Condition

Source file: condition.py

Root XPath

./hl7:component/hl7:structuredBody/hl7:component/hl7:section/hl7:templateId[@root='2.16.840.1.113883.10.20.22.2.5' or  @root='2.16.840.1.113883.10.20.22.2.5.1' ] /../hl7:entry/hl7:act/hl7:entryRelationship/hl7:observation

Expected OMOP domain: Condition

Fields

Field

Type

Order

Details

condition_occurrence_id

HASH

1

hash(person_id, provider_id, condition_concept_code, condition_concept_codeSystem, condition_start_date, condition_start_datetime, condition_end_date, condition_end_datetime, condition_id_root, condition_id_extension)

person_id

FK

2

FK → person_id

condition_concept_id

DERIVED

3

VT.codemap_xwalk_concept_id(concept_code=condition_concept_code, vocabulary_oid=condition_concept_codeSystem)

condition_start_date

PRIORITY

4

coalesce candidates by priority

condition_start_datetime

PRIORITY

5

coalesce candidates by priority

condition_end_date

PRIORITY

6

coalesce candidates by priority

condition_end_datetime

PRIORITY

7

coalesce candidates by priority

condition_type_concept_id

CONSTANT

8

32840

condition_status_concept_id

None

9

—

stop_reason

CONSTANT

10

provider_id

FK

11

FK → provider_id

visit_occurrence_id

FK

12

FK → visit_occurrence_id

visit_detail_id

None

13

—

condition_source_value

DERIVED

14

VT.concat_fields(first_field=condition_concept_code, second_field=condition_concept_codeSystem)

condition_source_concept_id

None

15

—

condition_status_source_value

CONSTANT

16

data_partner_id

DERIVED

20

VT.get_data_partner_id(filename=filename)

filename

FILENAME

100

source XML filename

cfg_name

CONSTANT

101

Condition

condition_concept_code

FIELD

hl7:value @code

condition_concept_codeSystem

FIELD

hl7:value @codeSystem

condition_end_date_high

FIELD

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

condition_end_datetime_high

FIELD

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

condition_id_extension

FIELD

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

condition_id_root

FIELD

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

condition_start_date_low

FIELD

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

condition_start_date_value

FIELD

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

condition_start_datetime_low

FIELD

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

condition_start_datetime_value

FIELD

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

domain_id

DERIVED

VT.codemap_xwalk_domain_id(concept_code=condition_concept_code, vocabulary_oid=condition_concept_codeSystem)

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)