Observational Health Data Sciences and Informatics

Meeting Notes August 13, 2019

Here is a link to a recording of the meeting: recording.

Topics

• Robert Miller shared and explained his code to convert NAACCR flat file-formatted data to the input format necessary for the generic ETL SQL. See here generic ETL SQL .
• Michael Gurley shared and explained his code to convert the data model from the popular tumor registry software Elekta METRIQ to the input format necessary for the generic ETL SQL.
• Andrew Williams raised the issue whether the two current NAACCR input formats sufficiently cover how tumor registry data will be encountered in the wild. It was countered that the best we can do is harvest efforts as new adopters encounter new scenarios.
• Andrew Williams and Maxim Moinat raised the issue of whether folks coming from non-NAACCR sources should map their tumor characteristics to the NAACCR vocabulary. It was argued folks should map to NAACCR so we can make tumor registry data and non-tumor registry data comparable. It was pointed out the problem arises that just saying that we should pick the “standard” concept for each tumor characteristic runs into the “Choose Your Own Adventure” problem that OMOP contains multiple “standard” concepts for many tumor characteristics semantic concepts. The approach we have agreed as a group to take is to choose NAACCR as our standard for tumor characteristics for the time being until we can map NAACCR to a more proper standardized vocabulary like SNOMED or LOINC. Hopefully via the Nebraska Lexicon. See the Presentation from June 18 where this issue was discussed. It sounds like this issue is still open for debate. An alternative to using NAACCR as the standardized tumor characteristics vocabulary is to let people use whatever seems right and depend on the mapping between concepts being worked out at the analysis stage. This issue can be discussed at the hackathon.
• The two-day OHDSI Oncology hackathon on August 21st and 22nd was re-announced. Details will be emailed to all members of the OHDIS Oncology Workgorup.