Observational Health Data Sciences and Informatics

Participants

Christian Reich, Rimma Belankaya, Dmytry Dymshyts, Andrew Williams, Robert Miller, Michael Gurley

Topics

• Reviewed Dmytry's latest progress on the NAACCR ingestion script.
  • Discussed the possibility of moving NAACCR schemas into a new structure to keep the CONCEPT.concept_code clean (not contain anything NOT in NAACCR source data). But we decided for version 1 we would include NAACCR schemas in the vocabulary, and include NAACCR schema IDs in site-dependent NAACCR items and NAACCR Item Codes. This means that ETL developers will have to know to use Rimma's ETL code to map NAACCR data into OMOP.
  • Agreed that mapping NAACCR schemas to ICD site/histology combinations is a must have for version 1 of NAACCR ingestion. Rimma's ETL SQL will not work without it.
  • Discussed whether NAACCR site-dependent variables should be duplicated across schemas. Dmytry's first version of NAACCR ingestion is duplicating them. We agreed that they should not. Dmytry said he can dedupe them.
  • Resolved “Curate NAACCR Items/Item Codes and OMOP domains”: https://github.com/OHDSI/OncologyWG/issues/26
  • Resolved “How should we handle long CONCEPT.concept_name entries that exceed 255 characters coming from NAACCR?”: https://github.com/OHDSI/OncologyWG/issues/28
  • Discussed: How should we handle 'Numeric' NAACCR items that define numeric ranges?:https://github.com/OHDSI/OncologyWG/issues/26
  • Resolved “How should we handle NAACCR provenance concepts?”: https://github.com/OHDSI/OncologyWG/issues/32
  • Discussed 'How should we handle versions of staging variables? For both TNM and AJCC variables?': https://github.com/OHDSI/OncologyWG/issues/31
  • Resolved “Should we record dates as a separate measurement record.(e.g. Date regional lymph node dissection NAACCR #682)?”:https://github.com/OHDSI/OncologyWG/issues/33
  • Resolved “How do we handle different versions of NAACCR?”: https://github.com/OHDSI/OncologyWG/issues/34