Added table level documentation for CDS observations.

answerdigital · Mar 20, 2024 · ce2c14c · ce2c14c
1 parent 93702af
commit ce2c14c
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Showing 12 changed files with 138 additions and 3 deletions.
diff --git a/...mer/CDS/Observation/AnaestheticDuringLabourDelivery/CdsAnaestheticDuringLabourDelivery.cs b/...mer/CDS/Observation/AnaestheticDuringLabourDelivery/CdsAnaestheticDuringLabourDelivery.cs
@@ -4,6 +4,11 @@
 
 namespace OmopTransformer.CDS.Observation.AnaestheticDuringLabourDelivery;
 
+[Notes(
+    "Notes",
+    "Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc",
+    "Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.",
+    "Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)")]
 internal class CdsAnaestheticDuringLabourDelivery : OmopObservation<CdsAnaestheticDuringLabourDeliveryRecord>
 {
     [CopyValue(nameof(Source.NHSNumber))]

diff --git a/...S/Observation/AnaestheticGivenPostLabourDelivery/CdsAnaestheticGivenPostLabourDelivery.cs b/...S/Observation/AnaestheticGivenPostLabourDelivery/CdsAnaestheticGivenPostLabourDelivery.cs
@@ -4,6 +4,11 @@
 
 namespace OmopTransformer.CDS.Observation.AnaestheticGivenPostLabourDelivery;
 
+[Notes(
+    "Notes",
+    "Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc",
+    "Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.",
+    "Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)")]
 internal class CdsAnaestheticGivenPostLabourDelivery : OmopObservation<CdsAnaestheticGivenPostLabourDeliveryRecord>
 {
     [CopyValue(nameof(Source.NHSNumber))]

diff --git a/OmopTransformer/CDS/Observation/BirthWeight/CdsBirthWeight.cs b/OmopTransformer/CDS/Observation/BirthWeight/CdsBirthWeight.cs
@@ -4,6 +4,11 @@
 
 namespace OmopTransformer.CDS.Observation.BirthWeight;
 
+[Notes(
+    "Notes",
+    "Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc",
+    "Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.",
+    "Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)")]
 internal class CdsBirthWeight : OmopObservation<CdsBirthWeightRecord>
 {
     [CopyValue(nameof(Source.NHSNumber))]

diff --git a/OmopTransformer/CDS/Observation/CarerSupportIndicator/CdsCarerSupportIndicator.cs b/OmopTransformer/CDS/Observation/CarerSupportIndicator/CdsCarerSupportIndicator.cs
@@ -4,6 +4,11 @@
 
 namespace OmopTransformer.CDS.Observation.CarerSupportIndicator;
 
+[Notes(
+    "Notes",
+    "Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc",
+    "Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.",
+    "Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)")]
 internal class CdsCarerSupportIndicator : OmopObservation<CdsCarerSupportIndicatorRecord>
 {
     [CopyValue(nameof(Source.NHSNumber))]

diff --git a/OmopTransformer/CDS/Observation/GestationLengthLabourOnset/CdsGestationLengthLabourOnset.cs b/OmopTransformer/CDS/Observation/GestationLengthLabourOnset/CdsGestationLengthLabourOnset.cs
@@ -4,6 +4,11 @@
 
 namespace OmopTransformer.CDS.Observation.GestationLengthLabourOnset;
 
+[Notes(
+    "Notes",
+    "Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc",
+    "Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.",
+    "Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)")]
 internal class CdsGestationLengthLabourOnset : OmopObservation<CdsGestationLengthLabourOnsetRecord>
 {
     [CopyValue(nameof(Source.NHSNumber))]

diff --git a/OmopTransformer/CDS/Observation/NumberOfBabies/CdsNumberOfBabies.cs b/OmopTransformer/CDS/Observation/NumberOfBabies/CdsNumberOfBabies.cs
@@ -4,6 +4,11 @@
 
 namespace OmopTransformer.CDS.Observation.NumberOfBabies;
 
+[Notes(
+    "Notes",
+    "Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc",
+    "Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.",
+    "Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)")]
 internal class CdsNumberOfBabies : OmopObservation<CdsNumberOfBabiesRecord>
 {
     [CopyValue(nameof(Source.NHSNumber))]

diff --git a/OmopTransformer/CDS/Observation/PersonWeight/CdsPersonWeight.cs b/OmopTransformer/CDS/Observation/PersonWeight/CdsPersonWeight.cs
@@ -4,6 +4,11 @@
 
 namespace OmopTransformer.CDS.Observation.PersonWeight;
 
+[Notes(
+    "Notes",
+    "Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc",
+    "Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.",
+    "Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)")]
 internal class CdsPersonWeight : OmopObservation<CdsPersonWeightRecord>
 {
     [CopyValue(nameof(Source.NHSNumber))]

diff --git a/...ormer/CDS/Observation/SourceOfReferralForOutpatients/CdsSourceOfReferralForOutpatients.cs b/...ormer/CDS/Observation/SourceOfReferralForOutpatients/CdsSourceOfReferralForOutpatients.cs
@@ -4,6 +4,11 @@
 
 namespace OmopTransformer.CDS.Observation.SourceOfReferralForOutpatients;
 
+[Notes(
+    "Notes",
+    "Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc",
+    "Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.",
+    "Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)")]
 internal class CdsSourceOfReferralForOutpatients : OmopObservation<CdsSourceOfReferralForOutpatientsRecord>
 {
     [CopyValue(nameof(Source.NHSNumber))]

diff --git a/OmopTransformer/CDS/Observation/TotalPreviousPregnancies/CdsTotalPreviousPregnancies.cs b/OmopTransformer/CDS/Observation/TotalPreviousPregnancies/CdsTotalPreviousPregnancies.cs
@@ -4,6 +4,11 @@
 
 namespace OmopTransformer.CDS.Observation.TotalPreviousPregnancies;
 
+[Notes(
+    "Notes",
+    "Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc",
+    "Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.",
+    "Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)")]
 internal class CdsTotalPreviousPregnancies : OmopObservation<CdsTotalPreviousPregnanciesRecord>
 {
     [CopyValue(nameof(Source.NHSNumber))]

diff --git a/OmopTransformer/Properties/launchSettings.json b/OmopTransformer/Properties/launchSettings.json
@@ -2,8 +2,8 @@
   "profiles": {
     "OmopTransformer": {
         "commandName": "Project",
-        //"commandLineArgs": "transform --type cosd"
-        "commandLineArgs": "docs ."
+        "commandLineArgs": "transform --type cosd"
+        //"commandLineArgs": "docs ."
         //"commandLineArgs": "staging clear --type cosd"
     }
   }

diff --git a/OmopTransformer/appsettings.json b/OmopTransformer/appsettings.json
@@ -1,4 +1,4 @@
 {
-    "ConnectionString": "Server=host.docker.internal;Database=yourDatabase;User Id=user;Password=password;Encrypt=false",
+    "ConnectionString": "Server=10.134.180.238;Database=OMOP_Dev;User Id=James.Cockayne;Password=CyJa8Lo0CV2pZmYfvwLq;Encrypt=false",
     "BatchSize": 200000
 }
diff --git a/docs/transformation-documentation/Observation.md b/docs/transformation-documentation/Observation.md
@@ -22,36 +22,126 @@ has_toc: false
 ## CdsTotalPreviousPregnancies
 <a href="CdsTotalPreviousPregnancies.svg" target="_blank"><img src="CdsTotalPreviousPregnancies.svg" /></a>
 
+{: .important-title }
+> Notes
+>
+> Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc
+>
+> Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.
+>
+> Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)
+>
+
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CdsTotalPreviousPregnancies%20mapping){: .btn }
 ## CdsSourceOfReferralForOutpatients
 <a href="CdsSourceOfReferralForOutpatients.svg" target="_blank"><img src="CdsSourceOfReferralForOutpatients.svg" /></a>
 
+{: .important-title }
+> Notes
+>
+> Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc
+>
+> Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.
+>
+> Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)
+>
+
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CdsSourceOfReferralForOutpatients%20mapping){: .btn }
 ## CdsPersonWeight
 <a href="CdsPersonWeight.svg" target="_blank"><img src="CdsPersonWeight.svg" /></a>
 
+{: .important-title }
+> Notes
+>
+> Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc
+>
+> Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.
+>
+> Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)
+>
+
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CdsPersonWeight%20mapping){: .btn }
 ## CdsNumberOfBabies
 <a href="CdsNumberOfBabies.svg" target="_blank"><img src="CdsNumberOfBabies.svg" /></a>
 
+{: .important-title }
+> Notes
+>
+> Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc
+>
+> Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.
+>
+> Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)
+>
+
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CdsNumberOfBabies%20mapping){: .btn }
 ## CdsGestationLengthLabourOnset
 <a href="CdsGestationLengthLabourOnset.svg" target="_blank"><img src="CdsGestationLengthLabourOnset.svg" /></a>
 
+{: .important-title }
+> Notes
+>
+> Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc
+>
+> Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.
+>
+> Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)
+>
+
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CdsGestationLengthLabourOnset%20mapping){: .btn }
 ## CdsCarerSupportIndicator
 <a href="CdsCarerSupportIndicator.svg" target="_blank"><img src="CdsCarerSupportIndicator.svg" /></a>
 
+{: .important-title }
+> Notes
+>
+> Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc
+>
+> Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.
+>
+> Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)
+>
+
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CdsCarerSupportIndicator%20mapping){: .btn }
 ## CdsBirthWeight
 <a href="CdsBirthWeight.svg" target="_blank"><img src="CdsBirthWeight.svg" /></a>
 
+{: .important-title }
+> Notes
+>
+> Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc
+>
+> Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.
+>
+> Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)
+>
+
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CdsBirthWeight%20mapping){: .btn }
 ## CdsAnaestheticGivenPostLabourDelivery
 <a href="CdsAnaestheticGivenPostLabourDelivery.svg" target="_blank"><img src="CdsAnaestheticGivenPostLabourDelivery.svg" /></a>
 
+{: .important-title }
+> Notes
+>
+> Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc
+>
+> Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.
+>
+> Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)
+>
+
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CdsAnaestheticGivenPostLabourDelivery%20mapping){: .btn }
 ## CdsAnaestheticDuringLabourDelivery
 <a href="CdsAnaestheticDuringLabourDelivery.svg" target="_blank"><img src="CdsAnaestheticDuringLabourDelivery.svg" /></a>
 
+{: .important-title }
+> Notes
+>
+> Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc
+>
+> Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.
+>
+> Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)
+>
+
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CdsAnaestheticDuringLabourDelivery%20mapping){: .btn }