Table name: stem_table
Reading from 3_covid19_tpp_gp_clinical.txt.gz.pure
Rows are skipped if:
codeis empty or ‘-1’dateis empty or in the year 2037
| Destination Field | Source field | Logic | Comment field |
|---|---|---|---|
| domain_id | ‘Measurement’ if the record has a value_as_number (which is not 0) or a value_as_concept_id. | As values can only be stored in the measurement (and observation) table, we enforce the domain if a value is given from the source. In other cases, the domain_id of the target concept_id will be used to determine the target table as per OMOP conventions. | |
| person_id | eid | ||
| visit_occurrence_id | eid event_dt | Create a new visit id string with the form: ‘covid prefix’(5000)+’eid’+’event_dt’ | |
| provider_id | |||
| id | Not used. | ||
| concept_id | code_type code | Combine the “code_type” with the “code” to use the correct lookup. If “code_type” = “0” use CTV3 lookup. If “code_type” = “1” use Local TPP lookup. If “code_type” = “-1” OR “-2”, discard that record. https://biobank.ndph.ox.ac.uk/showcase/coding.cgi?id=3175 | |
| source_value | code | ||
| source_concept_id | code_type code | ATHENA codes are not available for these CVT3 nor local TPP codes. All values are set to 0, as in gp_clinical_to_stem transformation. | |
| type_concept_id | 32817: EHR | ||
| start_date | event_dt | Fill with event date. If missing, discard the row. If 1902-02-02 or 1903-03-3, set date to yob-07-01 (field 34 in baseline) | |
| start_datetime | event_dt | ||
| end_date | |||
| end_datetime | |||
| verbatim_end_date | |||
| days_supply | |||
| dose_unit_source_value | |||
| lot_number | |||
| modifier_concept_id | |||
| modifier_source_value | |||
| operator_concept_id | |||
| modifier_source_value | |||
| quantity | |||
| range_high | |||
| range_low | |||
| refills | |||
| route_concept_id | |||
| route_source_value | |||
| sig | |||
| stop_reason | |||
| unique_device_id | |||
| unit_concept_id | |||
| unit_source_value | |||
| value_as_concept_id | |||
| value_as_number | value | If not a number, it is ‘None’. | |
| value_as_string | |||
| value_source_value | |||
| anatomic_site_concept_id | |||
| disease_status_concept_id | |||
| specimen_source_id | |||
| anatomic_site_source_value | |||
| disease_status_source_value | |||
| condition_status_concept_id | |||
| condition_status_source_value | |||
| qualifier_concept_id | |||
| qualifier_source_value |