Observational Health Data Sciences and Informatics

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Meeting Notes August 27, 2019

Topics

• Seng Chan You from Ajou University told the group about the code he and his colleagues have developed for extracting treatment cycle from single medication records in CDM databases 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