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Research Network Query Interoperation
James R. CampbellUniversity of Nebraska
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Requirements of Networked Query Semantic Interoperation
1. Standardized (agreed) formalism for query language
2. Shared (standardized) information modela) Top level ontology (data classes and attributes)b) Terminology model (domain ontology)
3. Domain data archetypes (data type specification)
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Query Interoperationi2b2 GPC 2014
Query formalism
Shared SQL Shared SQL
Top level ontology
ONTOLOGY metadata (MODIFIER_CD)
GPC metadata(BABEL)
Terminology model
CONCEPT_CD GPC ICD-9-CM
Data type specification
Metadataxml(MODIFIER_CD)
---
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EHR Healthcare Data InteroperationONC S&I Framework
EHR vendor Epic 2012 MU Stage 2(2012 )
Epic 2015
Query formalism
EDI (business) EDI HL7 QUERYEDI
HL7 HIE EDI Patient-CCDA
Top level ontology
Proprietary information model
Clarity tables HL7 RIMCCDA
CCDA
Terminology model
ICD-9-CMCPTHCPCS
ICD-9-CMCPTHCPCS
ICD-*-CMCPTHCPCSSNOMED CTLOINCRXNORM NDCMVX CVX
ICD-*-CMCPTHCPCSSNOMED CTLOINCRXNORM NDCMVX CVX
Data type specification
Site specific (Model system)Site specific
(Model system)Site specific
COGITO / i2b2 data specs
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UNMC Goals Implementing i2b2
• Deploy KU extracts updated to Clarity v2012 (now 2014)
• Take advantage of standard terminology that had appeared in Epic since KU started their project
• Develop Ontology metadata for MU domain ontologies to:– Meet PCORI requirements for network query management– Share and standardize for GPC network queries– Provide consistent data management interface to UNMC
research/public health communities
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GPC-Epic Research Standards Transformation Architecture
Meaningful UseMaps Clarity ETL Maps
i2b2 Ontology Metadata
Demographics LOINCLOINC(site)SNOMED CT
Problem ListSNOMED CT(IMO) SNOMED CT
Encounter diagnosesBilling diagnoses
ICD-9-CM(IMO) ICD-(*)-CM
Social historyLOINC
SNOMED CT
Laboratory results LOINC(site) LOINC
Clinical findingsLOINC(site)SNOMED CT
LOINC
Medication ordersPrescriptions
RxNORM(FDB) RxNORM
Medications AdministeredMedications Dispensed
NDC (Surescripts) RXNORMNDC
ProceduresCPT
ICD-9-PCSHCPCS
CPTICD-9-PCS
HCPCS(Colorado)
ImmunizationsCVX
MVX(site)
DocumentsLOINC(site)
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Issues within GPC re/interoperation
• Our sites have heterogeneous data resources and control/management of source data
• Sites are at different stages (?) of MU compliance within their EHR
• Problems with i2b2 metadata build for MU ontologies
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Problems of i2b2 metadata build for support of top level ontology
• Complex polyhierarchies like SNOMED CT require large metadata sets
• ‘LIKE’ string match queries for aggregation are prone to errors of metadata deployment
• Run-time aggregation queries are less efficient in polyhierarchy ‘tangles’
• Transitive closure tables improved run-time efficiency and provided an understandable formalism for distributing i2b2 ONTOLOGY metadata
• PATH-based queries were accurate but run-time varied substantially based upon PATH chosen
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Composed i2b2 SQL
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Metadata Structural DifferencesPATH vs TC
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UNMC Enterprise Research Information Models 2015
CHRONICLES
(Cache)
CLARITY
(SQL)
COGITOData
warehouse i2b2(SQL)
i2b2
(SQLStar
Schema)
PCORI
CDMv3
Popmednet SAS programs
SQL ODBC
Shared SQL ETLsStandards mapping
Meaningful Use Mapped
Standards
I2b2 OntologyMetadata
CDM V2SQL
SAS
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Query Interoperationi2b2 GPC 2014 UNMC 2014
Data CharacterztnGPC CDM V3
Query formalism Shared SQL Shared SQL Shared SQL SAS code
Top level ontology
ONTOLOGY metadata (MODIFIER_CD)
GPC metadata(BABEL)
ONC metadata (GPC metadata)CDM V2
CDM V3 SAS Datasets
Terminology model
CONCEPT_CD GPC CONCEPT_CDs
ICD-*-CMCPTHCPCSSNOMED CTLOINCRXNORM NDC
CDM V3 mixed subset ONC
Data type specification
Metadataxml --- Metadataxml (ONC datatypes)
CDM V3
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What UNMC can offer GPC colleagues today
• Metadata software for SNOMED CT, RxNORM, NDC incl some metadataxml
• Clarity extracts: Problems, Encounter dx, PMH, DRG, FS:Vital signs/exam/PRO/monitoring, Encounters, Procedures, Surgical history, Enrollment, Dispensing, Lab results, Outpt prescriptions,
• CDM SQL build: all V1, Dispensing, Conditions, Prescribing, (Lab_result_CM)
Questions?