Regenerate documentation. Split gender lookups between code systems.

answerdigital · Feb 12, 2024 · cd58dc7 · cd58dc7
1 parent 587c5fb
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diff --git a/Documentation/CdsLocation.json b/Documentation/CdsLocation.json
diff --git a/Documentation/CdsLocation.svg b/Documentation/CdsLocation.svg
diff --git a/Documentation/Location_location_source_value.md b/Documentation/Location_location_source_value.md
@@ -3,6 +3,26 @@
 * Value copied from `Patient_Postcode`
 
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Location%20table%20location_source_value%20field%20SACT%20mapping)
+### Rtds PAS Location
+* Value copied from `FirstOfNHSNUMBER`
+* `FirstOfNHSNUMBER` The patient's NHSNumber.
+<details>
+<summary>SQL</summary>
+
+```sql
+select
+	distinct
+		p.FirstOfNHSNUMBER,
+		p.FirstOfPOSTCODE
+from omop_staging.RTDS_PASDATA p
+where p.FirstOfPOSTCODE is not null
+	and p.FirstOfNHSNUMBER is not null;
+
+```
+</details>
+
+
+[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Location%20table%20location_source_value%20field%20Rtds%20PAS%20Location%20mapping)
 ### COSD Demographics
 Source columns  `StreetAddressLine1`, `StreetAddressLine2`, `StreetAddressLine3`, `StreetAddressLine4`, `Postcode`.
 Separates text with newlines. Trim whitespace.

diff --git a/Documentation/Location_nhs_number.md b/Documentation/Location_nhs_number.md
@@ -4,16 +4,16 @@
 
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Location%20table%20nhs_number%20field%20SACT%20mapping)
 ### Rtds PAS Location
-* Value copied from `NhsNumber`
-* `NhsNumber` The patient's NHSNumber.
+* Value copied from `FirstOfNHSNUMBER`
+* `FirstOfNHSNUMBER` The patient's NHSNumber.
 <details>
 <summary>SQL</summary>
 
 ```sql
 select
 	distinct
-		p.FirstOfNHSNUMBER as NhsNumber,
-		p.FirstOfPOSTCODE as Postcode
+		p.FirstOfNHSNUMBER,
+		p.FirstOfPOSTCODE
 from omop_staging.RTDS_PASDATA p
 where p.FirstOfPOSTCODE is not null
 	and p.FirstOfNHSNUMBER is not null;

diff --git a/Documentation/Location_zip.md b/Documentation/Location_zip.md
@@ -5,17 +5,17 @@ Uppercase the postcode then insert the space in the correct location, if needed.
 
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Location%20table%20zip%20field%20SACT%20mapping)
 ### Rtds PAS Location
-Source column  `Postcode`.
+Source column  `FirstOfPOSTCODE`.
 Uppercase the postcode then insert the space in the correct location, if needed.
-* `Postcode` The patient's Postcode.
+* `FirstOfPOSTCODE` The patient's Postcode.
 <details>
 <summary>SQL</summary>
 
 ```sql
 select
 	distinct
-		p.FirstOfNHSNUMBER as NhsNumber,
-		p.FirstOfPOSTCODE as Postcode
+		p.FirstOfNHSNUMBER,
+		p.FirstOfPOSTCODE
 from omop_staging.RTDS_PASDATA p
 where p.FirstOfPOSTCODE is not null
 	and p.FirstOfNHSNUMBER is not null;

diff --git a/Documentation/Person_ethnicity_concept_id.md b/Documentation/Person_ethnicity_concept_id.md
@@ -1,17 +1,21 @@
 # `Person` `ethnicity_concept_id`
 ### SACT
+Note: This is specific to US-based data mappings and is in regards to being “Hispanic “ and “Not Hispanic”. All our data is UK-based.
 * Constant value set to `0`. Unknown concept
 
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Person%20table%20ethnicity_concept_id%20field%20SACT%20mapping)
 ### Rtds Demographics
+Note: This is specific to US-based data mappings and is in regards to being “Hispanic “ and “Not Hispanic”. All our data is UK-based.
 * Constant value set to `0`. Unknown concept
 
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Person%20table%20ethnicity_concept_id%20field%20Rtds%20Demographics%20mapping)
 ### COSD Demographics
+Note: This is specific to US-based data mappings and is in regards to being “Hispanic “ and “Not Hispanic”. All our data is UK-based.
 * Constant value set to `0`. Unknown concept
 
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Person%20table%20ethnicity_concept_id%20field%20COSD%20Demographics%20mapping)
 ### CDS Person
+Note: This is specific to US-based data mappings and is in regards to being “Hispanic “ and “Not Hispanic”. All our data is UK-based.
 * Constant value set to `0`. Unknown concept
 
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Person%20table%20ethnicity_concept_id%20field%20CDS%20Person%20mapping)
diff --git a/Documentation/Person_gender_concept_id.md b/Documentation/Person_gender_concept_id.md
@@ -4,19 +4,14 @@ Source column  `Sex`.
 Lookup gender concept.
 
 
-|before|after|notes|
+|Sex|gender_concept_id|notes|
 |------|-----|-----|
 |Male|8507||
-|1|8507||
 |Female|8532||
-|2|8532||
-|9|8551||
-|X|8551||
 |Unknown|8551||
 |Not Stated|8551||
 
 Notes
-* [NHS Gender](https://www.datadictionary.nhs.uk/data_elements/person_stated_gender_code.html)
 * [OMOP Gender](https://athena.ohdsi.org/search-terms/terms?conceptClass=Gender&invalidReason=Valid&vocabulary=Gender&page=1&pageSize=50&query=)
 * `Sex` The patient's Sex.
 <details>
@@ -42,16 +37,12 @@ Source column  `PersonCurrentGenderCode`.
 Lookup gender concept.
 
 
-|before|after|notes|
+|PersonCurrentGenderCode|gender_concept_id|notes|
 |------|-----|-----|
-|Male|8507||
-|1|8507||
-|Female|8532||
-|2|8532||
-|9|8551||
-|X|8551||
-|Unknown|8551||
-|Not Stated|8551||
+|1|8507|Male|
+|2|8532|Female|
+|9|8551|Indeterminate (unable to be classified as either male or female)|
+|X|8551|Not known|
 
 Notes
 * [NHS Gender](https://www.datadictionary.nhs.uk/data_elements/person_stated_gender_code.html)

diff --git a/Documentation/Person_gender_source_concept_id.md b/Documentation/Person_gender_source_concept_id.md
@@ -4,16 +4,12 @@ Source column  `Person_Stated_Gender_Code`.
 Lookup gender concept.
 
 
-|before|after|notes|
+|Person_Stated_Gender_Code|gender_source_concept_id|notes|
 |------|-----|-----|
-|Male|8507||
-|1|8507||
-|Female|8532||
-|2|8532||
-|9|8551||
-|X|8551||
-|Unknown|8551||
-|Not Stated|8551||
+|1|8507|Male|
+|2|8532|Female|
+|9|8551|Indeterminate (unable to be classified as either male or female)|
+|X|8551|Not known|
 
 Notes
 * [NHS Gender](https://www.datadictionary.nhs.uk/data_elements/person_stated_gender_code.html)

diff --git a/Documentation/Person_race_concept_id.md b/Documentation/Person_race_concept_id.md
@@ -4,15 +4,15 @@ Source column  `EthnicCategory`.
 Lookup race concept.
 
 
-|before|after|notes|
+|EthnicCategory|race_concept_id|notes|
 |------|-----|-----|
 |A|8527|White - British|
 |B|8527|White - Irish|
 |C|8527|White - Any other White background|
-|D|700388|Mixed - White and Black Caribbean [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700388)|
-|E|700389|Mixed - White and Black African [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700389)|
-|F|700390|Mixed - White and Asian [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700390)|
-|G|700391|Mixed - Any other mixed background [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700391)|
+|D|8527|Mixed - White and Black Caribbean [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700388)|
+|E|8527|Mixed - White and Black African [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700389)|
+|F|8527|Mixed - White and Asian [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700390)|
+|G|8527|Mixed - Any other mixed background [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700391)|
 |H|38003574|Asian or Asian British - Indian|
 |J|38003589|Asian or Asian British - Pakistani|
 |K|38003575|Asian or Asian British - Bangladeshi|
@@ -106,15 +106,15 @@ Source column  `EthnicCategory`.
 Lookup race concept.
 
 
-|before|after|notes|
+|EthnicCategory|race_concept_id|notes|
 |------|-----|-----|
 |A|8527|White - British|
 |B|8527|White - Irish|
 |C|8527|White - Any other White background|
-|D|700388|Mixed - White and Black Caribbean [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700388)|
-|E|700389|Mixed - White and Black African [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700389)|
-|F|700390|Mixed - White and Asian [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700390)|
-|G|700391|Mixed - Any other mixed background [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700391)|
+|D|8527|Mixed - White and Black Caribbean [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700388)|
+|E|8527|Mixed - White and Black African [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700389)|
+|F|8527|Mixed - White and Asian [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700390)|
+|G|8527|Mixed - Any other mixed background [Athena mapping](https://athena.ohdsi.org/search-terms/terms/700391)|
 |H|38003574|Asian or Asian British - Indian|
 |J|38003589|Asian or Asian British - Pakistani|
 |K|38003575|Asian or Asian British - Bangladeshi|

diff --git a/Documentation/Person_race_source_concept_id.md b/Documentation/Person_race_source_concept_id.md
@@ -4,7 +4,7 @@ Source column  `EthnicCategory`.
 Lookup race source concept.
 
 
-|before|after|notes|
+|EthnicCategory|race_source_concept_id|notes|
 |------|-----|-----|
 |A|700385|White - British|
 |B|700386|White - Irish|
@@ -105,7 +105,7 @@ Source column  `EthnicCategory`.
 Lookup race source concept.
 
 
-|before|after|notes|
+|EthnicCategory|race_source_concept_id|notes|
 |------|-----|-----|
 |A|700385|White - British|
 |B|700386|White - Irish|

diff --git a/Documentation/RtdsLocation.json b/Documentation/RtdsLocation.json
@@ -5,13 +5,19 @@
     {
       "name": "zip",
       "sourceColumns": [
-        "Postcode"
+        "FirstOfPOSTCODE"
       ]
     },
     {
       "name": "nhs_number",
       "sourceColumns": [
-        "NhsNumber"
+        "FirstOfNHSNUMBER"
+      ]
+    },
+    {
+      "name": "location_source_value",
+      "sourceColumns": [
+        "FirstOfNHSNUMBER"
       ]
     }
   ]

diff --git a/Documentation/RtdsLocation.svg b/Documentation/RtdsLocation.svg
diff --git a/Documentation/VisitOccurrence_visit_concept_id.md b/Documentation/VisitOccurrence_visit_concept_id.md
@@ -3,7 +3,7 @@
 * Value copied from `VisitOccurenceConceptId`
 * `VisitOccurenceConceptId` 
 
-| Visit Occurrence Type (Info only)  | Location Class Condition                                                                                                                                                                   | Patient Classification Condition | Admission Method Code Condition |
+| Visit Occurrence Type             | Location Class Condition                                                                                                                                                                   | Patient Classification Condition | Admission Method Code Condition |
 |------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------|---------------------------------|
 | Emergency Room and Inpatient Visit | Is either 21 (Emergency Admission : Emergency Care Department or dental casualty department of the Health Care Provider) or 24 (Consultant Clinic of this or another Health Care Provider) | Is 1 (Ordinary admission)        | Is not 02 (Home Visit)          |
 | Emergency Room Visit               | Is either 21 (Emergency Admission : Emergency Care Department or dental casualty department of the Health Care Provider) or 24 (Consultant Clinic of this or another Health Care Provider) | Is not 1 (Ordinary admission)    | Is not 02 (Home Visit)          |
@@ -66,6 +66,6 @@ group by
 
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20VisitOccurrence%20table%20visit_concept_id%20field%20CDS%20VisitOccurrenceWithSpell%20mapping)
 ### CDS VisitOccurrenceWithoutSpell
-* Constant value set to `9202`. `Inpatient Visit`
+* Constant value set to `9202`. `Outpatient Visit`
 
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20VisitOccurrence%20table%20visit_concept_id%20field%20CDS%20VisitOccurrenceWithoutSpell%20mapping)
diff --git a/Documentation/VisitOccurrence_visit_type_concept_id.md b/Documentation/VisitOccurrence_visit_type_concept_id.md
@@ -57,6 +57,6 @@ group by
 
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20VisitOccurrence%20table%20visit_type_concept_id%20field%20CDS%20VisitOccurrenceWithSpell%20mapping)
 ### CDS VisitOccurrenceWithoutSpell
-* Constant value set to `32220`. `Still Patient`
+* Constant value set to `32818`. `EHR Administration Record`
 
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20VisitOccurrence%20table%20visit_type_concept_id%20field%20CDS%20VisitOccurrenceWithoutSpell%20mapping)