# Presentation: 779877

## caBIG Vocabulary and Common Data Elements Workspace

- UC Davis Cancer Center
- UC Davis Medical Informatics

## Clinical Workspace

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

## Research Workspace

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

## Public Health Workspace

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

## Interoperability Layers

- 1 	Physical

- 2 	Data Link

- 7 	Application

- 8 	Semantic

- 6	Presentation

- 5	Session

- 4	Transport

- 3	Network

- Vocabulary

- Semantic model

- Data exchange

- Data encoding

- Security

- Communication

- Medical Informatics

- Information
- Technology

- OSI Network Model

- *Concept for slide from Ted Klein and Tim Morris

## Patient Care

- Integration
- Hub

- Clinical
- Care
- Data

- Clinical
- Lab
- Data

- Imaging
- Data

- Pathology
- Lab
- Data

- LOINC

- SNOMED

- SNOMED

- DICOM

- RxNORM

- Central
- Terminology
- Server

## Cancer Research

- Integration
- Hub

- Clinical
- Care
- Data

- Clinical
- Lab
- Data

- Imaging
- Data

- Pathology
- Lab
- Data

- LOINC

- SNOMED

- SNOMED

- DICOM

- RxNORM

- Central
- Terminology
- Server

- Clinical Research
- Data

- Laboratory
- Research
- Data

## NCI Centric Components

- Patient
- Care Data

- Analysis
- Engine

- Clinician
- Registry

- GIS
- Engine

- Clinical
- Research
- Data

- Public Health
- Data

- Central
- Terminology
- Server

- Integration
- Hub

## Vocabulary

- 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

- Central
- Terminology
- Server

## HL7 Coded Data

- _[-](file:///../../../../Local%20Settings/Temporary%20Internet%20Files/OLK25/CDA%20-%20Botulism%20Case%20Report%20-%20Sample.xml##)_ <Observation>
-   <id root="**10.23.4573.90009**" />
-   <code code="**39154008**" codeSystem="**2.16.840.1.113883.6.96**" codeSystemName="**SNOMED CT**" codeSystemVersion="**0307core**" displayName="**clinical diagnosis**" />
**-** <value xsi:type="**CD**" code="**403385000**" codeSystem="**2.16.840.1.113883.6.5**" codeSystemName="**SNOMED**" displayName=“**lymphedema of leg**">
**-** <originalText> **mild postoperative lymphedema of leg**</originalText>
**-** <qualifier>
-   <name code="**246112005**" codeSystem="**2.16.840.1.113883.6.96**" codeSystemName="**SNOMED CT**" codeSystemVersion="**0307core**" displayName=“**severity**" />
-   <value code="**255604002**" codeSystem="**2.16.840.1.113883.6.96**" codeSystemName="**SNOMED CT**" codeSystemVersion="**0307core**" displayName=“**mild**" />
-   </qualifier>
**-** <qualifier>
-   <name code="**116684007**" codeSystem="**2.16.840.1.113883.6.96**" codeSystemName="**SNOMED CT**" codeSystemVersion="**0307core**" displayName=“**has time aspect**" />
-   <value code="**262061000**" codeSystem="**2.16.840.1.113883.6.96**" codeSystemName="**SNOMED CT**" codeSystemVersion="**0307core**" displayName=“**postoperative**" />
-   </qualifier>
**-** </Observation>

## Protégé Tool

- Open Source
- Distributed Authoring
- Multiple Plugins
- Domain specific
- Hierarchical classes
- Java API

## Build the Ontology

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

## Jterm Terminology Server

- Open Source
- Java API
- TQL language optimized
- for terminologies

## HL7 CTS 1.0

- Defines an API
- For HL7 V3
- Software applications
- To access terminology
- Services
- Message API
- Vocabulary API

## 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