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documentation:oncology:meeting_notes_2019_aug-06 [2019/08/07 12:39]
mgurley
documentation:oncology:meeting_notes_2019_aug-06 [2019/08/07 12:43] (current)
mgurley
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     * Michael Gurley shared updated DDL for the OMOP Oncology CDM extension. [[https://​github.com/​OHDSI/​OncologyWG/​tree/​master/​ddl|DDL]]. ​  The update included DDL for the CONCEPT_NUMERIC table and a CSV file and script to load the new table.     * Michael Gurley shared updated DDL for the OMOP Oncology CDM extension. [[https://​github.com/​OHDSI/​OncologyWG/​tree/​master/​ddl|DDL]]. ​  The update included DDL for the CONCEPT_NUMERIC table and a CSV file and script to load the new table.
     * It was announced that a new release of NAACCR within the OMOP vocabulary had been made.  Available at http://​athena.ohdsi.org/​. ​ This new release of NAACCR added support for relationships necessary to support numeric NAACCR concepts and some fixes to the NAACCR treatment items and item codes.     * It was announced that a new release of NAACCR within the OMOP vocabulary had been made.  Available at http://​athena.ohdsi.org/​. ​ This new release of NAACCR added support for relationships necessary to support numeric NAACCR concepts and some fixes to the NAACCR treatment items and item codes.
-    *  The group discussed how to handle overlapping NAACCR schemas. ​ This is technical issue for full vocabulary support of NAACCR. ​ The current approach is to collapse schemas when a site/​histology combination falls into more than one NAACCR schema. ​ There are cases where the same site/​histology combination is present in more than one schema. ​ In these cases, ​ NAACCR requires other variables to be looked at in order to reveal the semantics of some NAACCR items and/or NAACCR item codes.  Sometimes ​a NAACCR variable schema discriminator, ​one other time Gender.  This is a consequence of NAACCR'​s design flaw in reusing codes across unique semantic concepts. ​ The group agreed that collapsing schemas is OK in cases where it does not corrupt semantics but a solution must be come up for the non-collapsible cases. ​ Once possible solution would be to associate the other NAACCR ​variable ​necessary for mapping to a NAACCR ​schemes ​within the OMOP vocabulary.+    *  The group discussed how to handle overlapping NAACCR schemas. ​ This is technical issue for full vocabulary support of NAACCR. ​ The current approach is to collapse schemas when a site/​histology combination falls into more than one NAACCR schema. ​ There are cases where the same site/​histology combination is present in more than one schema. ​ In these cases, ​ NAACCR requires other variables to be looked at in order to reveal the semantics of some NAACCR items and/or NAACCR item codes: sometimes ​a NAACCR variable schema discriminator ​1, 2 or 3 (NAACCR items 3926, 3927, 3928), other time Sex (NAACCR item 220).  There might be others.  This is a consequence of NAACCR'​s design flaw in reusing codes across unique semantic concepts. ​ The group agreed that collapsing schemas is OK in cases where it does not corrupt semantics but a solution must be come up for the non-collapsible cases. ​ Once possible solution would be to associate the other NAACCR ​variables ​necessary for mapping to a NAACCR ​schema ​within the OMOP vocabulary.
     * It was announced that a OMOP Oncology Hackathon will take place on August 21st and August 22nd in the offices of IQVIA in New York city.  Details on exact timing and location to follow.     * It was announced that a OMOP Oncology Hackathon will take place on August 21st and August 22nd in the offices of IQVIA in New York city.  Details on exact timing and location to follow.
documentation/oncology/meeting_notes_2019_aug-06.txt ยท Last modified: 2019/08/07 12:43 by mgurley