Observational Health Data Sciences and Informatics

Documentation Planning

• Oncology Documentation Scope (Word document)

PROJECT PLANNING

• Current Task List
• List of Use Cases

ONCOLOGY WG PRODUCTS

OMOP CDM Oncology Module

• OMOP CDM Oncology Extension (Complete PDF)
• Part 1: "Oncology Extension Summary" (Power Point presentation)
• Part 2: "Oncology Extension Detailed" (Word document)

OMOP CDM Extension Implementing Oncology Module

• DDL for EPISODE, EPISODE_EVENT and MEASUREMENT tables

ETL Instructions for converting Tumor Registry Data to OMOP

• Crosswalk from Tumor Registry to OMOP
• High Level ETL Steps
• ETL Instructions for Mapping ICD-O diagnoses to SNOMED
• ETL of NAACCR diagnosis and diagnostic modifiers
• Ingestion of NAACCR into the OMOP vocabulary

WORK IN-PROGRESS

• Proposal for Ingestion of NAACCR into OMOP Vocabulary - Diagnostic Modifiers - in progress

PUBLICATIONS AND PRESENTATIONS BY WG MEMBERS

• OMOP CDM Oncology Module at Work 
• HemOnc: A New Standard Vocabulary for Oncology Drug Regimen Representation in the OMOP Common Data Model
• Conversion of Diagnosis and Chemotherapy Data in Electronic Health Records to Episode-based Oncology Extension of OMOP-CDM 
• HemOnc: A new standard vocabulary for chemotherapy regimen representation in the OMOP common data model
• Standardized Observational Cancer Research Using the OMOP CDM Oncology Module
• AMIA 2018: panel "Data Standardization in Cancer: Challenges and Opportunities"

• OHDSI 2018 European Symposium: poster "Improvement of cancer diagnosis representation in OMOP CDM"

• OHDSI 2018 Symposium: poster "SNOMED Extensions"

• 2018 OHDSI State of Collaborative: presentation
• 2017 Report to NCI: "Oncology Data Representation Challenges"

References and Archive

• Genomic Recording (zip)