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

Todays Agenda TopicTime 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 Experts Shawn Murphy i2B2 (Cont.) 3:05 - 3:15 Stan Huff CMIO Intermountain Health 3:15 3:30 Rick Biehl DOQS 3:30 3:45 Oliver Bodenreider - NLM 3:45 - 4:00 2

Proposed Timeline Meeting 1 Dec 6Meeting 2 Dec 13Meeting 3 Dec 20Meeting 4 Jan 03Meeting 5 Jan 10Meeting 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 3 Tasks Presentation from 3-4 SMEs on Concept Mapping in their organizations Starting Jan 3 rd, meeting times extended from 2:30-4:00pm Link - http://wiki.siframework.org/C2C+SME+Presentation+Schedule

Questions for Considerations Frameworks (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? 4

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 5

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

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 7

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 8

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

Example Using BioPortal SNOMED_CT to populate i2b2 ontology 10

Bioportal Clinical Finding view 11

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

Extracted SNOMED terms 13

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/ Mapper Cell Request to map local code ICD9 SNOMED_CT NCBO REST XML NCBO REST XML Locally Mapped data 14

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 ICD9 into SNOMED_CT SNOMED with ICD9 Data Mapper Cell Add new terms with SNOMED hierarchy, ICD9 name, basecode NCBO REST XML NCBO REST XML 15

SNOMED folder with ICD9 terms 16

ICD10 folder with ICD9 terms 17

Stanley M. Huff, MD Intermountain Healthcare 18

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 19

Information models Since 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 20

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) 21

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 dont understand the question We can use terminology services Can also use Java, Java Script 22

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 23

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

Query Health Clinical WG, 2011-12-20 25

Query Health Clinical WG, 2011-12-20 CLINICAL PHENOTYPE GENOTYPE 26

Query Health Clinical WG, 2011-12-20 CLINICAL PHENOTYPE GENOTYPE 27

Query Health Clinical WG, 2011-12-20 CATEGORY Hospital Physician Drug 31

Query Health Clinical WG, 2011-12-20 ROLE Admitting Hospital Transferring Hospital Attending Physician Consulting Physician Admitting Physician Ordered Drug Administered Drug 32

Query Health Clinical WG, 2011-12-20 PERSPECTIVE TYPE : Network, Directed Acyclic Graph, or Hierarchy 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

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. 34

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. 35

Query Health Clinical WG, 2011-12-20 Who? What? Where? When? How? Why? QUERY 36

Query Health Clinical WG, 2011-12-20 Spatiotemporal Region SNAP Continuant SPAN Occurrent Spatial Region Independent Continuant Dependent Continuant Processual Entity Temporal Region Site Object Object Aggregate Fiat Part of Object Boundary of Object 3D, 2D, 1D, 0D Quality Realizable Entity Function Role Disposition Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Scattered Temporal Region Connected Temporal Region Temporal Interval Temporal Instant Basic Formal Ontology (BFO) 37

Query Health Clinical WG, 2011-12-20 Spatiotemporal Region SNAP Continuant SPAN Occurrent Spatial Region Independent Continuant Dependent Continuant Processual Entity Temporal Region Site Object Object Aggregate Fiat Part of Object Boundary of Object 3D, 2D, 1D, 0D Quality Realizable Entity Function Role Disposition Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Scattered Temporal Region Connected Temporal Region Temporal Interval Temporal Instant Basic Formal Ontology (BFO) Calendar Clock Clinical Data Warehouse (CDW) (a) 38

Query Health Clinical WG, 2011-12-20 Spatiotemporal Region SNAP Continuant SPAN Occurrent Spatial Region Independent Continuant Dependent Continuant Processual Entity Temporal Region Site Object Object Aggregate Fiat Part of Object Boundary of Object 3D, 2D, 1D, 0D Quality Realizable Entity Function Role Disposition Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Scattered Temporal Region Connected Temporal Region Temporal Interval Temporal Instant Basic Formal Ontology (BFO) Geopolitics Calendar Clock Clinical Data Warehouse (CDW) (a) (b) 39

Query Health Clinical WG, 2011-12-20 Spatiotemporal Region SNAP Continuant SPAN Occurrent Spatial Region Independent Continuant Dependent Continuant Processual Entity Temporal Region Site Object Object Aggregate Fiat Part of Object Boundary of Object 3D, 2D, 1D, 0D Quality Realizable Entity Function Role Disposition Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Scattered Temporal Region Connected 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) 40

Query Health Clinical WG, 2011-12-20 Spatiotemporal Region SNAP Continuant SPAN Occurrent Spatial Region Independent Continuant Dependent Continuant Processual Entity Temporal Region Site Object Object Aggregate Fiat Part of Object Boundary of Object 3D, 2D, 1D, 0D Quality Realizable Entity Function Role Disposition Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Scattered Temporal Region Connected 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) 41

Query Health Clinical WG, 2011-12-20 Spatiotemporal Region SNAP Continuant SPAN Occurrent Spatial Region Independent Continuant Dependent Continuant Processual Entity Temporal Region Site Object Object Aggregate Fiat Part of Object Boundary of Object 3D, 2D, 1D, 0D Quality Realizable Entity Function Role Disposition Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Scattered Temporal Region Connected 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) 42

Query Health Clinical WG, 2011-12-20 Spatiotemporal Region SNAP Continuant SPAN Occurrent Spatial Region Independent Continuant Dependent Continuant Processual Entity Temporal Region Site Object Object Aggregate Fiat Part of Object Boundary of Object 3D, 2D, 1D, 0D Quality Realizable Entity Function Role Disposition Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Scattered Temporal Region Connected 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) 43

Query Health Clinical WG, 2011-12-20 Spatiotemporal Region SNAP Continuant SPAN Occurrent Spatial Region Independent Continuant Dependent Continuant Processual Entity Temporal Region Site Object Object Aggregate Fiat Part of Object Boundary of Object 3D, 2D, 1D, 0D Quality Realizable Entity Function Role Disposition Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Scattered Temporal Region Connected 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) 44

Query Health Clinical WG, 2011-12-20 Spatiotemporal Region SNAP Continuant SPAN Occurrent Spatial Region Independent Continuant Dependent Continuant Processual Entity Temporal Region Site Object Object Aggregate Fiat Part of Object Boundary of Object 3D, 2D, 1D, 0D Quality Realizable Entity Function Role Disposition Scattered Spatiotemporal Region Connected Spatiotemporal Region Spatiotemporal Interval Spatiotemporal Instant Processual Context Process Aggregate Process Fiat Part of Process Boundary of Process Scattered Temporal Region Connected 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! 45

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 Solutions [email protected] 46

Oliver Bodenreider, M.D. NLM 47

NLM resources for Clinical 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

Use cases Addisons disease translationquerydatabase ndc:16590052730 umls:C0001403 fdb:019188 rxnorm:854873 snomedct: 363732003 text-to-reference code-to-reference reference-to-code Zolpidem tartrate 10 MG Oral Tablet fdb:019188 snomedct: 363732003 49

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

Integrating vocabularies Biomedical literature Biomedical literature Genome annotations Genome annotations Model organisms Model organisms Genetic knowledge bases Clinical repositories Clinical repositories Other subdomains Other subdomains Anatomy 51

Integrating vocabularies Genome annotations Genome annotations GO Model organisms Model organisms NCBI Taxonomy Genetic knowledge bases OMIM Other subdomains Other subdomains Anatomy FMA UMLS Addison Disease (D000224) Addison's disease (363732003) Biomedical literature Biomedical literature MeSH Clinical repositories Clinical repositories SNOMED CT UMLS C0001403 52

What does UMLS stand for? Unified Medical Language System UMLS Unified Medical Language System UMLS Metathesaurus 53

Organize terms Synonymous terms clustered into a concept Preferred term Unique identifier (CUI) Addison's disease Addison DiseaseMeSHD000224 Primary hypoadrenalismMedDRA10036696 Primary adrenocortical insufficiencyICD-10E27.1 Addison's disease (disorder)SNOMED CT363732003 C0001403 54

Source Vocabularies 160 source vocabularies 21 languages Broad coverage of biomedicine 8M names (normalized) 2.6M concepts >10M relations Common presentation (2011AB) 55

Source Vocabularies in UMLS General 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) 56

Source Vocabularies in UMLS Specialized 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) The UMLS serves as a vehicle for the regulatory standards (HIPAA, HITSP, Meaningful Use) 57

Source vocabularies in RxNorm Gold Standard Alchemy Master Drug Data Base (Medi-Span, Wolters Kluwer Health) Multum MediSource Lexicon Micromedex DRUGDEX Medical Subject Headings FDA National Drug Code Directory FDA Structured Product Labels Natl Drug Data File (First DataBank Inc.) VHA National Drug File RT SNOMED 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 58

Application Programming Interfaces UMLS SOAP-based Supports term-to-cui, code-to-cui and cui-to code (+ mapping relations) https://uts.nlm.nih.gov//doc/devGuide/index.html 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/ http://rxnav.nlm.nih.gov/ 59

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? 60

References 61

References: UMLS home page UMLS home page http://www.nlm.nih.gov/research/umls/ http://www.nlm.nih.gov/research/umls/ UMLS documentation Reference manual http://www.ncbi.nlm.nih.gov/books/NBK9676/ http://www.ncbi.nlm.nih.gov/books/NBK9676/ Source documentation http://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html http://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html UMLS online tutorials http://www.nlm.nih.gov/research/umls/user_education/index.html http://www.nlm.nih.gov/research/umls/user_education/index.html 62

Other things you would need to know UMLS license agreement https://uts.nlm.nih.gov/help/license/LicenseAgreement.pdf https://uts.nlm.nih.gov/help/license/LicenseAgreement.pdf MetamorphoSys http://www.nlm.nih.gov/research/umls/implementation_resource s/metamorphosys/index.html http://www.nlm.nih.gov/research/umls/implementation_resource s/metamorphosys/index.html UMLS Terminology Services (UTS) https://uts.nlm.nih.gov/ https://uts.nlm.nih.gov/ 63

References: RxNorm RxNorm home page Content http://www.nlm.nih.gov/research/umls/ http://www.nlm.nih.gov/research/umls/ RxNav home page Browser + APIs http://rxnav.nlm.nih.gov/ http://rxnav.nlm.nih.gov/ 64

Documents

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