diff --git a/OmopTransformer/CDS/Observation/AnaestheticDuringLabourDelivery/CdsAnaestheticDuringLabourDelivery.cs b/OmopTransformer/CDS/Observation/AnaestheticDuringLabourDelivery/CdsAnaestheticDuringLabourDelivery.cs index 0c1a56c..fbacdb2 100644 --- a/OmopTransformer/CDS/Observation/AnaestheticDuringLabourDelivery/CdsAnaestheticDuringLabourDelivery.cs +++ b/OmopTransformer/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 { [CopyValue(nameof(Source.NHSNumber))] diff --git a/OmopTransformer/CDS/Observation/AnaestheticGivenPostLabourDelivery/CdsAnaestheticGivenPostLabourDelivery.cs b/OmopTransformer/CDS/Observation/AnaestheticGivenPostLabourDelivery/CdsAnaestheticGivenPostLabourDelivery.cs index 3d95765..4c67614 100644 --- a/OmopTransformer/CDS/Observation/AnaestheticGivenPostLabourDelivery/CdsAnaestheticGivenPostLabourDelivery.cs +++ b/OmopTransformer/CDS/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 { [CopyValue(nameof(Source.NHSNumber))] diff --git a/OmopTransformer/CDS/Observation/BirthWeight/CdsBirthWeight.cs b/OmopTransformer/CDS/Observation/BirthWeight/CdsBirthWeight.cs index a6b47a0..fd02769 100644 --- 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 { [CopyValue(nameof(Source.NHSNumber))] diff --git a/OmopTransformer/CDS/Observation/CarerSupportIndicator/CdsCarerSupportIndicator.cs b/OmopTransformer/CDS/Observation/CarerSupportIndicator/CdsCarerSupportIndicator.cs index 045ba4c..646ae3b 100644 --- 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 { [CopyValue(nameof(Source.NHSNumber))] diff --git a/OmopTransformer/CDS/Observation/GestationLengthLabourOnset/CdsGestationLengthLabourOnset.cs b/OmopTransformer/CDS/Observation/GestationLengthLabourOnset/CdsGestationLengthLabourOnset.cs index 5ca49d3..a980295 100644 --- 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 { [CopyValue(nameof(Source.NHSNumber))] diff --git a/OmopTransformer/CDS/Observation/NumberOfBabies/CdsNumberOfBabies.cs b/OmopTransformer/CDS/Observation/NumberOfBabies/CdsNumberOfBabies.cs index 047154e..d8d6e59 100644 --- 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 { [CopyValue(nameof(Source.NHSNumber))] diff --git a/OmopTransformer/CDS/Observation/PersonWeight/CdsPersonWeight.cs b/OmopTransformer/CDS/Observation/PersonWeight/CdsPersonWeight.cs index 2a77c4c..5d30523 100644 --- 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 { [CopyValue(nameof(Source.NHSNumber))] diff --git a/OmopTransformer/CDS/Observation/SourceOfReferralForOutpatients/CdsSourceOfReferralForOutpatients.cs b/OmopTransformer/CDS/Observation/SourceOfReferralForOutpatients/CdsSourceOfReferralForOutpatients.cs index 47d648f..7c247a4 100644 --- a/OmopTransformer/CDS/Observation/SourceOfReferralForOutpatients/CdsSourceOfReferralForOutpatients.cs +++ b/OmopTransformer/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 { [CopyValue(nameof(Source.NHSNumber))] diff --git a/OmopTransformer/CDS/Observation/TotalPreviousPregnancies/CdsTotalPreviousPregnancies.cs b/OmopTransformer/CDS/Observation/TotalPreviousPregnancies/CdsTotalPreviousPregnancies.cs index 83d51de..c639500 100644 --- 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 { [CopyValue(nameof(Source.NHSNumber))] diff --git a/OmopTransformer/Properties/launchSettings.json b/OmopTransformer/Properties/launchSettings.json index 33644d4..e8a62e1 100644 --- 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 index 819c807..d63de86 100644 --- 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 index 0aca18d..1a0b70e 100644 --- a/docs/transformation-documentation/Observation.md +++ b/docs/transformation-documentation/Observation.md @@ -22,36 +22,126 @@ has_toc: false ## CdsTotalPreviousPregnancies +{: .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 +{: .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 +{: .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 +{: .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 +{: .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 +{: .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 +{: .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 +{: .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 +{: .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 }