Medication_medication_activity

Source file: medication_medication_activity.py

Root XPath

./hl7:component/hl7:structuredBody/hl7:component/hl7:section/hl7:templateId[@root='2.16.840.1.113883.10.20.22.2.1' or @root='2.16.840.1.113883.10.20.22.2.1.1']/../hl7:entry/hl7:substanceAdministration[@moodCode='EVN']/hl7:consumable/hl7:manufacturedProduct/hl7:manufacturedMaterial

Expected OMOP domain: Drug

Fields

Field

Type

Order

Details

drug_exposure_id

HASH

1

hash(person_id, provider_id, drug_concept_code_code, drug_concept_codeSystem_code, drug_concept_code_translation, drug_concept_codeSystem_translation, drug_exposure_start_date, drug_exposure_start_datetime, drug_exposure_end_date, drug_exposure_end_datetime, quantity, drug_exposure_id_root, drug_exposure_id_extension)

person_id

FK

2

FK → person_id

drug_concept_id

PRIORITY

3

coalesce candidates by priority

drug_exposure_start_date

PRIORITY

4

coalesce candidates by priority

drug_exposure_start_datetime

PRIORITY

5

coalesce candidates by priority

drug_exposure_end_date

PRIORITY

6

coalesce candidates by priority

drug_exposure_end_datetime

PRIORITY

7

coalesce candidates by priority

verbatim_end_date

PRIORITY

8

coalesce candidates by priority

drug_type_concept_id

CONSTANT

9

32818

stop_reason

CONSTANT

10

refills

None

11

—

quantity

FIELD

12

../../../hl7:doseQuantity @value [FLOAT]

days_supply

None

13

—

sig

None

14

—

route_concept_id

DERIVED

15

VT.codemap_xwalk_concept_id(concept_code=route_concept_code, vocabulary_oid=route_concept_codeSystem)

lot_number

None

16

—

provider_id

FK

17

FK → provider_id

visit_occurrence_id

FK

18

FK → visit_occurrence_id

visit_detail_id

None

19

—

drug_source_value

PRIORITY

20

coalesce candidates by priority

drug_source_concept_id

PRIORITY

21

coalesce candidates by priority

route_source_value

DERIVED

22

VT.concat_fields(first_field=route_concept_code, second_field=route_concept_codeSystem)

dose_unit_source_value

FIELD

23

../../../hl7:doseQuantity @unit

data_partner_id

DERIVED

24

VT.get_data_partner_id(filename=filename)

filename

FILENAME

100

source XML filename

cfg_name

CONSTANT

101

Medication_medication_activity

domain_id

PRIORITY

coalesce candidates by priority

domain_id_code

DERIVED

VT.codemap_xwalk_domain_id(concept_code=drug_concept_code_code, vocabulary_oid=drug_concept_codeSystem_code)

domain_id_translation

DERIVED

VT.codemap_xwalk_domain_id(concept_code=drug_concept_code_translation, vocabulary_oid=drug_concept_codeSystem_translation)

drug_concept_codeSystem_code

FIELD

hl7:code @codeSystem

drug_concept_codeSystem_translation

FIELD

hl7:code/hl7:translation @codeSystem

drug_concept_code_code

FIELD

hl7:code @code

drug_concept_code_translation

FIELD

hl7:translation @code

drug_concept_id_code

DERIVED

VT.codemap_xwalk_concept_id(concept_code=drug_concept_code_code, vocabulary_oid=drug_concept_codeSystem_code)

drug_concept_id_translation

DERIVED

VT.codemap_xwalk_concept_id(concept_code=drug_concept_code_translation, vocabulary_oid=drug_concept_codeSystem_translation)

drug_exposure_end_date_high

FIELD

../../../hl7:effectiveTime/hl7:high[not(@nullFlavor='UNK')] @value [DATE] → priority (‘drug_exposure_end_date’, 1)

drug_exposure_end_date_low

FIELD

../../../hl7:effectiveTime/hl7:low[not(@nullFlavor='UNK')] @value [DATE] → priority (‘drug_exposure_end_date’, 3)

drug_exposure_end_date_value

FIELD

../../../hl7:effectiveTime @value [DATE] → priority (‘drug_exposure_end_date’, 2)

drug_exposure_end_datetime_high

FIELD

../../../hl7:effectiveTime/hl7:high[not(@nullFlavor='UNK')] @value [DATETIME_HIGH] → priority (‘drug_exposure_end_datetime’, 1)

drug_exposure_end_datetime_low

FIELD

../../../hl7:effectiveTime/hl7:low[not(@nullFlavor='UNK')] @value [DATETIME_HIGH] → priority (‘drug_exposure_end_datetime’, 3)

drug_exposure_end_datetime_value

FIELD

../../../hl7:effectiveTime @value [DATETIME_HIGH] → priority (‘drug_exposure_end_datetime’, 2)

drug_exposure_id_extension

FIELD

../../../hl7:id[not(@nullFlavor="UNK")] @extension

drug_exposure_id_root

FIELD

../../../hl7:id[not(@nullFlavor="UNK")] @root

drug_exposure_start_date_high

FIELD

../../../hl7:effectiveTime/hl7:high @value [DATE] → priority [‘drug_exposure_start_date’, 3]

drug_exposure_start_date_low

FIELD

../../../hl7:effectiveTime/hl7:low[not(@nullFlavor="UNK")] @value [DATE] → priority (‘drug_exposure_start_date’, 1)

drug_exposure_start_date_value

FIELD

../../../hl7:effectiveTime @value [DATE] → priority (‘drug_exposure_start_date’, 2)

drug_exposure_start_datetime_high

FIELD

../../../hl7:effectiveTime/hl7:high @value [DATETIME_LOW] → priority [‘drug_exposure_start_datetime’, 3]

drug_exposure_start_datetime_low

FIELD

../../../hl7:effectiveTime/hl7:low[not(@nullFlavor='UNK')] @value [DATETIME_LOW] → priority (‘drug_exposure_start_datetime’, 1)

drug_exposure_start_datetime_value

FIELD

../../../hl7:effectiveTime @value [DATETIME_LOW] → priority (‘drug_exposure_start_datetime’, 2)

drug_source_concept_id_code

DERIVED

VT.codemap_xwalk_source_concept_id(concept_code=drug_concept_code_code, vocabulary_oid=drug_concept_codeSystem_code)

drug_source_concept_id_translation

DERIVED

VT.codemap_xwalk_source_concept_id(concept_code=drug_concept_code_translation, vocabulary_oid=drug_concept_codeSystem_translation)

drug_source_value_code

DERIVED

VT.concat_fields(first_field=drug_concept_code_code, second_field=drug_concept_codeSystem_code)

drug_source_value_translation

DERIVED

VT.concat_fields(first_field=drug_concept_code_translation, second_field=drug_concept_codeSystem_translation)

route_concept_code

FIELD

../../../hl7:routeCode @code

route_concept_codeSystem

FIELD

../../../hl7:routeCode @codeSystem

verbatim_end_date_high

FIELD

../../../hl7:effectiveTime/hl7:high[not(@nullFlavor='UNK')] @value [DATE] → priority (‘verbatim_end_date’, 1)

verbatim_end_date_value

FIELD

../../../hl7:effectiveTime[not(@nullFlavor='UNK')] @value [DATE] → priority (‘verbatim_end_date’, 2)

Config type reference

config_type

Meaning

ROOT

Defines the XPath root element for this config

FIELD

Extracts an XML attribute value via XPath

DERIVED

Computed by a Python function from other fields

HASH

MD5/hash of a set of fields, used as a surrogate key

FK

Foreign key copied from a joined dataset

CONSTANT

Fixed literal value written to every row

PRIORITY

Coalesces the first non-null value from prioritized candidates

FILENAME

The source XML filename

None

Not populated (placeholder)