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


  • 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”:
    • Resolved “How should we handle long CONCEPT.concept_name entries that exceed 255 characters coming from NAACCR?”:
    • Discussed: How should we handle 'Numeric' NAACCR items that define numeric ranges?:
    • Resolved “How should we handle NAACCR provenance concepts?”:
    • Discussed 'How should we handle versions of staging variables? For both TNM and AJCC variables?':
    • Resolved “Should we record dates as a separate measurement record.(e.g. Date regional lymph node dissection NAACCR #682)?”:
    • Resolved “How do we handle different versions of NAACCR?”:
documentation/oncology/meeting_notes_2019_mar-12.txt · Last modified: 2019/03/13 13:38 by mgurley