From e98d56c37be1336653010c4f7481b91be0d3ab2e Mon Sep 17 00:00:00 2001 From: clairblacketer Date: Tue, 20 Jun 2017 09:09:22 -0400 Subject: [PATCH 1/9] Updated Home (markdown) --- Home.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Home.md b/Home.md index 23497a9..1bbaab0 100644 --- a/Home.md +++ b/Home.md @@ -29,8 +29,8 @@ Welcome to the Common Data Model wiki! This wiki houses all of the documentation
[COHORT_DEFINITION](wiki/COHORT_DEFINITION)
[ATTRIBUTE_DEFINITION](wiki/ATTRIBUTE_DEFINITION)
-
**Standardized Metadata** -
CDM_SOURCE +
**[Standardized Metadata](wiki/Standardized-Metadata)** +
[CDM_SOURCE](wiki/CDM_SOURCE)

**Standardized Clinical Data Tables**
PERSON From 376b8733851f8396352f1c06169aa5c2334a15ce Mon Sep 17 00:00:00 2001 From: clairblacketer Date: Tue, 20 Jun 2017 09:12:31 -0400 Subject: [PATCH 2/9] Updated Standardized Metadata (markdown) --- StandardizedMetadata/Standardized-Metadata.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/StandardizedMetadata/Standardized-Metadata.md b/StandardizedMetadata/Standardized-Metadata.md index 644f1b0..4810ed9 100644 --- a/StandardizedMetadata/Standardized-Metadata.md +++ b/StandardizedMetadata/Standardized-Metadata.md @@ -1 +1,5 @@ -# Standardized Vocabularies \ No newline at end of file +All metadata about the data should be derived from the data themselves. However, the folowing contains a few key pieces of information that are convenient especially for software applications utilizing the CDM data. + +Below provides and entity-relationship diagram highlighting the tables withing the Standardized Metadata portion of the OMOP Common Data Model: + +![](http://www.ohdsi.org/web/wiki/lib/exe/fetch.php?w=200&tok=f95343&media=documentation:cdm:standard_meta_data.png) \ No newline at end of file From 2d56a753fd247e361fc5ad777002c1e8fa33e289 Mon Sep 17 00:00:00 2001 From: clairblacketer Date: Tue, 20 Jun 2017 09:13:40 -0400 Subject: [PATCH 3/9] Updated Standardized Metadata (markdown) --- StandardizedMetadata/Standardized-Metadata.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/StandardizedMetadata/Standardized-Metadata.md b/StandardizedMetadata/Standardized-Metadata.md index 4810ed9..d482e48 100644 --- a/StandardizedMetadata/Standardized-Metadata.md +++ b/StandardizedMetadata/Standardized-Metadata.md @@ -1,3 +1,5 @@ +[CDM_SOURCE](wiki/CDM_SOURCE) + All metadata about the data should be derived from the data themselves. However, the folowing contains a few key pieces of information that are convenient especially for software applications utilizing the CDM data. Below provides and entity-relationship diagram highlighting the tables withing the Standardized Metadata portion of the OMOP Common Data Model: From 61a05e126a5ea3bc7cd3f26c30da251c3667dab3 Mon Sep 17 00:00:00 2001 From: clairblacketer Date: Tue, 20 Jun 2017 09:13:56 -0400 Subject: [PATCH 4/9] Updated Standardized Metadata (markdown) --- StandardizedMetadata/Standardized-Metadata.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/StandardizedMetadata/Standardized-Metadata.md b/StandardizedMetadata/Standardized-Metadata.md index d482e48..1e8217f 100644 --- a/StandardizedMetadata/Standardized-Metadata.md +++ b/StandardizedMetadata/Standardized-Metadata.md @@ -1,4 +1,4 @@ -[CDM_SOURCE](wiki/CDM_SOURCE) +[CDM_SOURCE](CDM_SOURCE) All metadata about the data should be derived from the data themselves. However, the folowing contains a few key pieces of information that are convenient especially for software applications utilizing the CDM data. From 023212b65e1d006148e21a84bcb94d1461e22cb4 Mon Sep 17 00:00:00 2001 From: clairblacketer Date: Tue, 20 Jun 2017 09:15:11 -0400 Subject: [PATCH 5/9] Updated CDM_SOURCE (markdown) --- StandardizedMetadata/CDM_SOURCE.md | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) diff --git a/StandardizedMetadata/CDM_SOURCE.md b/StandardizedMetadata/CDM_SOURCE.md index 80efb7d..c994d9c 100644 --- a/StandardizedMetadata/CDM_SOURCE.md +++ b/StandardizedMetadata/CDM_SOURCE.md @@ -1 +1,20 @@ -#CDM_SOURCE \ No newline at end of file +The CDM_SOURCE table contains detail about the source database and the process used to transform the data into the OMOP Common Data Model. + +Field|Required|Type|Description +:----|:----|:-----|:----- +|cdm_source_name|Yes|varchar(255)|The full name of the source| +|cdm_source_abbreviation|No|varchar(25)|An abbreviation of the name| +|cdm_holder|No|varchar(255)|The name of the organization responsible for the development of the CDM instance| +|source_description|No|CLOB|A description of the source data origin and purpose for collection. The description may contain a summary of the period of time that is expected to be covered by this dataset.| +|source_documentation_reference|No|varchar(255)|URL or other external reference to location of source documentation| +|cdm_etl _reference|No|varchar(255)|URL or other external reference to location of ETL specification documentation and ETL source code| +|source_release_date|No|date|The date for which the source data are most current, such as the last day of data capture| +|cdm_release_date|No|date|The date when the CDM was instantiated| +|cdm_version|No|varchar(10)|The version of CDM used| +|vocabulary_version|No|varchar(20)|The version of the vocabulary used| + +## Conventions + + * If a source database is derived from multiple data feeds, the integration of those disparate sources is expected to be documented in the ETL specifications. The source information on each of the databases can be represented as separate records in the CDM_SOURCE table. + * Currently, there is no mechanism to link individual records in the CDM tables to their source record in the CDM_SOURCE table. + * The version of the vocabulary can be obtained from the vocabulary_name field in the VOCABULARY table for the record where vocabulary_id='None'. \ No newline at end of file From 529d93f2118a7caba2a2884ec494bbc708ae43f6 Mon Sep 17 00:00:00 2001 From: clairblacketer Date: Tue, 20 Jun 2017 09:17:09 -0400 Subject: [PATCH 6/9] Updated Standardized Vocabularies (markdown) --- Standardized-Vocabularies.md | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/Standardized-Vocabularies.md b/Standardized-Vocabularies.md index fa2df72..e17b168 100644 --- a/Standardized-Vocabularies.md +++ b/Standardized-Vocabularies.md @@ -1,15 +1,15 @@ -
[CONCEPT](wiki/CONCEPT) -
[VOCABULARY](wiki/VOCABULARY) -
[DOMAIN](wiki/DOMAIN) -
[CONCEPT_CLASS](wiki/CONCEPT_CLASS) -
3.5 CONCEPT_RELATIONSHIP -
3.6 RELATIONSHIP -
3.7 CONCEPT_SYNONYM -
3.8 CONCEPT_ANCESTOR -
3.9 SOURCE_TO_CONCEPT_MAP -
3.10 DRUG_STRENGTH -
3.11 COHORT_DEFINITION -
3.12 ATTRIBUTE_DEFINITION +
[CONCEPT](CONCEPT) +
[VOCABULARY](VOCABULARY) +
[DOMAIN](DOMAIN) +
[CONCEPT_CLASS](CONCEPT_CLASS) +
[CONCEPT_RELATIONSHIP](CONCEPT_RELATIONSHIP) +
[RELATIONSHIP](RELATIONSHIP) +
[CONCEPT_SYNONYM](CONCEPT_SYNONYM) +
[CONCEPT_ANCESTOR](CONCEPT_ANCESTOR) +
[SOURCE_TO_CONCEPT_MAP](SOURCE_TO_CONCEPT_MAP) +
[DRUG_STRENGTH](DRUG_STRENGTH) +
[COHORT_DEFINITION](COHORT_DEFINITION) +
[ATTRIBUTE_DEFINITION](ATTRIBUTE_DEFINITION) These tables contain detailed information about the Concepts used in all of the CDM fact tables. The content of the Standardized Vocabularies tables is not generated anew by each CDM implementation. Instead, it is maintained centrally as a service to the community. From 5da62408aac87d7704e2fd9a1b8cef2cf3e744f2 Mon Sep 17 00:00:00 2001 From: clairblacketer Date: Tue, 20 Jun 2017 09:18:01 -0400 Subject: [PATCH 7/9] Updated Background (markdown) --- Background/Background.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Background/Background.md b/Background/Background.md index 15dccc7..c9f52ea 100644 --- a/Background/Background.md +++ b/Background/Background.md @@ -1,6 +1,6 @@ -
[The Role of the Common Data Model](TheRoleoftheCommonDataModel.md) -
[Design Principles](DesignPrinciples.md) -
[Data Model Conventions](DataModelConventions.md) +
[The Role of the Common Data Model](The Role of the Common Data Model) +
[Design Principles](Design Principles) +
[Data Model Conventions](Data Model Conventions) The Observational Medical Outcomes Partnership (OMOP) was a public-private partnership established to inform the appropriate use of observational healthcare databases for studying the effects of medical products. Over the course of the 5-year project and through its community of researchers from industry, government, and academia, OMOP successfully achieved its aims to: From 4f3df3215afe27aa6dc4f7307d10ee88a89e1dcf Mon Sep 17 00:00:00 2001 From: clairblacketer Date: Tue, 20 Jun 2017 09:18:23 -0400 Subject: [PATCH 8/9] Updated Background (markdown) --- Background/Background.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Background/Background.md b/Background/Background.md index c9f52ea..6a19245 100644 --- a/Background/Background.md +++ b/Background/Background.md @@ -1,6 +1,6 @@ -
[The Role of the Common Data Model](The Role of the Common Data Model) -
[Design Principles](Design Principles) -
[Data Model Conventions](Data Model Conventions) +
[The Role of the Common Data Model](The-Role-of-the-Common-Data-Model) +
[Design Principles](Design-Principles) +
[Data Model Conventions](Data-Model-Conventions) The Observational Medical Outcomes Partnership (OMOP) was a public-private partnership established to inform the appropriate use of observational healthcare databases for studying the effects of medical products. Over the course of the 5-year project and through its community of researchers from industry, government, and academia, OMOP successfully achieved its aims to: From b8c3981ca293087fe114fdc0bb4555d49d9e66e2 Mon Sep 17 00:00:00 2001 From: clairblacketer Date: Tue, 20 Jun 2017 09:21:59 -0400 Subject: [PATCH 9/9] Updated Home (markdown) --- Home.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Home.md b/Home.md index 1bbaab0..11461a9 100644 --- a/Home.md +++ b/Home.md @@ -32,8 +32,8 @@ Welcome to the Common Data Model wiki! This wiki houses all of the documentation
**[Standardized Metadata](wiki/Standardized-Metadata)**
[CDM_SOURCE](wiki/CDM_SOURCE)
-
**Standardized Clinical Data Tables** -
PERSON +
**[Standardized Clinical Data Tables]()** +
[PERSON]
OBSERVATION_PERIOD
SPECIMEN
DEATH