CDM v5.3.1 updates

Author: clairblacketer

BigQuery/OMOP CDM bigquery ddl.txt

@@ -1,3 +1,4 @@
+/*OMOP CDM v5.3.1 14June2018*/
 #standardsql
 create table concept (
   concept_id			    INT64			  not null ,
@@ -9,7 +10,7 @@ create table concept (
   concept_code			  STRING  		not null ,
   valid_start_DATE		DATE			  not null ,
   valid_end_DATE		  DATE			  not null ,
-  invalid_reason		  STRING  		
+  invalid_reason		  STRING
 )
 ;
 
@@ -46,7 +47,7 @@ create table concept_relationship (
   relationship_id		STRING  	not null,
   valid_start_DATE	DATE			not null,
   valid_end_DATE		DATE			not null,
-  invalid_reason		STRING  	
+  invalid_reason		STRING
   )
 ;
 
@@ -88,7 +89,7 @@ create table source_to_concept_map (
   target_vocabulary_id		STRING  		not null,
   valid_start_DATE			  DATE		    not null,
   valid_end_DATE			    DATE		    not null,
-  invalid_reason			    STRING  		
+  invalid_reason			    STRING
 )
 ;
 
@@ -107,7 +108,7 @@ create table drug_strength (
   box_size						        INT64		          ,
   valid_start_DATE				    DATE		   not null,
   valid_end_DATE				      DATE		   not null,
-  invalid_reason				      STRING     
+  invalid_reason				      STRING
 )
 ;
 
@@ -120,7 +121,7 @@ create table cohort_definition (
   definition_type_concept_id		  INT64			  not null,
   cohort_definition_syntax			  STRING     	        ,
   subject_concept_id				      INT64			  not null,
-  cohort_initiation_DATE			    DATE			  
+  cohort_initiation_DATE			    DATE
 )
 ;
 
@@ -130,7 +131,7 @@ create table attribute_definition (
   attribute_name				      STRING    	not null,
   attribute_description			  STRING    	        ,
   attribute_type_concept_id		INT64			  not null,
-  attribute_syntax				    STRING    	
+  attribute_syntax				    STRING
 )
 ;
 
@@ -146,7 +147,7 @@ create table cdm_source
   source_release_DATE				      DATE			         ,
   cdm_release_DATE					      DATE			         ,
   cdm_version						          STRING    		     ,
-  vocabulary_version					    STRING    		
+  vocabulary_version					    STRING
 )
 ;
 
@@ -159,7 +160,7 @@ create table metadata
   value_as_string           STRING               ,
   value_as_concept_id       INT64                ,
   metadata_DATE             DATE                 ,
-  metadata_DATETIME         DATETIME      
+  metadata_DATETIME         DATETIME
 )
 ;
 
@@ -185,7 +186,7 @@ create table person
   race_source_value				    STRING             ,
   race_source_concept_id		  INT64		           ,
   ethnicity_source_value		  STRING             ,
-  ethnicity_source_concept_id	INT64		  
+  ethnicity_source_concept_id	INT64
 )
 ;
 
@@ -219,7 +220,7 @@ create table specimen
   specimen_source_value				STRING  	         ,
   unit_source_value					  STRING  	         ,
   anatomic_site_source_value	STRING  	         ,
-  disease_status_source_value STRING  	
+  disease_status_source_value STRING
 )
 ;
 
@@ -233,7 +234,7 @@ create table death
   death_type_concept_id   INT64			not null ,
   cause_concept_id			  INT64			         ,
   cause_source_value			STRING  	         ,
-  cause_source_concept_id INT64			
+  cause_source_concept_id INT64
 )
 ;
 
@@ -257,33 +258,33 @@ create table visit_occurrence
   admitting_source_value		    STRING  	         ,
   discharge_to_concept_id		    INT64   	         ,
   discharge_to_source_value		  STRING  	         ,
-  preceding_visit_occurrence_id	INT64			
+  preceding_visit_occurrence_id	INT64
 )
 ;
 
 
 --HINT DISTRIBUTE_ON_KEY(person_id)
 create table visit_detail
 (
-  visit_detail_id             INT64     not null ,
-  person_id                   INT64     not null ,
-  visit_detail_concept_id     INT64     not null ,
-  visit_start_DATE            DATE      not null ,
-  visit_start_DATETIME        DATETIME           ,
-  visit_end_DATE              DATE      not null ,
-  visit_end_DATETIME          DATETIME           ,
-  visit_type_concept_id       INT64     not null ,
-  provider_id                 INT64              ,
-  care_site_id                INT64              ,
-  admitting_source_concept_id INT64              ,
-  discharge_to_concept_id     INT64              ,
-  preceding_visit_detail_id   INT64              ,
-  visit_source_value          STRING             ,
-  visit_source_concept_id     INT64              ,
-  admitting_source_value      STRING             ,
-  discharge_to_source_value   STRING             ,
-  visit_detail_parent_id      INT64              ,
-  visit_occurrence_id         INT64     not null
+  visit_detail_id                    INT64     not null ,
+  person_id                          INT64     not null ,
+  visit_detail_concept_id            INT64     not null ,
+  visit_detail_start_DATE            DATE      not null ,
+  visit_detail_start_DATETIME        DATETIME           ,
+  visit_detail_end_DATE              DATE      not null ,
+  visit_detail_end_DATETIME          DATETIME           ,
+  visit_deatil_type_concept_id       INT64     not null ,
+  provider_id                        INT64              ,
+  care_site_id                       INT64              ,
+  admitting_source_concept_id        INT64              ,
+  discharge_to_concept_id            INT64              ,
+  preceding_visit_detail_id          INT64              ,
+  visit_detail_source_value          STRING             ,
+  visit_deatil_source_concept_id     INT64              ,
+  admitting_source_value             STRING             ,
+  discharge_to_source_value          STRING             ,
+  visit_detail_parent_id             INT64              ,
+  visit_occurrence_id                INT64     not null
 )
 ;
 
@@ -304,7 +305,7 @@ create table procedure_occurrence
   visit_detail_id             INT64              ,
   procedure_source_value		  STRING  	         ,
   procedure_source_concept_id	INT64			         ,
-  modifier_source_value		   STRING   	  
+  modifier_source_value		   STRING
 )
 ;
 
@@ -334,7 +335,7 @@ create table drug_exposure
   drug_source_value				      STRING  	           ,
   drug_source_concept_id		    INT64			           ,
   route_source_value			      STRING  	           ,
-  dose_unit_source_value		    STRING  	  
+  dose_unit_source_value		    STRING
 )
 ;
 
@@ -356,7 +357,7 @@ create table device_exposure
   visit_occurrence_id			        INT64			           ,
   visit_detail_id                 INT64                ,
   device_source_value			        STRING    	         ,
-  device_source_concept_id		    INT64			  
+  device_source_concept_id		    INT64
 )
 ;
 
@@ -379,7 +380,7 @@ create table condition_occurrence
   condition_source_value		    STRING  	         ,
   condition_source_concept_id	  INT64			         ,
   condition_status_source_value	STRING             ,
-  condition_status_concept_id	  INT64			
+  condition_status_concept_id	  INT64
 )
 ;
 
@@ -406,7 +407,7 @@ create table measurement
   measurement_source_value		  STRING             ,
   measurement_source_concept_id	INT64			         ,
   unit_source_value				      STRING  	         ,
-  value_source_value			      STRING  	
+  value_source_value			      STRING
 )
 ;
 
@@ -427,7 +428,7 @@ create table note
   provider_id					  INT64			           ,
   visit_occurrence_id		INT64			           ,
   visit_detail_id       INT64                ,
-  note_source_value			STRING  		
+  note_source_value			STRING
 )
 ;
 
@@ -448,7 +449,7 @@ create table note_nlp
   nlp_DATETIME					      DATETIME		         ,
   term_exists					        STRING   		         ,
   term_temporal					      STRING   		         ,
-  term_modifiers				      STRING    	
+  term_modifiers				      STRING
 )
 ;
 
@@ -473,7 +474,7 @@ create table observation
   observation_source_value		  STRING  	     ,
   observation_source_concept_id	INT64			     ,
   unit_source_value				      STRING  	     ,
-  qualifier_source_value			  STRING  	
+  qualifier_source_value			  STRING
 )
 ;
 
@@ -498,7 +499,7 @@ create table location
   state							    STRING   		       ,
   zip							      STRING   	         ,
   county							  STRING    		     ,
-  location_source_value STRING    		
+  location_source_value STRING
 )
 ;
 
@@ -510,7 +511,7 @@ create table care_site
   place_of_service_concept_id	  INT64			           ,
   location_id						        INT64			           ,
   care_site_source_value			  STRING    		       ,
-  place_of_service_source_value STRING    		
+  place_of_service_source_value STRING
 )
 ;
 
@@ -529,7 +530,7 @@ create table provider
   specialty_source_value			STRING    		       ,
   specialty_source_concept_id	INT64			           ,
   gender_source_value			    STRING    		       ,
-  gender_source_concept_id		INT64			  
+  gender_source_concept_id		INT64
 )
 ;
 
@@ -553,7 +554,7 @@ create table payer_plan_period
   family_source_value			      STRING    	       ,
   stop_reason_concept_id        INT64              ,
   stop_reason_source_value      STRING             ,
-  stop_reason_source_concept_id INT64       
+  stop_reason_source_concept_id INT64
 )
 ;
 
@@ -581,7 +582,7 @@ create table cost
   revenue_code_concept_id		INT64			         ,
   revenue_code_source_value  STRING            ,
   drg_concept_id			      INT64		           ,
-  drg_source_value			    STRING   	
+  drg_source_value			    STRING
 )
 ;
 
@@ -606,7 +607,7 @@ create table cohort_attribute
   cohort_end_DATE				  DATE			not null ,
   attribute_definition_id INT64		  not null ,
   value_as_number				  FLOAT64			       ,
-  value_as_concept_id			INT64		
+  value_as_concept_id			INT64
 )
 ;
 
@@ -620,7 +621,7 @@ create table drug_era
   drug_era_start_DATE	DATE			not null ,
   drug_era_end_DATE		DATE		  not null ,
   drug_exposure_count	INT64	             ,
-  gap_days						INT64			
+  gap_days						INT64
 )
 ;
 
@@ -647,6 +648,6 @@ create table condition_era
   condition_concept_id			  INT64			not null ,
   condition_era_start_DATE		DATE			not null ,
   condition_era_end_DATE			DATE			not null ,
-  condition_occurrence_count	INT64			
+  condition_occurrence_count	INT64
 )
 ;

Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/CONDITION_OCCURRENCE.md

@@ -16,11 +16,11 @@ Field|Required|Type|Description
 | stop_reason                    | No        | varchar(20)  | The reason that the condition was no longer present, as indicated in the source data.                                                                                                                            |
 | provider_id                    | No        | integer      | A foreign key to the Provider in the PROVIDER table who was responsible for capturing (diagnosing) the Condition.                                                                                                |
 | visit_occurrence_id            | No        | integer      | A foreign key to the visit in the VISIT_OCCURRENCE table during which the Condition was determined (diagnosed).                                                                                                  |
-| visit_detail_id                | No        | integer      | A foreign key to the visit in the VISIT_DETAIL table during which the Condition was determined (diagnosed).                                                                                                           | visit_detail_id            | No        | integer      | A foreign key to the visit in the VISIT_DETAIL table during which the Condition was determined (diagnosed).                                                                                                             |
+| visit_detail_id                | No        | integer      | A foreign key to the visit in the VISIT_DETAIL table during which the Condition was determined (diagnosed).    																								   |
 | condition_source_value         | No        | varchar(50)  | The source code for the condition as it appears in the source data. This code is mapped to a standard condition concept in the Standardized Vocabularies and the original code is stored here for reference.     |
 | condition_source_concept_id    | No        | integer      | A foreign key to a Condition Concept that refers to the code used in the source.                                                                                                                                 |
-| condition_status_source_value  | No        | varchar(50)  | The source code for the condition status as it appears in the source data.    |
-| condition_status_concept_id    | No        | integer      | A foreign key to the predefined Concept in the Standard Vocabulary reflecting the condition status |                                                                                                                               |
+| condition_status_source_value  | No        | varchar(50)  | The source code for the condition status as it appears in the source data.    																																   |
+| condition_status_concept_id    | No        | integer      | A foreign key to the predefined Concept in the Standard Vocabulary reflecting the condition status 																											   |                                                                                                                               
 
 ### Conventions 
 

Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/DEVICE_EXPOSURE.md

@@ -16,7 +16,7 @@ Field|Required|Type|Description
 |visit_occurrence_id|No|integer|A foreign key to the visit in the VISIT_OCCURRENCE table during which the device was used.|
 |visit_detail_id|No|integer|A foreign key to the visit detail in the VISIT_DETAIL table during which the Drug Exposure was initiated.|
 |device_source_value|No|varchar(50)|The source code for the Device as it appears in the source data. This code is mapped to a standard Device Concept in the Standardized Vocabularies and the original code is stored here for reference.|
-|device_source_ concept_id|No|integer|A foreign key to a Device Concept that refers to the code used in the source.|
+|device_source_concept_id|No|integer|A foreign key to a Device Concept that refers to the code used in the source.|
 
 ### Conventions 
 

Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/NOTE_NLP.md

@@ -12,8 +12,8 @@ note_nlp_concept_id 		| No | integer | A foreign key to the predefined Concept i
 note_nlp_source_concept_id  | No | integer | A foreign key to a Concept that refers to the code in the source vocabulary used by the NLP system
 nlp_system 					| No | varchar(250) | Name and version of the NLP system that extracted the term.Useful for data provenance.
 nlp_date 					| Yes | date | The date of the note processing.Useful for data provenance.
-nlp_date_time 				| No | datetime | The date and time of the note processing. Useful for data provenance.
-term_exists 				| No | varchar(1) | A summary modifier that signifies presence or absence of the term for a given patient. Useful for quick querying. *
+nlp_datetime 				| No | datetime | The date and time of the note processing. Useful for data provenance.
+term_exists 				| No | varchar(1) | A summary modifier that signifies presence or absence of the term for a given patient. Useful for quick querying.
 term_temporal 				| No | varchar(50) | An optional time modifier associated with the extracted term. (for now “past” or “present” only). Standardize it later.
 term_modifiers 				| No | varchar(2000) | A compact description of all the modifiers of the specific term extracted by the NLP system. (e.g. “son has rash” ? “negated=no,subject=family, certainty=undef,conditional=false,general=false”).
 

Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/Standardized-Clinical-Data-Tables.md

@@ -3,6 +3,7 @@
 [SPECIMEN](https://github.com/OHDSI/CommonDataModel/wiki/SPECIMEN)  
 [DEATH](https://github.com/OHDSI/CommonDataModel/wiki/DEATH)  
 [VISIT_OCCURRENCE](https://github.com/OHDSI/CommonDataModel/wiki/VISIT_OCCURRENCE)  
+[VISIT_DETAIL](https://github.com/OHDSI/CommonDataModel/wiki/VISIT_DETAIL)  
 [PROCEDURE_OCCURRENCE](https://github.com/OHDSI/CommonDataModel/wiki/PROCEDURE_OCCURRENCE)  
 [DRUG_EXPOSURE](https://github.com/OHDSI/CommonDataModel/wiki/DRUG_EXPOSURE)  
 [DEVICE_EXPOSURE](https://github.com/OHDSI/CommonDataModel/wiki/DEVICE_EXPOSURE)  

Documentation/CommonDataModel_Wiki_Files/StandardizedMetadata/CDM_SOURCE.md

@@ -7,7 +7,7 @@ Field|Required|Type|Description
 |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|
+|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|

Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md

@@ -1,7 +1,7 @@
 The ATTRIBUTE_DEFINITION table contains records defining Attributes, or covariates, to members of a Cohort through an associated description and syntax and upon instantiation (execution of the algorithm) placed into the COHORT_ATTRIBUTE table. Attributes are derived elements that can be selected or calculated for a subject in a Cohort. The ATTRIBUTE_DEFINITION table provides a standardized structure for maintaining the rules governing the calculation of covariates for a subject in a Cohort, and can store operational programming code to instantiate the Attributes for a given Cohort within the OMOP Common Data Model.
 
 Field|Required|Type|Description
-:-------------------------|:--------|:-----|:--------------------------------------
+:-------------------------|:------|:--------------|:--------------------------------------
 |attribute_definition_id|Yes|integer|A unique identifier for each Attribute.|
 |attribute_name|Yes|varchar(255)|A short description of the Attribute.|
 |attribute_description|No|varchar(MAX)|A complete description of the Attribute definition|

Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md

@@ -1,14 +1,14 @@
 The COHORT_DEFINITION table contains records defining a Cohort derived from the data through the associated description and syntax and upon instantiation (execution of the algorithm) placed into the COHORT table. Cohorts are a set of subjects that satisfy a given combination of inclusion criteria for a duration of time. The COHORT_DEFINITION table provides a standardized structure for maintaining the rules governing the inclusion of a subject into a cohort, and can store operational programming code to instantiate the cohort within the OMOP Common Data Model.
 
 Field|Required|Type|Description
-:------------------------------|:--------|:-----|:-----------------------------------------------
+:------------------------------|:--------|:--------------|:-----------------------------------------------
 |cohort_definition_id|Yes|integer|A unique identifier for each Cohort.|
 |cohort_definition_name|Yes|varchar(255)|A short description of the Cohort.|
 |cohort_definition_description|No|varchar(MAX)|A complete description of the 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|
 |cohort_definition_syntax|No|varchar(MAX)|Syntax or code to operationalize the Cohort definition|
 |subject_concept_id|Yes|integer|A foreign key to the Concept to which defines the domain of subjects that are members of the cohort (e.g., Person, Provider, Visit).|
-|cohort_initiation_date|No|Date|A date to indicate when the Cohort was instantiated in the COHORT table|
+|cohort_initiation_date|No|Date|A date to indicate when the Cohort was initiated in the COHORT table|
 
 ### Conventions
   * The cohort_definition_syntax does not prescribe any specific syntax or programming language. Typically, it would be any flavor SQL, a cohort definition language, or a free-text description of the algorithm. 

Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md

@@ -1,6 +1,6 @@
 The CONCEPT_SYNONYM table is used to store alternate names and descriptions for Concepts. 
 
-|Field|Required|Type|Description|
+Field|Required|Type|Description
 :---------------------|:---------|:------------|:------------------------
 |concept_id|Yes|Integer|A foreign key to the Concept in the CONCEPT table.|
 |concept_synonym_name|Yes|varchar(1000)|The alternative name for the Concept.|