Observational Health Data Sciences and Informatics

This is an old revision of the document!

Meeting Notes August 27, 2019

Topics

• Seng Chan You from Ajou University told the group about the code he and his colleagues have developed to extract oncology drug regimens from OMOP data. See here: https://github.com/ABMI/treatmentCycleExtraction
• We reviewed the vocabulary tasks from the workshop.
  • Add the EPISODE table and field concepts to the vocabulary for metadata field reference. Like ‘episode.episode_id’. See here: https://github.com/OHDSI/OncologyWG/issues/66
  • Create new 'Regimen' domain, move all the Hemonc.org regimens into the new domain, create entries in the new domain for NAACCR high-level drug concepts and non-standardize existing drug NAACCR item codes. See here:https://github.com/OHDSI/OncologyWG/issues/69.
  • Put ‘did not happen’ NAACCR concepts in the Observation domain. For example, ‘Patient did not have chemotherapy’. See here: https://github.com/OHDSI/OncologyWG/issues/68
  • Fix missing leading zeros in the concept_codes for Treatment NAACCR item codes. See here: https://github.com/OHDSI/OncologyWG/issues/60
  • The 'NAACCR Proc Schema' entries do not have all the necessary relationships to ICDO codes via 'Proc Schema to ICDO' See here: https://github.com/OHDSI/OncologyWG/issues/60
• We made a decision on a convention for making a non-ambiguous reference between a 'Disease Episode' and 'Treatment. Convention: Populate parent_id of a ‘Treatment Episode’ with the ‘Disease Episode’ it is 'treating'.
• For the symposium, we decided to skip all the ICDO codes that participate in multiple NAACCR schemas. Until we can create a mapping table to be used for handling ambiguous ICDO site/histology combinations present in multiple schemas. See here: https://github.com/OHDSI/OncologyWG/issues/59. See here for SQL to identify the ambiguous ICDO Site/Histology combinations: https://github.com/OHDSI/OncologyWG/blob/master/documentation/debug_naaccr_ambiguites.sql