OMOP 5.3 - PostgreSQL MAJ (Visit Detail)

Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/CONDITION_OCCURRENCE.md

@@ -15,11 +15,12 @@ Field|Required|Type|Description
 | condition_type_concept_id      | Yes       | integer      | A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the source data from which the condition was recorded, the level of standardization, and the type of occurrence.  |
 | 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_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).                                                                                                             |
 | 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_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

@@ -15,7 +15,7 @@ Field|Required|Type|Description
 |provider_id|No|integer|A foreign key to the provider in the PROVIDER table who initiated of administered the Device.|
 |visit_occurrence_id|No|integer|A foreign key to the visit in the VISIT table during which the device was used.|
 |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.|
 |visit_detail_id|No|integer|A foreign key to the visit in the visit-detail table during which the Drug Exposure was initiated.|
 
 ### Conventions 

Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/NOTE_NLP.md

@@ -2,20 +2,20 @@ The NOTE_NLP table will encode all output of NLP on clinical notes. Each row rep
 
 Field | Required | Type | Description
 :------------------------------- | :-------- | :------------ | :---------------------------------------------------
-note_nlp_id | Yes | Big Integer | A unique identifier for each term extracted from a note.
-note_id | Yes | integer | A foreign key to the Note table note the term was extracted from.
-section_concept_id | No | integer | A foreign key to the predefined Concept in the Standardized Vocabularies representing the section of the extracted term.
-snippet | No | varchar(250) | A small window of text surrounding the term.
-offset | No | varchar(50) | Character offset of the extracted term in the input note.
-lexical_variant | Yes | varchar(250) | Raw text extracted from the NLP tool.
-note_nlp_concept_id | No | integer | A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the normalized concept for the extracted term. Domain of the term is represented as part of the Concept table.
-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. *
-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�).
+|note_nlp_id | Yes | Big Integer | A unique identifier for each term extracted from a note.|
+|note_id | Yes | integer | A foreign key to the Note table note the term was extracted from.|
+|section_concept_id | No | integer | A foreign key to the predefined Concept in the Standardized Vocabularies representing the section of the extracted term.|
+|snippet | No | varchar(250) | A small window of text surrounding the term.|
+|offset | No | varchar(50) | Character offset of the extracted term in the input note.|
+|lexical_variant | Yes | varchar(250) | Raw text extracted from the NLP tool.|
+|note_nlp_concept_id | No | integer | A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the normalized concept for the extracted term. Domain of the term is represented as part of the Concept table.|
+|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_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�).|
 
 ### Conventions
 

Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/VISIT_DETAIL.md

@@ -16,7 +16,7 @@ Field|Required|Type|Description
 |visit_source_value|No|string(50)|The source code for the visit as it appears in the source data.|
 |visit_source_concept_id|No|Integer|A foreign key to a Concept that refers to the code used in the source.|
 |admitting_source_value	|Varchar(50)|	No|	The source code for the admitting source as it appears in the source data.|
-|admitting_source_concept_id|	|Integer	|No	|A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the admitting source for a visit.|
+|admitting_source_concept_id	|Integer	|No	|A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the admitting source for a visit.|
 |discharge_to_source_value|	Varchar(50)|	No|	The source code for the discharge disposition as it appears in the source data.|
 |discharge_to_concept_id|	Integer	|No	|A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the discharge disposition for a visit.|
 |preceding_visit_detail_id	|Integer|	No	|A foreign key to the VISIT_DETAIL table of the visit immediately preceding this visit|

Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/VISIT_OCCURRENCE.md

@@ -14,7 +14,7 @@ Field|Required|Type|Description
 |care_site_id|No|integer|A foreign key to the care site in the care site table that was visited.|
 |visit_source_value|No|string(50)|The source code for the visit as it appears in the source data.|
 |visit_source_concept_id|No|Integer|A foreign key to a Concept that refers to the code used in the source.|
-|admitting_source_concept_id|	|Integer	|No	|A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the admitting source for a visit.|
+|admitting_source_concept_id|	Integer	|No	|A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the admitting source for a visit.|
 |admitting_source_value	|Varchar(50)|	No|	The source code for the admitting source as it appears in the source data.|
 |discharge_to_concept_id|	Integer	|No	|A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the discharge disposition for a visit.|
 |discharge_to_source_value|	Varchar(50)|	No|	The source code for the discharge disposition as it appears in the source data.|
@@ -39,4 +39,4 @@ Field|Required|Type|Description
 	* Patient self-discharge against medical advice: 4021968
   * In the case where a patient died during admission (Visit_Occurrence.discharge_disposition_concept_id = 4216643 �Patient died�), a record in the Death table should be created with death_type_concept_id = 44818516 (�EHR discharge status "Expired").
   * PRECEDING_VISIT_ID can be used to link a visit immediately preceding the current visit
-  * Some EMR systems combine emergency room followed by inpatient admission into one visit, and it is close to impossible to separate the two. To annotate this visit type, a new visit concept �Emergency Room and Inpatient Visit� was added (CONCEPT_ID 262).
+  * Some EMR systems combine emergency room followed by inpatient admission into one visit, and it is close to impossible to separate the two. To annotate this visit type, a new visit concept �Emergency Room and Inpatient Visit� was added (CONCEPT_ID 262).

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|
@@ -17,4 +17,4 @@ Field|Required|Type|Description
 
   * 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'.
+  * The version of the vocabulary can be obtained from the vocabulary_name field in the VOCABULARY table for the record where vocabulary_id='None'.

Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md

@@ -8,7 +8,7 @@ Field|Required|Type|Description
 |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|CLOB|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_instantiation_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.|

Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/RELATIONSHIP.md

@@ -1,6 +1,6 @@
 The RELATIONSHIP table provides a reference list of all types of relationships that can be used to associate any two concepts in the CONCEPT_RELATIONSHP table. 
 
-|Field|Required|Type|Description|
+Field|Required|Type|Description|
 :-----------------------|:--------|:------------|:-----------------------------------------
 |relationship_id|Yes|varchar(20)| The type of relationship captured by the relationship record.|
 |relationship_name|Yes|varchar(255)| The text that describes the relationship type.|
@@ -289,4 +289,4 @@ Previous Relationship_id|Version 5 Relationship_id
 |357|SNOMED meas - HCPCS|
 |358|HCPCS - SNOMED meas|
 |359|Domain subsumes|
-|360|Is domain|
+|360|Is domain|