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

Query Health Concept-to-Codes (C2C) SWG Meeting #3. December 20, 2011. Today’s Agenda . Proposed Timeline . TODAY. Starting Jan 3 rd , meeting times extended from 2:30-4:00pm. Tasks Introductions Scope Proposed Approach Identify SME and presentation timeline for next few meetings.

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

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  1. Query Health Concept-to-Codes (C2C) SWGMeeting #3 December 20, 2011

  2. Today’s Agenda

  3. Proposed Timeline TODAY Starting Jan 3rd, meeting times extended from 2:30-4:00pm • Tasks • Introductions • Scope • Proposed Approach • Identify SME and presentation timeline for next few meetings • 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 • Presentation from 3-4 SMEs on Concept Mapping in their organizations • Tasks • Presentation from 3-4 additional SMEs on Concept Mapping in their organizations (if needed) • Tasks • Review of presented concept mapping frameworks to develop a proposed approach • Presentation and review of Draft Deliverable with the SWG Coordinate offline activities to summarize approaches and develop draft deliverable from presenters Link - http://wiki.siframework.org/C2C+SME+Presentation+Schedule

  4. Questions for Considerations

  5. 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

  6. Shawn Murphy (Cont.) Distributed Query Framework - i2B2

  7. Use cases for i2b2 Ontology Services 1 - Mapping a Global to a Local Terminology for SHRINE queries 2 - Merging one terminology into another to enable queries using two terminologies simultaneously

  8. Ontology Use Case in i2b2 for Shared Health Research Information Network (SHRINE) Queries are created using ontology presented in web client Queries are distributed to multiple sites using central ontology Central ontology is transformed to local ontology at each site

  9. Distributed Query System Dark Blue = core i2b2 technology Light Blue = SHRINE modules (“cells”)

  10. Example – Using BioPortal SNOMED_CT to populate i2b2 ontology

  11. Bioportal Clinical Finding view

  12. NCBO Extraction workflow Extraction Workflow Request to extract ontology NCBOREST XML SNOMED view Process Extracted Data i2b2 Metadata

  13. Extracted SNOMED terms

  14. 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/ NCBOREST XML MapperCell Request to map local code Locally Mapped data ICD9  SNOMED_CT

  15. Integrating two i2b2 ontologies with NCBO services • Integrate ICD-9 into SNOMED • For each SNOMED term, find a mapped ICD9 term: Request to integrate Integration Workflow MapperCell ICD9 into SNOMED_CT Add new terms with SNOMED hierarchy, ICD9 name, basecode NCBOREST XML SNOMED with ICD9 Data

  16. SNOMED folder with ICD9 terms

  17. ICD10 folder with ICD9 terms

  18. Stanley M. Huff, MD Intermountain Healthcare

  19. Define concept mapping? • Concept mapping is typically to support data transformation • Concept mapping is always purpose specific • Clinical care • Public health reporting • Billing • Secondary use of data

  20. Information models • Since mappings are typically for data transformation or conversion, detailed clinical data models provide context SystolicBPObs 138 mmHg data quals BodyLocation Right Arm data PatientPosition Sitting data

  21. Kinds of mappings • Structure 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)

  22. Mapping Tools • Internal tools • Lexical matching using Dice Coefficient • External tools • RELMA • Preservation 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

  23. Maintenance of mappings • We maintain our own mappings • Cost • 14 FTEs that create models, terminology, and mappings • 1,200 HL7 interfaces • 3 million patients • 31,000 employees • No one else uses our mappings

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

  25. 25

  26. CLINICAL PHENOTYPE GENOTYPE 26

  27. CLINICAL PHENOTYPE GENOTYPE 27

  28. 28

  29. All of the dimensions are the same 6-table implementation. 29

  30. Largely inspired by the work of Ralph Kimball 30

  31. CATEGORY Hospital Physician Drug The categories represent the LOGICAL subdimensions of the data warehouse. 31

  32. ROLE Admitting Hospital Transferring Hospital Attending Physician Consulting Physician Admitting Physician Ordered Drug Administered Drug 32

  33. TYPE : Network, Directed Acyclic Graph, or Hierarchy Ontologieshappenhere! PERSPECTIVE ICD-9 384.6 decomposes ICD-9 384 Acetaminophen is an Analgesic Tylenol brands Acetaminophen Tylenol 350 Caps instantiates Tylenol Vesicle is an Organelle Lower jaw bone is synonym of Mandible 33

  34. CATEGORY PERSPECTIVE ROLE How many analgesics were administered? Query all facts where a drug (category) was administered (role) and Analgesic was available in any higher perspective. 34

  35. 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 35

  36. Who? What? Where? When? How? Why? QUERY 36

  37. Basic Formal Ontology (BFO) SpatialRegion 3D, 2D, 1D, 0D IndependentContinuant SNAPContinuant SiteObject Object Aggregate Fiat Part of Object Boundary of Object DependentContinuant Quality Realizable Entity Function Role Disposition ProcessualEntity Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process SPANOccurrent Spatiotemporal Region Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant TemporalRegion Scattered Temporal Region Connected Temporal Region Temporal Interval Temporal Instant 37

  38. Clinical Data Warehouse (CDW) Basic Formal Ontology (BFO) SpatialRegion 3D, 2D, 1D, 0D IndependentContinuant SNAPContinuant SiteObject Object Aggregate Fiat Part of Object Boundary of Object DependentContinuant Quality Realizable Entity Function Role Disposition ProcessualEntity Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process SPANOccurrent Spatiotemporal Region Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant (a) TemporalRegion Calendar Scattered Temporal Region Connected Temporal Region Temporal Interval Temporal Instant Clock 38

  39. Clinical Data Warehouse (CDW) Basic Formal Ontology (BFO) (b) Geopolitics SpatialRegion 3D, 2D, 1D, 0D IndependentContinuant SNAPContinuant SiteObject Object Aggregate Fiat Part of Object Boundary of Object DependentContinuant Quality Realizable Entity Function Role Disposition ProcessualEntity Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process SPANOccurrent Spatiotemporal Region Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant (a) TemporalRegion Calendar Scattered Temporal Region Connected Temporal Region Temporal Interval Temporal Instant Clock 39

  40. Clinical Data Warehouse (CDW) Basic Formal Ontology (BFO) (b) Geopolitics SpatialRegion 3D, 2D, 1D, 0D (c) Organization IndependentContinuant SNAPContinuant Caregiver SiteObject Object Aggregate Fiat Part of Object Boundary of Object Patient DependentContinuant Anatomy Quality Realizable Entity Function Role Disposition Diagnosis Procedure ProcessualEntity Material Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Facility SPANOccurrent Accounting Spatiotemporal Region Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant (a) TemporalRegion Calendar Scattered Temporal Region Connected Temporal Region Temporal Interval Temporal Instant Clock 40

  41. Clinical Data Warehouse (CDW) Basic Formal Ontology (BFO) Geopolitics SpatialRegion 3D, 2D, 1D, 0D Organization IndependentContinuant SNAPContinuant Caregiver SiteObject Object Aggregate Fiat Part of Object Boundary of Object Patient (d) DependentContinuant Anatomy Quality Realizable Entity Function Role Disposition Diagnosis Procedure ProcessualEntity Material Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Facility SPANOccurrent Accounting Spatiotemporal Region Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant TemporalRegion Calendar Scattered Temporal Region Connected Temporal Region Temporal Interval Temporal Instant Clock 41

  42. Clinical Data Warehouse (CDW) Basic Formal Ontology (BFO) Geopolitics SpatialRegion 3D, 2D, 1D, 0D Organization IndependentContinuant SNAPContinuant Caregiver SiteObject Object Aggregate Fiat Part of Object Boundary of Object Patient (d) DependentContinuant Anatomy Quality Realizable Entity Function Role Disposition Diagnosis Procedure ProcessualEntity (e) Material Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Facility SPANOccurrent Accounting Spatiotemporal Region Encounter Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant Operation TemporalRegion Calendar Scattered Temporal Region Connected Temporal Region Temporal Interval Temporal Instant Clock 42

  43. Clinical Data Warehouse (CDW) Basic Formal Ontology (BFO) Geopolitics SpatialRegion 3D, 2D, 1D, 0D Organization IndependentContinuant SNAPContinuant Caregiver SiteObject Object Aggregate Fiat Part of Object Boundary of Object Patient (d) DependentContinuant Anatomy (f) Quality Realizable Entity Function Role Disposition Diagnosis Procedure ProcessualEntity (e) Material Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Facility SPANOccurrent Accounting Spatiotemporal Region Encounter Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant Operation Facts TemporalRegion Calendar Scattered Temporal Region Connected Temporal Region Temporal Interval Temporal Instant Clock 43

  44. Clinical Data Warehouse (CDW) Basic Formal Ontology (BFO) Geopolitics SpatialRegion 3D, 2D, 1D, 0D Organization IndependentContinuant SNAPContinuant Caregiver SiteObject Object Aggregate Fiat Part of Object Boundary of Object Patient (d) DependentContinuant Anatomy (f) Quality Realizable Entity Function Role Disposition Diagnosis Procedure ProcessualEntity (e) Material Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Facility SPANOccurrent Accounting (g) Spatiotemporal Region Encounter Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant Operation Facts TemporalRegion Calendar Scattered Temporal Region Connected Temporal Region Temporal Interval Temporal Instant Clock 44

  45. Clinical Data Warehouse (CDW) Basic Formal Ontology (BFO) Geopolitics SpatialRegion 3D, 2D, 1D, 0D Organization IndependentContinuant SNAPContinuant Caregiver SiteObject Object Aggregate Fiat Part of Object Boundary of Object Patient DependentContinuant Anatomy Quality Realizable Entity Function Role Disposition Diagnosis Procedure ProcessualEntity Material Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Facility Queries happen here! SPANOccurrent Accounting Spatiotemporal Region Encounter Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant Operation Facts TemporalRegion Calendar Scattered Temporal Region Connected Temporal Region Temporal Interval Temporal Instant Clock 45

  46. Coming in 2012-2013! 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 46

  47. Oliver Bodenreider, M.D. NLM

  48. NLM resources forClinical Concept Mapping Standards and Interoperability (S&I) Framework Clinical Concept Mapping (Sub-Work Group) December 20, 2011 Dr. Olivier Bodenreider U.S. National Library of Medicine, Bethesda, MD 48

  49. text-to-reference code-to-reference reference-to-code Use cases query translation database “Addison’s disease” umls:C0001403 snomedct: 363732003 snomedct: 363732003 fdb:019188 fdb:019188 ndc:16590052730 rxnorm:854873 Zolpidem tartrate 10 MG Oral Tablet 49

  50. Clinical repositories Geneticknowledge bases Other subdomains SNOMED CT OMIM … Biomedical literature MeSH NCBI Taxonomy GO Model organisms FMA Genome annotations Anatomy Integrating vocabularies UMLS 50

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