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Hello, I am a brand new member (just joined today) and am helping implement OMOP CDM v6.0 for my organization. I am looking for a mapping document from CDM v5.2.2 to CDM v6.0. Is there a document that provides detailed, table-to-table mapping between the two versions? I can access the PostgreSQL scripts to create v6.0 on GitHub fine, but it’s the mapping document I cannot find anywhere. Thank you for any help.
To my knowledge, there is no such document on v5.2 to v6.0 mapping. And in my personal opinion, such document may not be necessary. A major difference of v5 and v6 is that v6 has several new tables being added to CDM, such as SURVEY_CONDUCT, and LOCATION_HISTORY. However, if your source data does not carry these information, nothing need to be done there. Another variation is that in v6, some new fields are added to the existing tables, e.g., Latitude and longitude added to LOCATION table, NOTE_EVENT_ID and NOTE_DOMAIN_ID (NOTE_EVENT_TABLE_CONCEPT_ID) added to NOTE table etc. Again, if your source data does not have these information, you don’t have worry about them.
Having said above, I do think several things needs to be changed when moving from v5 to v6. For example, DEATH table removed and cause of death now stored in CONDITION_OCCURRENCE. Also if your v5 has COST table populated, person_id should be added to this table in v6. Without knowing what your v5 CDM and source data look like, it is hard to give more detailed instruction.
One other thing to note is that an Oncology Extension Model is added to v5.3 and v6. If your v5.2 has oncology data, your may consider using this extension. But that is a whole new topic.
Hope this helps. My two cents,
Qi Yang, thank you so much for the knowledge!
Speaking of “cost”, do you know if/how DEVICE_COST, DRUG_COST, PROCEDURE_COST and VISIT_COST tables in v5 map to COST table in v6? It looks like [COST].cost_event_id (foreign key) may be what establishes the link, but I am not sure.
On a separate note (sorry to use the same thread) - does anyone know where the vocabulary for v6 is stored that can be downloaded?
Thanks again!
Speaking of “cost”, do you know if/how DEVICE_COST, DRUG_COST, PROCEDURE_COST and VISIT_COST tables in v5 map to COST table in v6? It looks like [COST].cost_event_id (foreign key) may be what establishes the link, but I am not sure.
Correct! In v5.3 and v6, all the individual COST tables are combined into one COST table and cost_event_id and cost_event_field_concept_id provide the link to their respective tables
On a separate note (sorry to use the same thread) - does anyone know where the vocabulary for v6 is stored that can be downloaded?
Athena. The same place where you downloaded the vocabulary for v5. There is no separate v6 vocabulary version. Whatever in Athena is the latest and it is compatible with v6 CDM
In Athena, just like for V5. The tables are still identical, so there is no separate download for V6 right now. That might change soon.