From 066b872ee11499424648f5bbf4b068fb58b4e39b Mon Sep 17 00:00:00 2001 From: Andryc Date: Tue, 17 Aug 2021 15:26:11 -0400 Subject: [PATCH 1/6] Added CDM v5.4 menu item --- rmd/_site.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/rmd/_site.yml b/rmd/_site.yml index 328ba6f..387b8be 100644 --- a/rmd/_site.yml +++ b/rmd/_site.yml @@ -29,6 +29,8 @@ navbar: href: cdm30.html - text: "CDM v5.3.1" href: cdm531.html + - text: "CDM v5.4" + href: cdm531.html - text: "CDM v6.0" href: cdm60.html - text: "Proposals" From 41bda9c907db7c14e9bbc861676659e06bf04e6a Mon Sep 17 00:00:00 2001 From: Andryc Date: Wed, 18 Aug 2021 11:27:56 -0400 Subject: [PATCH 2/6] Issue 329 updated visit_detail_parent_id --- inst/csv/OMOP_CDMv5.4_Field_Level.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/csv/OMOP_CDMv5.4_Field_Level.csv b/inst/csv/OMOP_CDMv5.4_Field_Level.csv index f719620..203a04f 100644 --- a/inst/csv/OMOP_CDMv5.4_Field_Level.csv +++ b/inst/csv/OMOP_CDMv5.4_Field_Level.csv @@ -68,7 +68,7 @@ VISIT_DETAIL,admitting_source_concept_id,No,Integer,"Use this field to determine VISIT_DETAIL,discharge_to_source_value,No,Varchar(50),,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was discharged to after a visit, as in they went home or were moved to long-term care. Typically this applies only to visits that have a length of stay of a day or more.",No,No,,,,, VISIT_DETAIL,discharge_to_concept_id,No,integer,"Use this field to determine where the patient was discharged to after a visit detail record. This concept is part of the visit domain and can indicate if a patient was discharged to home or sent to a long-term care facility, for example.","If available, map the DISCHARGE_TO_SOURCE_VALUE to a Standard Concept in the Visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,, VISIT_DETAIL,preceding_visit_detail_id,No,integer,Use this field to find the visit detail that occurred for the person prior to the given visit detail record. There could be a few days or a few years in between.,"The PRECEDING_VISIT_DETAIL_ID can be used to link a visit immediately preceding the current Visit Detail. Note this is not symmetrical, and there is no such thing as a ""following_visit_id"".",No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, -VISIT_DETAIL,visit_detail_parent_id,No,integer,Use this field to find the visit detail that subsumes the given visit detail record. This is used in the case that a visit detail record needs to be nested beyond the VISIT_OCCURRENCE/VISIT_DETAIL relationship.,"If there are multiple nested levels to how Visits are represented in the source, the VISIT_DETAIL_PARENT_ID can be used to record this relationship. ",No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, +VISIT_DETAIL,parent_visit_detail_id,No,integer,Use this field to find the visit detail that subsumes the given visit detail record. This is used in the case that a visit detail record needs to be nested beyond the VISIT_OCCURRENCE/VISIT_DETAIL relationship.,"If there are multiple nested levels to how Visits are represented in the source, the PARENT_VISIT_DETAIL_ID can be used to record this relationship. ",No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, VISIT_DETAIL,visit_occurrence_id,Yes,integer,Use this field to link the VISIT_DETAIL record to its VISIT_OCCURRENCE.,Put the VISIT_OCCURRENCE_ID that subsumes the VISIT_DETAIL record here.,No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, CONDITION_OCCURRENCE,condition_occurrence_id,Yes,integer,The unique key given to a condition record for a person. Refer to the ETL for how duplicate conditions during the same visit were handled.,"Each instance of a condition present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same condition within the same visit. It is valid to keep these duplicates and assign them individual, unique, CONDITION_OCCURRENCE_IDs, though it is up to the ETL how they should be handled.",Yes,No,,,,, CONDITION_OCCURRENCE,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the condition is recorded.,,No,Yes,PERSON,PERSON_ID,,, @@ -523,4 +523,4 @@ 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 0941a0783cfee1ef521305cf058a2d48bcdddc71 Mon Sep 17 00:00:00 2001 From: unknown Date: Wed, 18 Aug 2021 11:55:08 -0400 Subject: [PATCH 3/6] 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 4/6] 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 5/6] 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 6/6] 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