mz-health/OMOP
mz-health
/
OMOP
mirror of https://github.com/OHDSI/CommonDataModel.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Add all comments

This commit is contained in:
parisni 2017-09-10 00:48:28 +02:00
parent 2614905905
commit 2420ca1301
6 changed files with 452 additions and 138 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/CONDITION_OCCURRENCE.md
View File

@ -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

28
Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/NOTE_NLP.md
View File

@ -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_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”).|
### Conventions

41
Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/CONDITION_OCCURRENCE.md
View File

@ -1,41 +0,0 @@
Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization, for example:
* Medical claims data include diagnoses coded in ICD-9-CM that are submitted as part of a reimbursement claim for health services and
* EHRs may capture Person Conditions in the form of diagnosis codes or symptoms.
Field|Required|Type|Description
:--------------------------------|:--------|:------------|:------------------------------------------------------------
| condition_occurrence_id | Yes | integer | A unique identifier for each Condition Occurrence event. |
| person_id | Yes | integer | A foreign key identifier to the Person who is experiencing the condition. The demographic details of that Person are stored in the PERSON table. |
| condition_concept_id | Yes | integer | A foreign key that refers to a Standard Condition Concept identifier in the Standardized Vocabularies. |
| condition_start_date | Yes | date | The date when the instance of the Condition is recorded. |
| condition_start_datetime | No | datetime | The date and time when the instance of the Condition is recorded. |
| condition_end_date | No | date | The date when the instance of the Condition is considered to have ended. |
| condition_end_datetime | No | date | The date when the instance of the Condition is considered to have ended. |
| 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). |
| 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 |
### Conventions
* Valid Condition Concepts belong to the "Condition" domain.
* Condition records are typically inferred from diagnostic codes recorded in the source data. Such code system, like ICD-9-CM, ICD-10-CM, Read etc., provide a comprehensive coverage of conditions. However, if the diagnostic code in the source does not define a condition, but rather an observation or a procedure, then such information is not stored in the CONDITION_OCCURRENCE table, but in the respective tables instead.
* Source Condition identifiers are mapped to Standard Concepts for Conditions in the Standardized Vocabularies. When the source code cannot be translated into a Standard Concept, a CONDITION_OCCURRENCE entry is stored with only the corresponding source_concept_id and source_value, while the condition_concept_id is set to 0.
* Family history and past diagnoses ("history of") are not recorded in the CONDITION_OCCURRENCE table. Instead, they are listed in the OBSERVATION table.
* Codes written in the process of establishing the diagnosis, such as "question of" of and "rule out", are not represented here. Instead, they are listed in the OBSERVATION table, if they are used for analyses.
* A Condition Occurrence Type is assigned based on the data source and type of condition attribute, for example:
* ICD-9-CM Primary Diagnosis from inpatient and outpatient Claims
* ICD-9-CM Secondary Diagnoses from inpatient and outpatient Claims
* Diagnoses or problems recorded in an EHR.
* The Stop Reason indicates why a Condition is no longer valid with respect to the purpose within the source data. Typical values include "Discharged", "Resolved", etc. Note that a Stop Reason does not necessarily imply that the condition is no longer occurring.
* Condition source codes are typically ICD-9-CM, Read or ICD-10 diagnosis codes from medical claims or discharge status/visit diagnosis codes from EHRs.
* Presently, there is no designated vocabulary, domain, or class that represents condition status. The following concepts from SNOMED are recommended:
* Admitting diagnosis: 4203942
* Final diagnosis: 4230359 <20> should also be used for <20>Discharge diagnosis<69>
* Preliminary diagnosis: 4033240

50
Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/NOTE_NLP.md
View File

@ -1,50 +0,0 @@
The NOTE_NLP table will encode all output of NLP on clinical notes. Each row represents a single extracted term from a note.
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”).|
### Conventions
**Term_exists**
Term_exists is defined as a flag that indicates if the patient actually has or had the condition. Any of the following modifiers would make Term_exists false:
* Negation = true
* Subject = [anything other than the patient]
* Conditional = true
* Rule_out = true
* Uncertain = very low certainty or any lower certainties
A complete lack of modifiers would make Term_exists true.
For the modifiers that are there, they would have to have these values:
* Negation = false
* Subject = patient
* Conditional = false
* Rule_out = false
* Uncertain = true or high or moderate or even low (could argue about low)
**Term_temporal**
Term_temporal is to indicate if a condition is “present” or just in the “past”.
The following would be past:
* History = true
* Concept_date = anything before the time of the report
**Term_modifiers**
Term_modifiers will concatenate all modifiers for different types of entities (conditions, drugs, labs etc) into one string. Lab values will be saved as one of the modifiers. A list of allowable modifiers (e.g., signature for medications) and their possible values will be standardized later.

308
PostgreSQL/OMOP CDM comments - PostgreSQL.sql
View File

@ -1,3 +1,11 @@
--
--CLINICAL
--
-- VISIT_OCCURENCE
COMMENT ON COLUMN omop.visit_occurence.visit_occurrence_id IS 'A unique identifier for each Person'';s visit or encounter at a healthcare provider.';
COMMENT ON COLUMN omop.visit_occurence.person_id IS 'A foreign key identifier to the Person for whom the visit is recorded. The demographic details of that Person are stored in the PERSON table.';
@ -16,6 +24,8 @@ COMMENT ON COLUMN omop.visit_occurence.admitting_source_value IS ' The source c
COMMENT ON COLUMN omop.visit_occurence.discharge_to_concept_id IS 'A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the discharge disposition for a visit.';
COMMENT ON COLUMN omop.visit_occurence.discharge_to_source_value IS ' The source code for the discharge disposition as it appears in the source data.';
COMMENT ON COLUMN omop.visit_occurence.preceding_visit_occurrence_id IS 'A foreign key to the VISIT_OCCURRENCE table of the visit immediately preceding this visit';
-- CONDITION_OCCURENCE
COMMENT ON COLUMN omop.condition_occurence. condition_occurrence_id IS ' A unique identifier for each Condition Occurrence event. ';
COMMENT ON COLUMN omop.condition_occurence. person_id IS ' A foreign key identifier to the Person who is experiencing the condition. The demographic details of that Person are stored in the PERSON table. ';
@ -33,6 +43,8 @@ COMMENT ON COLUMN omop.condition_occurence. condition_source_value IS '
COMMENT ON COLUMN omop.condition_occurence. condition_source_concept_id IS ' A foreign key to a Condition Concept that refers to the code used in the source. ';
COMMENT ON COLUMN omop.condition_occurence. condition_status_source_value IS ' The source code for the condition status as it appears in the source data. ';
COMMENT ON COLUMN omop.condition_occurence. condition_status_concept_id IS ' A foreign key to the predefined concept in the standard vocabulary reflecting the condition status ';
-- DEATH
COMMENT ON COLUMN omop.death.person_id IS 'A foreign key identifier to the deceased person. The demographic details of that person are stored in the person table.';
COMMENT ON COLUMN omop.death.death_date IS 'The date the person was deceased. If the precise date including day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day.';
@ -41,6 +53,8 @@ COMMENT ON COLUMN omop.death.death_type_concept_id IS 'A foreign key referring t
COMMENT ON COLUMN omop.death.cause_concept_id IS 'A foreign key referring to a standard concept identifier in the Standardized Vocabularies for conditions.';
COMMENT ON COLUMN omop.death.cause_source_value IS 'The source code for the cause of death as it appears in the source data. This code is mapped to a standard concept in the Standardized Vocabularies and the original code is, stored here for reference.';
COMMENT ON COLUMN omop.death.cause_source_concept_id IS 'A foreign key to the concept that refers to the code used in the source. Note, this variable name is abbreviated to ensure it will be allowable across database platforms.';
-- DEVICE_EXPOSURE
COMMENT ON COLUMN omop.device_exposure.device_exposure_id IS 'A system-generated unique identifier for each Device Exposure.';
COMMENT ON COLUMN omop.device_exposure.person_id IS 'A foreign key identifier to the Person who is subjected to the Device. The demographic details of that person are stored in the Person table.';
@ -57,6 +71,8 @@ COMMENT ON COLUMN omop.device_exposure.visit_occurrence_id IS 'A foreign key to
COMMENT ON COLUMN omop.device_exposure.device_source_value IS '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.';
COMMENT ON COLUMN omop.device_exposure.device_source_ concept_id IS 'A foreign key to a Device Concept that refers to the code used in the source.';
COMMENT ON COLUMN omop.device_exposure.visit_detail_id IS 'A foreign key to the visit in the visit-detail table during which the Drug Exposure was initiated.';
-- DRUG_EXPOSURE
COMMENT ON COLUMN omop.drug_exposure.drug_exposure_id IS 'A system-generated unique identifier for each Drug utilization event.';
COMMENT ON COLUMN omop.drug_exposure.person_id IS 'A foreign key identifier to the person who is subjected to the Drug. The demographic details of that person are stored in the person table.';
@ -81,12 +97,16 @@ COMMENT ON COLUMN omop.drug_exposure.drug_source_concept_id IS 'A foreign key to
COMMENT ON COLUMN omop.drug_exposure.route_source_value IS 'The information about the route of administration as detailed in the source.';
COMMENT ON COLUMN omop.drug_exposure.dose_unit_source_value IS 'The information about the dose unit as detailed in the source.';
COMMENT ON COLUMN omop.drug_exposure.visit_detail_id IS 'A foreign key to the visit in the VISIT_DETAIL table during which the Drug Exposure was initiated.';
-- FACT_RELATIONSHIP
COMMENT ON COLUMN omop.FACT_RELATIONSHIP.domain_concept_id_1 IS 'The concept representing the domain of fact one, from which the corresponding table can be inferred.';
COMMENT ON COLUMN omop.FACT_RELATIONSHIP.fact_id_1 IS 'The unique identifier in the table corresponding to the domain of fact one.';
COMMENT ON COLUMN omop.FACT_RELATIONSHIP.domain_concept_id_2 IS 'The concept representing the domain of fact two, from which the corresponding table can be inferred.';
COMMENT ON COLUMN omop.FACT_RELATIONSHIP.fact_id_2 IS 'The unique identifier in the table corresponding to the domain of fact two.';
COMMENT ON COLUMN omop.FACT_RELATIONSHIP.relationship_concept_id IS 'A foreign key to a Standard Concept ID of relationship in the Standardized Vocabularies.';
-- MEASUREMENT
COMMENT ON COLUMN omop.MEASUREMENT.measurement_id IS 'A unique identifier for each Measurement.';
COMMENT ON COLUMN omop.MEASUREMENT.person_id IS 'A foreign key identifier to the Person about whom the measurement was recorded. The demographic details of that Person are stored in the PERSON table.';
@ -107,6 +127,8 @@ COMMENT ON COLUMN omop.MEASUREMENT.measurement_source_value IS 'The Measurement
COMMENT ON COLUMN omop.MEASUREMENT.measurement_source_concept_id IS 'A foreign key to a Concept in the Standard Vocabularies that refers to the code used in the source.';
COMMENT ON COLUMN omop.MEASUREMENT.unit_source_value IS 'The source code for the unit as it appears in the source data. This code is mapped to a standard unit concept in the Standardized Vocabularies and the original code is stored here for reference.';
COMMENT ON COLUMN omop.MEASUREMENT.value_source_value IS 'The source value associated with the content of the value_as_number or value_as_concept_id as stored in the source data.';
-- NOTE
COMMENT ON COLUMN omop.NOTE.note_id IS 'A unique identifier for each note.';
COMMENT ON COLUMN omop.NOTE.person_id IS 'A foreign key identifier to the Person about whom the Note was recorded. The demographic details of that Person are stored in the PERSON table.';
@ -121,6 +143,8 @@ COMMENT ON COLUMN omop.NOTE.language_concept_id IS 'A foreign key to the predef
COMMENT ON COLUMN omop.NOTE.provider_id IS 'A foreign key to the Provider in the PROVIDER table who took the Note.';
COMMENT ON COLUMN omop.NOTE.note_source_value IS 'The source value associated with the origin of the note';
COMMENT ON COLUMN omop.NOTE.visit_occurrence_id IS 'Foreign key to the Visit in the VISIT_OCCURRENCE table when the Note was taken.';
-- VISIT_DETAIL
COMMENT ON COLUMN omop.VISIT_DETAIL.visit_detail_id IS 'A unique identifier for each Person'';s visit or encounter at a healthcare provider.';
COMMENT ON COLUMN omop.VISIT_DETAIL.person_id IS 'A foreign key identifier to the Person for whom the visit is recorded. The demographic details of that Person are stored in the PERSON table.';
@ -141,6 +165,8 @@ COMMENT ON COLUMN omop.VISIT_DETAIL.discharge_to_concept_id IS 'A foreign key to
COMMENT ON COLUMN omop.VISIT_DETAIL.preceding_visit_detail_id IS 'A foreign key to the VISIT_DETAIL table of the visit immediately preceding this visit';
COMMENT ON COLUMN omop.VISIT_DETAIL.visit_detail_parent_id IS 'A foreign key to the VISIT_DETAIL table record to represent the immediate parent visit-detail record.';
COMMENT ON COLUMN omop.VISIT_DETAIL.visit_occurrence_id IS 'A foreign key that refers to the record in the VISIT_OCCURRENCE table. This is a required field, because for every visit_detail is a child of visit_occurrence and cannot exist without a corresponding parent record in visit_occurrence.';
-- SPECIMEN
COMMENT ON COLUMN omop.SPECIMEN.specimen_id IS 'A unique identifier for each specimen.';
COMMENT ON COLUMN omop.SPECIMEN.person_id IS 'A foreign key identifier to the Person for whom the Specimen is recorded.';
@ -157,6 +183,8 @@ COMMENT ON COLUMN omop.SPECIMEN.specimen_source_value IS 'The Specimen value as
COMMENT ON COLUMN omop.SPECIMEN.unit_source_value IS 'The information about the Unit as detailed in the source.';
COMMENT ON COLUMN omop.SPECIMEN.anatomic_site_source_value IS 'The information about the anatomic site as detailed in the source.';
COMMENT ON COLUMN omop.SPECIMEN.disease_status_source_value IS 'The information about the disease status as detailed in the source.';
-- PROCEDURE_OCCURRENCE
COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.procedure_occurrence_id IS 'A system-generated unique identifier for each Procedure Occurrence.';
COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.person_id IS 'A foreign key identifier to the Person who is subjected to the Procedure. The demographic details of that Person are stored in the PERSON table.';
@ -172,6 +200,8 @@ COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.procedure_source_value IS 'The sourc
COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.procedure_source_concept_id IS 'A foreign key to a Procedure Concept that refers to the code used in the source.';
COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.qualifier_source_value IS 'The source code for the qualifier as it appears in the source data.';
COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.visit_detail_id IS 'A foreign key to the visit in the visit table during which the Procedure was carried out.';
-- PERSON
COMMENT ON COLUMN omop.PERSON.person_id IS 'A unique identifier for each person.';
COMMENT ON COLUMN omop.PERSON.gender_concept_id IS 'A foreign key that refers to an identifier in the CONCEPT table for the unique gender of the person.';
@ -191,12 +221,16 @@ COMMENT ON COLUMN omop.PERSON.race_source_value IS 'The source code for the race
COMMENT ON COLUMN omop.PERSON.race_source_concept_id IS 'A foreign key to the race concept that refers to the code used in the source.';
COMMENT ON COLUMN omop.PERSON.ethnicity_source_value IS 'The source code for the ethnicity of the person as it appears in the source data. The person ethnicity is mapped to a standard ethnicity concept in the Standardized Vocabularies and the original code is, stored here for reference.';
COMMENT ON COLUMN omop.PERSON.ethnicity_source_concept_id IS 'A foreign key to the ethnicity concept that refers to the code used in the source.';
-- OBSERVATION_PERIOD
COMMENT ON COLUMN omop.OBSERVATION_PERIOD.observation_period_id IS 'A unique identifier for each observation period.';
COMMENT ON COLUMN omop.OBSERVATION_PERIOD.person_id IS 'A foreign key identifier to the person for whom the observation period is defined. The demographic details of that person are stored in the person table.';
COMMENT ON COLUMN omop.OBSERVATION_PERIOD.observation_period_start_date IS 'The start date of the observation period for which data are available from the data source.';
COMMENT ON COLUMN omop.OBSERVATION_PERIOD.observation_period_end_date IS 'The end date of the observation period for which data are available from the data source.';
COMMENT ON COLUMN omop.OBSERVATION_PERIOD.period_type_concept_id IS 'A foreign key identifier to the predefined concept in the Standardized Vocabularies reflecting the source of the observation period information';
-- OBSERVATION
COMMENT ON COLUMN omop.OBSERVATION.observation_id IS 'A unique identifier for each observation.';
COMMENT ON COLUMN omop.OBSERVATION.person_id IS 'A foreign key identifier to the Person about whom the observation was recorded. The demographic details of that Person are stored in the PERSON table.';
@ -216,6 +250,8 @@ COMMENT ON COLUMN omop.OBSERVATION.observation_source_value IS 'The observation
COMMENT ON COLUMN omop.OBSERVATION.observation_source_concept_id IS 'A foreign key to a Concept that refers to the code used in the source.';
COMMENT ON COLUMN omop.OBSERVATION.unit_source_value IS 'The source code for the unit as it appears in the source data. This code is mapped to a standard unit concept in the Standardized Vocabularies and the original code is, stored here for reference.';
COMMENT ON COLUMN omop.OBSERVATION.qualifier_source_value IS 'The source value associated with a qualifier to characterize the observation';
-- NOTE_NLP
COMMENT ON COLUMN omop.NOTE_NLP.note_nlp_id IS ' A unique identifier for each term extracted from a note.';
COMMENT ON COLUMN omop.NOTE_NLP.note_id IS ' A foreign key to the Note table note the term was extracted from.';
@ -229,4 +265,274 @@ COMMENT ON COLUMN omop.NOTE_NLP.nlp_system IS ' Name and version of the NLP sys
COMMENT ON COLUMN omop.NOTE_NLP.nlp_date IS ' The date of the note processing.Useful for data provenance.';
COMMENT ON COLUMN omop.NOTE_NLP.nlp_date_time IS ' The date and time of the note processing. Useful for data provenance.';
COMMENT ON COLUMN omop.NOTE_NLP.term_exists IS ' A summary modifier that signifies presence or absence of the term for a given patient. Useful for quick querying. *';
Fichier binaire Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/NOTE_NLP.md correspondant
--
--ECONOMIC
--
-- COST
COMMENT ON COLUMN omop.COST.cost_id IS 'A unique identifier for each COST record.';
COMMENT ON COLUMN omop.COST.cost_event_id IS 'A foreign key identifier to the event (e.g. Measurement, Procedure, Visit, Drug Exposure, etc) record for which cost data are recorded.';
COMMENT ON COLUMN omop.COST.cost_domain_id IS 'The concept representing the domain of the cost event, from which the corresponding table can be inferred that contains the entity for which cost information is recorded.';
COMMENT ON COLUMN omop.COST.cost_type_concept_id IS 'A foreign key identifier to a concept in the CONCEPT table for the provenance or the source of the COST data: Calculated from insurance claim information, provider revenue, calculated from cost-to-charge ratio, reported from accounting database, etc.';
COMMENT ON COLUMN omop.COST.currency_concept_id IS 'A foreign key identifier to the concept representing the 3-letter code used to delineate international currencies, such as USD for US Dollar.';
COMMENT ON COLUMN omop.COST.total_charge IS 'The total amount charged by some provider of goods or services (e.g. hospital, physician pharmacy, dme provider) to payers (insurance companies, the patient).';
COMMENT ON COLUMN omop.COST.total_cost IS 'The cost incurred by the provider of goods or services.';
COMMENT ON COLUMN omop.COST.total_paid IS 'The total amount actually paid from all payers for goods or services of the provider.';
COMMENT ON COLUMN omop.COST.paid_by_payer IS 'The amount paid by the Payer for the goods or services.';
COMMENT ON COLUMN omop.COST.paid_by_patient IS 'The total amount paid by the Person as a share of the expenses.';
COMMENT ON COLUMN omop.COST.paid_patient_copay IS 'The amount paid by the Person as a fixed contribution to the expenses.';
COMMENT ON COLUMN omop.COST.paid_patient_coinsurance IS 'The amount paid by the Person as a joint assumption of risk. Typically, this is a percentage of the expenses defined by the Payer Plan after the Person'';s deductible is exceeded.';
COMMENT ON COLUMN omop.COST.paid_patient_deductible IS 'The amount paid by the Person that is counted toward the deductible defined by the Payer Plan. paid_patient_deductible does contribute to the paid_by_patient variable.';
COMMENT ON COLUMN omop.COST.paid_by_primary IS 'The amount paid by a primary Payer through the coordination of benefits.';
COMMENT ON COLUMN omop.COST.paid_ingredient_cost IS 'The amount paid by the Payer to a pharmacy for the drug, excluding the amount paid for dispensing the drug. paid_ingredient_cost contributes to the paid_by_payer field if this field is populated with a nonzero value.';
COMMENT ON COLUMN omop.COST.paid_dispensing_fee IS 'The amount paid by the Payer to a pharmacy for dispensing a drug, excluding the amount paid for the drug ingredient. paid_dispensing_fee contributes to the paid_by_payer field if this field is populated with a nonzero value.';
COMMENT ON COLUMN omop.COST.payer_plan_period_id IS 'A foreign key to the PAYER_PLAN_PERIOD table, where the details of the Payer, Plan and Family are stored. Record the payer_plan_id that relates to the payer who contributed to the paid_by_payer field.';
COMMENT ON COLUMN omop.COST.amount_allowed IS 'The contracted amount agreed between the payer and provider.';
COMMENT ON COLUMN omop.COST.revenue_code_concept_id IS 'A foreign key referring to a Standard Concept ID in the Standardized Vocabularies for Revenue codes.';
COMMENT ON COLUMN omop.COST.revenue_code_source_value IS 'The source code for the Revenue code as it appears in the source data, stored here for reference.';
COMMENT ON COLUMN omop.COST.drg_concept_id IS 'A foreign key to the predefined concept in the DRG Vocabulary reflecting the DRG for a visit.';
COMMENT ON COLUMN omop.COST.drg_source_value IS ' The 3-digit DRG source code as it appears in the source data.';
-- PAYER_PLAN_PERIOD
COMMENT ON COLUMN omop.PAYER_PLAN_PERIOD.payer_plan_period_id IS 'A identifier for each unique combination of payer, plan, family code and time span.';
COMMENT ON COLUMN omop.PAYER_PLAN_PERIOD.person_id IS 'A foreign key identifier to the Person covered by the payer. The demographic details of that Person are stored in the PERSON table.';
COMMENT ON COLUMN omop.PAYER_PLAN_PERIOD.payer_plan_period_start_date IS 'The start date of the payer plan period.';
COMMENT ON COLUMN omop.PAYER_PLAN_PERIOD.payer_plan_period_end_date IS 'The end date of the payer plan period.';
COMMENT ON COLUMN omop.PAYER_PLAN_PERIOD.payer_source_value IS 'The source code for the payer as it appears in the source data.';
COMMENT ON COLUMN omop.PAYER_PLAN_PERIOD.plan_source_value IS 'The source code for the Person'';s health benefit plan as it appears in the source data.';
COMMENT ON COLUMN omop.PAYER_PLAN_PERIOD.family_source_value IS 'The source code for the Person'';s family as it appears in the source data.';
--
--METADATA
--
-- CDM_SOURCE
COMMENT ON COLUMN omop.CDM_SOURCE.cdm_source_name IS 'The full name of the source';
COMMENT ON COLUMN omop.CDM_SOURCE.cdm_source_abbreviation IS 'An abbreviation of the name';
COMMENT ON COLUMN omop.CDM_SOURCE.cdm_holder IS 'The name of the organization responsible for the development of the CDM instance';
COMMENT ON COLUMN omop.CDM_SOURCE.source_description IS '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.';
COMMENT ON COLUMN omop.CDM_SOURCE.source_documentation_reference IS 'URL or other external reference to location of source documentation';
COMMENT ON COLUMN omop.CDM_SOURCE.cdm_etl _reference IS 'URL or other external reference to location of ETL specification documentation and ETL source code';
COMMENT ON COLUMN omop.CDM_SOURCE.source_release_date IS 'The date for which the source data are most current, such as the last day of data capture';
COMMENT ON COLUMN omop.CDM_SOURCE.cdm_release_date IS 'The date when the CDM was instantiated';
COMMENT ON COLUMN omop.CDM_SOURCE.cdm_version IS 'The version of CDM used';
COMMENT ON COLUMN omop.CDM_SOURCE.vocabulary_version IS 'The version of the vocabulary used';
--
--DERIVED
--
-- COHORT_ATTRIBUTE
COMMENT ON COLUMN omop.COHORT_ATTRIBUTE.cohort_definition_id IS 'A foreign key to a record in the [COHORT_DEFINITION](https://github.com/OHDSI/CommonDataModel/wiki/COHORT_DEFINITION) table containing relevant Cohort Definition information.';
COMMENT ON COLUMN omop.COHORT_ATTRIBUTE.subject_id IS 'A foreign key to the subject in the Cohort. These could be referring to records in the PERSON, PROVIDER, VISIT_OCCURRENCE table.';
COMMENT ON COLUMN omop.COHORT_ATTRIBUTE.cohort_start_date IS 'The date when the Cohort Definition criteria for the Person, Provider or Visit first match.';
COMMENT ON COLUMN omop.COHORT_ATTRIBUTE.cohort_end_date IS 'The date when the Cohort Definition criteria for the Person, Provider or Visit no longer match or the Cohort membership was terminated.';
COMMENT ON COLUMN omop.COHORT_ATTRIBUTE.attribute_definition_id IS 'A foreign key to a record in the [ATTRIBUTE_DEFINITION](https://github.com/OHDSI/CommonDataModel/wiki/ATTRIBUTE_DEFINITION) table containing relevant Attribute Definition information.';
COMMENT ON COLUMN omop.COHORT_ATTRIBUTE.value_as_number IS 'The attribute result stored as a number. This is applicable to attributes where the result is expressed as a numeric value.';
COMMENT ON COLUMN omop.COHORT_ATTRIBUTE.value_as_concept_id IS 'The attribute result stored as a Concept ID. This is applicable to attributes where the result is expressed as a categorical value.';
-- COHORT
COMMENT ON COLUMN omop.COHORT.cohort_definition_id IS 'A foreign key to a record in the COHORT_DEFINITION table containing relevant Cohort Definition information.';
COMMENT ON COLUMN omop.COHORT.subject_id IS 'A foreign key to the subject in the cohort. These could be referring to records in the PERSON, PROVIDER, VISIT_OCCURRENCE table.';
COMMENT ON COLUMN omop.COHORT.cohort_start_date IS 'The date when the Cohort Definition criteria for the Person, Provider or Visit first match.';
COMMENT ON COLUMN omop.COHORT.cohort_end_date IS 'The date when the Cohort Definition criteria for the Person, Provider or Visit no longer match or the Cohort membership was terminated.';
-- CONDITION_ERA
COMMENT ON COLUMN omop.CONDITION_ERA.condition_era_id IS 'A unique identifier for each Condition Era.';
COMMENT ON COLUMN omop.CONDITION_ERA.person_id IS 'A foreign key identifier to the Person who is experiencing the Condition during the Condition Era. The demographic details of that Person are stored in the PERSON table.';
COMMENT ON COLUMN omop.CONDITION_ERA.condition_concept_id IS 'A foreign key that refers to a standard Condition Concept identifier in the Standardized Vocabularies.';
COMMENT ON COLUMN omop.CONDITION_ERA.condition_era_start_date IS 'The start date for the Condition Era constructed from the individual instances of Condition Occurrences. It is the start date of the very first chronologically recorded instance of the condition.';
COMMENT ON COLUMN omop.CONDITION_ERA.condition_era_end_date IS 'The end date for the Condition Era constructed from the individual instances of Condition Occurrences. It is the end date of the final continuously recorded instance of the Condition.';
COMMENT ON COLUMN omop.CONDITION_ERA.condition_occurrence_count IS 'The number of individual Condition Occurrences used to construct the condition era.';
-- DOSE_ERA
COMMENT ON COLUMN omop.DOSE_ERA.dose_era_id IS 'A unique identifier for each Dose Era.';
COMMENT ON COLUMN omop.DOSE_ERA.person_id IS 'A foreign key identifier to the Person who is subjected to the drug during the drug era. The demographic details of that Person are stored in the PERSON table.';
COMMENT ON COLUMN omop.DOSE_ERA.drug_concept_id IS 'A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies for the active Ingredient Concept.';
COMMENT ON COLUMN omop.DOSE_ERA.unit_concept_id IS 'A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies for the unit concept.';
COMMENT ON COLUMN omop.DOSE_ERA.dose_value IS 'The numeric value of the dose.';
COMMENT ON COLUMN omop.DOSE_ERA.dose_era_start_date IS 'The start date for the drug era constructed from the individual instances of drug exposures. It is the start date of the very first chronologically recorded instance of utilization of a drug.';
COMMENT ON COLUMN omop.DOSE_ERA.dose_era_end_date IS 'The end date for the drug era constructed from the individual instance of drug exposures. It is the end date of the final continuously recorded instance of utilization of a drug.';
-- DRUG_ERA
COMMENT ON COLUMN omop.DRUG_ERA.drug_era_id IS 'A unique identifier for each Drug Era.';
COMMENT ON COLUMN omop.DRUG_ERA.person_id IS 'A foreign key identifier to the Person who is subjected to the Drug during the fDrug Era. The demographic details of that Person are stored in the PERSON table.';
COMMENT ON COLUMN omop.DRUG_ERA.drug_concept_id IS 'A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies for the Ingredient Concept.';
COMMENT ON COLUMN omop.DRUG_ERA.drug_era_start_date IS 'The start date for the Drug Era constructed from the individual instances of Drug Exposures. It is the start date of the very first chronologically recorded instance of conutilization of a Drug.';
COMMENT ON COLUMN omop.DRUG_ERA.drug_era_end_date IS 'The end date for the drug era constructed from the individual instance of drug exposures. It is the end date of the final continuously recorded instance of utilization of a drug.';
COMMENT ON COLUMN omop.DRUG_ERA.drug_exposure_count IS 'The number of individual Drug Exposure occurrences used to construct the Drug Era.';
COMMENT ON COLUMN omop.DRUG_ERA.gap_days IS 'The number of days that are not covered by DRUG_EXPOSURE records that were used to make up the era record.';
--
--SYSTEM
--
-- CARE_SITE
COMMENT ON COLUMN omop.CARE_SITE.care_site_id IS 'A unique identifier for each Care Site.';
COMMENT ON COLUMN omop.CARE_SITE.care_site_name IS 'The verbatim description or name of the Care Site as in data source';
COMMENT ON COLUMN omop.CARE_SITE.place_of_service_concept_id IS 'A foreign key that refers to a Place of Service Concept ID in the Standardized Vocabularies.';
COMMENT ON COLUMN omop.CARE_SITE.location_id IS 'A foreign key to the geographic Location in the LOCATION table, where the detailed address information is stored.';
COMMENT ON COLUMN omop.CARE_SITE.care_site_source_value IS 'The identifier for the Care Site in the source data, stored here for reference.';
COMMENT ON COLUMN omop.CARE_SITE.place_of_service_source_value IS 'The source code for the Place of Service as it appears in the source data, stored here for reference.';
-- LOCATION
COMMENT ON COLUMN omop.LOCATION.location_id IS 'A unique identifier for each geographic location.';
COMMENT ON COLUMN omop.LOCATION.address_1 IS 'The address field 1, typically used for the street address, as it appears in the source data.';
COMMENT ON COLUMN omop.LOCATION.address_2 IS 'The address field 2, typically used for additional detail such as buildings, suites, floors, as it appears in the source data.';
COMMENT ON COLUMN omop.LOCATION.city IS 'The city field as it appears in the source data.';
COMMENT ON COLUMN omop.LOCATION.state IS 'The state field as it appears in the source data.';
COMMENT ON COLUMN omop.LOCATION.zip IS 'The zip or postal code.';
COMMENT ON COLUMN omop.LOCATION.county IS 'The county.';
COMMENT ON COLUMN omop.LOCATION.location_source_value IS 'The verbatim information that is used to uniquely identify the location as it appears in the source data.';
-- PROVIDER
COMMENT ON COLUMN omop.PROVIDER.provider_id IS 'A unique identifier for each Provider.';
COMMENT ON COLUMN omop.PROVIDER.provider_name IS 'A description of the Provider.';
COMMENT ON COLUMN omop.PROVIDER.npi IS 'The National Provider Identifier (NPI) of the provider.';
COMMENT ON COLUMN omop.PROVIDER.dea IS 'The Drug Enforcement Administration (DEA) number of the provider.';
COMMENT ON COLUMN omop.PROVIDER.specialty_concept_id IS 'A foreign key to a Standard Specialty Concept ID in the Standardized Vocabularies.';
COMMENT ON COLUMN omop.PROVIDER.care_site_id IS 'A foreign key to the main Care Site where the provider is practicing.';
COMMENT ON COLUMN omop.PROVIDER.year_of_birth IS 'The year of birth of the Provider.';
COMMENT ON COLUMN omop.PROVIDER.gender_concept_id IS 'The gender of the Provider.';
COMMENT ON COLUMN omop.PROVIDER.provider_source_value IS 'The identifier used for the Provider in the source data, stored here for reference.';
COMMENT ON COLUMN omop.PROVIDER.specialty_source_value IS 'The source code for the Provider specialty as it appears in the source data, stored here for reference.';
COMMENT ON COLUMN omop.PROVIDER.specialty_source_concept_id IS 'A foreign key to a Concept that refers to the code used in the source.';
COMMENT ON COLUMN omop.PROVIDER.gender_source_value IS 'The gender code for the Provider as it appears in the source data, stored here for reference.';
COMMENT ON COLUMN omop.PROVIDER.gender_source_concept_id IS 'A foreign key to a Concept that refers to the code used in the source.';
--
--SYSTEM
--
-- ATTRIBUTE_DEFINITION
COMMENT ON COLUMN omop.ATTRIBUTE_DEFINITION.attribute_definition_id IS 'A unique identifier for each Attribute.';
COMMENT ON COLUMN omop.ATTRIBUTE_DEFINITION.attribute_name IS 'A short description of the Attribute.';
COMMENT ON COLUMN omop.ATTRIBUTE_DEFINITION.attribute_description IS 'A complete description of the Attribute definition';
COMMENT ON COLUMN omop.ATTRIBUTE_DEFINITION.attribute_type_concept_id IS 'Type defining what kind of Attribute Definition the record represents and how the syntax may be executed';
COMMENT ON COLUMN omop.ATTRIBUTE_DEFINITION.attribute_syntax IS 'Syntax or code to operationalize the Attribute definition';
-- COHORT_DEFINITION
COMMENT ON COLUMN omop.COHORT_DEFINITION.cohort_definition_id IS 'A unique identifier for each Cohort.';
COMMENT ON COLUMN omop.COHORT_DEFINITION.cohort_definition_name IS 'A short description of the Cohort.';
COMMENT ON COLUMN omop.COHORT_DEFINITION.cohort_definition_description IS 'A complete description of the Cohort definition';
COMMENT ON COLUMN omop.COHORT_DEFINITION.definition_type_concept_id IS 'Type defining what kind of Cohort Definition the record represents and how the syntax may be executed';
COMMENT ON COLUMN omop.COHORT_DEFINITION.cohort_definition_syntax IS 'Syntax or code to operationalize the Cohort definition';
COMMENT ON COLUMN omop.COHORT_DEFINITION.subject_concept_id IS 'A foreign key to the Concept to which defines the domain of subjects that are members of the cohort (e.g., Person, Provider, Visit).';
COMMENT ON COLUMN omop.COHORT_DEFINITION.cohort_instantiation_date IS 'A date to indicate when the Cohort was instantiated in the COHORT table';
-- CONCEPT_ANCESTOR
COMMENT ON COLUMN omop.CONCEPT_ANCESTOR.ancestor_concept_id IS 'A foreign key to the concept in the concept table for the higher-level concept that forms the ancestor in the relationship.';
COMMENT ON COLUMN omop.CONCEPT_ANCESTOR.descendant_concept_id IS 'A foreign key to the concept in the concept table for the lower-level concept that forms the descendant in the relationship.';
COMMENT ON COLUMN omop.CONCEPT_ANCESTOR.min_levels_of_separation IS 'The minimum separation in number of levels of hierarchy between ancestor and descendant concepts. This is an attribute that is used to simplify hierarchic analysis.';
COMMENT ON COLUMN omop.CONCEPT_ANCESTOR.max_levels_of_separation IS 'The maximum separation in number of levels of hierarchy between ancestor and descendant concepts. This is an attribute that is used to simplify hierarchic analysis.';
-- CONCEPT_CLASS
COMMENT ON COLUMN omop.CONCEPT_CLASS.concept_class_id IS 'A unique key for each class.';
COMMENT ON COLUMN omop.CONCEPT_CLASS.concept_class_name IS 'The name describing the Concept Class, e.g. "Clinical Finding", "Ingredient", etc.';
COMMENT ON COLUMN omop.CONCEPT_CLASS.concept_class_concept_id IS 'A foreign key that refers to an identifier in the [CONCEPT](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT) table for the unique Concept Class the record belongs to.';
-- CONCEPT
COMMENT ON COLUMN omop.CONCEPT.concept_id IS 'A unique identifier for each Concept across all domains.';
COMMENT ON COLUMN omop.CONCEPT.concept_name IS 'An unambiguous, meaningful and descriptive name for the Concept.';
COMMENT ON COLUMN omop.CONCEPT.domain_id IS 'A foreign key to the [DOMAIN](https://github.com/OHDSI/CommonDataModel/wiki/DOMAIN) table the Concept belongs to.';
COMMENT ON COLUMN omop.CONCEPT.vocabulary_id IS 'A foreign key to the [VOCABULARY](https://github.com/OHDSI/CommonDataModel/wiki/VOCABULARY) table indicating from which source the Concept has been adapted.';
COMMENT ON COLUMN omop.CONCEPT.concept_class_id IS 'The attribute or concept class of the Concept. Examples are '';Clinical Drug'';, '';Ingredient'';, '';Clinical Finding''; etc.';
COMMENT ON COLUMN omop.CONCEPT.standard_concept IS 'This flag determines where a Concept is a Standard Concept, i.e. is used in the data, a Classification Concept, or a non-standard Source Concept. The allowables values are '';S''; (Standard Concept) and '';C''; (Classification Concept), otherwise the content is NULL.';
COMMENT ON COLUMN omop.CONCEPT.concept_code IS 'The concept code represents the identifier of the Concept in the source vocabulary, such as SNOMED-CT concept IDs, RxNorm RXCUIs etc. Note that concept codes are not unique across vocabularies.';
COMMENT ON COLUMN omop.CONCEPT.valid_start_date IS 'The date when the Concept was first recorded. The default value is 1-Jan-1970, meaning, the Concept has no (known) date of inception.';
COMMENT ON COLUMN omop.CONCEPT.valid_end_date IS 'The date when the Concept became invalid because it was deleted or superseded (updated) by a new concept. The default value is 31-Dec-2099, meaning, the Concept is valid until it becomes deprecated.';
COMMENT ON COLUMN omop.CONCEPT.invalid_reason IS 'Reason the Concept was invalidated. Possible values are D (deleted), U (replaced with an update) or NULL when valid_end_date has the default value.';
-- CONCEPT_RELATIONSHIP
COMMENT ON COLUMN omop.CONCEPT_RELATIONSHIP.concept_id_1 IS 'A foreign key to a Concept in the [CONCEPT](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT) table associated with the relationship. Relationships are directional, and this field represents the source concept designation.';
COMMENT ON COLUMN omop.CONCEPT_RELATIONSHIP.concept_id_2 IS 'A foreign key to a Concept in the [CONCEPT](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT) table associated with the relationship. Relationships are directional, and this field represents the destination concept designation.';
COMMENT ON COLUMN omop.CONCEPT_RELATIONSHIP.relationship_id IS 'A unique identifier to the type or nature of the Relationship as defined in the [RELATIONSHIP](https://github.com/OHDSI/CommonDataModel/wiki/RELATIONSHIP) table.';
COMMENT ON COLUMN omop.CONCEPT_RELATIONSHIP.valid_start_date IS 'The date when the instance of the Concept Relationship is first recorded.';
COMMENT ON COLUMN omop.CONCEPT_RELATIONSHIP.valid_end_date IS 'The date when the Concept Relationship became invalid because it was deleted or superseded (updated) by a new relationship. Default value is 31-Dec-2099.';
COMMENT ON COLUMN omop.CONCEPT_RELATIONSHIP.invalid_reason IS 'Reason the relationship was invalidated. Possible values are '';D''; (deleted), '';U''; (replaced with an update) or NULL when valid_end_date has the default value.';
-- CONCEPT_SYNONYM
COMMENT ON COLUMN omop.CONCEPT_SYNONYM.Field IS 'Description';
COMMENT ON COLUMN omop.CONCEPT_SYNONYM.concept_id IS 'A foreign key to the Concept in the CONCEPT table.';
COMMENT ON COLUMN omop.CONCEPT_SYNONYM.concept_synonym_name IS 'The alternative name for the Concept.';
COMMENT ON COLUMN omop.CONCEPT_SYNONYM.language_concept_id IS 'A foreign key to a Concept representing the language.';
-- DOMAIN
COMMENT ON COLUMN omop.DOMAIN.domain_id IS 'A unique key for each domain.';
COMMENT ON COLUMN omop.DOMAIN.domain_name IS 'The name describing the Domain, e.g. "Condition", "Procedure", "Measurement" etc.';
COMMENT ON COLUMN omop.DOMAIN.domain_concept_id IS 'A foreign key that refers to an identifier in the [CONCEPT](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT) table for the unique Domain Concept the Domain record belongs to.';
-- DRUG_STRENGTH
COMMENT ON COLUMN omop.DRUG_STRENGTH.drug_concept_id IS 'A foreign key to the Concept in the CONCEPT table representing the identifier for Branded Drug or Clinical Drug Concept.';
COMMENT ON COLUMN omop.DRUG_STRENGTH.ingredient_concept_id IS 'A foreign key to the Concept in the CONCEPT table, representing the identifier for drug Ingredient Concept contained within the drug product.';
COMMENT ON COLUMN omop.DRUG_STRENGTH.amount_value IS 'The numeric value associated with the amount of active ingredient contained within the product.';
COMMENT ON COLUMN omop.DRUG_STRENGTH.amount_unit_concept_id IS 'A foreign key to the Concept in the CONCEPT table representing the identifier for the Unit for the absolute amount of active ingredient.';
COMMENT ON COLUMN omop.DRUG_STRENGTH.numerator_value IS 'The numeric value associated with the concentration of the active ingredient contained in the product';
COMMENT ON COLUMN omop.DRUG_STRENGTH.numerator_unit_concept_id IS 'A foreign key to the Concept in the CONCEPT table representing the identifier for the numerator Unit for the concentration of active ingredient.';
COMMENT ON COLUMN omop.DRUG_STRENGTH.denominator_value IS 'The amount of total liquid (or other divisible product, such as ointment, gel, spray, etc.).';
COMMENT ON COLUMN omop.DRUG_STRENGTH.denominator_unit_concept_id IS 'A foreign key to the Concept in the CONCEPT table representing the identifier for the denominator Unit for the concentration of active ingredient.';
COMMENT ON COLUMN omop.DRUG_STRENGTH.box_size IS 'The number of units of Clinical of Branded Drug, or Quantified Clinical or Branded Drug contained in a box as dispensed to the patient';
COMMENT ON COLUMN omop.DRUG_STRENGTH.valid_start_date IS 'The date when the Concept was first recorded. The default value is 1-Jan-1970.';
COMMENT ON COLUMN omop.DRUG_STRENGTH.valid_end_date IS 'The date when the concept became invalid because it was deleted or superseded (updated) by a new Concept. The default value is 31-Dec-2099.';
COMMENT ON COLUMN omop.DRUG_STRENGTH.invalid_reason IS 'Reason the concept was invalidated. Possible values are '';D''; (deleted), '';U''; (replaced with an update) or NULL when valid_end_date has the default value.';
-- RELATIONSHIP
COMMENT ON COLUMN omop.RELATIONSHIP.Field IS 'Description';
COMMENT ON COLUMN omop.RELATIONSHIP.relationship_id IS ' The type of relationship captured by the relationship record.';
COMMENT ON COLUMN omop.RELATIONSHIP.relationship_name IS ' The text that describes the relationship type.';
COMMENT ON COLUMN omop.RELATIONSHIP.is_hierarchical IS 'Defines whether a relationship defines concepts into classes or hierarchies. Values are 1 for hierarchical relationship or 0 if not.';
COMMENT ON COLUMN omop.RELATIONSHIP.defines_ancestry IS 'Defines whether a hierarchical relationship contributes to the concept_ancestor table. These are subsets of the hierarchical relationships. Valid values are 1 or 0.';
COMMENT ON COLUMN omop.RELATIONSHIP.reverse_relationship_id IS 'The identifier for the relationship used to define the reverse relationship between two concepts.';
COMMENT ON COLUMN omop.RELATIONSHIP.relationship_concept_id IS 'A foreign key that refers to an identifier in the CONCEPT table for the unique relationship concept.';
-- SOURCE_TO_CONCEPT_MAP
COMMENT ON COLUMN omop.SOURCE_TO_CONCEPT_MAP.source_code IS 'The source code being translated into a Standard Concept.';
COMMENT ON COLUMN omop.SOURCE_TO_CONCEPT_MAP.source_concept_id IS 'A foreign key to the Source Concept that is being translated into a Standard Concept.';
COMMENT ON COLUMN omop.SOURCE_TO_CONCEPT_MAP.source_vocabulary_id IS 'A foreign key to the VOCABULARY table defining the vocabulary of the source code that is being translated to a Standard Concept.';
COMMENT ON COLUMN omop.SOURCE_TO_CONCEPT_MAP.source_code_description IS 'An optional description for the source code. This is included as a convenience to compare the description of the source code to the name of the concept.';
COMMENT ON COLUMN omop.SOURCE_TO_CONCEPT_MAP.target_concept_id IS 'A foreign key to the target Concept to which the source code is being mapped.';
COMMENT ON COLUMN omop.SOURCE_TO_CONCEPT_MAP.target_vocabulary_id IS 'A foreign key to the VOCABULARY table defining the vocabulary of the target Concept.';
COMMENT ON COLUMN omop.SOURCE_TO_CONCEPT_MAP.valid_start_date IS 'The date when the mapping instance was first recorded.';
COMMENT ON COLUMN omop.SOURCE_TO_CONCEPT_MAP.valid_end_date IS 'The date when the mapping instance became invalid because it was deleted or superseded (updated) by a new relationship. Default value is 31-Dec-2099.';
COMMENT ON COLUMN omop.SOURCE_TO_CONCEPT_MAP.invalid_reason IS 'Reason the mapping instance was invalidated. Possible values are D (deleted), U (replaced with an update) or NULL when valid_end_date has the default value.';
-- VOCABULARY
COMMENT ON COLUMN omop.VOCABULARY.vocabulary_id IS 'A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit.';
COMMENT ON COLUMN omop.VOCABULARY.vocabulary_name IS 'The name describing the vocabulary, for example "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)" etc.';
COMMENT ON COLUMN omop.VOCABULARY.vocabulary_reference IS 'External reference to documentation or available download of the about the vocabulary.';
COMMENT ON COLUMN omop.VOCABULARY.vocabulary_version IS 'Version of the Vocabulary as indicated in the source.';
COMMENT ON COLUMN omop.VOCABULARY.vocabulary_concept_id IS 'A foreign key that refers to a standard concept identifier in the CONCEPT table for the Vocabulary the VOCABULARY record belongs to.';

158
PostgreSQL/extract_comments.sh
View File

@ -1,46 +1,144 @@
#!/bin/bash
echo "-- VISIT_OCCURENCE" > "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/VISIT_OCCURRENCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.visit_occurence.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
#
#CLINICAL
#
echo "\n\n--\n--CLINICAL\n--\n" > "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- VISIT_OCCURENCE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/VISIT_OCCURRENCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.visit_occurence.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- CONDITION_OCCURENCE" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/CONDITION_OCCURRENCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.condition_occurence.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- CONDITION_OCCURENCE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/CONDITION_OCCURRENCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.condition_occurence.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- DEATH" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/DEATH.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.death.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- DEATH" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/DEATH.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.death.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- DEVICE_EXPOSURE" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/DEVICE_EXPOSURE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.device_exposure.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- DEVICE_EXPOSURE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/DEVICE_EXPOSURE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.device_exposure.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- DRUG_EXPOSURE" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/DRUG_EXPOSURE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.drug_exposure.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- DRUG_EXPOSURE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/DRUG_EXPOSURE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.drug_exposure.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- FACT_RELATIONSHIP" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/FACT_RELATIONSHIP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.FACT_RELATIONSHIP.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- FACT_RELATIONSHIP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/FACT_RELATIONSHIP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.FACT_RELATIONSHIP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- MEASUREMENT" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/MEASUREMENT.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.MEASUREMENT.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- MEASUREMENT" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/MEASUREMENT.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.MEASUREMENT.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- NOTE" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/NOTE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.NOTE.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- NOTE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/NOTE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.NOTE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- VISIT_DETAIL" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/VISIT_DETAIL.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.VISIT_DETAIL.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- VISIT_DETAIL" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/VISIT_DETAIL.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.VISIT_DETAIL.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- SPECIMEN" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/SPECIMEN.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.SPECIMEN.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- SPECIMEN" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/SPECIMEN.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.SPECIMEN.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- PROCEDURE_OCCURRENCE" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/PROCEDURE_OCCURRENCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- PROCEDURE_OCCURRENCE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/PROCEDURE_OCCURRENCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- PERSON" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/PERSON.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.PERSON.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- PERSON" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/PERSON.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.PERSON.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- OBSERVATION_PERIOD" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/OBSERVATION_PERIOD.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.OBSERVATION_PERIOD.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- OBSERVATION_PERIOD" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/OBSERVATION_PERIOD.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.OBSERVATION_PERIOD.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- OBSERVATION" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/OBSERVATION.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.OBSERVATION.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- OBSERVATION" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/OBSERVATION.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.OBSERVATION.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "-- NOTE_NLP" >> "PostgreSQL/pg_comments.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/NOTE_NLP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.NOTE_NLP.\1 IS '\2';/g" >> "PostgreSQL/pg_comments.sql"
echo "\n\n-- NOTE_NLP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/NOTE_NLP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.NOTE_NLP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
#
#ECONOMIC
#
echo "\n\n--\n--ECONOMIC\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- COST" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/COST.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.COST.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- PAYER_PLAN_PERIOD" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.PAYER_PLAN_PERIOD.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
#
#METADATA
#
echo "\n\n--\n--METADATA\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CDM_SOURCE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedMetadata/CDM_SOURCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CDM_SOURCE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
#
#DERIVED
#
echo "\n\n--\n--DERIVED\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- COHORT_ATTRIBUTE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT_ATTRIBUTE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.COHORT_ATTRIBUTE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- COHORT" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.COHORT.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CONDITION_ERA" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/CONDITION_ERA.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CONDITION_ERA.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- DOSE_ERA" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/DOSE_ERA.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.DOSE_ERA.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- DRUG_ERA" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/DRUG_ERA.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.DRUG_ERA.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
#
#SYSTEM
#
echo "\n\n--\n--SYSTEM\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CARE_SITE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/CARE_SITE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CARE_SITE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- LOCATION" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/LOCATION.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.LOCATION.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- PROVIDER" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/PROVIDER.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.PROVIDER.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
#
#SYSTEM
#
echo "\n\n--\n--SYSTEM\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- ATTRIBUTE_DEFINITION" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.ATTRIBUTE_DEFINITION.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- COHORT_DEFINITION" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.COHORT_DEFINITION.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CONCEPT_ANCESTOR" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_ANCESTOR.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CONCEPT_ANCESTOR.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CONCEPT_CLASS" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_CLASS.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CONCEPT_CLASS.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CONCEPT" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CONCEPT.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CONCEPT_RELATIONSHIP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CONCEPT_RELATIONSHIP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CONCEPT_SYNONYM" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.CONCEPT_SYNONYM.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- DOMAIN" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/DOMAIN.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.DOMAIN.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- DRUG_STRENGTH" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/DRUG_STRENGTH.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.DRUG_STRENGTH.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- RELATIONSHIP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/RELATIONSHIP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.RELATIONSHIP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- SOURCE_TO_CONCEPT_MAP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.SOURCE_TO_CONCEPT_MAP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- VOCABULARY" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/VOCABULARY.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/|\(.*\)|.*|.*|\(.*\)|/COMMENT ON COLUMN omop.VOCABULARY.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"