ukbiobank-omop-etl
Resources and documentation for UK Biobank to OMOP CDM v5.3.1 conversion
Table name: observation
Reading from Baseline characteristics
| Destination Field | Source field | Logic | Comment field |
|---|---|---|---|
| observation_id | |||
| person_id | Use eid (not included) | ||
| observation_concept_id | 189-0.0 | TBD, custom 2B+ concept? | No concept for Townsend index (UK specific) |
| observation_date | 189-0.0 | Date of attending assessment center (field 53-0.0) | |
| observation_datetime | |||
| observation_type_concept_id | In between patient reported and clinical study? = population study Best fit would be from visit types = Health Examination Current options: 45905771 - Observation Recorded from a Survey or 581413 - Observation from Measurement | ||
| value_as_number | 189-0.0 | ||
| value_as_string | |||
| value_as_concept_id | |||
| qualifier_concept_id | |||
| unit_concept_id | |||
| provider_id | |||
| visit_occurrence_id | Lookup visit occurrence belonging to this person (eid) and this instance_id. | ||
| visit_detail_id | |||
| observation_source_value | 189-0.0 | ||
| observation_source_concept_id | |||
| unit_source_value | |||
| qualifier_source_value |
Reading from Hand grip strength
| Destination Field | Source field | Logic | Comment field |
|---|---|---|---|
| observation_id | |||
| person_id | Use eid (not included) | ||
| observation_concept_id | 46-3.0 47-3.0 |
44805438 - SNOMED observation | |
| observation_date | 46-3.0 47-3.0 |
Use corresponding date of attending assessment center. If instance 0: 53-0.0 If instance 1: 53-1.0 If instance 2: 53-2.0 If instance 3: 53-3.0 |
|
| observation_datetime | |||
| observation_type_concept_id | In between patient reported and clinical study? = population study Best fit would be from visit types = Health Examination Current options: 45905771 - Observation Recorded from a Survey or 581413 - Observation from Measurement | ||
| value_as_number | 46-3.0 47-3.0 |
kg (UCUM concept) | |
| value_as_string | |||
| value_as_concept_id | |||
| qualifier_concept_id | |||
| unit_concept_id | 46-3.0 47-3.0 |
kg (UCUM concept) |
|
| provider_id | |||
| visit_occurrence_id | Lookup visit occurrence belonging to this person (eid) and this instance_id. | ||
| visit_detail_id | |||
| observation_source_value | 46-3.0 47-3.0 |
||
| observation_source_concept_id | |||
| unit_source_value | |||
| qualifier_source_value |
Reading from Ongoing characteristics
| Destination Field | Source field | Logic | Comment field |
|---|---|---|---|
| observation_id | |||
| person_id | Use eid (not included) | ||
| observation_concept_id | 190-0.0 | ‘Reason Lost to follow-up’ (45956528, CEIL, non-standard) | |
| observation_date | 191-0.0 | ||
| observation_datetime | |||
| observation_type_concept_id | In between patient reported and clinical study? = population study Best fit would be from visit types = Health Examination Current options: 45905771 - Observation Recorded from a Survey or 581413 - Observation from Measurement | ||
| value_as_number | |||
| value_as_string | 190-0.0 | Description of the value | |
| value_as_concept_id | 190-0.0 | Map values to concept_id | |
| qualifier_concept_id | |||
| unit_concept_id | |||
| provider_id | |||
| visit_occurrence_id | Lookup visit occurrence belonging to this person (eid) and this instance_id. | ||
| visit_detail_id | |||
| observation_source_value | |||
| observation_source_concept_id | |||
| unit_source_value | |||
| qualifier_source_value |