity

TemporalRegion


3D, 2D, 1D, 0D





Basic Formal Ontology (BFO)Geopolitics

Calendar

Clock


(a)

(b)

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SNAPContinuant

SPANOccurrent

SpatialRegion


DependentContinuant

ProcessualEntity

TemporalRegion


3D, 2D, 1D, 0D






Organization

Caregiver

Patient

Anatomy

Diagnosis

Procedure

Material

Facility

Accounting

Geopolitics

Calendar

Clock


(a)

(b)

(c)

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SNAPContinuant

SPANOccurrent

SpatialRegion


DependentContinuant

ProcessualEntity

TemporalRegion


3D, 2D, 1D, 0D






Organization

Caregiver

Patient

Anatomy

Diagnosis

Procedure

Material

Facility

Accounting

Geopolitics

Calendar

Clock


(d)

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SNAPContinuant

SPANOccurrent

SpatialRegion


DependentContinuant

ProcessualEntity

TemporalRegion


3D, 2D, 1D, 0D






Organization

Caregiver

Patient

Encounter

Anatomy

Diagnosis

Procedure

Material

Facility

Accounting

Geopolitics

Calendar

Clock


Operation

(d)

(e)

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SNAPContinuant

SPANOccurrent

SpatialRegion


DependentContinuant

ProcessualEntity

TemporalRegion


3D, 2D, 1D, 0D






Organization

Caregiver

Patient

Encounter

Anatomy

Diagnosis

Procedure

Material

Facility

Accounting

Geopolitics

Calendar

Clock


Operation

Facts

(d)(f)

(e)

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SNAPContinuant

SPANOccurrent

SpatialRegion


DependentContinuant

ProcessualEntity

TemporalRegion


3D, 2D, 1D, 0D






Organization

Caregiver

Patient

Encounter

Anatomy

Diagnosis

Procedure

Material

Facility

Accounting

Geopolitics

Calendar

Clock


Operation

Facts

(d)

(g)

(f)

(e)

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SNAPContinuant

SPANOccurrent

SpatialRegion


DependentContinuant

ProcessualEntity

TemporalRegion


3D, 2D, 1D, 0D






Organization

Caregiver

Patient

Encounter

Anatomy

Diagnosis

Procedure

Material

Facility

Accounting

Geopolitics

Calendar

Clock


Operation

Facts

Queries happen

here!

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Thank You!• You are welcome to contact me for

additional information at any time:

Richard E. Biehl, Ph.D.

Data-Oriented Quality [email protected]

Coming in

2012-2013!

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Oliver Bodenreider, M.D.NLM

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48U.S. National Library of Medicine

NLM resources forClinical Concept Mapping

Standards and Interoperability (S&I) FrameworkClinical Concept Mapping (Sub-Work Group)December 20, 2011

Dr. Olivier BodenreiderU.S. National Library of Medicine,Bethesda, MD

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Use cases

“Addison’s disease”

translationquery database

ndc:16590052730

umls:C0001403

fdb:019188

rxnorm:854873

snomedct: 363732003

text-to-referencecode-to-referencereference-to-code

Zolpidem tartrate 10 MG Oral Tablet

fdb:019188

snomedct:

363732003

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Integrating vocabularies

BiomedicalliteratureMeS

H

Genomeannotations

GO

Modelorganisms

NCBITaxonomy

Geneticknowledge bases

OMIM

Clinicalrepositories

SNOMED CT

Othersubdomains

…

Anatomy

FMA

UMLS

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Biomedicalliterature

Genomeannotations

Modelorganisms



Othersubdomains

Anatomy

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Genomeannotations

GO

Modelorganisms

NCBITaxonomy


OMIM

Othersubdomains

…

Anatomy

FMA

UMLSAddison Disease (D000224)

Addison's disease (363732003)

BiomedicalliteratureMeS

H


SNOMED CT

UMLSC0001403

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What does UMLS stand for?UnifiedMedicalLanguageSystem

UMLS®

Unified Medical Language System®

UMLS Metathesaurus®

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Organize termsSynonymous terms clustered into

a conceptPreferred termUnique identifier (CUI)

Addison's disease

Addison Disease MeSH D000224Primary hypoadrenalism MedDRA 10036696Primary adrenocortical insufficiency ICD-10 E27.1Addison's disease (disorder) SNOMED CT 363732003

C0001403

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Source Vocabularies160 source vocabularies21 languagesBroad coverage of biomedicine

◦8M names (normalized)◦2.6M concepts◦>10M relations

Common presentation

(2011AB)

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Source Vocabularies in UMLSGeneral vocabularies

◦anatomy (FMA, Neuronames)◦drugs (RxNorm, First DataBank,

Micromedex)◦medical devices (UMD, SPN)

Several perspectives◦clinical terms (SNOMED CT)◦ information sciences (MeSH)◦administrative terminologies

(ICD-9-CM, ICD-10-CM, CPT-4)◦data exchange terminologies (HL7, LOINC)

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Source Vocabularies in UMLSSpecialized vocabularies

◦nursing (NIC, NOC, NANDA, Omaha, ICNP)◦dentistry (CDT)◦oncology (PDQ)◦psychiatry (DSM, APA)◦adverse reactions (MedDRA, WHO ART)◦primary care (ICPC)

Terminology of knowledge bases (AI/Rheum, DXplain, QMR)

The UMLS serves as a vehicle for the regulatory standards (HIPAA, HITSP, Meaningful Use)

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Source vocabularies in RxNormGold Standard AlchemyMaster Drug Data Base (Medi-Span, Wolters Kluwer Health)Multum MediSource LexiconMicromedex DRUGDEXMedical Subject HeadingsFDA National Drug Code DirectoryFDA Structured Product LabelsNat’l Drug Data File (First DataBank Inc.)VHA National Drug File – RTSNOMED Clinical Terms (drug information)VHA National Drug File

26

67

46

66

55

38

85

88*

13

(terms in thousands, as of October 2011)

116*

19

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Application Programming InterfacesUMLS

◦SOAP-based◦Supports term-to-cui, code-to-cui and

cui-to code (+ mapping relations)◦https://uts.nlm.nih.gov//doc/devGuide/index.html

RxNorm◦SOAP-based and RESTful◦Supports term-to-rxcui, code-to-rxcui

and rxcui-to code◦http://rxnav.nlm.nih.gov/

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https://uts.nlm.nih.gov/doc/devGuide/index.html

http://rxnav.nlm.nih.gov/


Questions for Considerations

Frameworks (Ex. - i2B2, PMN, hQuery)

Resources and Tools(UMLS/UTS, RxNorm/RxNav)

Standards

Overview and Current Status

• How do you define concept mapping within your system (e.g. are you mapping in between standards, or are you mapping from standards to your local data dictionary)?

• Are there any internal mechanism?• Do you use any external tools?• Are you able to maintain the

integrity of the original data in its native form (i.e. data as collected and not modified)?

• Terminology integration system

• Source transparency (most original terminologies can be recreated from the UMLS; generally not the case for RxNorm)

• How do your standards relate to concept mapping?

• Are you able to maintain the integrity of the original data in its native form (i.e. data as collected and not modified)?

Integration and

Infrastructure

• How can you integrate with external tools for mapping? JavaScript library? Java? Web Services API?

• UMLS: - GUI: UTS - API: SOAP-based• RxNorm

- GUI: RxNav- API: SOAP-based + RESTful

• What infrastructure is necessary to implement / utilize your standard?

Alignment to Query Health

• Is your framework geared towards the Data Source? The Information Requestor? Or Both?

• Includes all major clinical terminologies

• Bridges between query (text, code) and data source (standard code)

• Are the standards developed around concept mapping at the data source level? The Information Requestor level? Or Both?

Maintenance

• Who maintains your concept mapping tool?

• Who maintains the mappings and how often are they released?

• What is the associated cost with maintenance?

• NLM develops the UMLS and RxNorm (data + tooling)

• Release schedule - UMLS: twice yearly - RxNorm: monthly• No fee to the end user

(but license agreement required*)

• Who maintains the development of standards?

• Who maintains the mappings and how often are they released?

• What is the associated cost with maintenance and periodic releases?

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References

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References: UMLS home pageUMLS home page

◦http://www.nlm.nih.gov/research/umls/

UMLS documentation◦Reference manual

http://www.ncbi.nlm.nih.gov/books/NBK9676/

◦Source documentationhttp://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html

UMLS online tutorials◦ http://www.nlm.nih.gov/research/umls/user_education/index.html

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http://www.nlm.nih.gov/research/umls/



http://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html

http://www.nlm.nih.gov/research/umls/user_education/index.html


Other things you would need to knowUMLS license agreement

◦ https://uts.nlm.nih.gov/help/license/LicenseAgreement.pdf

MetamorphoSys◦ http://www.nlm.nih.gov/research/umls/implementati

on_resources/metamorphosys/index.htmlUMLS Terminology Services (UTS)

◦ https://uts.nlm.nih.gov/

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https://uts.nlm.nih.gov/help/license/LicenseAgreement.pdf

https://uts.nlm.nih.gov/help/license/LicenseAgreement.pdf

http://www.nlm.nih.gov/research/umls/implementation_resources/metamorphosys/index.html

http://www.nlm.nih.gov/research/umls/implementation_resources/metamorphosys/index.html

https://uts.nlm.nih.gov/


References: RxNormRxNorm home page

◦Content◦http://www.nlm.nih.gov/research/uml

s/

RxNav home page◦Browser + APIs◦http://rxnav.nlm.nih.gov/

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http://rxnav.nlm.nih.gov/

Query Health Concept-to-Codes (C2C) SWG Meeting #3

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