documentation:oncology:meeting_notes_2019_jul-02
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documentation:oncology:meeting_notes_2019_jul-02 [2019/07/03 11:23] mgurley |
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| https://github.com/OHDSI/OncologyWG/issues?q=is%3Aopen+is%3Aissue+milestone%3A%22Beta+testing+preparation%22 | https://github.com/OHDSI/OncologyWG/issues?q=is%3Aopen+is%3Aissue+milestone%3A%22Beta+testing+preparation%22 | ||
| - | * We discussed scoping NAACCR items to schemas. This is the requirement that all the necessary NAACCR items to diagnose a site/histology combination are linked and represented within the OMOP vocabulary. Example: Gleason Score for Prostate Cancer; HER2 for Breast Cancer. And so on. Rimma argued that this is a feature that all oncology information models need to suport. Dmytry confirmed that this is not currently done in the staging NAACCR ingestion. Michael argued that it is important but expectational and not necessary for ETLing, so it can be done in the next version. Dmytry agreed to try to accomplish this for version one of ingestion but will defer it to the next version if it is too much work. See here: https://github.com/OHDSI/OncologyWG/issues/54 | + | * We discussed scoping NAACCR items to schemas. This is the requirement that all the necessary NAACCR items to diagnose a site/histology combination are linked and represented within the OMOP vocabulary. Example: Gleason Score for Prostate Cancer; HER2 for Breast Cancer. And so on. Rimma argued that this is a feature that all oncology information models need to suport. Dmytry confirmed that this is not currently done in the staging NAACCR ingestion. Michael argued that it is important but expectational and not necessary for ETLing, so it can be done in the next version. Dmytry agreed to try to accomplish this for version one of ingestion but will defer it to the next version if it is too much work. See here: https://github.com/OHDSI/OncologyWG/issues/54. |
| * We discussed how the fundamental site/histology data points, NAACCR item 400 'Primary Site' and NAACCR 522 'HISTOLOGIC TYPE ICD-O-3' are represented within the OMOP vocabulary. Dmytry and Michael confirmed that these NAACCR items had been curated into the 'Observation' domain and marked as non-standard. The group agreed that the ETL documentation will need to specify how to handle these "special" NAACCR items. | * We discussed how the fundamental site/histology data points, NAACCR item 400 'Primary Site' and NAACCR 522 'HISTOLOGIC TYPE ICD-O-3' are represented within the OMOP vocabulary. Dmytry and Michael confirmed that these NAACCR items had been curated into the 'Observation' domain and marked as non-standard. The group agreed that the ETL documentation will need to specify how to handle these "special" NAACCR items. | ||
| * We discussed that the best way to provide feedback to Dmytry on the NAACCR ingestion is to query the staging tables. | * We discussed that the best way to provide feedback to Dmytry on the NAACCR ingestion is to query the staging tables. | ||
documentation/oncology/meeting_notes_2019_jul-02.txt ยท Last modified: 2019/07/03 11:28 by mgurley
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