Post on 24-Feb-2016
description
Query Health Concept-to-Codes (C2C) SWGMeeting #3
December 20, 2011
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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 •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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Tasks •Presentation from 3-4 SMEs on Concept Mapping in their organizations
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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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
Query Health – Clinical WG, 2011-12-20
CLINICAL
PHENOTYPE
GENOTYPE
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Query Health – Clinical WG, 2011-12-20
CLINICAL
PHENOTYPE
GENOTYPE
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Query Health – Clinical WG, 2011-12-2028
Query Health – Clinical WG, 2011-12-20
All of the dimensions
are the same 6-table
implementation.
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Query Health – Clinical WG, 2011-12-20
Largely inspired by the
work of Ralph Kimball
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Query Health – Clinical WG, 2011-12-20
CATEGORY
HospitalPhysicianDrug
The categories represent the LOGICAL subdimensions of the data warehouse.31
Query Health – Clinical WG, 2011-12-20
ROLE
Admitting HospitalTransferring HospitalAttending PhysicianConsulting PhysicianAdmitting PhysicianOrdered DrugAdministered Drug
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Query Health – Clinical WG, 2011-12-20
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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Query Health – Clinical WG, 2011-12-20
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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Query Health – Clinical WG, 2011-12-20
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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Query Health – Clinical WG, 2011-12-20
Who?What?Where?When?How?Why?
QUERY
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Query Health – Clinical WG, 2011-12-20
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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Query Health – Clinical WG, 2011-12-20
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)
Calendar
Clock
Clinical Data Warehouse (CDW)
(a)
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Query Health – Clinical WG, 2011-12-20
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)Geopolitics
Calendar
Clock
Clinical Data Warehouse (CDW)
(a)
(b)
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Query Health – Clinical WG, 2011-12-20
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)
Organization
Caregiver
Patient
Anatomy
Diagnosis
Procedure
Material
Facility
Accounting
Geopolitics
Calendar
Clock
Clinical Data Warehouse (CDW)
(a)
(b)
(c)
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Query Health – Clinical WG, 2011-12-20
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)
Organization
Caregiver
Patient
Anatomy
Diagnosis
Procedure
Material
Facility
Accounting
Geopolitics
Calendar
Clock
Clinical Data Warehouse (CDW)
(d)
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Query Health – Clinical WG, 2011-12-20
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)
Organization
Caregiver
Patient
Encounter
Anatomy
Diagnosis
Procedure
Material
Facility
Accounting
Geopolitics
Calendar
Clock
Clinical Data Warehouse (CDW)
Operation
(d)
(e)
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Query Health – Clinical WG, 2011-12-20
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)
Organization
Caregiver
Patient
Encounter
Anatomy
Diagnosis
Procedure
Material
Facility
Accounting
Geopolitics
Calendar
Clock
Clinical Data Warehouse (CDW)
Operation
Facts
(d)(f)
(e)
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Query Health – Clinical WG, 2011-12-20
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)
Organization
Caregiver
Patient
Encounter
Anatomy
Diagnosis
Procedure
Material
Facility
Accounting
Geopolitics
Calendar
Clock
Clinical Data Warehouse (CDW)
Operation
Facts
(d)
(g)
(f)
(e)
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Query Health – Clinical WG, 2011-12-20
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)
Organization
Caregiver
Patient
Encounter
Anatomy
Diagnosis
Procedure
Material
Facility
Accounting
Geopolitics
Calendar
Clock
Clinical Data Warehouse (CDW)
Operation
Facts
Queries happen
here!
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Query Health – Clinical WG, 2011-12-20
Thank You!• You are welcome to contact me for
additional information at any time:
Richard E. Biehl, Ph.D.
Data-Oriented Quality Solutionsrbiehl@doqs.com
Coming in
2012-2013!
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Oliver Bodenreider, M.D.NLM
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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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51U.S. National Library of Medicine
Integrating vocabularies
Biomedicalliterature
Genomeannotations
Modelorganisms
Geneticknowledge bases
Clinicalrepositories
Othersubdomains
Anatomy
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52U.S. National Library of Medicine
Integrating vocabularies
Genomeannotations
GO
Modelorganisms
NCBITaxonomy
Geneticknowledge bases
OMIM
Othersubdomains
…
Anatomy
FMA
UMLSAddison Disease (D000224)
Addison's disease (363732003)
BiomedicalliteratureMeS
H
Clinicalrepositories
SNOMED CT
UMLSC0001403
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53U.S. National Library of Medicine
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
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67
46
66
55
38
85
88*
13
(terms in thousands, as of October 2011)
116*
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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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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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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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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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