From 3b10bbcce03478db94aa759148081ec4b3b4050b Mon Sep 17 00:00:00 2001 From: holtyad Date: Thu, 11 Dec 2025 16:48:07 +0000 Subject: [PATCH 1/5] update lookup misses --- OmopTransformer/Transformation/MetastasisSiteLookup.cs | 1 + OmopTransformer/Transformation/SurgicalAccessTypeLungLookup.cs | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/OmopTransformer/Transformation/MetastasisSiteLookup.cs b/OmopTransformer/Transformation/MetastasisSiteLookup.cs index 95723f91..ee3603b9 100644 --- a/OmopTransformer/Transformation/MetastasisSiteLookup.cs +++ b/OmopTransformer/Transformation/MetastasisSiteLookup.cs @@ -8,6 +8,7 @@ internal class MetastasisSiteLookup : ILookup public Dictionary Mappings { get; } = new() { + { "01", new ValueWithNote("36769301", "Metastasis to bone") }, { "02", new ValueWithNote("36768862", "Metastasis to brain") }, { "03", new ValueWithNote("36770544", "Metastasis to liver") }, { "04", new ValueWithNote("36770283", "Metastasis to lung") }, diff --git a/OmopTransformer/Transformation/SurgicalAccessTypeLungLookup.cs b/OmopTransformer/Transformation/SurgicalAccessTypeLungLookup.cs index b1cc0b2c..c502c31a 100644 --- a/OmopTransformer/Transformation/SurgicalAccessTypeLungLookup.cs +++ b/OmopTransformer/Transformation/SurgicalAccessTypeLungLookup.cs @@ -12,7 +12,8 @@ internal class SurgicalAccessTypeLungLookup : ILookup { "2", new ValueWithNote("4044378", "Laparoscopic/Thoracoscopic with planned conversion to open surgery") }, { "3", new ValueWithNote("4044378", "Laparoscopic/Thoracoscopic with unplanned conversion to open surgery") }, { "4", new ValueWithNote("44808608", "Laparoscopic/Thoracoscopic completed") }, - { "5", new ValueWithNote("44790026", "Robotic surgery") } + { "5", new ValueWithNote("44790026", "Robotic surgery") }, + { "Z", new ValueWithNote("0", "Other") } }; public string[] ColumnNotes => From 1b083292615d76e34f59172aa6c9d02efa90d4fa Mon Sep 17 00:00:00 2001 From: holtyad Date: Wed, 17 Dec 2025 14:45:56 +0000 Subject: [PATCH 2/5] add measurements --- ...surementMcategoryFinalPreTreatmentStage.cs | 29 +++++++++++++++ ...urementMcategoryFinalPreTreatmentStage.xml | 35 +++++++++++++++++++ ...ntMcategoryFinalPreTreatmentStageRecord.cs | 13 +++++++ ...eastMeasurementMcategoryIntegratedStage.cs | 29 +++++++++++++++ ...astMeasurementMcategoryIntegratedStage.xml | 35 +++++++++++++++++++ ...asurementMcategoryIntegratedStageRecord.cs | 13 +++++++ ...surementNcategoryFinalPreTreatmentStage.cs | 29 +++++++++++++++ ...urementNcategoryFinalPreTreatmentStage.xml | 35 +++++++++++++++++++ ...ntNcategoryFinalPreTreatmentStageRecord.cs | 13 +++++++ ...eastMeasurementNcategoryIntegratedStage.cs | 29 +++++++++++++++ ...astMeasurementNcategoryIntegratedStage.xml | 34 ++++++++++++++++++ ...asurementNcategoryIntegratedStageRecord.cs | 13 +++++++ OmopTransformer/COSD/CosdTransformer.cs | 28 +++++++++++++++ OmopTransformer/OmopTransformer.csproj | 12 +++++++ .../Transformation/MetastasisSiteLookup.cs | 6 ++-- 15 files changed, 350 insertions(+), 3 deletions(-) create mode 100644 OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.cs create mode 100644 OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.xml create mode 100644 OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStageRecord.cs create mode 100644 OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStage.cs create mode 100644 OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStage.xml create mode 100644 OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStageRecord.cs create mode 100644 OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.cs create mode 100644 OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.xml create mode 100644 OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStageRecord.cs create mode 100644 OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStage.cs create mode 100644 OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStage.xml create mode 100644 OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStageRecord.cs diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.cs b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.cs new file mode 100644 index 00000000..09d1b697 --- /dev/null +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.cs @@ -0,0 +1,29 @@ +using OmopTransformer.Annotations; +using OmopTransformer.Omop.Measurement; +using OmopTransformer.Transformation; + +namespace OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage; + +internal class CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage : OmopMeasurement +{ + [CopyValue(nameof(Source.NhsNumber))] + public override string? nhs_number { get; set; } + + [Transform(typeof(DateConverter), nameof(Source.MeasurementDate))] + public override DateTime? measurement_date { get; set; } + + [Transform(typeof(DateConverter), nameof(Source.MeasurementDate))] + public override DateTime? measurement_datetime { get; set; } + + [ConstantValue(32828, "EHR episode record")] + public override int? measurement_type_concept_id { get; set; } + + [CopyValue(nameof(Source.McategoryFinalPreTreatment))] + public override string? measurement_source_value { get; set; } + + [Transform(typeof(MCategoryLookup), nameof(Source.McategoryFinalPreTreatment))] + public override int[]? measurement_concept_id { get; set; } + + [ConstantValue(2000500014, "MCategoryFinalPreTreatmentStage")] + public override int? measurement_source_concept_id { get; set; } +} diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.xml b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.xml new file mode 100644 index 00000000..2d967760 --- /dev/null +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.xml @@ -0,0 +1,35 @@ + + +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentMCategory' as McategoryFinalPreTreatment, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NHSNumber, + coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + McategoryFinalPreTreatment +from BR +where McategoryFinalPreTreatment is not null +and NHSNumber is not null; + + + + Patient NHS Number + NHS NUMBER + + + Measurement Date is the date on which TNM Stage Grouping (Final pre-treatment) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed. + DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED) + TNM STAGE GROUPING DATE (FINAL PRETREATMENT) + + + Is the code, using a TNM CODING EDITION, which classifies the absence or presence of distant metastases before treatment during a Cancer Care Spell. + M CATEGORY (FINAL PRETREATMENT) + + + diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStageRecord.cs b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStageRecord.cs new file mode 100644 index 00000000..dc4314d8 --- /dev/null +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStageRecord.cs @@ -0,0 +1,13 @@ +using OmopTransformer.Annotations; + +namespace OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage; + +[DataOrigin("COSD")] +[Description("COSD V8 Breast Measurement M Category Final Pre Treatment Stage")] +[SourceQuery("CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.xml")] +internal class CosdV8BreastMeasurementMcategoryFinalPreTreatmentStageRecord +{ + public string? NhsNumber { get; set; } + public string? MeasurementDate { get; set; } + public string? McategoryFinalPreTreatment { get; set; } +} diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStage.cs b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStage.cs new file mode 100644 index 00000000..6f5d68f2 --- /dev/null +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStage.cs @@ -0,0 +1,29 @@ +using OmopTransformer.Annotations; +using OmopTransformer.Omop.Measurement; +using OmopTransformer.Transformation; + +namespace OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementMcategoryIntegratedStage; + +internal class CosdV8BreastMeasurementMcategoryIntegratedStage : OmopMeasurement +{ + [CopyValue(nameof(Source.NhsNumber))] + public override string? nhs_number { get; set; } + + [Transform(typeof(DateConverter), nameof(Source.MeasurementDate))] + public override DateTime? measurement_date { get; set; } + + [Transform(typeof(DateConverter), nameof(Source.MeasurementDate))] + public override DateTime? measurement_datetime { get; set; } + + [ConstantValue(32828, "EHR episode record")] + public override int? measurement_type_concept_id { get; set; } + + [CopyValue(nameof(Source.MCategoryIntegratedStage))] + public override string? measurement_source_value { get; set; } + + [Transform(typeof(MCategoryLookup), nameof(Source.MCategoryIntegratedStage))] + public override int[]? measurement_concept_id { get; set; } + + [ConstantValue(2000500018, "MCategoryIntegratedStage")] + public override int? measurement_source_concept_id { get; set; } +} diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStage.xml b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStage.xml new file mode 100644 index 00000000..a74adb1d --- /dev/null +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStage.xml @@ -0,0 +1,35 @@ + + +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + MCategoryIntegratedStage +from BR +where MCategoryIntegratedStage is not null +and NhsNumber is not null; + + + + Patient NHS Number + NHS NUMBER + + + Measurement Date is the date on which TNM Stage Grouping (Integrated) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed. + DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED) + TNM STAGE GROUPING DATE (INTEGRATED) + + + Is the code, using a TNM CODING EDITION, which classifies the absence or presence of distant metastases after all information from treatment is available during a Cancer Care Spell. + M CATEGORY (INTEGRATED STAGE) + + + diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStageRecord.cs b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStageRecord.cs new file mode 100644 index 00000000..6b60d224 --- /dev/null +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStageRecord.cs @@ -0,0 +1,13 @@ +using OmopTransformer.Annotations; + +namespace OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementMcategoryIntegratedStage; + +[DataOrigin("COSD")] +[Description("COSD V8 Breast Measurement M Category Integrated Stage")] +[SourceQuery("CosdV8BreastMeasurementMcategoryIntegratedStage.xml")] +internal class CosdV8BreastMeasurementMcategoryIntegratedStageRecord +{ + public string? NhsNumber { get; set; } + public string? MeasurementDate { get; set; } + public string? MCategoryIntegratedStage { get; set; } +} diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.cs b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.cs new file mode 100644 index 00000000..d1890508 --- /dev/null +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.cs @@ -0,0 +1,29 @@ +using OmopTransformer.Annotations; +using OmopTransformer.Omop.Measurement; +using OmopTransformer.Transformation; + +namespace OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage; + +internal class CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage : OmopMeasurement +{ + [CopyValue(nameof(Source.NhsNumber))] + public override string? nhs_number { get; set; } + + [Transform(typeof(DateConverter), nameof(Source.MeasurementDate))] + public override DateTime? measurement_date { get; set; } + + [Transform(typeof(DateConverter), nameof(Source.MeasurementDate))] + public override DateTime? measurement_datetime { get; set; } + + [ConstantValue(32828, "EHR episode record")] + public override int? measurement_type_concept_id { get; set; } + + [CopyValue(nameof(Source.NcategoryFinalPreTreatment))] + public override string? measurement_source_value { get; set; } + + [Transform(typeof(NCategoryLookup), nameof(Source.NcategoryFinalPreTreatment))] + public override int[]? measurement_concept_id { get; set; } + + [ConstantValue(2000500015, "NCategoryFinalPreTreatmentStage")] + public override int? measurement_source_concept_id { get; set; } +} diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.xml b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.xml new file mode 100644 index 00000000..86686f78 --- /dev/null +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.xml @@ -0,0 +1,35 @@ + + +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + NcategoryFinalPreTreatment +from BR +where NcategoryFinalPreTreatment is not null +and NhsNumber is not null; + + + + Patient NHS Number + NHS NUMBER + + + Measurement Date is the date on which TNM Stage Grouping (Final pre-treatment) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed. + DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED) + TNM STAGE GROUPING DATE (FINAL PRETREATMENT) + + + Is the code, using a TNM CODING EDITION, which classifies the presence or absence of regional lymph node metastases before treatment during a Cancer Care Spell. + N CATEGORY (FINAL PRETREATMENT) + + + diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStageRecord.cs b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStageRecord.cs new file mode 100644 index 00000000..64a2b4ad --- /dev/null +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStageRecord.cs @@ -0,0 +1,13 @@ +using OmopTransformer.Annotations; + +namespace OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage; + +[DataOrigin("COSD")] +[Description("COSD V8 Breast Measurement N Category Final Pre Treatment Stage")] +[SourceQuery("CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.xml")] +internal class CosdV8BreastMeasurementNcategoryFinalPreTreatmentStageRecord +{ + public string? NhsNumber { get; set; } + public string? MeasurementDate { get; set; } + public string? NcategoryFinalPreTreatment { get; set; } +} diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStage.cs b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStage.cs new file mode 100644 index 00000000..672fb7ca --- /dev/null +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStage.cs @@ -0,0 +1,29 @@ +using OmopTransformer.Annotations; +using OmopTransformer.Omop.Measurement; +using OmopTransformer.Transformation; + +namespace OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementNcategoryIntegratedStage; + +internal class CosdV8BreastMeasurementNcategoryIntegratedStage : OmopMeasurement +{ + [CopyValue(nameof(Source.NhsNumber))] + public override string? nhs_number { get; set; } + + [Transform(typeof(DateConverter), nameof(Source.MeasurementDate))] + public override DateTime? measurement_date { get; set; } + + [Transform(typeof(DateConverter), nameof(Source.MeasurementDate))] + public override DateTime? measurement_datetime { get; set; } + + [ConstantValue(32828, "EHR episode record")] + public override int? measurement_type_concept_id { get; set; } + + [CopyValue(nameof(Source.NCategoryIntegratedStage))] + public override string? measurement_source_value { get; set; } + + [Transform(typeof(NCategoryLookup), nameof(Source.NCategoryIntegratedStage))] + public override int[]? measurement_concept_id { get; set; } + + [ConstantValue(2000500019, "NCategoryIntegratedStage")] + public override int? measurement_source_concept_id { get; set; } +} diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStage.xml b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStage.xml new file mode 100644 index 00000000..3ff83f8d --- /dev/null +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStage.xml @@ -0,0 +1,34 @@ + + +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + NCategoryIntegratedStage +from BR +where NCategoryIntegratedStage is not null; + + + + Patient NHS Number + NHS NUMBER + + + Measurement Date is the date on which TNM Stage Grouping (Integrated) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed. + DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED) + TNM STAGE GROUPING DATE (INTEGRATED) + + + Is the code, using a TNM CODING EDITION, which classifies the presence or absence of regional lymph node metastases after all information from treatment is available during a Cancer Care Spell. + N CATEGORY (INTEGRATED STAGE) + + + diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStageRecord.cs b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStageRecord.cs new file mode 100644 index 00000000..81d23965 --- /dev/null +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStageRecord.cs @@ -0,0 +1,13 @@ +using OmopTransformer.Annotations; + +namespace OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementNcategoryIntegratedStage; + +[DataOrigin("COSD")] +[Description("COSD V8 Breast Measurement N Category Integrated Stage")] +[SourceQuery("CosdV8BreastMeasurementNcategoryIntegratedStage.xml")] +internal class CosdV8BreastMeasurementNcategoryIntegratedStageRecord +{ + public string? NhsNumber { get; set; } + public string? MeasurementDate { get; set; } + public string? NCategoryIntegratedStage { get; set; } +} diff --git a/OmopTransformer/COSD/CosdTransformer.cs b/OmopTransformer/COSD/CosdTransformer.cs index dde615fa..09658fea 100644 --- a/OmopTransformer/COSD/CosdTransformer.cs +++ b/OmopTransformer/COSD/CosdTransformer.cs @@ -19,6 +19,10 @@ using OmopTransformer.COSD.Breast.ProcedureOccurrence.CosdV9BreastProcedureOccurrenceProcedureOpcs; using OmopTransformer.COSD.Breast.ProcedureOccurrence.CosdV9BreastProcedureOccurrencePrimaryProcedureOpcs; using OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementGradeOfDifferentiation; +using OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage; +using OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementMcategoryIntegratedStage; +using OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage; +using OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementNcategoryIntegratedStage; using OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV8LungConditionOccurrencePrimaryDiagnosis; using OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopography; using OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV8LungConditionOccurrenceProgression; @@ -1033,5 +1037,29 @@ await Transform( + _measurementRecorder.InsertUpdateMeasurements, + "CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage", + runId, + cancellationToken); + + await Transform( + _measurementRecorder.InsertUpdateMeasurements, + "CosdV8BreastMeasurementMcategoryIntegratedStage", + runId, + cancellationToken); + + await Transform( + _measurementRecorder.InsertUpdateMeasurements, + "CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage", + runId, + cancellationToken); + + await Transform( + _measurementRecorder.InsertUpdateMeasurements, + "CosdV8BreastMeasurementNcategoryIntegratedStage", + runId, + cancellationToken); } } \ No newline at end of file diff --git a/OmopTransformer/OmopTransformer.csproj b/OmopTransformer/OmopTransformer.csproj index 20d8e7c3..1f48cef5 100644 --- a/OmopTransformer/OmopTransformer.csproj +++ b/OmopTransformer/OmopTransformer.csproj @@ -89,6 +89,18 @@ Always + + Always + + + Always + + + Always + + + Always + Always diff --git a/OmopTransformer/Transformation/MetastasisSiteLookup.cs b/OmopTransformer/Transformation/MetastasisSiteLookup.cs index ee3603b9..984f2fe9 100644 --- a/OmopTransformer/Transformation/MetastasisSiteLookup.cs +++ b/OmopTransformer/Transformation/MetastasisSiteLookup.cs @@ -8,15 +8,15 @@ internal class MetastasisSiteLookup : ILookup public Dictionary Mappings { get; } = new() { - { "01", new ValueWithNote("36769301", "Metastasis to bone") }, + { "01", new ValueWithNote("36769301", "Metastasis to bone") }, // Bone (Retired 1 July 2012) { "02", new ValueWithNote("36768862", "Metastasis to brain") }, { "03", new ValueWithNote("36770544", "Metastasis to liver") }, { "04", new ValueWithNote("36770283", "Metastasis to lung") }, { "07", new ValueWithNote("36769180", "Metastasis to the Unknown Site") }, { "08", new ValueWithNote("35225673", "Metastasis to skin") }, { "09", new ValueWithNote("36769243", "Distant spread to lymph node") }, - { "10", new ValueWithNote("36769301", "Metastasis to bone") }, - { "11", new ValueWithNote("35226074", "Metastasis to bone marrow") }, + { "10", new ValueWithNote("36769301", "Metastasis to bone") }, // Bone (excluding Bone Marrow) + { "11", new ValueWithNote("35226074", "Metastasis to bone marrow") }, // Bone marrow { "12", new ValueWithNote("36769269", "Regional spread to lymph node") }, { "98", new ValueWithNote("36769180", "Metastasis") }, { "99", new ValueWithNote("36769180", "Metastasis") } From ba4d2e3855599175ee52731c5b72a636ccf8cebf Mon Sep 17 00:00:00 2001 From: holtyad Date: Wed, 17 Dec 2025 14:46:20 +0000 Subject: [PATCH 3/5] build docs --- ...rementMcategoryFinalPreTreatmentStage.json | 118 +++++++++++ ...urementMcategoryFinalPreTreatmentStage.svg | 89 ++++++++ ...stMeasurementMcategoryIntegratedStage.json | 118 +++++++++++ ...astMeasurementMcategoryIntegratedStage.svg | 89 ++++++++ ...rementNcategoryFinalPreTreatmentStage.json | 118 +++++++++++ ...urementNcategoryFinalPreTreatmentStage.svg | 89 ++++++++ ...stMeasurementNcategoryIntegratedStage.json | 118 +++++++++++ ...astMeasurementNcategoryIntegratedStage.svg | 89 ++++++++ ...easurementNonPrimaryPathwayMetastasis.json | 2 +- ...ngMeasurementPrimaryPathwayMetastasis.json | 2 +- .../CosdV8LungSurgicalAccessType.json | 2 +- ...easurementNonPrimaryPathwayMetastasis.json | 2 +- ...V8MeasurementPrimaryPathwayMetastasis.json | 2 +- ...onPrimaryPathwayProgressionMetastasis.json | 2 +- ...NonPrimaryPathwayRecurrenceMetastasis.json | 2 +- ...ngMeasurementPrimaryPathwayMetastasis.json | 2 +- .../CosdV9LungSurgicalAccessType.json | 2 +- ...onPrimaryPathwayProgressionMetastasis.json | 2 +- ...NonPrimaryPathwayRecurrenceMetastasis.json | 2 +- ...V9MeasurementPrimaryPathwayMetastasis.json | 2 +- .../Measurement.md | 16 ++ .../Measurement_measurement_concept_id.md | 197 ++++++++++++++++++ .../Measurement_measurement_date.md | 111 ++++++++++ .../Measurement_measurement_datetime.md | 111 ++++++++++ ...asurement_measurement_source_concept_id.md | 16 ++ .../Measurement_measurement_source_value.md | 107 ++++++++++ ...Measurement_measurement_type_concept_id.md | 16 ++ .../Measurement_nhs_number.md | 107 ++++++++++ .../Observation_qualifier_concept_id.md | 2 + 29 files changed, 1523 insertions(+), 12 deletions(-) create mode 100644 docs/transformation-documentation/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.json create mode 100644 docs/transformation-documentation/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.svg create mode 100644 docs/transformation-documentation/CosdV8BreastMeasurementMcategoryIntegratedStage.json create mode 100644 docs/transformation-documentation/CosdV8BreastMeasurementMcategoryIntegratedStage.svg create mode 100644 docs/transformation-documentation/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.json create mode 100644 docs/transformation-documentation/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.svg create mode 100644 docs/transformation-documentation/CosdV8BreastMeasurementNcategoryIntegratedStage.json create mode 100644 docs/transformation-documentation/CosdV8BreastMeasurementNcategoryIntegratedStage.svg diff --git a/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.json b/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.json new file mode 100644 index 00000000..4a3efc7e --- /dev/null +++ b/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.json @@ -0,0 +1,118 @@ +{ + "omopTable": "Measurement", + "origin": "COSD", + "omopColumns": [ + { + "name": "nhs_number", + "operation_description": "Value copied from `NhsNumber`", + "dataSource": [ + { + "name": "NhsNumber", + "description": "Patient NHS Number", + "origins": [ + { + "origin": "NHS NUMBER", + "url": "https://www.datadictionary.nhs.uk/data_elements/nhs_number.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentMCategory' as McategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n McategoryFinalPreTreatment\nfrom BR\nwhere McategoryFinalPreTreatment is not null\nand NHSNumber is not null;\n\t", + "lookup_table_markdown": null + }, + { + "name": "measurement_date", + "operation_description": "Converts text to dates.", + "dataSource": [ + { + "name": "MeasurementDate", + "description": "Measurement Date is the date on which TNM Stage Grouping (Final pre-treatment) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed.", + "origins": [ + { + "origin": "DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)", + "url": "https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html" + }, + { + "origin": "TNM STAGE GROUPING DATE (FINAL PRETREATMENT)", + "url": "https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__final_pretreatment_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentMCategory' as McategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n McategoryFinalPreTreatment\nfrom BR\nwhere McategoryFinalPreTreatment is not null\nand NHSNumber is not null;\n\t", + "lookup_table_markdown": null + }, + { + "name": "measurement_datetime", + "operation_description": "Converts text to dates.", + "dataSource": [ + { + "name": "MeasurementDate", + "description": "Measurement Date is the date on which TNM Stage Grouping (Final pre-treatment) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed.", + "origins": [ + { + "origin": "DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)", + "url": "https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html" + }, + { + "origin": "TNM STAGE GROUPING DATE (FINAL PRETREATMENT)", + "url": "https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__final_pretreatment_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentMCategory' as McategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n McategoryFinalPreTreatment\nfrom BR\nwhere McategoryFinalPreTreatment is not null\nand NHSNumber is not null;\n\t", + "lookup_table_markdown": null + }, + { + "name": "measurement_type_concept_id", + "operation_description": "Constant value set to `32828`. EHR episode record", + "dataSource": null, + "query": null, + "lookup_table_markdown": null + }, + { + "name": "measurement_source_concept_id", + "operation_description": "Constant value set to `2000500014`. MCategoryFinalPreTreatmentStage", + "dataSource": null, + "query": null, + "lookup_table_markdown": null + }, + { + "name": "measurement_concept_id", + "operation_description": "Lookup concepts.", + "dataSource": [ + { + "name": "McategoryFinalPreTreatment", + "description": "Is the code, using a TNM CODING EDITION, which classifies the absence or presence of distant metastases before treatment during a Cancer Care Spell.", + "origins": [ + { + "origin": "M CATEGORY (FINAL PRETREATMENT)", + "url": "https://www.datadictionary.nhs.uk/data_elements/m_category__final_pretreatment_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentMCategory' as McategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n McategoryFinalPreTreatment\nfrom BR\nwhere McategoryFinalPreTreatment is not null\nand NHSNumber is not null;\n\t", + "lookup_table_markdown": "\r\n\r\n|McategoryFinalPreTreatment|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|0|1635624|AJCC/UICC M0 Category|\r\n|1|1635142|AJCC/UICC M1 Category|\r\n|1a|1635100|AJCC/UICC M1a Category|\r\n|1b|1634463|AJCC/UICC M1b Category|\r\n|1c|1635519|AJCC/UICC M1c Category|\r\n|1d|1634064|AJCC/UICC M1d Category|\r\n|X |1633547|AJCC/UICC MX Category|\r\n\r\nNotes\r\n* [OMOP Laterality](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=tnm&boosts)\r\n" + }, + { + "name": "measurement_source_value", + "operation_description": "Value copied from `McategoryFinalPreTreatment`", + "dataSource": [ + { + "name": "McategoryFinalPreTreatment", + "description": "Is the code, using a TNM CODING EDITION, which classifies the absence or presence of distant metastases before treatment during a Cancer Care Spell.", + "origins": [ + { + "origin": "M CATEGORY (FINAL PRETREATMENT)", + "url": "https://www.datadictionary.nhs.uk/data_elements/m_category__final_pretreatment_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentMCategory' as McategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n McategoryFinalPreTreatment\nfrom BR\nwhere McategoryFinalPreTreatment is not null\nand NHSNumber is not null;\n\t", + "lookup_table_markdown": null + } + ] +} \ No newline at end of file diff --git a/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.svg b/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.svg new file mode 100644 index 00000000..02e6f4db --- /dev/null +++ b/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage.svg @@ -0,0 +1,89 @@ + + + + + NHS NUMBER + + + + + + Copy value + + + + nhs_number + + + + DATE OF PRIMARY + CANCER DIAGNOSIS (CLINICALLY + AGREED) + + + + TNM STAGE GROUPING + DATE (FINAL PRETREATMENT) + + + + + + Converts text to dates. + + + + measurement_date + + + + DATE OF PRIMARY + CANCER DIAGNOSIS (CLINICALLY + AGREED) + + + + TNM STAGE GROUPING + DATE (FINAL PRETREATMENT) + + + + + + Converts text to dates. + + + + measurement_datetime + + + + M CATEGORY (FINAL + PRETREATMENT) + + + + + + Lookup concepts. + + + + measurement_concept_id + + + + M CATEGORY (FINAL + PRETREATMENT) + + + + + + Copy value + + + + measurement_source_value + + \ No newline at end of file diff --git a/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryIntegratedStage.json b/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryIntegratedStage.json new file mode 100644 index 00000000..21258e4c --- /dev/null +++ b/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryIntegratedStage.json @@ -0,0 +1,118 @@ +{ + "omopTable": "Measurement", + "origin": "COSD", + "omopColumns": [ + { + "name": "nhs_number", + "operation_description": "Value copied from `NhsNumber`", + "dataSource": [ + { + "name": "NhsNumber", + "description": "Patient NHS Number", + "origins": [ + { + "origin": "NHS NUMBER", + "url": "https://www.datadictionary.nhs.uk/data_elements/nhs_number.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NhsNumber is not null;\n\t", + "lookup_table_markdown": null + }, + { + "name": "measurement_date", + "operation_description": "Converts text to dates.", + "dataSource": [ + { + "name": "MeasurementDate", + "description": "Measurement Date is the date on which TNM Stage Grouping (Integrated) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed.", + "origins": [ + { + "origin": "DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)", + "url": "https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html" + }, + { + "origin": "TNM STAGE GROUPING DATE (INTEGRATED)", + "url": "https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__integrated_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NhsNumber is not null;\n\t", + "lookup_table_markdown": null + }, + { + "name": "measurement_datetime", + "operation_description": "Converts text to dates.", + "dataSource": [ + { + "name": "MeasurementDate", + "description": "Measurement Date is the date on which TNM Stage Grouping (Integrated) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed.", + "origins": [ + { + "origin": "DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)", + "url": "https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html" + }, + { + "origin": "TNM STAGE GROUPING DATE (INTEGRATED)", + "url": "https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__integrated_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NhsNumber is not null;\n\t", + "lookup_table_markdown": null + }, + { + "name": "measurement_type_concept_id", + "operation_description": "Constant value set to `32828`. EHR episode record", + "dataSource": null, + "query": null, + "lookup_table_markdown": null + }, + { + "name": "measurement_source_concept_id", + "operation_description": "Constant value set to `2000500018`. MCategoryIntegratedStage", + "dataSource": null, + "query": null, + "lookup_table_markdown": null + }, + { + "name": "measurement_concept_id", + "operation_description": "Lookup concepts.", + "dataSource": [ + { + "name": "MCategoryIntegratedStage", + "description": "Is the code, using a TNM CODING EDITION, which classifies the absence or presence of distant metastases after all information from treatment is available during a Cancer Care Spell.", + "origins": [ + { + "origin": "M CATEGORY (INTEGRATED STAGE)", + "url": "https://www.datadictionary.nhs.uk/data_elements/m_category__integrated_stage_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NhsNumber is not null;\n\t", + "lookup_table_markdown": "\r\n\r\n|MCategoryIntegratedStage|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|0|1635624|AJCC/UICC M0 Category|\r\n|1|1635142|AJCC/UICC M1 Category|\r\n|1a|1635100|AJCC/UICC M1a Category|\r\n|1b|1634463|AJCC/UICC M1b Category|\r\n|1c|1635519|AJCC/UICC M1c Category|\r\n|1d|1634064|AJCC/UICC M1d Category|\r\n|X |1633547|AJCC/UICC MX Category|\r\n\r\nNotes\r\n* [OMOP Laterality](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=tnm&boosts)\r\n" + }, + { + "name": "measurement_source_value", + "operation_description": "Value copied from `MCategoryIntegratedStage`", + "dataSource": [ + { + "name": "MCategoryIntegratedStage", + "description": "Is the code, using a TNM CODING EDITION, which classifies the absence or presence of distant metastases after all information from treatment is available during a Cancer Care Spell.", + "origins": [ + { + "origin": "M CATEGORY (INTEGRATED STAGE)", + "url": "https://www.datadictionary.nhs.uk/data_elements/m_category__integrated_stage_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NhsNumber is not null;\n\t", + "lookup_table_markdown": null + } + ] +} \ No newline at end of file diff --git a/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryIntegratedStage.svg b/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryIntegratedStage.svg new file mode 100644 index 00000000..f1a0413b --- /dev/null +++ b/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryIntegratedStage.svg @@ -0,0 +1,89 @@ + + + + + NHS NUMBER + + + + + + Copy value + + + + nhs_number + + + + DATE OF PRIMARY + CANCER DIAGNOSIS (CLINICALLY + AGREED) + + + + TNM STAGE GROUPING + DATE (INTEGRATED) + + + + + + Converts text to dates. + + + + measurement_date + + + + DATE OF PRIMARY + CANCER DIAGNOSIS (CLINICALLY + AGREED) + + + + TNM STAGE GROUPING + DATE (INTEGRATED) + + + + + + Converts text to dates. + + + + measurement_datetime + + + + M CATEGORY (INTEGRATED + STAGE) + + + + + + Lookup concepts. + + + + measurement_concept_id + + + + M CATEGORY (INTEGRATED + STAGE) + + + + + + Copy value + + + + measurement_source_value + + \ No newline at end of file diff --git a/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.json b/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.json new file mode 100644 index 00000000..d959f434 --- /dev/null +++ b/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.json @@ -0,0 +1,118 @@ +{ + "omopTable": "Measurement", + "origin": "COSD", + "omopColumns": [ + { + "name": "nhs_number", + "operation_description": "Value copied from `NhsNumber`", + "dataSource": [ + { + "name": "NhsNumber", + "description": "Patient NHS Number", + "origins": [ + { + "origin": "NHS NUMBER", + "url": "https://www.datadictionary.nhs.uk/data_elements/nhs_number.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NhsNumber is not null;\n\t", + "lookup_table_markdown": null + }, + { + "name": "measurement_date", + "operation_description": "Converts text to dates.", + "dataSource": [ + { + "name": "MeasurementDate", + "description": "Measurement Date is the date on which TNM Stage Grouping (Final pre-treatment) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed.", + "origins": [ + { + "origin": "DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)", + "url": "https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html" + }, + { + "origin": "TNM STAGE GROUPING DATE (FINAL PRETREATMENT)", + "url": "https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__final_pretreatment_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NhsNumber is not null;\n\t", + "lookup_table_markdown": null + }, + { + "name": "measurement_datetime", + "operation_description": "Converts text to dates.", + "dataSource": [ + { + "name": "MeasurementDate", + "description": "Measurement Date is the date on which TNM Stage Grouping (Final pre-treatment) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed.", + "origins": [ + { + "origin": "DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)", + "url": "https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html" + }, + { + "origin": "TNM STAGE GROUPING DATE (FINAL PRETREATMENT)", + "url": "https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__final_pretreatment_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NhsNumber is not null;\n\t", + "lookup_table_markdown": null + }, + { + "name": "measurement_type_concept_id", + "operation_description": "Constant value set to `32828`. EHR episode record", + "dataSource": null, + "query": null, + "lookup_table_markdown": null + }, + { + "name": "measurement_source_concept_id", + "operation_description": "Constant value set to `2000500015`. NCategoryFinalPreTreatmentStage", + "dataSource": null, + "query": null, + "lookup_table_markdown": null + }, + { + "name": "measurement_concept_id", + "operation_description": "Lookup NCategory concepts.", + "dataSource": [ + { + "name": "NcategoryFinalPreTreatment", + "description": "Is the code, using a TNM CODING EDITION, which classifies the presence or absence of regional lymph node metastases before treatment during a Cancer Care Spell.", + "origins": [ + { + "origin": "N CATEGORY (FINAL PRETREATMENT)", + "url": "https://www.datadictionary.nhs.uk/data_elements/n_category__final_pretreatment_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NhsNumber is not null;\n\t", + "lookup_table_markdown": "\r\n\r\n|NcategoryFinalPreTreatment|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|0|1633440|AJCC/UICC N0 Category|\r\n|0a|1633621|AJCC/UICC N0a Category|\r\n|0b|1635244|AJCC/UICC N0b Category|\r\n|1|1634434|AJCC/UICC N1 Category|\r\n|1a|1633735|AJCC/UICC N1a Category|\r\n|1b|1635130|AJCC/UICC N1b Category|\r\n|1c|1634620|AJCC/UICC N1c Category|\r\n|2|1634119|AJCC/UICC N2 Category|\r\n|2a|1635644|AJCC/UICC N2a Category|\r\n|2b|1634134|AJCC/UICC N2b Category|\r\n|2c|1634080|AJCC/UICC N2c Category|\r\n|3|1635320|AJCC/UICC N3 Category|\r\n|3a|1635590|AJCC/UICC N3a Category|\r\n|3b|1633422|AJCC/UICC N3b Category|\r\n|3c|1634735|AJCC/UICC N3c Category|\r\n|4|1635445|AJCC/UICC N4 Category|\r\n|X|1633885|AJCC/UICC NX Category|\r\n\r\nNotes\r\n* [OMOP Laterality](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=tnm&boosts)\r\n" + }, + { + "name": "measurement_source_value", + "operation_description": "Value copied from `NcategoryFinalPreTreatment`", + "dataSource": [ + { + "name": "NcategoryFinalPreTreatment", + "description": "Is the code, using a TNM CODING EDITION, which classifies the presence or absence of regional lymph node metastases before treatment during a Cancer Care Spell.", + "origins": [ + { + "origin": "N CATEGORY (FINAL PRETREATMENT)", + "url": "https://www.datadictionary.nhs.uk/data_elements/n_category__final_pretreatment_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NhsNumber is not null;\n\t", + "lookup_table_markdown": null + } + ] +} \ No newline at end of file diff --git a/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.svg b/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.svg new file mode 100644 index 00000000..d4ba3108 --- /dev/null +++ b/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.svg @@ -0,0 +1,89 @@ + + + + + NHS NUMBER + + + + + + Copy value + + + + nhs_number + + + + DATE OF PRIMARY + CANCER DIAGNOSIS (CLINICALLY + AGREED) + + + + TNM STAGE GROUPING + DATE (FINAL PRETREATMENT) + + + + + + Converts text to dates. + + + + measurement_date + + + + DATE OF PRIMARY + CANCER DIAGNOSIS (CLINICALLY + AGREED) + + + + TNM STAGE GROUPING + DATE (FINAL PRETREATMENT) + + + + + + Converts text to dates. + + + + measurement_datetime + + + + N CATEGORY (FINAL + PRETREATMENT) + + + + + + Lookup NCategory concepts. + + + + measurement_concept_id + + + + N CATEGORY (FINAL + PRETREATMENT) + + + + + + Copy value + + + + measurement_source_value + + \ No newline at end of file diff --git a/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryIntegratedStage.json b/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryIntegratedStage.json new file mode 100644 index 00000000..8f458026 --- /dev/null +++ b/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryIntegratedStage.json @@ -0,0 +1,118 @@ +{ + "omopTable": "Measurement", + "origin": "COSD", + "omopColumns": [ + { + "name": "nhs_number", + "operation_description": "Value copied from `NhsNumber`", + "dataSource": [ + { + "name": "NhsNumber", + "description": "Patient NHS Number", + "origins": [ + { + "origin": "NHS NUMBER", + "url": "https://www.datadictionary.nhs.uk/data_elements/nhs_number.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", + "lookup_table_markdown": null + }, + { + "name": "measurement_date", + "operation_description": "Converts text to dates.", + "dataSource": [ + { + "name": "MeasurementDate", + "description": "Measurement Date is the date on which TNM Stage Grouping (Integrated) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed.", + "origins": [ + { + "origin": "DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)", + "url": "https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html" + }, + { + "origin": "TNM STAGE GROUPING DATE (INTEGRATED)", + "url": "https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__integrated_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", + "lookup_table_markdown": null + }, + { + "name": "measurement_datetime", + "operation_description": "Converts text to dates.", + "dataSource": [ + { + "name": "MeasurementDate", + "description": "Measurement Date is the date on which TNM Stage Grouping (Integrated) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed.", + "origins": [ + { + "origin": "DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)", + "url": "https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html" + }, + { + "origin": "TNM STAGE GROUPING DATE (INTEGRATED)", + "url": "https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__integrated_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", + "lookup_table_markdown": null + }, + { + "name": "measurement_type_concept_id", + "operation_description": "Constant value set to `32828`. EHR episode record", + "dataSource": null, + "query": null, + "lookup_table_markdown": null + }, + { + "name": "measurement_source_concept_id", + "operation_description": "Constant value set to `2000500019`. NCategoryIntegratedStage", + "dataSource": null, + "query": null, + "lookup_table_markdown": null + }, + { + "name": "measurement_concept_id", + "operation_description": "Lookup NCategory concepts.", + "dataSource": [ + { + "name": "NCategoryIntegratedStage", + "description": "Is the code, using a TNM CODING EDITION, which classifies the presence or absence of regional lymph node metastases after all information from treatment is available during a Cancer Care Spell.", + "origins": [ + { + "origin": "N CATEGORY (INTEGRATED STAGE)", + "url": "https://www.datadictionary.nhs.uk/data_elements/n_category__integrated_stage_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", + "lookup_table_markdown": "\r\n\r\n|NCategoryIntegratedStage|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|0|1633440|AJCC/UICC N0 Category|\r\n|0a|1633621|AJCC/UICC N0a Category|\r\n|0b|1635244|AJCC/UICC N0b Category|\r\n|1|1634434|AJCC/UICC N1 Category|\r\n|1a|1633735|AJCC/UICC N1a Category|\r\n|1b|1635130|AJCC/UICC N1b Category|\r\n|1c|1634620|AJCC/UICC N1c Category|\r\n|2|1634119|AJCC/UICC N2 Category|\r\n|2a|1635644|AJCC/UICC N2a Category|\r\n|2b|1634134|AJCC/UICC N2b Category|\r\n|2c|1634080|AJCC/UICC N2c Category|\r\n|3|1635320|AJCC/UICC N3 Category|\r\n|3a|1635590|AJCC/UICC N3a Category|\r\n|3b|1633422|AJCC/UICC N3b Category|\r\n|3c|1634735|AJCC/UICC N3c Category|\r\n|4|1635445|AJCC/UICC N4 Category|\r\n|X|1633885|AJCC/UICC NX Category|\r\n\r\nNotes\r\n* [OMOP Laterality](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=tnm&boosts)\r\n" + }, + { + "name": "measurement_source_value", + "operation_description": "Value copied from `NCategoryIntegratedStage`", + "dataSource": [ + { + "name": "NCategoryIntegratedStage", + "description": "Is the code, using a TNM CODING EDITION, which classifies the presence or absence of regional lymph node metastases after all information from treatment is available during a Cancer Care Spell.", + "origins": [ + { + "origin": "N CATEGORY (INTEGRATED STAGE)", + "url": "https://www.datadictionary.nhs.uk/data_elements/n_category__integrated_stage_.html" + } + ] + } + ], + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", + "lookup_table_markdown": null + } + ] +} \ No newline at end of file diff --git a/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryIntegratedStage.svg b/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryIntegratedStage.svg new file mode 100644 index 00000000..e1210456 --- /dev/null +++ b/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryIntegratedStage.svg @@ -0,0 +1,89 @@ + + + + + NHS NUMBER + + + + + + Copy value + + + + nhs_number + + + + DATE OF PRIMARY + CANCER DIAGNOSIS (CLINICALLY + AGREED) + + + + TNM STAGE GROUPING + DATE (INTEGRATED) + + + + + + Converts text to dates. + + + + measurement_date + + + + DATE OF PRIMARY + CANCER DIAGNOSIS (CLINICALLY + AGREED) + + + + TNM STAGE GROUPING + DATE (INTEGRATED) + + + + + + Converts text to dates. + + + + measurement_datetime + + + + N CATEGORY (INTEGRATED + STAGE) + + + + + + Lookup NCategory concepts. + + + + measurement_concept_id + + + + N CATEGORY (INTEGRATED + STAGE) + + + + + + Copy value + + + + measurement_source_value + + \ No newline at end of file diff --git a/docs/transformation-documentation/CosdV8LungMeasurementNonPrimaryPathwayMetastasis.json b/docs/transformation-documentation/CosdV8LungMeasurementNonPrimaryPathwayMetastasis.json index bf32700e..05568a64 100644 --- a/docs/transformation-documentation/CosdV8LungMeasurementNonPrimaryPathwayMetastasis.json +++ b/docs/transformation-documentation/CosdV8LungMeasurementNonPrimaryPathwayMetastasis.json @@ -79,7 +79,7 @@ } ], "query": "\nwith lung as (\n select distinct\n Record ->> '$.Lung.LungCore.LungCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Lung.LungCore.LungCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n unnest(\n [\n [ Record ->> '$.Lung.LungCore.LungCoreNonPrimaryCancerPathwayRoute.MetastaticSite.@code' ],\n Record ->> '$.Lung.LungCore.LungCoreNonPrimaryCancerPathwayRoute.MetastaticSite[*].@code'\n ],\n recursive := true\n ) as MetastaticSite\n from omop_staging.cosd_staging_81\n where type = 'LU'\n)\nselect distinct\n NhsNumber,\n DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n MetastaticSite\nfrom lung\nwhere MetastaticSite is not null\n and MetastaticSite != '97'\n and NhsNumber is not null;\n\n\t", - "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" + "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|01|36769301|Metastasis to bone|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" }, { "name": "measurement_source_value", diff --git a/docs/transformation-documentation/CosdV8LungMeasurementPrimaryPathwayMetastasis.json b/docs/transformation-documentation/CosdV8LungMeasurementPrimaryPathwayMetastasis.json index 609659e8..3a4e2f81 100644 --- a/docs/transformation-documentation/CosdV8LungMeasurementPrimaryPathwayMetastasis.json +++ b/docs/transformation-documentation/CosdV8LungMeasurementPrimaryPathwayMetastasis.json @@ -79,7 +79,7 @@ } ], "query": "\nwith lung as (\nselect \n Record ->> '$.Lung.LungCore.LungCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Lung.LungCore.LungCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n unnest(\n [\n [\n Record ->> '$.Lung.LungCore.LungCoreDiagnosis.MetastaticSite.@code'\n ], \n Record ->> '$.Lung.LungCore.LungCoreDiagnosis.MetastaticSite[*].@code'\n ], recursive := true\n ) as MetastaticSite\nfrom omop_staging.cosd_staging_81\nwhere Type = 'LU'\n)\nselect distinct\n NhsNumber,\n ClinicalDateCancerDiagnosis,\n MetastaticSite\nfrom lung\nwhere MetastaticSite is not null\n and MetastaticSite != 97\n and NhsNumber is not null;\n\n\t", - "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" + "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|01|36769301|Metastasis to bone|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" }, { "name": "measurement_source_value", diff --git a/docs/transformation-documentation/CosdV8LungSurgicalAccessType.json b/docs/transformation-documentation/CosdV8LungSurgicalAccessType.json index 4b77a456..f85296da 100644 --- a/docs/transformation-documentation/CosdV8LungSurgicalAccessType.json +++ b/docs/transformation-documentation/CosdV8LungSurgicalAccessType.json @@ -134,7 +134,7 @@ } ], "query": "\nwith LU as (\n select \n Record ->> '$.Lung.LungCore.LungCoreReferralAndFirstStageOfPatientPathway.DateFirstSeen' as DateFirstSeen,\n Record ->> '$.Lung.LungCore.LungCoreReferralAndFirstStageOfPatientPathway.SpecialistDateFirstSeen' as SpecialistDateFirstSeen,\n Record ->> '$.Lung.LungCore.LungCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Lung.LungCore.LungCoreStaging.IntegratedStageTNMStageGroupingDate' as IntegratedStageTNMStageGroupingDate,\n Record ->> '$.Lung.LungCore.LungCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as FinalPreTreatmentTNMStageGroupingDate,\n unnest ([[Record ->> '$.Lung.LungCore.LungCoreTreatment.CancerTreatmentStartDate'], Record ->> '$.Lung.LungCore.LungCoreTreatment[*].CancerTreatmentStartDate'], recursive := true) as CancerTreatmentStartDate,\n Record ->> '$.Lung.LungCore.LungCoreTreatment.LungCoreSurgeryAndOtherProcedures.ProcedureDate' as ProcedureDate,\n Record ->> '$.Lung.LungCore.LungCoreTreatment.LungCoreSurgeryAndOtherProcedures.SurgicalAccessType.@code' as SurgicalAccessType,\n Record ->> '$.Lung.LungCore.LungCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber\n from omop_staging.cosd_staging_81\n where Type = 'LU'\n)\nselect\n distinct\n SurgicalAccessType,\n NhsNumber,\n least(\n cast (DateFirstSeen as date),\n cast (SpecialistDateFirstSeen as date),\n cast (ClinicalDateCancerDiagnosis as date),\n cast (IntegratedStageTNMStageGroupingDate as date),\n cast (FinalPreTreatmentTNMStageGroupingDate as date),\n cast (CancerTreatmentStartDate as date),\n cast (ProcedureDate as date)\n ) as Date\nfrom LU o\nwhere o.SurgicalAccessType is not null\n and not (\n DateFirstSeen is null and\n SpecialistDateFirstSeen is null and\n ClinicalDateCancerDiagnosis is null and\n IntegratedStageTNMStageGroupingDate is null and\n FinalPreTreatmentTNMStageGroupingDate is null and\n CancerTreatmentStartDate is null and\n ProcedureDate is null\n )\n ", - "lookup_table_markdown": "\r\n\r\n|SurgicalAccessType|qualifier_concept_id|notes|\r\n|------|-----|-----|\r\n|1|4044378|Open approach|\r\n|2|4044378|Laparoscopic/Thoracoscopic with planned conversion to open surgery|\r\n|3|4044378|Laparoscopic/Thoracoscopic with unplanned conversion to open surgery|\r\n|4|44808608|Laparoscopic/Thoracoscopic completed|\r\n|5|44790026|Robotic surgery|\r\n\r\nNotes\r\n* [OMOP Open approach](https://athena.ohdsi.org/search-terms/terms/4044378)\r\n* [OMOP Laparoscopic/Thoracoscopic](https://athena.ohdsi.org/search-terms/terms/44808608)\r\n* [OMOP Robotic surgery](https://athena.ohdsi.org/search-terms/terms/44790026)\r\n* [SURGICAL ACCESS TYPE](https://www.datadictionary.nhs.uk/data_elements/surgical_access_type.html)\r\n" + "lookup_table_markdown": "\r\n\r\n|SurgicalAccessType|qualifier_concept_id|notes|\r\n|------|-----|-----|\r\n|1|4044378|Open approach|\r\n|2|4044378|Laparoscopic/Thoracoscopic with planned conversion to open surgery|\r\n|3|4044378|Laparoscopic/Thoracoscopic with unplanned conversion to open surgery|\r\n|4|44808608|Laparoscopic/Thoracoscopic completed|\r\n|5|44790026|Robotic surgery|\r\n|Z|0|Other|\r\n\r\nNotes\r\n* [OMOP Open approach](https://athena.ohdsi.org/search-terms/terms/4044378)\r\n* [OMOP Laparoscopic/Thoracoscopic](https://athena.ohdsi.org/search-terms/terms/44808608)\r\n* [OMOP Robotic surgery](https://athena.ohdsi.org/search-terms/terms/44790026)\r\n* [SURGICAL ACCESS TYPE](https://www.datadictionary.nhs.uk/data_elements/surgical_access_type.html)\r\n" }, { "name": "qualifier_source_value", diff --git a/docs/transformation-documentation/CosdV8MeasurementNonPrimaryPathwayMetastasis.json b/docs/transformation-documentation/CosdV8MeasurementNonPrimaryPathwayMetastasis.json index 6b86976f..5789273d 100644 --- a/docs/transformation-documentation/CosdV8MeasurementNonPrimaryPathwayMetastasis.json +++ b/docs/transformation-documentation/CosdV8MeasurementNonPrimaryPathwayMetastasis.json @@ -79,7 +79,7 @@ } ], "query": "\nwith co as (\n select distinct\n Record ->> '$.Colorectal.ColorectalCore.ColorectalCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Colorectal.ColorectalCore.ColorectalCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n unnest(\n [\n [ Record ->> '$.Colorectal.ColorectalCore.ColorectalCoreNonPrimaryCancerPathwayRoute.MetastaticSite.@code' ],\n Record ->> '$.Colorectal.ColorectalCore.ColorectalCoreNonPrimaryCancerPathwayRoute.MetastaticSite[*].@code'\n ],\n recursive := true\n ) as MetastaticSite\n from omop_staging.cosd_staging_81\n where type = 'CO'\n)\nselect distinct\n NhsNumber,\n DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n MetastaticSite\nfrom co\nwhere MetastaticSite is not null\n and MetastaticSite != '97';\n\t", - "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" + "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|01|36769301|Metastasis to bone|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" }, { "name": "measurement_source_value", diff --git a/docs/transformation-documentation/CosdV8MeasurementPrimaryPathwayMetastasis.json b/docs/transformation-documentation/CosdV8MeasurementPrimaryPathwayMetastasis.json index b0e4fdc2..88560158 100644 --- a/docs/transformation-documentation/CosdV8MeasurementPrimaryPathwayMetastasis.json +++ b/docs/transformation-documentation/CosdV8MeasurementPrimaryPathwayMetastasis.json @@ -79,7 +79,7 @@ } ], "query": "\nwith co as (\nselect \n Record ->> '$.Colorectal.ColorectalCore.ColorectalCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Colorectal.ColorectalCore.ColorectalCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n unnest(\n [\n [\n Record ->> '$.Colorectal.ColorectalCore.ColorectalCoreDiagnosis.MetastaticSite.@code'\n ], \n Record ->> '$.Colorectal.ColorectalCore.ColorectalCoreDiagnosis.MetastaticSite[*].@code'\n ], recursive := true\n ) as MetastaticSite\nfrom omop_staging.cosd_staging_81\nwhere Type = 'CO'\n)\nselect distinct\n NhsNumber,\n ClinicalDateCancerDiagnosis,\n MetastaticSite\nfrom co\nwhere MetastaticSite is not null\n and MetastaticSite != 97;\n\t", - "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" + "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|01|36769301|Metastasis to bone|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" }, { "name": "measurement_source_value", diff --git a/docs/transformation-documentation/CosdV9LungMeasurementNonPrimaryPathwayProgressionMetastasis.json b/docs/transformation-documentation/CosdV9LungMeasurementNonPrimaryPathwayProgressionMetastasis.json index 60f2a013..96c14f1c 100644 --- a/docs/transformation-documentation/CosdV9LungMeasurementNonPrimaryPathwayProgressionMetastasis.json +++ b/docs/transformation-documentation/CosdV9LungMeasurementNonPrimaryPathwayProgressionMetastasis.json @@ -86,7 +86,7 @@ } ], "query": "\nwith lung as (\n select distinct\n Record ->> '$.LinkagePatientId.NhsNumber.@extension' as NHSNumber,\n Record ->> '$.NonPrimaryPathway.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n unnest ([[Record ->> '$.NonPrimaryPathway.Progression.MetastaticTypeAndSiteProgression.MetastaticSite.@code'], Record ->> '$.NonPrimaryPathway.Progression.MetastaticTypeAndSiteProgression[*].MetastaticSite.@code'], recursive := true) as MetastaticSite\n from omop_staging.cosd_staging_901\n where type = 'LU'\n)\nselect\n distinct\n NHSNumber,\n DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n MetastaticSite\nfrom lung\nwhere MetastaticSite is not null\n and MetastaticSite != '97'\n\t", - "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" + "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|01|36769301|Metastasis to bone|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" }, { "name": "measurement_source_value", diff --git a/docs/transformation-documentation/CosdV9LungMeasurementNonPrimaryPathwayRecurrenceMetastasis.json b/docs/transformation-documentation/CosdV9LungMeasurementNonPrimaryPathwayRecurrenceMetastasis.json index 3cf83405..449a5f9d 100644 --- a/docs/transformation-documentation/CosdV9LungMeasurementNonPrimaryPathwayRecurrenceMetastasis.json +++ b/docs/transformation-documentation/CosdV9LungMeasurementNonPrimaryPathwayRecurrenceMetastasis.json @@ -86,7 +86,7 @@ } ], "query": "\nwith lung as (\n select distinct\n Record ->> '$.LinkagePatientId.NhsNumber.@extension' as NHSNumber,\n Record ->> '$.NonPrimaryPathway.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n unnest ([[Record ->> '$.NonPrimaryPathway.Recurrence.MetastaticTypeAndSiteRecurrence.MetastaticSite.@code'], Record ->> '$.NonPrimaryPathway.Recurrence.MetastaticTypeAndSiteRecurrence[*].MetastaticSite.@code'], recursive := true) as MetastaticSite\n from omop_staging.cosd_staging_901\n where type = 'LU'\n)\nselect distinct\n NHSNumber,\n DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n MetastaticSite\nfrom lung\nwhere MetastaticSite is not null\n and MetastaticSite != '97'\n\t", - "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" + "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|01|36769301|Metastasis to bone|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" }, { "name": "measurement_source_value", diff --git a/docs/transformation-documentation/CosdV9LungMeasurementPrimaryPathwayMetastasis.json b/docs/transformation-documentation/CosdV9LungMeasurementPrimaryPathwayMetastasis.json index 62ad8146..8976ffd3 100644 --- a/docs/transformation-documentation/CosdV9LungMeasurementPrimaryPathwayMetastasis.json +++ b/docs/transformation-documentation/CosdV9LungMeasurementPrimaryPathwayMetastasis.json @@ -86,7 +86,7 @@ } ], "query": "\nwith lung as (\n select distinct\n Record ->> '$.LinkagePatientId.NhsNumber.@extension' as NHSNumber,\n Record ->> '$.PrimaryPathway.LinkageDiagnosticDetails.DateOfPrimaryDiagnosisClinicallyAgreed' as DateOfPrimaryDiagnosisClinicallyAgreed,\n unnest ([[Record ->> '$.PrimaryPathway.Diagnosis.MetastaticTypeAndSiteDiagnosis.MetastaticType.@code'], Record ->> '$.PrimaryPathway.Diagnosis.MetastaticTypeAndSiteDiagnosis[*].MetastaticType.@code'], recursive := true) as MetastaticSite\n from omop_staging.cosd_staging_901\n where type = 'LU'\n)\nselect distinct\n NHSNumber,\n DateOfPrimaryDiagnosisClinicallyAgreed,\n MetastaticSite\nfrom lung\nwhere MetastaticSite is not null\n and MetastaticSite != '97'\n\t", - "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" + "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|01|36769301|Metastasis to bone|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" }, { "name": "measurement_source_value", diff --git a/docs/transformation-documentation/CosdV9LungSurgicalAccessType.json b/docs/transformation-documentation/CosdV9LungSurgicalAccessType.json index 99bc48a8..d9a6be8d 100644 --- a/docs/transformation-documentation/CosdV9LungSurgicalAccessType.json +++ b/docs/transformation-documentation/CosdV9LungSurgicalAccessType.json @@ -134,7 +134,7 @@ } ], "query": "\nwith LU as (\n select\n Record ->> '$.PrimaryPathway.ReferralAndFirstStageOfPatientPathway.DateFirstSeen' as DateFirstSeen,\n Record ->> '$.PrimaryPathway.ReferralAndFirstStageOfPatientPathway.DateFirstSeenCancerSpecialist' as DateFirstSeenCancerSpecialist,\n Record ->> '$.PrimaryPathway.LinkageDiagnosticDetails.DateOfPrimaryDiagnosisClinicallyAgreed' as DateOfPrimaryDiagnosisClinicallyAgreed,\n Record ->> '$.PrimaryPathway.Staging.StageDateFinalPretreatmentStage' as StageDateFinalPretreatmentStage,\n Record ->> '$.PrimaryPathway.Staging.StageDateIntegratedStage' as StageDateIntegratedStage,\n Record ->> '$.Treatment.TreatmentStartDateCancer' as TreatmentStartDateCancer,\n Record ->> '$.Treatment.Surgery.ProcedureDate' as ProcedureDate,\n Record ->> '$.Treatment.Surgery.SurgicalAccessType.@code' as SurgicalAccessType,\n Record ->> '$.LinkagePatientId.NhsNumber.@extension' as NhsNumber\n from omop_staging.cosd_staging_901\n where type = 'LU'\n)\nselect\n distinct\n SurgicalAccessType,\n NhsNumber,\n least(\n cast(DateFirstSeen as date),\n cast(DateFirstSeenCancerSpecialist as date),\n cast(DateOfPrimaryDiagnosisClinicallyAgreed as date),\n cast(StageDateFinalPretreatmentStage as date),\n cast(StageDateIntegratedStage as date),\n cast(TreatmentStartDateCancer as date),\n cast(ProcedureDate as date)\n ) as Date\nfrom LU o\nwhere o.SurgicalAccessType is not null\n and not (\n DateFirstSeen is null and\n DateFirstSeenCancerSpecialist is null and\n DateOfPrimaryDiagnosisClinicallyAgreed is null and\n StageDateFinalPretreatmentStage is null and\n StageDateIntegratedStage is null and\n TreatmentStartDateCancer is null and\n ProcedureDate is null\n )\n ", - "lookup_table_markdown": "\r\n\r\n|SurgicalAccessType|qualifier_concept_id|notes|\r\n|------|-----|-----|\r\n|1|4044378|Open approach|\r\n|2|4044378|Laparoscopic/Thoracoscopic with planned conversion to open surgery|\r\n|3|4044378|Laparoscopic/Thoracoscopic with unplanned conversion to open surgery|\r\n|4|44808608|Laparoscopic/Thoracoscopic completed|\r\n|5|44790026|Robotic surgery|\r\n\r\nNotes\r\n* [OMOP Open approach](https://athena.ohdsi.org/search-terms/terms/4044378)\r\n* [OMOP Laparoscopic/Thoracoscopic](https://athena.ohdsi.org/search-terms/terms/44808608)\r\n* [OMOP Robotic surgery](https://athena.ohdsi.org/search-terms/terms/44790026)\r\n* [SURGICAL ACCESS TYPE](https://www.datadictionary.nhs.uk/data_elements/surgical_access_type.html)\r\n" + "lookup_table_markdown": "\r\n\r\n|SurgicalAccessType|qualifier_concept_id|notes|\r\n|------|-----|-----|\r\n|1|4044378|Open approach|\r\n|2|4044378|Laparoscopic/Thoracoscopic with planned conversion to open surgery|\r\n|3|4044378|Laparoscopic/Thoracoscopic with unplanned conversion to open surgery|\r\n|4|44808608|Laparoscopic/Thoracoscopic completed|\r\n|5|44790026|Robotic surgery|\r\n|Z|0|Other|\r\n\r\nNotes\r\n* [OMOP Open approach](https://athena.ohdsi.org/search-terms/terms/4044378)\r\n* [OMOP Laparoscopic/Thoracoscopic](https://athena.ohdsi.org/search-terms/terms/44808608)\r\n* [OMOP Robotic surgery](https://athena.ohdsi.org/search-terms/terms/44790026)\r\n* [SURGICAL ACCESS TYPE](https://www.datadictionary.nhs.uk/data_elements/surgical_access_type.html)\r\n" }, { "name": "qualifier_source_value", diff --git a/docs/transformation-documentation/CosdV9MeasurementNonPrimaryPathwayProgressionMetastasis.json b/docs/transformation-documentation/CosdV9MeasurementNonPrimaryPathwayProgressionMetastasis.json index 1c1fc408..16bd257f 100644 --- a/docs/transformation-documentation/CosdV9MeasurementNonPrimaryPathwayProgressionMetastasis.json +++ b/docs/transformation-documentation/CosdV9MeasurementNonPrimaryPathwayProgressionMetastasis.json @@ -86,7 +86,7 @@ } ], "query": "\nwith CO as (\n select distinct\n Record ->> '$.LinkagePatientId.NhsNumber.@extension' as NhsNumber,\n Record ->> '$.NonPrimaryPathway.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n unnest(\n [\n [ Record ->> '$.NonPrimaryPathway.Progression.MetastaticTypeAndSiteProgression.MetastaticSite.@code' ],\n Record ->> '$.NonPrimaryPathway.Progression.MetastaticTypeAndSiteProgression[*].MetastaticSite.@code'\n ],\n recursive := true\n ) as MetastaticSite\n from omop_staging.cosd_staging_901\n where type = 'CO'\n)\nselect\n distinct\n NhsNumber,\n DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n MetastaticSite\nfrom CO\nwhere MetastaticSite is not null\n and MetastaticSite != '97';\n\t", - "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" + "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|01|36769301|Metastasis to bone|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" }, { "name": "measurement_source_value", diff --git a/docs/transformation-documentation/CosdV9MeasurementNonPrimaryPathwayRecurrenceMetastasis.json b/docs/transformation-documentation/CosdV9MeasurementNonPrimaryPathwayRecurrenceMetastasis.json index 8e31b33e..9a0e46bb 100644 --- a/docs/transformation-documentation/CosdV9MeasurementNonPrimaryPathwayRecurrenceMetastasis.json +++ b/docs/transformation-documentation/CosdV9MeasurementNonPrimaryPathwayRecurrenceMetastasis.json @@ -86,7 +86,7 @@ } ], "query": "\nwith CO as (\n select distinct\n Record ->> '$.LinkagePatientId.NhsNumber.@extension' as NhsNumber,\n Record ->> '$.NonPrimaryPathway.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n unnest(\n [\n [ Record ->> '$.NonPrimaryPathway.Recurrence.MetastaticTypeAndSiteRecurrence.MetastaticSite.@code' ],\n Record ->> '$.NonPrimaryPathway.Recurrence.MetastaticTypeAndSiteRecurrence[*].MetastaticSite.@code'\n ],\n recursive := true\n ) as MetastaticSite\n from omop_staging.cosd_staging_901\n where type = 'CO'\n)\nselect distinct\n NhsNumber,\n DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n MetastaticSite\nfrom CO\nwhere MetastaticSite is not null\n and MetastaticSite != '97';\n\t", - "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" + "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|01|36769301|Metastasis to bone|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" }, { "name": "measurement_source_value", diff --git a/docs/transformation-documentation/CosdV9MeasurementPrimaryPathwayMetastasis.json b/docs/transformation-documentation/CosdV9MeasurementPrimaryPathwayMetastasis.json index 74e76fd9..6015b0aa 100644 --- a/docs/transformation-documentation/CosdV9MeasurementPrimaryPathwayMetastasis.json +++ b/docs/transformation-documentation/CosdV9MeasurementPrimaryPathwayMetastasis.json @@ -86,7 +86,7 @@ } ], "query": "\nwith CO as (\n select distinct\n Record ->> '$.LinkagePatientId.NhsNumber.@extension' as NhsNumber,\n Record ->> '$.PrimaryPathway.LinkageDiagnosticDetails.DateOfPrimaryDiagnosisClinicallyAgreed' as DateOfPrimaryDiagnosisClinicallyAgreed,\n unnest(\n [\n [ Record ->> '$.PrimaryPathway.Diagnosis.MetastaticTypeAndSiteDiagnosis.MetastaticSite.@code' ],\n Record ->> '$.PrimaryPathway.Diagnosis.MetastaticTypeAndSiteDiagnosis[*].MetastaticSite.@code'\n ],\n recursive := true\n ) as MetastaticSite\n from omop_staging.cosd_staging_901\n where type = 'CO'\n)\nselect distinct\n NhsNumber,\n DateOfPrimaryDiagnosisClinicallyAgreed,\n MetastaticSite\nfrom CO\nwhere MetastaticSite is not null\n and MetastaticSite != '97';\n\t", - "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" + "lookup_table_markdown": "\r\n\r\n|MetastaticSite|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|01|36769301|Metastasis to bone|\r\n|02|36768862|Metastasis to brain|\r\n|03|36770544|Metastasis to liver|\r\n|04|36770283|Metastasis to lung|\r\n|07|36769180|Metastasis to the Unknown Site|\r\n|08|35225673|Metastasis to skin|\r\n|09|36769243|Distant spread to lymph node|\r\n|10|36769301|Metastasis to bone|\r\n|11|35226074|Metastasis to bone marrow|\r\n|12|36769269|Regional spread to lymph node|\r\n|98|36769180|Metastasis|\r\n|99|36769180|Metastasis|\r\n\r\nNotes\r\n* [OMOP Metastasis](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=metastasis&boosts)\r\n* [NHS - Metastasis](https://www.datadictionary.nhs.uk/data_elements/metastatic_site__at_diagnosis_.html?hl=metastatic%2Csite%2Cdiagnosis)\r\n" }, { "name": "measurement_source_value", diff --git a/docs/transformation-documentation/Measurement.md b/docs/transformation-documentation/Measurement.md index 8387707c..98415c2e 100644 --- a/docs/transformation-documentation/Measurement.md +++ b/docs/transformation-documentation/Measurement.md @@ -267,6 +267,22 @@ has_toc: false [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CosdV8MeasurementGradeOfDifferentiation%20mapping){: .btn } +## CosdV8BreastMeasurementNcategoryIntegratedStage + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CosdV8BreastMeasurementNcategoryIntegratedStage%20mapping){: .btn } +## CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage%20mapping){: .btn } +## CosdV8BreastMeasurementMcategoryIntegratedStage + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CosdV8BreastMeasurementMcategoryIntegratedStage%20mapping){: .btn } +## CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CosdV8BreastMeasurementMcategoryFinalPreTreatmentStage%20mapping){: .btn } ## CosdV8BreastMeasurementGradeOfDifferentiation diff --git a/docs/transformation-documentation/Measurement_measurement_concept_id.md b/docs/transformation-documentation/Measurement_measurement_concept_id.md index 8ebcc32d..a0044d6e 100644 --- a/docs/transformation-documentation/Measurement_measurement_concept_id.md +++ b/docs/transformation-documentation/Measurement_measurement_concept_id.md @@ -323,6 +323,7 @@ Lookup MetastasisSite concepts. |MetastaticSite|measurement_concept_id|notes| |------|-----|-----| +|01|36769301|Metastasis to bone| |02|36768862|Metastasis to brain| |03|36770544|Metastasis to liver| |04|36770283|Metastasis to lung| @@ -369,6 +370,7 @@ Lookup MetastasisSite concepts. |MetastaticSite|measurement_concept_id|notes| |------|-----|-----| +|01|36769301|Metastasis to bone| |02|36768862|Metastasis to brain| |03|36770544|Metastasis to liver| |04|36770283|Metastasis to lung| @@ -415,6 +417,7 @@ Lookup MetastasisSite concepts. |MetastaticSite|measurement_concept_id|notes| |------|-----|-----| +|01|36769301|Metastasis to bone| |02|36768862|Metastasis to brain| |03|36770544|Metastasis to liver| |04|36770283|Metastasis to lung| @@ -974,6 +977,7 @@ Lookup MetastasisSite concepts. |MetastaticSite|measurement_concept_id|notes| |------|-----|-----| +|01|36769301|Metastasis to bone| |02|36768862|Metastasis to brain| |03|36770544|Metastasis to liver| |04|36770283|Metastasis to lung| @@ -1029,6 +1033,7 @@ Lookup MetastasisSite concepts. |MetastaticSite|measurement_concept_id|notes| |------|-----|-----| +|01|36769301|Metastasis to bone| |02|36768862|Metastasis to brain| |03|36770544|Metastasis to liver| |04|36770283|Metastasis to lung| @@ -1622,6 +1627,7 @@ Lookup MetastasisSite concepts. |MetastaticSite|measurement_concept_id|notes| |------|-----|-----| +|01|36769301|Metastasis to bone| |02|36768862|Metastasis to brain| |03|36770544|Metastasis to liver| |04|36770283|Metastasis to lung| @@ -1674,6 +1680,7 @@ Lookup MetastasisSite concepts. |MetastaticSite|measurement_concept_id|notes| |------|-----|-----| +|01|36769301|Metastasis to bone| |02|36768862|Metastasis to brain| |03|36770544|Metastasis to liver| |04|36770283|Metastasis to lung| @@ -1726,6 +1733,7 @@ Lookup MetastasisSite concepts. |MetastaticSite|measurement_concept_id|notes| |------|-----|-----| +|01|36769301|Metastasis to bone| |02|36768862|Metastasis to brain| |03|36770544|Metastasis to liver| |04|36770283|Metastasis to lung| @@ -2323,6 +2331,7 @@ Lookup MetastasisSite concepts. |MetastaticSite|measurement_concept_id|notes| |------|-----|-----| +|01|36769301|Metastasis to bone| |02|36768862|Metastasis to brain| |03|36770544|Metastasis to liver| |04|36770283|Metastasis to lung| @@ -2376,6 +2385,7 @@ Lookup MetastasisSite concepts. |MetastaticSite|measurement_concept_id|notes| |------|-----|-----| +|01|36769301|Metastasis to bone| |02|36768862|Metastasis to brain| |03|36770544|Metastasis to liver| |04|36770283|Metastasis to lung| @@ -2647,6 +2657,193 @@ where GradeOfDifferentiationAtDiagnosis is not null; [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_concept_id%20field%20COSD%20V8%20Measurement%20Grade%20of%20Differentiation%20(At%20Diagnosis)%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Integrated Stage +Source column `NCategoryIntegratedStage`. +Lookup NCategory concepts. + + +|NCategoryIntegratedStage|measurement_concept_id|notes| +|------|-----|-----| +|0|1633440|AJCC/UICC N0 Category| +|0a|1633621|AJCC/UICC N0a Category| +|0b|1635244|AJCC/UICC N0b Category| +|1|1634434|AJCC/UICC N1 Category| +|1a|1633735|AJCC/UICC N1a Category| +|1b|1635130|AJCC/UICC N1b Category| +|1c|1634620|AJCC/UICC N1c Category| +|2|1634119|AJCC/UICC N2 Category| +|2a|1635644|AJCC/UICC N2a Category| +|2b|1634134|AJCC/UICC N2b Category| +|2c|1634080|AJCC/UICC N2c Category| +|3|1635320|AJCC/UICC N3 Category| +|3a|1635590|AJCC/UICC N3a Category| +|3b|1633422|AJCC/UICC N3b Category| +|3c|1634735|AJCC/UICC N3c Category| +|4|1635445|AJCC/UICC N4 Category| +|X|1633885|AJCC/UICC NX Category| + +Notes +* [OMOP Laterality](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=tnm&boosts) + +* `NCategoryIntegratedStage` Is the code, using a TNM CODING EDITION, which classifies the presence or absence of regional lymph node metastases after all information from treatment is available during a Cancer Care Spell. [N CATEGORY (INTEGRATED STAGE)](https://www.datadictionary.nhs.uk/data_elements/n_category__integrated_stage_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + NCategoryIntegratedStage +from BR +where NCategoryIntegratedStage is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_concept_id%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Final Pre Treatment Stage +Source column `NcategoryFinalPreTreatment`. +Lookup NCategory concepts. + + +|NcategoryFinalPreTreatment|measurement_concept_id|notes| +|------|-----|-----| +|0|1633440|AJCC/UICC N0 Category| +|0a|1633621|AJCC/UICC N0a Category| +|0b|1635244|AJCC/UICC N0b Category| +|1|1634434|AJCC/UICC N1 Category| +|1a|1633735|AJCC/UICC N1a Category| +|1b|1635130|AJCC/UICC N1b Category| +|1c|1634620|AJCC/UICC N1c Category| +|2|1634119|AJCC/UICC N2 Category| +|2a|1635644|AJCC/UICC N2a Category| +|2b|1634134|AJCC/UICC N2b Category| +|2c|1634080|AJCC/UICC N2c Category| +|3|1635320|AJCC/UICC N3 Category| +|3a|1635590|AJCC/UICC N3a Category| +|3b|1633422|AJCC/UICC N3b Category| +|3c|1634735|AJCC/UICC N3c Category| +|4|1635445|AJCC/UICC N4 Category| +|X|1633885|AJCC/UICC NX Category| + +Notes +* [OMOP Laterality](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=tnm&boosts) + +* `NcategoryFinalPreTreatment` Is the code, using a TNM CODING EDITION, which classifies the presence or absence of regional lymph node metastases before treatment during a Cancer Care Spell. [N CATEGORY (FINAL PRETREATMENT)](https://www.datadictionary.nhs.uk/data_elements/n_category__final_pretreatment_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + NcategoryFinalPreTreatment +from BR +where NcategoryFinalPreTreatment is not null +and NhsNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_concept_id%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Integrated Stage +Source column `MCategoryIntegratedStage`. +Lookup concepts. + + +|MCategoryIntegratedStage|measurement_concept_id|notes| +|------|-----|-----| +|0|1635624|AJCC/UICC M0 Category| +|1|1635142|AJCC/UICC M1 Category| +|1a|1635100|AJCC/UICC M1a Category| +|1b|1634463|AJCC/UICC M1b Category| +|1c|1635519|AJCC/UICC M1c Category| +|1d|1634064|AJCC/UICC M1d Category| +|X |1633547|AJCC/UICC MX Category| + +Notes +* [OMOP Laterality](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=tnm&boosts) + +* `MCategoryIntegratedStage` Is the code, using a TNM CODING EDITION, which classifies the absence or presence of distant metastases after all information from treatment is available during a Cancer Care Spell. [M CATEGORY (INTEGRATED STAGE)](https://www.datadictionary.nhs.uk/data_elements/m_category__integrated_stage_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + MCategoryIntegratedStage +from BR +where MCategoryIntegratedStage is not null +and NhsNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_concept_id%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Final Pre Treatment Stage +Source column `McategoryFinalPreTreatment`. +Lookup concepts. + + +|McategoryFinalPreTreatment|measurement_concept_id|notes| +|------|-----|-----| +|0|1635624|AJCC/UICC M0 Category| +|1|1635142|AJCC/UICC M1 Category| +|1a|1635100|AJCC/UICC M1a Category| +|1b|1634463|AJCC/UICC M1b Category| +|1c|1635519|AJCC/UICC M1c Category| +|1d|1634064|AJCC/UICC M1d Category| +|X |1633547|AJCC/UICC MX Category| + +Notes +* [OMOP Laterality](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=tnm&boosts) + +* `McategoryFinalPreTreatment` Is the code, using a TNM CODING EDITION, which classifies the absence or presence of distant metastases before treatment during a Cancer Care Spell. [M CATEGORY (FINAL PRETREATMENT)](https://www.datadictionary.nhs.uk/data_elements/m_category__final_pretreatment_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentMCategory' as McategoryFinalPreTreatment, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NHSNumber, + coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + McategoryFinalPreTreatment +from BR +where McategoryFinalPreTreatment is not null +and NHSNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_concept_id%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } ### COSD V8 Breast Measurement Grade of Differentiation (At Diagnosis) Source column `GradeOfDifferentiationAtDiagnosis`. Lookup GradeDifferentiation concepts. diff --git a/docs/transformation-documentation/Measurement_measurement_date.md b/docs/transformation-documentation/Measurement_measurement_date.md index b75b4087..de7b5b77 100644 --- a/docs/transformation-documentation/Measurement_measurement_date.md +++ b/docs/transformation-documentation/Measurement_measurement_date.md @@ -1579,6 +1579,117 @@ where GradeOfDifferentiationAtDiagnosis is not null; [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_date%20field%20COSD%20V8%20Measurement%20Grade%20of%20Differentiation%20(At%20Diagnosis)%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Integrated Stage +Source column `MeasurementDate`. +Converts text to dates. + +* `MeasurementDate` Measurement Date is the date on which TNM Stage Grouping (Integrated) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed. [DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)](https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html), [TNM STAGE GROUPING DATE (INTEGRATED)](https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__integrated_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + NCategoryIntegratedStage +from BR +where NCategoryIntegratedStage is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_date%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Final Pre Treatment Stage +Source column `MeasurementDate`. +Converts text to dates. + +* `MeasurementDate` Measurement Date is the date on which TNM Stage Grouping (Final pre-treatment) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed. [DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)](https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html), [TNM STAGE GROUPING DATE (FINAL PRETREATMENT)](https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__final_pretreatment_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + NcategoryFinalPreTreatment +from BR +where NcategoryFinalPreTreatment is not null +and NhsNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_date%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Integrated Stage +Source column `MeasurementDate`. +Converts text to dates. + +* `MeasurementDate` Measurement Date is the date on which TNM Stage Grouping (Integrated) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed. [DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)](https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html), [TNM STAGE GROUPING DATE (INTEGRATED)](https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__integrated_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + MCategoryIntegratedStage +from BR +where MCategoryIntegratedStage is not null +and NhsNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_date%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Final Pre Treatment Stage +Source column `MeasurementDate`. +Converts text to dates. + +* `MeasurementDate` Measurement Date is the date on which TNM Stage Grouping (Final pre-treatment) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed. [DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)](https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html), [TNM STAGE GROUPING DATE (FINAL PRETREATMENT)](https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__final_pretreatment_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentMCategory' as McategoryFinalPreTreatment, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NHSNumber, + coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + McategoryFinalPreTreatment +from BR +where McategoryFinalPreTreatment is not null +and NHSNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_date%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } ### COSD V8 Breast Measurement Grade of Differentiation (At Diagnosis) Source column `MeasurementDate`. Converts text to dates. diff --git a/docs/transformation-documentation/Measurement_measurement_datetime.md b/docs/transformation-documentation/Measurement_measurement_datetime.md index 8a22149a..4b50e1c2 100644 --- a/docs/transformation-documentation/Measurement_measurement_datetime.md +++ b/docs/transformation-documentation/Measurement_measurement_datetime.md @@ -1583,6 +1583,117 @@ where GradeOfDifferentiationAtDiagnosis is not null; [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_datetime%20field%20COSD%20V8%20Measurement%20Grade%20of%20Differentiation%20(At%20Diagnosis)%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Integrated Stage +Source column `MeasurementDate`. +Converts text to dates. + +* `MeasurementDate` Measurement Date is the date on which TNM Stage Grouping (Integrated) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed. [DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)](https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html), [TNM STAGE GROUPING DATE (INTEGRATED)](https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__integrated_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + NCategoryIntegratedStage +from BR +where NCategoryIntegratedStage is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_datetime%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Final Pre Treatment Stage +Source column `MeasurementDate`. +Converts text to dates. + +* `MeasurementDate` Measurement Date is the date on which TNM Stage Grouping (Final pre-treatment) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed. [DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)](https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html), [TNM STAGE GROUPING DATE (FINAL PRETREATMENT)](https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__final_pretreatment_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + NcategoryFinalPreTreatment +from BR +where NcategoryFinalPreTreatment is not null +and NhsNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_datetime%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Integrated Stage +Source column `MeasurementDate`. +Converts text to dates. + +* `MeasurementDate` Measurement Date is the date on which TNM Stage Grouping (Integrated) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed. [DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)](https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html), [TNM STAGE GROUPING DATE (INTEGRATED)](https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__integrated_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + MCategoryIntegratedStage +from BR +where MCategoryIntegratedStage is not null +and NhsNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_datetime%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Final Pre Treatment Stage +Source column `MeasurementDate`. +Converts text to dates. + +* `MeasurementDate` Measurement Date is the date on which TNM Stage Grouping (Final pre-treatment) was recorded, but if this is not available, then it is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed. [DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)](https://www.datadictionary.nhs.uk/data_elements/date_of_primary_cancer_diagnosis__clinically_agreed_.html), [TNM STAGE GROUPING DATE (FINAL PRETREATMENT)](https://www.datadictionary.nhs.uk/data_elements/tnm_stage_grouping_date__final_pretreatment_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentMCategory' as McategoryFinalPreTreatment, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NHSNumber, + coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + McategoryFinalPreTreatment +from BR +where McategoryFinalPreTreatment is not null +and NHSNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_datetime%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } ### COSD V8 Breast Measurement Grade of Differentiation (At Diagnosis) Source column `MeasurementDate`. Converts text to dates. diff --git a/docs/transformation-documentation/Measurement_measurement_source_concept_id.md b/docs/transformation-documentation/Measurement_measurement_source_concept_id.md index cd74b7e4..8cc2676c 100644 --- a/docs/transformation-documentation/Measurement_measurement_source_concept_id.md +++ b/docs/transformation-documentation/Measurement_measurement_source_concept_id.md @@ -1776,3 +1776,19 @@ where lower(EVENT) not like '%comment%' * Constant value set to `2000500014`. MCategoryFinalPreTreatmentStage [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_source_concept_id%20field%20COSD%20V8%20Measurement%20M%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Integrated Stage +* Constant value set to `2000500019`. NCategoryIntegratedStage + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_source_concept_id%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Final Pre Treatment Stage +* Constant value set to `2000500015`. NCategoryFinalPreTreatmentStage + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_source_concept_id%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Integrated Stage +* Constant value set to `2000500018`. MCategoryIntegratedStage + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_source_concept_id%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Final Pre Treatment Stage +* Constant value set to `2000500014`. MCategoryFinalPreTreatmentStage + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_source_concept_id%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } diff --git a/docs/transformation-documentation/Measurement_measurement_source_value.md b/docs/transformation-documentation/Measurement_measurement_source_value.md index 4e192bbb..7d825bd6 100644 --- a/docs/transformation-documentation/Measurement_measurement_source_value.md +++ b/docs/transformation-documentation/Measurement_measurement_source_value.md @@ -1428,6 +1428,113 @@ where GradeOfDifferentiationAtDiagnosis is not null; [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_source_value%20field%20COSD%20V8%20Measurement%20Grade%20of%20Differentiation%20(At%20Diagnosis)%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Integrated Stage +* Value copied from `NCategoryIntegratedStage` + +* `NCategoryIntegratedStage` Is the code, using a TNM CODING EDITION, which classifies the presence or absence of regional lymph node metastases after all information from treatment is available during a Cancer Care Spell. [N CATEGORY (INTEGRATED STAGE)](https://www.datadictionary.nhs.uk/data_elements/n_category__integrated_stage_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + NCategoryIntegratedStage +from BR +where NCategoryIntegratedStage is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_source_value%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Final Pre Treatment Stage +* Value copied from `NcategoryFinalPreTreatment` + +* `NcategoryFinalPreTreatment` Is the code, using a TNM CODING EDITION, which classifies the presence or absence of regional lymph node metastases before treatment during a Cancer Care Spell. [N CATEGORY (FINAL PRETREATMENT)](https://www.datadictionary.nhs.uk/data_elements/n_category__final_pretreatment_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + NcategoryFinalPreTreatment +from BR +where NcategoryFinalPreTreatment is not null +and NhsNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_source_value%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Integrated Stage +* Value copied from `MCategoryIntegratedStage` + +* `MCategoryIntegratedStage` Is the code, using a TNM CODING EDITION, which classifies the absence or presence of distant metastases after all information from treatment is available during a Cancer Care Spell. [M CATEGORY (INTEGRATED STAGE)](https://www.datadictionary.nhs.uk/data_elements/m_category__integrated_stage_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + MCategoryIntegratedStage +from BR +where MCategoryIntegratedStage is not null +and NhsNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_source_value%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Final Pre Treatment Stage +* Value copied from `McategoryFinalPreTreatment` + +* `McategoryFinalPreTreatment` Is the code, using a TNM CODING EDITION, which classifies the absence or presence of distant metastases before treatment during a Cancer Care Spell. [M CATEGORY (FINAL PRETREATMENT)](https://www.datadictionary.nhs.uk/data_elements/m_category__final_pretreatment_.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentMCategory' as McategoryFinalPreTreatment, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NHSNumber, + coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + McategoryFinalPreTreatment +from BR +where McategoryFinalPreTreatment is not null +and NHSNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_source_value%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } ### COSD V8 Breast Measurement Grade of Differentiation (At Diagnosis) * Value copied from `GradeOfDifferentiationAtDiagnosis` diff --git a/docs/transformation-documentation/Measurement_measurement_type_concept_id.md b/docs/transformation-documentation/Measurement_measurement_type_concept_id.md index 06658afd..4ffe0400 100644 --- a/docs/transformation-documentation/Measurement_measurement_type_concept_id.md +++ b/docs/transformation-documentation/Measurement_measurement_type_concept_id.md @@ -250,6 +250,22 @@ has_toc: false * Constant value set to `32828`. EHR episode record [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_type_concept_id%20field%20COSD%20V8%20Measurement%20Grade%20of%20Differentiation%20(At%20Diagnosis)%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Integrated Stage +* Constant value set to `32828`. EHR episode record + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_type_concept_id%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Final Pre Treatment Stage +* Constant value set to `32828`. EHR episode record + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_type_concept_id%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Integrated Stage +* Constant value set to `32828`. EHR episode record + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_type_concept_id%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Final Pre Treatment Stage +* Constant value set to `32828`. EHR episode record + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20measurement_type_concept_id%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } ### COSD V8 Breast Measurement Grade of Differentiation (At Diagnosis) * Constant value set to `32828`. EHR episode record diff --git a/docs/transformation-documentation/Measurement_nhs_number.md b/docs/transformation-documentation/Measurement_nhs_number.md index 666d042c..c240583b 100644 --- a/docs/transformation-documentation/Measurement_nhs_number.md +++ b/docs/transformation-documentation/Measurement_nhs_number.md @@ -1518,6 +1518,113 @@ where GradeOfDifferentiationAtDiagnosis is not null; [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20nhs_number%20field%20COSD%20V8%20Measurement%20Grade%20of%20Differentiation%20(At%20Diagnosis)%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Integrated Stage +* Value copied from `NhsNumber` + +* `NhsNumber` Patient NHS Number [NHS NUMBER](https://www.datadictionary.nhs.uk/data_elements/nhs_number.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + NCategoryIntegratedStage +from BR +where NCategoryIntegratedStage is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20nhs_number%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement N Category Final Pre Treatment Stage +* Value copied from `NhsNumber` + +* `NhsNumber` Patient NHS Number [NHS NUMBER](https://www.datadictionary.nhs.uk/data_elements/nhs_number.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + NcategoryFinalPreTreatment +from BR +where NcategoryFinalPreTreatment is not null +and NhsNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20nhs_number%20field%20COSD%20V8%20Breast%20Measurement%20N%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Integrated Stage +* Value copied from `NhsNumber` + +* `NhsNumber` Patient NHS Number [NHS NUMBER](https://www.datadictionary.nhs.uk/data_elements/nhs_number.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NhsNumber, + coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + MCategoryIntegratedStage +from BR +where MCategoryIntegratedStage is not null +and NhsNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20nhs_number%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Integrated%20Stage%20mapping){: .btn } +### COSD V8 Breast Measurement M Category Final Pre Treatment Stage +* Value copied from `NhsNumber` + +* `NhsNumber` Patient NHS Number [NHS NUMBER](https://www.datadictionary.nhs.uk/data_elements/nhs_number.html) + +```sql +with BR as ( + select + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentMCategory' as McategoryFinalPreTreatment, + Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage + from omop_staging.cosd_staging_81 + where Type = 'BR' +) +select distinct + NHSNumber, + coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, + McategoryFinalPreTreatment +from BR +where McategoryFinalPreTreatment is not null +and NHSNumber is not null; + +``` + + +[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Measurement%20table%20nhs_number%20field%20COSD%20V8%20Breast%20Measurement%20M%20Category%20Final%20Pre%20Treatment%20Stage%20mapping){: .btn } ### COSD V8 Breast Measurement Grade of Differentiation (At Diagnosis) * Value copied from `NhsNumber` diff --git a/docs/transformation-documentation/Observation_qualifier_concept_id.md b/docs/transformation-documentation/Observation_qualifier_concept_id.md index 1b7e480d..eb49afe1 100644 --- a/docs/transformation-documentation/Observation_qualifier_concept_id.md +++ b/docs/transformation-documentation/Observation_qualifier_concept_id.md @@ -18,6 +18,7 @@ Lookup SurgicalAccessType concepts for lung cancer procedures. |3|4044378|Laparoscopic/Thoracoscopic with unplanned conversion to open surgery| |4|44808608|Laparoscopic/Thoracoscopic completed| |5|44790026|Robotic surgery| +|Z|0|Other| Notes * [OMOP Open approach](https://athena.ohdsi.org/search-terms/terms/4044378) @@ -82,6 +83,7 @@ Lookup SurgicalAccessType concepts for lung cancer procedures. |3|4044378|Laparoscopic/Thoracoscopic with unplanned conversion to open surgery| |4|44808608|Laparoscopic/Thoracoscopic completed| |5|44790026|Robotic surgery| +|Z|0|Other| Notes * [OMOP Open approach](https://athena.ohdsi.org/search-terms/terms/4044378) From 2826dfa0dc995fb8d426d4781a64ac07b2442edc Mon Sep 17 00:00:00 2001 From: holtyad Date: Mon, 22 Dec 2025 13:23:51 +0000 Subject: [PATCH 4/5] update NHSNumber queries --- .../CosdV8BreastMeasurementGradeOfDifferentiation.xml | 4 ++-- .../CosdV8BreastMeasurementMcategoryIntegratedStage.xml | 8 ++++---- ...V8BreastMeasurementNcategoryFinalPreTreatmentStage.xml | 8 ++++---- .../CosdV8BreastMeasurementNcategoryIntegratedStage.xml | 6 +++--- 4 files changed, 13 insertions(+), 13 deletions(-) diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementGradeOfDifferentiation/CosdV8BreastMeasurementGradeOfDifferentiation.xml b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementGradeOfDifferentiation/CosdV8BreastMeasurementGradeOfDifferentiation.xml index 9ebf1963..c003dac6 100644 --- a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementGradeOfDifferentiation/CosdV8BreastMeasurementGradeOfDifferentiation.xml +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementGradeOfDifferentiation/CosdV8BreastMeasurementGradeOfDifferentiation.xml @@ -2,7 +2,7 @@ with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed, Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis @@ -10,7 +10,7 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate, GradeOfDifferentiationAtDiagnosis from BR diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStage.xml b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStage.xml index a74adb1d..b8edc6f7 100644 --- a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStage.xml +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementMcategoryIntegratedStage/CosdV8BreastMeasurementMcategoryIntegratedStage.xml @@ -2,7 +2,7 @@ with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage @@ -10,15 +10,15 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, MCategoryIntegratedStage from BR where MCategoryIntegratedStage is not null -and NhsNumber is not null; +and NHSNumber is not null; - + Patient NHS Number NHS NUMBER diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.xml b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.xml index 86686f78..72d0dd2c 100644 --- a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.xml +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.xml @@ -2,7 +2,7 @@ with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment, Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage @@ -10,15 +10,15 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, NcategoryFinalPreTreatment from BR where NcategoryFinalPreTreatment is not null -and NhsNumber is not null; +and NHSNumber is not null; - + Patient NHS Number NHS NUMBER diff --git a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStage.xml b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStage.xml index 3ff83f8d..ecc2eb12 100644 --- a/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStage.xml +++ b/OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementNcategoryIntegratedStage/CosdV8BreastMeasurementNcategoryIntegratedStage.xml @@ -2,7 +2,7 @@ with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage @@ -10,14 +10,14 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, NCategoryIntegratedStage from BR where NCategoryIntegratedStage is not null; - + Patient NHS Number NHS NUMBER From 0e79f0a7ba9f03ecf83f4354e5db30829249ff2a Mon Sep 17 00:00:00 2001 From: holtyad Date: Mon, 22 Dec 2025 13:23:57 +0000 Subject: [PATCH 5/5] build docs --- ...eastMeasurementGradeOfDifferentiation.json | 10 +++++----- ...stMeasurementMcategoryIntegratedStage.json | 10 +++++----- ...rementNcategoryFinalPreTreatmentStage.json | 10 +++++----- ...stMeasurementNcategoryIntegratedStage.json | 10 +++++----- .../Measurement_measurement_concept_id.md | 20 +++++++++---------- .../Measurement_measurement_date.md | 20 +++++++++---------- .../Measurement_measurement_datetime.md | 20 +++++++++---------- .../Measurement_measurement_source_value.md | 20 +++++++++---------- .../Measurement_nhs_number.md | 20 +++++++++---------- 9 files changed, 70 insertions(+), 70 deletions(-) diff --git a/docs/transformation-documentation/CosdV8BreastMeasurementGradeOfDifferentiation.json b/docs/transformation-documentation/CosdV8BreastMeasurementGradeOfDifferentiation.json index 5f9499f8..83d4c08d 100644 --- a/docs/transformation-documentation/CosdV8BreastMeasurementGradeOfDifferentiation.json +++ b/docs/transformation-documentation/CosdV8BreastMeasurementGradeOfDifferentiation.json @@ -17,7 +17,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate,\n GradeOfDifferentiationAtDiagnosis\nfrom BR\nwhere GradeOfDifferentiationAtDiagnosis is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate,\n GradeOfDifferentiationAtDiagnosis\nfrom BR\nwhere GradeOfDifferentiationAtDiagnosis is not null;\n\t", "lookup_table_markdown": null }, { @@ -39,7 +39,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate,\n GradeOfDifferentiationAtDiagnosis\nfrom BR\nwhere GradeOfDifferentiationAtDiagnosis is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate,\n GradeOfDifferentiationAtDiagnosis\nfrom BR\nwhere GradeOfDifferentiationAtDiagnosis is not null;\n\t", "lookup_table_markdown": null }, { @@ -61,7 +61,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate,\n GradeOfDifferentiationAtDiagnosis\nfrom BR\nwhere GradeOfDifferentiationAtDiagnosis is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate,\n GradeOfDifferentiationAtDiagnosis\nfrom BR\nwhere GradeOfDifferentiationAtDiagnosis is not null;\n\t", "lookup_table_markdown": null }, { @@ -86,7 +86,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate,\n GradeOfDifferentiationAtDiagnosis\nfrom BR\nwhere GradeOfDifferentiationAtDiagnosis is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate,\n GradeOfDifferentiationAtDiagnosis\nfrom BR\nwhere GradeOfDifferentiationAtDiagnosis is not null;\n\t", "lookup_table_markdown": "\r\n\r\n|GradeOfDifferentiationAtDiagnosis|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|GX||GX grade|\r\n|G1|36768162|Grade 1: Well differentiated|\r\n|G2|36770626|Grade 2: Moderately differentiated|\r\n|G3|36769666|Grade 3: Poorly differentiated|\r\n|G4|36769737|Grade 4: Undifferentiated|\r\n\r\nNotes\r\n* [OMOP Grade Differentiation](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&conceptClass=Histopattern&page=1&pageSize=500&query=grade&boosts)\r\n* [NHS - Grade of Differentiation (At Diagnosis)](https://www.datadictionary.nhs.uk/data_elements/grade_of_differentiation__at_diagnosis_.html?hl=grade%2Cdifferentiation)\r\n" }, { @@ -104,7 +104,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate,\n GradeOfDifferentiationAtDiagnosis\nfrom BR\nwhere GradeOfDifferentiationAtDiagnosis is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,\n Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate,\n GradeOfDifferentiationAtDiagnosis\nfrom BR\nwhere GradeOfDifferentiationAtDiagnosis is not null;\n\t", "lookup_table_markdown": null } ] diff --git a/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryIntegratedStage.json b/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryIntegratedStage.json index 21258e4c..215e68ea 100644 --- a/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryIntegratedStage.json +++ b/docs/transformation-documentation/CosdV8BreastMeasurementMcategoryIntegratedStage.json @@ -17,7 +17,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NhsNumber is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NHSNumber is not null;\n\t", "lookup_table_markdown": null }, { @@ -39,7 +39,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NhsNumber is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NHSNumber is not null;\n\t", "lookup_table_markdown": null }, { @@ -61,7 +61,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NhsNumber is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NHSNumber is not null;\n\t", "lookup_table_markdown": null }, { @@ -93,7 +93,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NhsNumber is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NHSNumber is not null;\n\t", "lookup_table_markdown": "\r\n\r\n|MCategoryIntegratedStage|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|0|1635624|AJCC/UICC M0 Category|\r\n|1|1635142|AJCC/UICC M1 Category|\r\n|1a|1635100|AJCC/UICC M1a Category|\r\n|1b|1634463|AJCC/UICC M1b Category|\r\n|1c|1635519|AJCC/UICC M1c Category|\r\n|1d|1634064|AJCC/UICC M1d Category|\r\n|X |1633547|AJCC/UICC MX Category|\r\n\r\nNotes\r\n* [OMOP Laterality](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=tnm&boosts)\r\n" }, { @@ -111,7 +111,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NhsNumber is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n MCategoryIntegratedStage\nfrom BR\nwhere MCategoryIntegratedStage is not null\nand NHSNumber is not null;\n\t", "lookup_table_markdown": null } ] diff --git a/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.json b/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.json index d959f434..65a60c48 100644 --- a/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.json +++ b/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryFinalPreTreatmentStage.json @@ -17,7 +17,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NhsNumber is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NHSNumber is not null;\n\t", "lookup_table_markdown": null }, { @@ -39,7 +39,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NhsNumber is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NHSNumber is not null;\n\t", "lookup_table_markdown": null }, { @@ -61,7 +61,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NhsNumber is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NHSNumber is not null;\n\t", "lookup_table_markdown": null }, { @@ -93,7 +93,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NhsNumber is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NHSNumber is not null;\n\t", "lookup_table_markdown": "\r\n\r\n|NcategoryFinalPreTreatment|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|0|1633440|AJCC/UICC N0 Category|\r\n|0a|1633621|AJCC/UICC N0a Category|\r\n|0b|1635244|AJCC/UICC N0b Category|\r\n|1|1634434|AJCC/UICC N1 Category|\r\n|1a|1633735|AJCC/UICC N1a Category|\r\n|1b|1635130|AJCC/UICC N1b Category|\r\n|1c|1634620|AJCC/UICC N1c Category|\r\n|2|1634119|AJCC/UICC N2 Category|\r\n|2a|1635644|AJCC/UICC N2a Category|\r\n|2b|1634134|AJCC/UICC N2b Category|\r\n|2c|1634080|AJCC/UICC N2c Category|\r\n|3|1635320|AJCC/UICC N3 Category|\r\n|3a|1635590|AJCC/UICC N3a Category|\r\n|3b|1633422|AJCC/UICC N3b Category|\r\n|3c|1634735|AJCC/UICC N3c Category|\r\n|4|1635445|AJCC/UICC N4 Category|\r\n|X|1633885|AJCC/UICC NX Category|\r\n\r\nNotes\r\n* [OMOP Laterality](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=tnm&boosts)\r\n" }, { @@ -111,7 +111,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NhsNumber is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NcategoryFinalPreTreatment\nfrom BR\nwhere NcategoryFinalPreTreatment is not null\nand NHSNumber is not null;\n\t", "lookup_table_markdown": null } ] diff --git a/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryIntegratedStage.json b/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryIntegratedStage.json index 8f458026..9bc09f84 100644 --- a/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryIntegratedStage.json +++ b/docs/transformation-documentation/CosdV8BreastMeasurementNcategoryIntegratedStage.json @@ -17,7 +17,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", "lookup_table_markdown": null }, { @@ -39,7 +39,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", "lookup_table_markdown": null }, { @@ -61,7 +61,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", "lookup_table_markdown": null }, { @@ -93,7 +93,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", "lookup_table_markdown": "\r\n\r\n|NCategoryIntegratedStage|measurement_concept_id|notes|\r\n|------|-----|-----|\r\n|0|1633440|AJCC/UICC N0 Category|\r\n|0a|1633621|AJCC/UICC N0a Category|\r\n|0b|1635244|AJCC/UICC N0b Category|\r\n|1|1634434|AJCC/UICC N1 Category|\r\n|1a|1633735|AJCC/UICC N1a Category|\r\n|1b|1635130|AJCC/UICC N1b Category|\r\n|1c|1634620|AJCC/UICC N1c Category|\r\n|2|1634119|AJCC/UICC N2 Category|\r\n|2a|1635644|AJCC/UICC N2a Category|\r\n|2b|1634134|AJCC/UICC N2b Category|\r\n|2c|1634080|AJCC/UICC N2c Category|\r\n|3|1635320|AJCC/UICC N3 Category|\r\n|3a|1635590|AJCC/UICC N3a Category|\r\n|3b|1633422|AJCC/UICC N3b Category|\r\n|3c|1634735|AJCC/UICC N3c Category|\r\n|4|1635445|AJCC/UICC N4 Category|\r\n|X|1633885|AJCC/UICC NX Category|\r\n\r\nNotes\r\n* [OMOP Laterality](https://athena.ohdsi.org/search-terms/terms?vocabulary=Cancer+Modifier&page=1&pageSize=500&query=tnm&boosts)\r\n" }, { @@ -111,7 +111,7 @@ ] } ], - "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NhsNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", + "query": "\nwith BR as (\n select \n Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,\n Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage,\n Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage\n from omop_staging.cosd_staging_81\n where Type = 'BR'\n)\nselect distinct\n NHSNumber,\n coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate,\n NCategoryIntegratedStage\nfrom BR\nwhere NCategoryIntegratedStage is not null;\n\t", "lookup_table_markdown": null } ] diff --git a/docs/transformation-documentation/Measurement_measurement_concept_id.md b/docs/transformation-documentation/Measurement_measurement_concept_id.md index a0044d6e..57666a30 100644 --- a/docs/transformation-documentation/Measurement_measurement_concept_id.md +++ b/docs/transformation-documentation/Measurement_measurement_concept_id.md @@ -2690,7 +2690,7 @@ Notes ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage @@ -2698,7 +2698,7 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, NCategoryIntegratedStage from BR @@ -2741,7 +2741,7 @@ Notes ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment, Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage @@ -2749,12 +2749,12 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, NcategoryFinalPreTreatment from BR where NcategoryFinalPreTreatment is not null -and NhsNumber is not null; +and NHSNumber is not null; ``` @@ -2783,7 +2783,7 @@ Notes ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage @@ -2791,12 +2791,12 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, MCategoryIntegratedStage from BR where MCategoryIntegratedStage is not null -and NhsNumber is not null; +and NHSNumber is not null; ``` @@ -2866,7 +2866,7 @@ Notes ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed, Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis @@ -2874,7 +2874,7 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate, GradeOfDifferentiationAtDiagnosis from BR diff --git a/docs/transformation-documentation/Measurement_measurement_date.md b/docs/transformation-documentation/Measurement_measurement_date.md index de7b5b77..2dd53603 100644 --- a/docs/transformation-documentation/Measurement_measurement_date.md +++ b/docs/transformation-documentation/Measurement_measurement_date.md @@ -1588,7 +1588,7 @@ Converts text to dates. ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage @@ -1596,7 +1596,7 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, NCategoryIntegratedStage from BR @@ -1615,7 +1615,7 @@ Converts text to dates. ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment, Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage @@ -1623,12 +1623,12 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, NcategoryFinalPreTreatment from BR where NcategoryFinalPreTreatment is not null -and NhsNumber is not null; +and NHSNumber is not null; ``` @@ -1643,7 +1643,7 @@ Converts text to dates. ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage @@ -1651,12 +1651,12 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, MCategoryIntegratedStage from BR where MCategoryIntegratedStage is not null -and NhsNumber is not null; +and NHSNumber is not null; ``` @@ -1699,7 +1699,7 @@ Converts text to dates. ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed, Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis @@ -1707,7 +1707,7 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate, GradeOfDifferentiationAtDiagnosis from BR diff --git a/docs/transformation-documentation/Measurement_measurement_datetime.md b/docs/transformation-documentation/Measurement_measurement_datetime.md index 4b50e1c2..c0876d1a 100644 --- a/docs/transformation-documentation/Measurement_measurement_datetime.md +++ b/docs/transformation-documentation/Measurement_measurement_datetime.md @@ -1592,7 +1592,7 @@ Converts text to dates. ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage @@ -1600,7 +1600,7 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, NCategoryIntegratedStage from BR @@ -1619,7 +1619,7 @@ Converts text to dates. ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment, Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage @@ -1627,12 +1627,12 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, NcategoryFinalPreTreatment from BR where NcategoryFinalPreTreatment is not null -and NhsNumber is not null; +and NHSNumber is not null; ``` @@ -1647,7 +1647,7 @@ Converts text to dates. ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage @@ -1655,12 +1655,12 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, MCategoryIntegratedStage from BR where MCategoryIntegratedStage is not null -and NhsNumber is not null; +and NHSNumber is not null; ``` @@ -1703,7 +1703,7 @@ Converts text to dates. ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed, Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis @@ -1711,7 +1711,7 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate, GradeOfDifferentiationAtDiagnosis from BR diff --git a/docs/transformation-documentation/Measurement_measurement_source_value.md b/docs/transformation-documentation/Measurement_measurement_source_value.md index 7d825bd6..62923d02 100644 --- a/docs/transformation-documentation/Measurement_measurement_source_value.md +++ b/docs/transformation-documentation/Measurement_measurement_source_value.md @@ -1436,7 +1436,7 @@ where GradeOfDifferentiationAtDiagnosis is not null; ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage @@ -1444,7 +1444,7 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, NCategoryIntegratedStage from BR @@ -1462,7 +1462,7 @@ where NCategoryIntegratedStage is not null; ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment, Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage @@ -1470,12 +1470,12 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, NcategoryFinalPreTreatment from BR where NcategoryFinalPreTreatment is not null -and NhsNumber is not null; +and NHSNumber is not null; ``` @@ -1489,7 +1489,7 @@ and NhsNumber is not null; ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage @@ -1497,12 +1497,12 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, MCategoryIntegratedStage from BR where MCategoryIntegratedStage is not null -and NhsNumber is not null; +and NHSNumber is not null; ``` @@ -1543,7 +1543,7 @@ and NHSNumber is not null; ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed, Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis @@ -1551,7 +1551,7 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate, GradeOfDifferentiationAtDiagnosis from BR diff --git a/docs/transformation-documentation/Measurement_nhs_number.md b/docs/transformation-documentation/Measurement_nhs_number.md index c240583b..cec6530a 100644 --- a/docs/transformation-documentation/Measurement_nhs_number.md +++ b/docs/transformation-documentation/Measurement_nhs_number.md @@ -1526,7 +1526,7 @@ where GradeOfDifferentiationAtDiagnosis is not null; ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageNCategory' as NCategoryIntegratedStage, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage @@ -1534,7 +1534,7 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, NCategoryIntegratedStage from BR @@ -1552,7 +1552,7 @@ where NCategoryIntegratedStage is not null; ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentNCategory' as NcategoryFinalPreTreatment, Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as StageDateFinalPretreatmentStage @@ -1560,12 +1560,12 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateFinalPretreatmentStage, ClinicalDateCancerDiagnosis) as MeasurementDate, NcategoryFinalPreTreatment from BR where NcategoryFinalPreTreatment is not null -and NhsNumber is not null; +and NHSNumber is not null; ``` @@ -1579,7 +1579,7 @@ and NhsNumber is not null; ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageMCategory' as MCategoryIntegratedStage, Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as StageDateIntegratedStage @@ -1587,12 +1587,12 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(StageDateIntegratedStage, ClinicalDateCancerDiagnosis) as MeasurementDate, MCategoryIntegratedStage from BR where MCategoryIntegratedStage is not null -and NhsNumber is not null; +and NHSNumber is not null; ``` @@ -1633,7 +1633,7 @@ and NHSNumber is not null; ```sql with BR as ( select - Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber, + Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis, Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed, Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.DiagnosisGradeOfDifferentiation.@code' as GradeOfDifferentiationAtDiagnosis @@ -1641,7 +1641,7 @@ with BR as ( where Type = 'BR' ) select distinct - NhsNumber, + NHSNumber, coalesce(ClinicalDateCancerDiagnosis, DateOfNonPrimaryCancerDiagnosisClinicallyAgreed) as MeasurementDate, GradeOfDifferentiationAtDiagnosis from BR