caBIG Vocabulary and Common Data Elements Workspace

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caBIG Vocabulary and Common Data Elements
Workspace

• UC Davis Cancer Center
• UC Davis Medical Informatics

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Clinical Workspace

• Clinical care
• Medical record data
• Laboratory information
• Image acquisition, display and storage
• Adverse event reporting
• Genetic counseling
• Genetic testing

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Research Workspace

• Research
• Clinical trials records
• Tumor registry
• Protocol linking
• Gene expression studies
• Biomarkers
• Cancer animal models
• Anatomy
• Study data
• Genomic data
• Therapeutics

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Public Health Workspace

• Public Health
• Provider reporting
• Cancer registries
• Population Co-morbidity
• GIS
• Death registries

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Interoperability Layers
Semantic model
Vocabulary
OSI Network Model
8 Semantic
Data exchange
7 Application
Medical Informatics
6 Presentation
Data encoding
5 Session
Security
4 Transport
Information Technology
3 Network
Communication
2 Data Link
1 Physical
Concept for slide from Ted Klein and Tim Morris
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Patient Care
Clinical Care Data
Clinical Lab Data
LOINC
SNOMED
RxNORM
Integration Hub
Central Terminology Server
Pathology Lab Data
Imaging Data
DICOM
SNOMED
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Cancer Research
Clinical Care Data
Clinical Lab Data
LOINC
SNOMED
RxNORM
Clinical Research Data
Laboratory Research Data
Integration Hub
Central Terminology Server
Pathology Lab Data
Imaging Data
DICOM
SNOMED
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NCI Centric Components
Public Health Data
Analysis Engine
Patient Care Data
Integration Hub
Central Terminology Server
Clinician Registry
GIS Engine
Clinical Research Data
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Vocabulary
Central Terminology Server

• HL7 V3 messaging is complex
• Byproduct of semantic necessity
• A library of post coordinated terms is essential
• Vocabulary mapping has not reached this level of
  detail yet
• Example
• mild postoperative lymphedema of leg

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HL7 Coded Data
- ltObservationgt   ltid root"10.23.4573.90009" /gt
  ltcode code"39154008" codeSystem"2.16.840.1.11
3883.6.96" codeSystemName"SNOMED CT"
codeSystemVersion"0307core" displayName"clinical
diagnosis" /gt - ltvalue xsitype"CD"
code"403385000" codeSystem"2.16.840.1.113883.6.5
" codeSystemName"SNOMED" displayNamelymphedema
of leg"gt - ltoriginalTextgt mild postoperative
lymphedema of leglt/originalTextgt - ltqualifiergt  
ltname code"246112005" codeSystem"2.16.840.1.1138
83.6.96" codeSystemName"SNOMED CT"
codeSystemVersion"0307core" displayNameseverity
" /gt   ltvalue code"255604002"
codeSystem"2.16.840.1.113883.6.96"
codeSystemName"SNOMED CT" codeSystemVersion"0307
core" displayNamemild" /gt   lt/qualifiergt -
ltqualifiergt   ltname code"116684007"
codeSystem"2.16.840.1.113883.6.96"
codeSystemName"SNOMED CT" codeSystemVersion"0307
core" displayNamehas time aspect" /gt   ltvalue
code"262061000" codeSystem"2.16.840.1.113883.6.9
6" codeSystemName"SNOMED CT" codeSystemVersion"0
307core" displayNamepostoperative" /gt  
lt/qualifiergt - lt/Observationgt
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Protégé Tool
Open Source Distributed Authoring Multiple
Plugins Domain specific Hierarchical classes Java
API
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Build the Ontology

• Infectious disease ontology
• Co-authored with the CDC
• Implemented in CA
• Coupled with Algernon rule-based inference system

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Jterm Terminology Server
Open Source Java API TQL language optimized for
terminologies
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HL7 CTS 1.0
Defines an API For HL7 V3 Software
applications To access terminology Services Messag
e API Vocabulary API
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Source

• Build term list
• NCI Thesaurus
• NLP with POS of clinical documents
• Mapping to NCVHS/CHI approved standard
  vocabularies
• Expand the standard vocabularies as needed