Map Oxygenation and ventilator data to device_exposure for three CDM sources

[stephanieshong]

• vent data from obs_gen to device
• If the O2 device maps to a SNOMED code, OBSGEN_TYPE should equal ‘SM’ and OBGEN_CODE should include the SNOMED code.
• If using either of the custom codes, OBSGEN_TYPE should equal ‘UD_N3C_O2_DEVICE’ and OBSGEN_CODE should include either ‘OT_O2_DEVICE’, or ‘ROOM_AIR’.

[stephanieshong]

PCORNet CDM

If using the custom code what should be the concept_id? -- If using either of the custom codes, OBSGEN_TYPE should equal ‘UD_N3C_O2_DEVICE’ and -- OBSGEN_CODE should include either ‘OT_O2_DEVICE’, or ‘ROOM_AIR’.

[stephanieshong]

• [x] PCORNet
• [x] ACT
• [x] TriNetX

[stephanieshong]

for PCORNet CDM: when obsgen_type is SM then use the code in the obsgen_code as the code to lookup the concept_id using the concept table. when obsgen_type = UD_N3C_O2_DEVICE then use the following rule if obsgen_code = room_air then use 2004208005 as the concept_id if obsgen_code = OT_O2_DEVICE then use 2004208004 as the concept_id raw_obsgen_name -> device_source_value

[stephanieshong]

PCORNet CDM -done. Generate xwalk lookup table for SNOMEDCT codes to concept_id for all the SM code types that the sites are submitting for the payload. and use the value to set the device_concept_id.

[stephanieshong]

for ACT CDM: vent2device observation_fact if concept_cd = N3C:ROOM_AIR' then use 2004208005 as the concept_id if concept_cd = ‘N3C:OT_O2_DEVICE' then use 2004208004 as the concept_id if they are prefixed with SNOMEDCT then use the lookup table

[stephanieshong]

still waiting on documentation from TriNetX CDM regarding this data enhancements.

[stephanieshong]

• [x] OMOP CDM - merge device_exposure to device_exposure completed.

[stephanieshong]

TriNetX was using "SNOMED CT" as the vocabulary id but the OMOP concept uses "SNOMED" as the vocabulary_id. TriNetX vocab mapping table has been updated to map local vocab SNOMED CT to SNOMED for OMOP concept table.