condition_source_concept_id

Cosd V8 Condition Occurrence Primary Diagnosis

Source column CancerDiagnosis. Resolve ICD10 codes to OMOP concepts. If code cannot be mapped, map using the parent code.

• CancerDiagnosis PRIMARY DIAGNOSIS (ICD) is the International Classification of Diseases (ICD) code used to identify the PRIMARY DIAGNOSIS. PRIMARY DIAGNOSIS (ICD)

;with XMLNAMESPACES('http://www.datadictionary.nhs.uk/messages/COSD-v8-1' AS COSD),
    CosdRecords as ( 
    select
            T.staging.value('(Id/@root)[1]', 'uniqueidentifier') as Id,
            T.staging.query('*[local-name() != "Id"][1]/*[1]') as Node -- Select the first inner element of the element that is not called Id.
    from omop_staging.cosd_staging
    cross apply content.nodes('COSD:COSD/*') as T(staging)
    where T.staging.exist('Id/@root') = 1
            and Content.value('namespace-uri((/*:COSD)[1])','nvarchar(max)') = 'http://www.datadictionary.nhs.uk/messages/COSD-v8-1'
            and substring (FileName, 15, 2) = 'CO'
), CO as (
	select 
        Id,
        Node,
        Node.value('(ColorectalCore/ColorectalCoreLinkagePatientId/NHSNumber/@extension)[1]', 'varchar(max)') as NhsNumber,
        Node.value('(ColorectalCore/ColorectalCoreLinkageDiagnosticDetails/ClinicalDateCancerDiagnosis)[1]', 'varchar(max)') as DiagnosisDate,
        Node.value('(ColorectalCore/ColorectalCoreLinkageDiagnosticDetails/DateOfNonPrimaryCancerDiagnosisClinicallyAgreed)[1]', 'varchar(max)') as NonPrimaryDiagnosisDate,
        Node.value('(ColorectalCore/ColorectalCoreDiagnosis/MorphologyICDODiagnosis/@code)[1]', 'varchar(max)') as CancerHistology,
        Node.value('(ColorectalCore/ColorectalCoreDiagnosis/TopographyICDO/@code)[1]', 'varchar(max)') as CancerTopography,
        Node.value('(ColorectalCore/ColorectalCoreDiagnosis/BasisOfCancerDiagnosis/@code)[1]', 'varchar(max)') as BasisOfDiagnosisCancer,
        Node.value('(ColorectalCore/ColorectalCoreLinkageDiagnosticDetails/PrimaryDiagnosis/@code)[1]', 'varchar(max)') as CancerDiagnosis
	from CosdRecords        
)
select 
	distinct
		NhsNumber,
		coalesce (DiagnosisDate, NonPrimaryDiagnosisDate) as DiagnosisDate,
		BasisOfDiagnosisCancer,
		CancerDiagnosis
from CO
where NhsNumber is not null and
	(
		DiagnosisDate is not null or 
		NonPrimaryDiagnosisDate is not null
	);
	

Comment or raise an issue for this mapping.

Cosd V8 Condition Occurrence Primary Diagnosis Histology Topography

Source columns CancerHistology, CancerTopography. Resolve ICD-o-3 codes to OMOP concepts.

• CancerHistology MORPHOLOGY (ICD-O CANCER TRANSFORMATION) is the morphology code of the Cancer Transformation using the ICD-O CODE. MORPHOLOGY (ICD-O CANCER TRANSFORMATION)

• CancerTopography TOPOGRAPHY (ICD-O) is the topographical site of the Tumour using the ICD-O CODE. TOPOGRAPHY (ICD-O)

;with XMLNAMESPACES('http://www.datadictionary.nhs.uk/messages/COSD-v8-1' AS COSD),
    CosdRecords as ( 
    select
            T.staging.value('(Id/@root)[1]', 'uniqueidentifier') as Id,
            T.staging.query('*[local-name() != "Id"][1]/*[1]') as Node -- Select the first inner element of the element that is not called Id.
    from omop_staging.cosd_staging
    cross apply content.nodes('COSD:COSD/*') as T(staging)
    where T.staging.exist('Id/@root') = 1
            and Content.value('namespace-uri((/*:COSD)[1])','nvarchar(max)') = 'http://www.datadictionary.nhs.uk/messages/COSD-v8-1'
            and substring (FileName, 15, 2) = 'CO'
), CO as (
	select 
        Id,
        Node,
        Node.value('(ColorectalCore/ColorectalCoreLinkagePatientId/NHSNumber/@extension)[1]', 'varchar(max)') as NhsNumber,
        Node.value('(ColorectalCore/ColorectalCoreLinkageDiagnosticDetails/ClinicalDateCancerDiagnosis)[1]', 'varchar(max)') as DiagnosisDate,
        Node.value('(ColorectalCore/ColorectalCoreLinkageDiagnosticDetails/DateOfNonPrimaryCancerDiagnosisClinicallyAgreed)[1]', 'varchar(max)') as NonPrimaryDiagnosisDate,
        Node.value('(ColorectalCore/ColorectalCoreDiagnosis/MorphologyICDODiagnosis/@code)[1]', 'varchar(max)') as CancerHistology,
        Node.value('(ColorectalCore/ColorectalCoreDiagnosis/TopographyICDO/@code)[1]', 'varchar(max)') as CancerTopography,
        Node.value('(ColorectalCore/ColorectalCoreDiagnosis/BasisOfCancerDiagnosis/@code)[1]', 'varchar(max)') as BasisOfDiagnosisCancer,
        Node.value('(ColorectalCore/ColorectalCoreLinkageDiagnosticDetails/PrimaryDiagnosis/@code)[1]', 'varchar(max)') as CancerDiagnosis
	from CosdRecords        
)
select 
	distinct
		NhsNumber,
		coalesce (DiagnosisDate, NonPrimaryDiagnosisDate) as DiagnosisDate,
		BasisOfDiagnosisCancer,
		CancerHistology,
		CancerTopography
from CO
where NhsNumber is not null and
	(
		DiagnosisDate is not null or 
		NonPrimaryDiagnosisDate is not null
	)
	and (CancerHistology is not null and CancerTopography is not null)
	

Comment or raise an issue for this mapping.

COSD V9 Condition Occurrence Recurrence

Source column SecondaryDiagnosis. Resolve ICD10 codes to OMOP concepts. If code cannot be mapped, map using the parent code.

• SecondaryDiagnosis SECONDARY DIAGNOSIS (ICD) is the International Classification of Diseases (ICD) code used to identify the secondary PATIENT DIAGNOSIS. SECONDARY DIAGNOSIS (ICD)

;with 
    XMLNAMESPACES('http://www.datadictionary.nhs.uk/messages/COSD-v9-0-1' AS COSD901),
    CosdRecords as ( 

    select
            T.staging.value('(Id/@root)[1]', 'uniqueidentifier') as Id,
            T.staging.query('.') as Node
    from omop_staging.cosd_staging
    cross apply content.nodes('COSD901:COSD/*') as T(staging)
    where T.staging.exist('Id/@root') = 1
            and Content.value('namespace-uri((/*:COSD)[1])','nvarchar(max)') = 'http://www.datadictionary.nhs.uk/messages/COSD-v9-0-1'
            and substring (FileName, 15, 2) = 'CO'
), CO as (
	select
		Id,
		Node,
		Node.value('(ColorectalRecord/LinkagePatientId/NhsNumber/@extension)[1]', 'varchar(max)') as NhsNumber,
		Node.value('(ColorectalRecord/PrimaryPathway/LinkageDiagnosticDetails/DateOfPrimaryDiagnosisClinicallyAgreed)[1]', 'varchar(max)') as DateOfPrimaryDiagnosisClinicallyAgreed,
		Node.value('(ColorectalRecord/PrimaryPathway/Diagnosis/DiagnosisAdditionalItems/SecondaryDiagnosisIcd/@code)[1]', 'varchar(max)') as SecondaryDiagnosis
	from CosdRecords
)
select
	NhsNumber,
	DateOfPrimaryDiagnosisClinicallyAgreed,
	max (SecondaryDiagnosis) as SecondaryDiagnosis
from CO
where DateOfPrimaryDiagnosisClinicallyAgreed is not null
	and SecondaryDiagnosis is not null
group by NhsNumber, DateOfPrimaryDiagnosisClinicallyAgreed;

	

Comment or raise an issue for this mapping.

COSD V9 Condition Occurrence Recurrence

Source column NonPrimaryRecurrenceOriginalDiagnosis. Resolve ICD10 codes to OMOP concepts. If code cannot be mapped, map using the parent code.

• NonPrimaryRecurrenceOriginalDiagnosis PRIMARY DIAGNOSIS (ICD ORIGINAL) is the International Classification of Diseases (ICD) code used to identify the original PRIMARY DIAGNOSIS. PRIMARY DIAGNOSIS (ICD ORIGINAL)

;with 
    XMLNAMESPACES('http://www.datadictionary.nhs.uk/messages/COSD-v9-0-1' AS COSD901),
    CosdRecords as ( 

    select
            T.staging.value('(Id/@root)[1]', 'uniqueidentifier') as Id,
            T.staging.query('.') as Node
    from omop_staging.cosd_staging
    cross apply content.nodes('COSD901:COSD/*') as T(staging)
    where T.staging.exist('Id/@root') = 1
            and Content.value('namespace-uri((/*:COSD)[1])','nvarchar(max)') = 'http://www.datadictionary.nhs.uk/messages/COSD-v9-0-1'
            and substring (FileName, 15, 2) = 'CO'
), CO as (
	select
		Id,
		Node,
		Node.value('(ColorectalRecord/LinkagePatientId/NhsNumber/@extension)[1]', 'varchar(max)') as NhsNumber,
		Node.value('(ColorectalRecord/NonPrimaryPathway/DateOfNonPrimaryCancerDiagnosisClinicallyAgreed)[1]', 'varchar(max)') as DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,
		Node.value('(ColorectalRecord/NonPrimaryPathway/Recurrence/OriginalPrimaryDiagnosisIcd/@code)[1]', 'varchar(max)') as NonPrimaryRecurrenceOriginalDiagnosis
	from CosdRecords
)
select 
	distinct 
        NhsNumber,
        DateOfNonPrimaryCancerDiagnosisClinicallyAgreed,
		NonPrimaryRecurrenceOriginalDiagnosis
from CO
where NonPrimaryRecurrenceOriginalDiagnosis is not null;
	

Comment or raise an issue for this mapping.

COSD V9 Condition Occurrence Progression

Source column NonPrimaryProgressionOriginalDiagnosis. Resolve ICD10 codes to OMOP concepts. If code cannot be mapped, map using the parent code.

• NonPrimaryProgressionOriginalDiagnosis CANCER PROGRESSION (ICD ORIGINAL) is the International Classification of Diseases (ICD) code of the original PATIENT DIAGNOSIS of the Cancer Progression. CANCER PROGRESSION (ICD ORIGINAL)

;with 
    XMLNAMESPACES('http://www.datadictionary.nhs.uk/messages/COSD-v9-0-1' AS COSD901),
    CosdRecords as ( 

    select
            T.staging.value('(Id/@root)[1]', 'uniqueidentifier') as Id,
            T.staging.query('.') as Node
    from omop_staging.cosd_staging
    cross apply content.nodes('COSD901:COSD/*') as T(staging)
    where T.staging.exist('Id/@root') = 1
            and Content.value('namespace-uri((/*:COSD)[1])','nvarchar(max)') = 'http://www.datadictionary.nhs.uk/messages/COSD-v9-0-1'
            and substring (FileName, 15, 2) = 'CO'
), CO as (
	select
		Id,
		Node,
		Node.value('(ColorectalRecord/LinkagePatientId/NhsNumber/@extension)[1]', 'varchar(max)') as NhsNumber,
		Node.value('(ColorectalRecord/NonPrimaryPathway/DateOfNonPrimaryCancerDiagnosisClinicallyAgreed)[1]', 'varchar(max)') as NonPrimaryDiagnosisDate,
		Node.value('(ColorectalRecord/NonPrimaryPathway/Progression/ProgressionIcd/@code)[1]', 'varchar(max)') as NonPrimaryProgressionOriginalDiagnosis
	from CosdRecords
)
select 
	distinct 
        NhsNumber,
        NonPrimaryDiagnosisDate,
		NonPrimaryProgressionOriginalDiagnosis
from CO
where NonPrimaryProgressionOriginalDiagnosis is not null;
	

Comment or raise an issue for this mapping.

COSD V9 Condition Occurrence Primary Diagnosis

Source column CancerDiagnosis. Resolve ICD10 codes to OMOP concepts. If code cannot be mapped, map using the parent code.

• CancerDiagnosis The basis of how a PATIENT DIAGNOSIS relating to cancer was identified. BASIS OF DIAGNOSIS (CANCER)

;with 
    XMLNAMESPACES('http://www.datadictionary.nhs.uk/messages/COSD-v9-0-1' AS COSD901),
    CosdRecords as ( 

    select
            T.staging.value('(Id/@root)[1]', 'uniqueidentifier') as Id,
            T.staging.query('.') as Node
    from omop_staging.cosd_staging
    cross apply content.nodes('COSD901:COSD/*') as T(staging)
    where T.staging.exist('Id/@root') = 1
            and Content.value('namespace-uri((/*:COSD)[1])','nvarchar(max)') = 'http://www.datadictionary.nhs.uk/messages/COSD-v9-0-1'
            and substring (FileName, 15, 2) = 'CO'
), CO as (
	select
		Id,
		Node,
		Node.value('(ColorectalRecord/LinkagePatientId/NhsNumber/@extension)[1]', 'varchar(max)') as NhsNumber,
		Node.value('(ColorectalRecord/PrimaryPathway/LinkageDiagnosticDetails/DateOfPrimaryDiagnosisClinicallyAgreed)[1]', 'varchar(max)') as DateOfPrimaryDiagnosisClinicallyAgreed,
		Node.value('(ColorectalRecord/PrimaryPathway/Diagnosis/MorphologyIcd-o-3/@code)[1]', 'varchar(max)') as CancerHistology,
		Node.value('(ColorectalRecord/PrimaryPathway/Diagnosis/TopographyIcd-o-3/@code)[1]', 'varchar(max)') as CancerTopography,
		Node.value('(ColorectalRecord/PrimaryPathway/Diagnosis/BasisOfDiagnosisCancer/@code)[1]', 'varchar(max)') as BasisOfDiagnosisCancer,
		Node.value('(ColorectalRecord/PrimaryPathway/LinkageDiagnosticDetails/PrimaryDiagnosisIcd/@code)[1]', 'varchar(max)') as CancerDiagnosis
	from CosdRecords
)
select
	NhsNumber,
	DateOfPrimaryDiagnosisClinicallyAgreed,
	max(BasisOfDiagnosisCancer) as BasisOfDiagnosisCancer,
	CancerDiagnosis
from CO
where DateOfPrimaryDiagnosisClinicallyAgreed is not null
group by NhsNumber, DateOfPrimaryDiagnosisClinicallyAgreed, CancerDiagnosis;
	

Comment or raise an issue for this mapping.

COSD V9 Condition Occurrence Primary Diagnosis Histology Topography

Source columns CancerHistology, CancerTopography. Resolve ICD-o-3 codes to OMOP concepts.

• CancerHistology MORPHOLOGY (ICD-O CANCER TRANSFORMATION) is the morphology code of the Cancer Transformation using the ICD-O CODE. MORPHOLOGY (ICD-O CANCER TRANSFORMATION)

• CancerTopography TOPOGRAPHY (ICD-O) is the topographical site of the Tumour using the ICD-O CODE. TOPOGRAPHY (ICD-O)

;with 
    XMLNAMESPACES('http://www.datadictionary.nhs.uk/messages/COSD-v9-0-1' AS COSD901),
    CosdRecords as ( 

    select
            T.staging.value('(Id/@root)[1]', 'uniqueidentifier') as Id,
            T.staging.query('.') as Node
    from omop_staging.cosd_staging
    cross apply content.nodes('COSD901:COSD/*') as T(staging)
    where T.staging.exist('Id/@root') = 1
            and Content.value('namespace-uri((/*:COSD)[1])','nvarchar(max)') = 'http://www.datadictionary.nhs.uk/messages/COSD-v9-0-1'
            and substring (FileName, 15, 2) = 'CO'
), CO as (
	select
		Id,
		Node,
		Node.value('(ColorectalRecord/LinkagePatientId/NhsNumber/@extension)[1]', 'varchar(max)') as NhsNumber,
		Node.value('(ColorectalRecord/PrimaryPathway/LinkageDiagnosticDetails/DateOfPrimaryDiagnosisClinicallyAgreed)[1]', 'varchar(max)') as DateOfPrimaryDiagnosisClinicallyAgreed,
		Node.value('(ColorectalRecord/PrimaryPathway/Diagnosis/MorphologyIcd-o-3/@code)[1]', 'varchar(max)') as CancerHistology,
		Node.value('(ColorectalRecord/PrimaryPathway/Diagnosis/TopographyIcd-o-3/@code)[1]', 'varchar(max)') as CancerTopography,
		Node.value('(ColorectalRecord/PrimaryPathway/Diagnosis/BasisOfDiagnosisCancer/@code)[1]', 'varchar(max)') as BasisOfDiagnosisCancer,
		Node.value('(ColorectalRecord/PrimaryPathway/LinkageDiagnosticDetails/PrimaryDiagnosisIcd/@code)[1]', 'varchar(max)') as CancerDiagnosis
	from CosdRecords
)
select
	distinct
		NhsNumber,
		DateOfPrimaryDiagnosisClinicallyAgreed,
		BasisOfDiagnosisCancer,
		CancerHistology,
		CancerTopography
from CO
where DateOfPrimaryDiagnosisClinicallyAgreed is not null
	and CancerHistology is not null
	and CancerTopography is not null;
	

Comment or raise an issue for this mapping.

CDS Condition Occurrence

Source column DiagnosisCode. Resolve ICD10 codes to OMOP concepts. If code cannot be mapped, map using the parent code.

• DiagnosisCode ICD10 diagnosis code PRIMARY DIAGNOSIS (ICD), SECONDARY DIAGNOSIS (ICD)

select
	distinct
		d.DiagnosisCode,
		line01.RecordConnectionIdentifier,
		line01.NHSNumber,
		line01.CDSActivityDate
from omop_staging.cds_diagnosis d
	inner join omop_staging.cds_line01 line01
		on d.MessageId = line01.MessageId
where line01.NHSNumber is not null;
	

Comment or raise an issue for this mapping.