Visit

Source file: visit.py

Root XPath

./hl7:component/hl7:structuredBody/hl7:component/hl7:section/hl7:templateId[ @root="2.16.840.1.113883.10.20.22.2.22" or @root="2.16.840.1.113883.10.20.22.2.22.1" ]/../hl7:entry/hl7:encounter[@moodCode="EVN"]

Expected OMOP domain: Visit

Fields

Field

Type

Order

Details

visit_occurrence_id

HASH

1

hash(visit_occurrence_id_root, visit_occurrence_id_extension, person_id, provider_id, visit_concept_id, visit_source_value, visit_start_date, visit_start_datetime, visit_end_date, visit_end_datetime, care_site_id_root, care_site_id_extension)

person_id

FK

2

FK → person_id

visit_concept_id

PRIORITY

3

coalesce candidates by priority

visit_start_date

PRIORITY

4

coalesce candidates by priority

visit_start_datetime

PRIORITY

5

coalesce candidates by priority

visit_end_date

PRIORITY

6

coalesce candidates by priority

visit_end_datetime

PRIORITY

7

coalesce candidates by priority

visit_type_concept_id

CONSTANT

8

32827

provider_id

HASH

9

hash(provider_id_street, provider_id_city, provider_id_state, provider_id_zip, provider_id_given, provider_id_family, provider_id_performer_root, provider_id_performer_extension)

care_site_id

HASH

10

hash(care_site_id_root, care_site_id_extension)

visit_source_value

PRIORITY

11

coalesce candidates by priority

visit_source_concept_id

PRIORITY

12

coalesce candidates by priority

admitting_source_concept_id

None

13

—

admitting_source_value

CONSTANT

14

discharge_to_concept_id

None

15

—

discharge_to_source_value

CONSTANT

16

preceding_visit_occurrence_id

None

17

—

data_partner_id

DERIVED

20

VT.get_data_partner_id(filename=filename)

filename

FILENAME

100

source XML filename

cfg_name

CONSTANT

101

Visit

care_site_id_extension

FIELD

hl7:participant/hl7:participantRole[@classCode="SDLOC"]/hl7:id @extension

care_site_id_root

FIELD

hl7:participant/hl7:participantRole[@classCode="SDLOC"]/hl7:id @root

domain_id

PRIORITY

coalesce candidates by priority

domain_id_default

CONSTANT

Visit

domain_id_encounter

DERIVED

VT.codemap_xwalk_domain_id(concept_code=visit_concept_code_encounter, vocabulary_oid=visit_concept_codeSystem_encounter, default=None)

domain_id_trans1

DERIVED

VT.codemap_xwalk_domain_id(concept_code=visit_concept_code_trans1, vocabulary_oid=visit_concept_system_trans1, default=None)

domain_id_trans2

DERIVED

VT.codemap_xwalk_domain_id(concept_code=visit_concept_code_trans2, vocabulary_oid=visit_concept_system_trans2, default=None)

domain_id_trans3

DERIVED

VT.codemap_xwalk_domain_id(concept_code=visit_concept_code_trans3, vocabulary_oid=visit_concept_system_trans3, default=None)

domain_id_trans4

DERIVED

VT.codemap_xwalk_domain_id(concept_code=visit_concept_code_trans4, vocabulary_oid=visit_concept_system_trans4, default=None)

provider_id_city

FIELD

hl7:performer/hl7:assignedEntity/hl7:addr/hl7:city @#text

provider_id_family

FIELD

hl7:performer/hl7:assignedEntity/hl7:assignedPerson/hl7:name/hl7:family @#text

provider_id_given

FIELD

hl7:performer/hl7:assignedEntity/hl7:assignedPerson/hl7:name/hl7:given @#text

provider_id_performer_extension

FIELD

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

provider_id_performer_root

FIELD

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

provider_id_state

FIELD

hl7:performer/hl7:assignedEntity/hl7:addr/hl7:state @#text

provider_id_street

FIELD

hl7:performer/hl7:assignedEntity/hl7:addr/hl7:streetAddressLine @#text

provider_id_zip

FIELD

hl7:performer/hl7:assignedEntity/hl7:addr/hl7:postalCode @#text

visit_concept_codeSystem_encounter

FIELD

hl7:code @codeSystem

visit_concept_code_encounter

FIELD

hl7:code @code

visit_concept_code_trans1

FIELD

hl7:code/hl7:translation[1] @code

visit_concept_code_trans2

FIELD

hl7:code/hl7:translation[2] @code

visit_concept_code_trans3

FIELD

hl7:code/hl7:translation[3] @code

visit_concept_code_trans4

FIELD

hl7:code/hl7:translation[4] @code

visit_concept_id_default

CONSTANT

0

visit_concept_id_encounter

DERIVED

VT.codemap_xwalk_concept_id(concept_code=visit_concept_code_encounter, vocabulary_oid=visit_concept_codeSystem_encounter, default=None)

visit_concept_id_trans1

DERIVED

VT.codemap_xwalk_concept_id(concept_code=visit_concept_code_trans1, vocabulary_oid=visit_concept_system_trans1, default=None)

visit_concept_id_trans2

DERIVED

VT.codemap_xwalk_concept_id(concept_code=visit_concept_code_trans2, vocabulary_oid=visit_concept_system_trans2, default=None)

visit_concept_id_trans3

DERIVED

VT.codemap_xwalk_concept_id(concept_code=visit_concept_code_trans3, vocabulary_oid=visit_concept_system_trans3, default=None)

visit_concept_id_trans4

DERIVED

VT.codemap_xwalk_concept_id(concept_code=visit_concept_code_trans4, vocabulary_oid=visit_concept_system_trans4, default=None)

visit_concept_system_trans1

FIELD

hl7:code/hl7:translation[1] @codeSystem

visit_concept_system_trans2

FIELD

hl7:code/hl7:translation[2] @codeSystem

visit_concept_system_trans3

FIELD

hl7:code/hl7:translation[3] @codeSystem

visit_concept_system_trans4

FIELD

hl7:code/hl7:translation[4] @codeSystem

visit_end_date_high

FIELD

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

visit_end_date_low

FIELD

hl7:effectiveTime/hl7:low @value [DATE] → priority [‘visit_end_date’, 3]

visit_end_date_value

FIELD

hl7:effectiveTime @value [DATE] → priority [‘visit_end_date’, 2]

visit_end_datetime_high

FIELD

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

visit_end_datetime_low

FIELD

hl7:effectiveTime/hl7:low @value [DATETIME_HIGH] → priority [‘visit_end_datetime’, 3]

visit_end_datetime_value

FIELD

hl7:effectiveTime @value [DATETIME_HIGH] → priority [‘visit_end_datetime’, 2]

visit_occurrence_id_extension

FIELD

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

visit_occurrence_id_root

FIELD

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

visit_source_concept_id_default

CONSTANT

None

visit_source_concept_id_encounter

DERIVED

VT.codemap_xwalk_source_concept_id(concept_code=visit_concept_code_encounter, vocabulary_oid=visit_concept_codeSystem_encounter)

visit_source_concept_id_trans1

DERIVED

VT.codemap_xwalk_source_concept_id(concept_code=visit_concept_code_trans1, vocabulary_oid=visit_concept_system_trans1)

visit_source_concept_id_trans2

DERIVED

VT.codemap_xwalk_source_concept_id(concept_code=visit_concept_code_trans2, vocabulary_oid=visit_concept_system_trans2)

visit_source_concept_id_trans3

DERIVED

VT.codemap_xwalk_source_concept_id(concept_code=visit_concept_code_trans3, vocabulary_oid=visit_concept_system_trans3)

visit_source_concept_id_trans4

DERIVED

VT.codemap_xwalk_source_concept_id(concept_code=visit_concept_code_trans4, vocabulary_oid=visit_concept_system_trans4)

visit_source_value_default

CONSTANT

visit_source_value_encounter

DERIVED

VT.concat_fields(first_field=visit_concept_codeSystem_encounter, second_field=visit_concept_code_encounter, default=None)

visit_source_value_trans1

DERIVED

VT.concat_fields(first_field=visit_concept_system_trans1, second_field=visit_concept_code_trans1, default=None)

visit_source_value_trans2

DERIVED

VT.concat_fields(first_field=visit_concept_system_trans2, second_field=visit_concept_code_trans2, default=None)

visit_source_value_trans3

DERIVED

VT.concat_fields(first_field=visit_concept_system_trans3, second_field=visit_concept_code_trans3, default=None)

visit_source_value_trans4

DERIVED

VT.concat_fields(first_field=visit_concept_system_trans4, second_field=visit_concept_code_trans4, default=None)

visit_start_date_low

FIELD

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

visit_start_date_value

FIELD

hl7:effectiveTime @value [DATE] → priority [‘visit_start_date’, 2]

visit_start_datetime_low

FIELD

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

visit_start_datetime_value

FIELD

hl7:effectiveTime @value [DATETIME_LOW] → priority [‘visit_start_datetime’, 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)