From 0941a0783cfee1ef521305cf058a2d48bcdddc71 Mon Sep 17 00:00:00 2001 From: unknown Date: Wed, 18 Aug 2021 11:55:08 -0400 Subject: [PATCH 1/4] Issue #259 [measurement table] added unit_source_concept_id --- inst/csv/OMOP_CDMv5.4_Field_Level.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/inst/csv/OMOP_CDMv5.4_Field_Level.csv b/inst/csv/OMOP_CDMv5.4_Field_Level.csv index f719620..866c707 100644 --- a/inst/csv/OMOP_CDMv5.4_Field_Level.csv +++ b/inst/csv/OMOP_CDMv5.4_Field_Level.csv @@ -165,6 +165,7 @@ MEASUREMENT,visit_detail_id,No,integer,"The VISIT_DETAIL record during which the MEASUREMENT,measurement_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the Measurement that occurred. For example, this could be an ICD10 or Read code.",This code is mapped to a Standard Measurement Concept in the Standardized Vocabularies and the original code is stored here for reference.,No,No,,,,, MEASUREMENT,measurement_source_concept_id,No,integer,"This is the concept representing the MEASUREMENT_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Measurement necessary for a given analytic use case. Consider using MEASUREMENT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the MEASUREMENT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,,, MEASUREMENT,unit_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the unit of the Measurement that occurred. ,This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.,No,No,,,,, +MEASUREMENT,unit_source_concept_id,No,integer,"This is the concept representing the UNIT_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Measurement necessary for a given analytic use case. Consider using UNIT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the UNIT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,,, MEASUREMENT,value_source_value,No,varchar(50),This field houses the verbatim result value of the Measurement from the source data . ,"If both a continuous and categorical result are given in the source data such that both VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID are both included, store the verbatim value that was mapped to VALUE_AS_CONCEPT_ID here.",No,No,,,,, OBSERVATION,observation_id,Yes,integer,The unique key given to an Observation record for a Person. Refer to the ETL for how duplicate Observations during the same Visit were handled.,Each instance of an observation present in the source data should be assigned this unique key. ,Yes,No,,,,, OBSERVATION,person_id,Yes,integer,The PERSON_ID of the Person for whom the Observation is recorded. This may be a system generated code.,,No,Yes,PERSON,PERSON_ID,,, @@ -523,4 +524,4 @@ ATTRIBUTE_DEFINITION,attribute_definition_id,Yes,integer,,,No,No,,,,, ATTRIBUTE_DEFINITION,attribute_name,Yes,varchar(255),,,No,No,,,,, ATTRIBUTE_DEFINITION,attribute_description,No,varchar(MAX),,,No,No,,,,, ATTRIBUTE_DEFINITION,attribute_type_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -ATTRIBUTE_DEFINITION,attribute_syntax,No,varchar(MAX),,,No,No,,,,, \ No newline at end of file +ATTRIBUTE_DEFINITION,attribute_syntax,No,varchar(MAX),,,No,No,,,,, From 826f6a923f5b2e60e04c6df5efa1f848ef2c21a6 Mon Sep 17 00:00:00 2001 From: unknown Date: Wed, 18 Aug 2021 12:55:26 -0400 Subject: [PATCH 2/4] Issue #149 fix for nullables in vocabulary table (vocabulary_reference and vocabulary_version both have isRequired=No) --- inst/csv/OMOP_CDMv5.3.1_Field_Level.csv | 4 ++-- inst/csv/OMOP_CDMv5.4_Field_Level.csv | 2 +- inst/csv/OMOP_CDMv6.0_Field_Level.csv | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/inst/csv/OMOP_CDMv5.3.1_Field_Level.csv b/inst/csv/OMOP_CDMv5.3.1_Field_Level.csv index da10426..e278fc7 100644 --- a/inst/csv/OMOP_CDMv5.3.1_Field_Level.csv +++ b/inst/csv/OMOP_CDMv5.3.1_Field_Level.csv @@ -407,7 +407,7 @@ VOCABULARY,vocabulary_name,Yes,varchar(255),"The name describing the vocabulary, example, International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS) etc.",,No,No,,,,, -VOCABULARY,vocabulary_reference,Yes,varchar(255),"External reference to documentation or +VOCABULARY,vocabulary_reference,No,varchar(255),"External reference to documentation or available download of the about the vocabulary.",,No,No,,,,, VOCABULARY,vocabulary_version,No,varchar(255),"Version of the Vocabulary as indicated in @@ -512,4 +512,4 @@ ATTRIBUTE_DEFINITION,attribute_definition_id,Yes,integer,,,No,No,,,,, ATTRIBUTE_DEFINITION,attribute_name,Yes,varchar(255),,,No,No,,,,, ATTRIBUTE_DEFINITION,attribute_description,No,varchar(MAX),,,No,No,,,,, ATTRIBUTE_DEFINITION,attribute_type_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -ATTRIBUTE_DEFINITION,attribute_syntax,No,varchar(MAX),,,No,No,,,,, \ No newline at end of file +ATTRIBUTE_DEFINITION,attribute_syntax,No,varchar(MAX),,,No,No,,,,, diff --git a/inst/csv/OMOP_CDMv5.4_Field_Level.csv b/inst/csv/OMOP_CDMv5.4_Field_Level.csv index 866c707..0a75e02 100644 --- a/inst/csv/OMOP_CDMv5.4_Field_Level.csv +++ b/inst/csv/OMOP_CDMv5.4_Field_Level.csv @@ -419,7 +419,7 @@ VOCABULARY,vocabulary_name,Yes,varchar(255),"The name describing the vocabulary, example, International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS) etc.",,No,No,,,,, -VOCABULARY,vocabulary_reference,Yes,varchar(255),"External reference to documentation or +VOCABULARY,vocabulary_reference,No,varchar(255),"External reference to documentation or available download of the about the vocabulary.",,No,No,,,,, VOCABULARY,vocabulary_version,No,varchar(255),"Version of the Vocabulary as indicated in diff --git a/inst/csv/OMOP_CDMv6.0_Field_Level.csv b/inst/csv/OMOP_CDMv6.0_Field_Level.csv index c3d2d1e..426d5b3 100644 --- a/inst/csv/OMOP_CDMv6.0_Field_Level.csv +++ b/inst/csv/OMOP_CDMv6.0_Field_Level.csv @@ -449,7 +449,7 @@ VOCABULARY,vocabulary_name,Yes,varchar(255),"The name describing the vocabulary, example International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS) etc.",,No,No,,,,, -VOCABULARY,vocabulary_reference,Yes,varchar(255),"External reference to documentation or +VOCABULARY,vocabulary_reference,No,varchar(255),"External reference to documentation or available download of the about the vocabulary.",,No,No,,,,, VOCABULARY,vocabulary_version,No,varchar(255),"Version of the Vocabulary as indicated in @@ -544,4 +544,4 @@ COHORT_DEFINITION,cohort_definition_description,No,varchar(MAX),A complete descr COHORT_DEFINITION,definition_type_concept_id,Yes,integer,Type defining what kind of Cohort Definition the record represents and how the syntax may be executed.,,No,Yes,CONCEPT,CONCEPT_ID,,, COHORT_DEFINITION,cohort_definition_syntax,No,varchar(MAX),Syntax or code to operationalize the Cohort Definition.,,No,No,,,,, COHORT_DEFINITION,subject_concept_id,Yes,integer,"This field contains a Concept that represents the domain of the subjects that are members of the cohort (e.g., Person, Provider, Visit).",,No,Yes,CONCEPT,CONCEPT_ID,,, -COHORT_DEFINITION,cohort_initiation_date,No,date,A date to indicate when the Cohort was initiated in the COHORT table.,,No,No,,,,, \ No newline at end of file +COHORT_DEFINITION,cohort_initiation_date,No,date,A date to indicate when the Cohort was initiated in the COHORT table.,,No,No,,,,, From 543893d406d8e3f827672a282bb12c781448634f Mon Sep 17 00:00:00 2001 From: unknown Date: Wed, 18 Aug 2021 14:23:54 -0400 Subject: [PATCH 3/4] Issue #149 fix for nullables in vocabulary table (vocabulary_reference isRequired=Yes vocabulary_version isRequired=No) --- inst/csv/OMOP_CDMv5.3.1_Field_Level.csv | 2 +- inst/csv/OMOP_CDMv6.0_Field_Level.csv | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/csv/OMOP_CDMv5.3.1_Field_Level.csv b/inst/csv/OMOP_CDMv5.3.1_Field_Level.csv index e278fc7..33a1ee8 100644 --- a/inst/csv/OMOP_CDMv5.3.1_Field_Level.csv +++ b/inst/csv/OMOP_CDMv5.3.1_Field_Level.csv @@ -407,7 +407,7 @@ VOCABULARY,vocabulary_name,Yes,varchar(255),"The name describing the vocabulary, example, International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS) etc.",,No,No,,,,, -VOCABULARY,vocabulary_reference,No,varchar(255),"External reference to documentation or +VOCABULARY,vocabulary_reference,Yes,varchar(255),"External reference to documentation or available download of the about the vocabulary.",,No,No,,,,, VOCABULARY,vocabulary_version,No,varchar(255),"Version of the Vocabulary as indicated in diff --git a/inst/csv/OMOP_CDMv6.0_Field_Level.csv b/inst/csv/OMOP_CDMv6.0_Field_Level.csv index 426d5b3..6c46e93 100644 --- a/inst/csv/OMOP_CDMv6.0_Field_Level.csv +++ b/inst/csv/OMOP_CDMv6.0_Field_Level.csv @@ -449,7 +449,7 @@ VOCABULARY,vocabulary_name,Yes,varchar(255),"The name describing the vocabulary, example International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS) etc.",,No,No,,,,, -VOCABULARY,vocabulary_reference,No,varchar(255),"External reference to documentation or +VOCABULARY,vocabulary_reference,Yes,varchar(255),"External reference to documentation or available download of the about the vocabulary.",,No,No,,,,, VOCABULARY,vocabulary_version,No,varchar(255),"Version of the Vocabulary as indicated in From b4661f637da61d88d3ca31f30603e149f8e98e50 Mon Sep 17 00:00:00 2001 From: unknown Date: Wed, 18 Aug 2021 14:37:43 -0400 Subject: [PATCH 4/4] Issue #149 saved fix for nullables in vocabulary table (vocabulary_reference and vocabulary_version both have isRequired=No) --- inst/csv/OMOP_CDMv5.4_Field_Level.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/csv/OMOP_CDMv5.4_Field_Level.csv b/inst/csv/OMOP_CDMv5.4_Field_Level.csv index 0a75e02..866c707 100644 --- a/inst/csv/OMOP_CDMv5.4_Field_Level.csv +++ b/inst/csv/OMOP_CDMv5.4_Field_Level.csv @@ -419,7 +419,7 @@ VOCABULARY,vocabulary_name,Yes,varchar(255),"The name describing the vocabulary, example, International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS) etc.",,No,No,,,,, -VOCABULARY,vocabulary_reference,No,varchar(255),"External reference to documentation or +VOCABULARY,vocabulary_reference,Yes,varchar(255),"External reference to documentation or available download of the about the vocabulary.",,No,No,,,,, VOCABULARY,vocabulary_version,No,varchar(255),"Version of the Vocabulary as indicated in