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added table comments

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parisni 2017-09-10 12:05:00 +02:00
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commit 1b5c53ac25
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PostgreSQL/OMOP CDM comments - PostgreSQL.sql
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@ -2,6 +2,7 @@
--CLINICAL
--
-- VISIT_OCCURRENCE
COMMENT ON TABLE visit_occurrence IS 'The VISIT_OCCURRENCE table contains the spans of time a Person continuously receives medical services from one or more providers at a Care Site in a given setting within the health care system. Visits are classified into 4 settings: outpatient care, inpatient confinement, emergency room, and long-term care. Persons may transition between these settings over the course of an episode of care (for example, treatment of a disease onset).';
COMMENT ON COLUMN visit_occurrence.visit_occurrence_id IS 'A unique identifier for each Person'';s visit or encounter at a healthcare provider.';
COMMENT ON COLUMN visit_occurrence.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.';
COMMENT ON COLUMN visit_occurrence.visit_concept_id IS 'A foreign key that refers to a visit Concept identifier in the Standardized Vocabularies.';
@ -20,6 +21,7 @@ COMMENT ON COLUMN visit_occurrence.discharge_to_concept_id IS 'A foreign key to
COMMENT ON COLUMN visit_occurrence.discharge_to_source_value IS 'The source code for the discharge disposition as it appears in the source data.';
COMMENT ON COLUMN visit_occurrence.preceding_visit_occurrence_id IS 'A foreign key to the VISIT_OCCURRENCE table of the visit immediately preceding this visit';
-- CONDITION_OCCURRENCE
COMMENT ON TABLE condition_occurrence IS '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:';
COMMENT ON COLUMN condition_occurrence. condition_occurrence_id IS 'A unique identifier for each Condition Occurrence event.';
COMMENT ON COLUMN condition_occurrence. 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.';
COMMENT ON COLUMN condition_occurrence. condition_concept_id IS 'A foreign key that refers to a Standard Condition Concept identifier in the Standardized Vocabularies.';
@ -37,6 +39,7 @@ COMMENT ON COLUMN condition_occurrence. condition_source_concept_id IS 'A fo
COMMENT ON COLUMN condition_occurrence. condition_status_source_value IS 'The source code for the condition status as it appears in the source data.';
COMMENT ON COLUMN condition_occurrence. condition_status_concept_id IS 'A foreign key to the predefined concept in the standard vocabulary reflecting the condition status';
-- DEATH
COMMENT ON TABLE death IS 'The death domain contains the clinical event for how and when a Person dies. A person can have up to one record if the source system contains evidence about the Death, such as:';
COMMENT ON COLUMN 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 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.';
COMMENT ON COLUMN death.death_datetime IS 'The date and time 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.';
@ -45,6 +48,7 @@ COMMENT ON COLUMN death.cause_concept_id IS 'A foreign key referring to a standa
COMMENT ON COLUMN 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 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 TABLE device_exposure IS 'The device exposure domain captures information about a person'';s exposure to a foreign physical object or instrument that which is used for diagnostic or therapeutic purposes through a mechanism beyond chemical action. Devices include implantable objects (e.g. pacemakers, stents, artificial joints), medical equipment and supplies (e.g. bandages, crutches, syringes), other instruments used in medical procedures (e.g. sutures, defibrillators) and material used in clinical care (e.g. adhesives, body material, dental material, surgical material).';
COMMENT ON COLUMN device_exposure.device_exposure_id IS 'A system-generated unique identifier for each Device Exposure.';
COMMENT ON COLUMN 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.';
COMMENT ON COLUMN device_exposure.device_concept_id IS 'A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies for the Device concept.';
@ -61,6 +65,7 @@ COMMENT ON COLUMN device_exposure.device_source_value IS 'The source code for th
COMMENT ON COLUMN 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 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 TABLE drug_exposure IS 'The drug exposure domain captures records about the utilization of a Drug when ingested or otherwise introduced into the body. A Drug is a biochemical substance formulated in such a way that when administered to a Person it will exert a certain physiological effect. Drugs include prescription and over-the-counter medicines, vaccines, and large-molecule biologic therapies. Radiological devices ingested or applied locally do not count as Drugs.';
COMMENT ON COLUMN drug_exposure.drug_exposure_id IS 'A system-generated unique identifier for each Drug utilization event.';
COMMENT ON COLUMN 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.';
COMMENT ON COLUMN drug_exposure.drug_concept_id IS 'A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies for the Drug concept.';
@ -85,12 +90,14 @@ COMMENT ON COLUMN drug_exposure.route_source_value IS 'The information about the
COMMENT ON COLUMN drug_exposure.dose_unit_source_value IS 'The information about the dose unit as detailed in the source.';
COMMENT ON COLUMN 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 TABLE FACT_RELATIONSHIP IS 'The FACT_RELATIONSHIP table contains records about the relationships between facts stored as records in any table of the CDM. Relationships can be defined between facts from the same domain (table), or different domains. Examples of Fact Relationships include: Person relationships (parent-child), care site relationships (hierarchical organizational structure of facilities within a health system), indication relationship (between drug exposures and associated conditions), usage relationships (of devices during the course of an associated procedure), or facts derived from one another (measurements derived from an associated specimen).';
COMMENT ON COLUMN 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 FACT_RELATIONSHIP.fact_id_1 IS 'The unique identifier in the table corresponding to the domain of fact one.';
COMMENT ON COLUMN 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 FACT_RELATIONSHIP.fact_id_2 IS 'The unique identifier in the table corresponding to the domain of fact two.';
COMMENT ON COLUMN FACT_RELATIONSHIP.relationship_concept_id IS 'A foreign key to a Standard Concept ID of relationship in the Standardized Vocabularies.';
-- MEASUREMENT
COMMENT ON TABLE MEASUREMENT IS 'The MEASUREMENT table contains records of Measurement, i.e. structured values (numerical or categorical) obtained through systematic and standardized examination or testing of a Person or Person'';s sample. The MEASUREMENT table contains both orders and results of such Measurements as laboratory tests, vital signs, quantitative findings from pathology reports, etc.';
COMMENT ON COLUMN MEASUREMENT.measurement_id IS 'A unique identifier for each Measurement.';
COMMENT ON COLUMN 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.';
COMMENT ON COLUMN MEASUREMENT.measurement_concept_id IS 'A foreign key to the standard measurement concept identifier in the Standardized Vocabularies.';
@ -111,6 +118,7 @@ COMMENT ON COLUMN MEASUREMENT.measurement_source_concept_id IS 'A foreign key to
COMMENT ON COLUMN 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 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 TABLE NOTE IS 'The NOTE table captures unstructured information that was recorded by a provider about a patient in free text notes on a given date.';
COMMENT ON COLUMN NOTE.note_id IS 'A unique identifier for each note.';
COMMENT ON COLUMN 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.';
COMMENT ON COLUMN NOTE.note_date IS 'The date the note was recorded.';
@ -125,6 +133,7 @@ COMMENT ON COLUMN NOTE.provider_id IS 'A foreign key to the Provider in the PROV
COMMENT ON COLUMN NOTE.note_source_value IS 'The source value associated with the origin of the note';
COMMENT ON COLUMN NOTE.visit_occurrence_id IS 'Foreign key to the Visit in the VISIT_OCCURRENCE table when the Note was taken.';
-- VISIT_DETAIL
COMMENT ON TABLE VISIT_DETAIL IS 'The VISIT_DETAIL table is an optional table used to represents details of each record in the parent visit_occurrence table. For every record in visit_occurrence table there may be 0 or more records in the visit_detail table with a 1:n relationship where n may be 0. The visit_detail table is structurally very similar to visit_occurrence table and belongs to the similar domain as the visit.';
COMMENT ON COLUMN VISIT_DETAIL.visit_detail_id IS 'A unique identifier for each Person'';s visit or encounter at a healthcare provider.';
COMMENT ON COLUMN 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.';
COMMENT ON COLUMN VISIT_DETAIL.visit_detail_concept_id IS 'A foreign key that refers to a visit Concept identifier in the Standardized Vocabularies.';
@ -145,6 +154,7 @@ COMMENT ON COLUMN VISIT_DETAIL.preceding_visit_detail_id IS 'A foreign key to t
COMMENT ON COLUMN 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 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 TABLE SPECIMEN IS 'The specimen domain contains the records identifying biological samples from a person.';
COMMENT ON COLUMN SPECIMEN.specimen_id IS 'A unique identifier for each specimen.';
COMMENT ON COLUMN SPECIMEN.person_id IS 'A foreign key identifier to the Person for whom the Specimen is recorded.';
COMMENT ON COLUMN SPECIMEN.specimen_concept_id IS 'A foreign key referring to a Standard Concept identifier in the Standardized Vocabularies for the Specimen.';
@ -161,6 +171,7 @@ COMMENT ON COLUMN SPECIMEN.unit_source_value IS 'The information about the Unit
COMMENT ON COLUMN SPECIMEN.anatomic_site_source_value IS 'The information about the anatomic site as detailed in the source.';
COMMENT ON COLUMN SPECIMEN.disease_status_source_value IS 'The information about the disease status as detailed in the source.';
-- PROCEDURE_OCCURRENCE
COMMENT ON TABLE PROCEDURE_OCCURRENCE IS 'The PROCEDURE_OCCURRENCE table contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. For example:';
COMMENT ON COLUMN PROCEDURE_OCCURRENCE.procedure_occurrence_id IS 'A system-generated unique identifier for each Procedure Occurrence.';
COMMENT ON COLUMN 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.';
COMMENT ON COLUMN PROCEDURE_OCCURRENCE.procedure_concept_id IS 'A foreign key that refers to a standard procedure Concept identifier in the Standardized Vocabularies.';
@ -176,6 +187,7 @@ COMMENT ON COLUMN PROCEDURE_OCCURRENCE.procedure_source_concept_id IS 'A foreign
COMMENT ON COLUMN PROCEDURE_OCCURRENCE.qualifier_source_value IS 'The source code for the qualifier as it appears in the source data.';
COMMENT ON COLUMN 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 TABLE PERSON IS 'The Person Domain contains records that uniquely identify each patient in the source data who is time at-risk to have clinical observations recorded within the source systems.';
COMMENT ON COLUMN PERSON.person_id IS 'A unique identifier for each person.';
COMMENT ON COLUMN PERSON.gender_concept_id IS 'A foreign key that refers to an identifier in the CONCEPT table for the unique gender of the person.';
COMMENT ON COLUMN PERSON.year_of_birth IS 'The year of birth of the person. For data sources with date of birth, the year is extracted. For data sources where the year of birth is not available, the approximate year of birth is derived based on any age group categorization available.';
@ -195,12 +207,14 @@ COMMENT ON COLUMN PERSON.race_source_concept_id IS 'A foreign key to the race co
COMMENT ON COLUMN 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 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 TABLE OBSERVATION_PERIOD IS 'The OBSERVATION_PERIOD table contains records which uniquely define the spans of time for which a Person is at-risk to have clinical events recorded within the source systems, even if no events in fact are recorded (healthy patient with no healthcare interactions).';
COMMENT ON COLUMN OBSERVATION_PERIOD.observation_period_id IS 'A unique identifier for each observation period.';
COMMENT ON COLUMN 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 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 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 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 TABLE OBSERVATION IS 'The OBSERVATION table captures clinical facts about a Person obtained in the context of examination, questioning or a procedure. Any data that cannot be represented by any other domains, such as social and lifestyle facts, medical history, family history, etc. are recorded here.';
COMMENT ON COLUMN OBSERVATION.observation_id IS 'A unique identifier for each observation.';
COMMENT ON COLUMN 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.';
COMMENT ON COLUMN OBSERVATION.observation_concept_id IS 'A foreign key to the standard observation concept identifier in the Standardized Vocabularies.';
@ -220,6 +234,7 @@ COMMENT ON COLUMN OBSERVATION.observation_source_concept_id IS 'A foreign key to
COMMENT ON COLUMN 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 OBSERVATION.qualifier_source_value IS 'The source value associated with a qualifier to characterize the observation';
-- NOTE_NLP
COMMENT ON TABLE NOTE_NLP IS 'The NOTE_NLP table will encode all output of NLP on clinical notes. Each row represents a single extracted term from a note.';
COMMENT ON COLUMN NOTE_NLP.note_nlp_id IS 'A unique identifier for each term extracted from a note.';
COMMENT ON COLUMN NOTE_NLP.note_id IS 'A foreign key to the Note table note the term was extracted from.';
COMMENT ON COLUMN NOTE_NLP.section_concept_id IS 'A foreign key to the predefined Concept in the Standardized Vocabularies representing the section of the extracted term.';
@ -236,6 +251,7 @@ COMMENT ON COLUMN NOTE_NLP.term_exists IS 'A summary modifier that signifies pr
--ECONOMIC
--
-- COST
COMMENT ON TABLE COST IS 'The COST table captures records containing the cost of any medical entity recorded in one of the DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, VISIT_OCCURRENCE or DEVICE_OCCURRENCE tables. It replaces the corresponding DRUG_COST, PROCEDURE_COST, VISIT_COST or DEVICE_COST tables that were initially defined for the OMOP CDM V5. However, it also allows to capture cost information for records of the OBSERVATION and MEASUREMENT tables.';
COMMENT ON COLUMN COST.cost_id IS 'A unique identifier for each COST record.';
COMMENT ON COLUMN 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 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.';
@ -259,6 +275,7 @@ COMMENT ON COLUMN COST.revenue_code_source_value IS 'The source code for the Rev
COMMENT ON COLUMN 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 COST.drg_source_value IS 'The 3-digit DRG source code as it appears in the source data.';
-- PAYER_PLAN_PERIOD
COMMENT ON TABLE PAYER_PLAN_PERIOD IS 'The PAYER_PLAN_PERIOD table captures details of the period of time that a Person is continuously enrolled under a specific health Plan benefit structure from a given Payer. Each Person receiving healthcare is typically covered by a health benefit plan, which pays for (fully or partially), or directly provides, the care. These benefit plans are provided by payers, such as health insurances or state or government agencies. In each plan the details of the health benefits are defined for the Person or her family, and the health benefit Plan might change over time typically with increasing utilization (reaching certain cost thresholds such as deductibles), plan availability and purchasing choices of the Person. The unique combinations of Payer organizations, health benefit Plans and time periods in which they are valid for a Person are recorded in this table.';
COMMENT ON COLUMN 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 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 PAYER_PLAN_PERIOD.payer_plan_period_start_date IS 'The start date of the payer plan period.';
@ -270,6 +287,7 @@ COMMENT ON COLUMN PAYER_PLAN_PERIOD.family_source_value IS 'The source code for
--METADATA
--
-- CDM_SOURCE
COMMENT ON TABLE CDM_SOURCE IS 'The CDM_SOURCE table contains detail about the source database and the process used to transform the data into the OMOP Common Data Model.';
COMMENT ON COLUMN CDM_SOURCE.cdm_source_name IS 'The full name of the source';
COMMENT ON COLUMN CDM_SOURCE.cdm_source_abbreviation IS 'An abbreviation of the name';
COMMENT ON COLUMN CDM_SOURCE.cdm_holder IS 'The name of the organization responsible for the development of the CDM instance';
@ -284,6 +302,7 @@ COMMENT ON COLUMN CDM_SOURCE.vocabulary_version IS 'The version of the vocabular
--DERIVED
--
-- COHORT_ATTRIBUTE
COMMENT ON TABLE COHORT_ATTRIBUTE IS 'The COHORT_ATTRIBUTE table contains attributes associated with each subject within a cohort, as defined by a given set of criteria for a duration of time. The definition of the Cohort Attribute is contained in the ATTRIBUTE_DEFINITION table.';
COMMENT ON COLUMN 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 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 COHORT_ATTRIBUTE.cohort_start_date IS 'The date when the Cohort Definition criteria for the Person, Provider or Visit first match.';
@ -292,11 +311,13 @@ COMMENT ON COLUMN COHORT_ATTRIBUTE.attribute_definition_id IS 'A foreign key to
COMMENT ON COLUMN 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 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 TABLE COHORT IS 'The COHORT table contains records of subjects that satisfy a given set of criteria for a duration of time. The definition of the cohort is contained within the COHORT_DEFINITION table. Cohorts can be constructed of patients (Persons), Providers or Visits.';
COMMENT ON COLUMN COHORT.cohort_definition_id IS 'A foreign key to a record in the COHORT_DEFINITION table containing relevant Cohort Definition information.';
COMMENT ON COLUMN 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 COHORT.cohort_start_date IS 'The date when the Cohort Definition criteria for the Person, Provider or Visit first match.';
COMMENT ON COLUMN 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 TABLE CONDITION_ERA IS 'A Condition Era is defined as a span of time when the Person is assumed to have a given condition.';
COMMENT ON COLUMN CONDITION_ERA.condition_era_id IS 'A unique identifier for each Condition Era.';
COMMENT ON COLUMN 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 CONDITION_ERA.condition_concept_id IS 'A foreign key that refers to a standard Condition Concept identifier in the Standardized Vocabularies.';
@ -304,6 +325,7 @@ COMMENT ON COLUMN CONDITION_ERA.condition_era_start_date IS 'The start date for
COMMENT ON COLUMN 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 CONDITION_ERA.condition_occurrence_count IS 'The number of individual Condition Occurrences used to construct the condition era.';
-- DOSE_ERA
COMMENT ON TABLE DOSE_ERA IS 'A Dose Era is defined as a span of time when the Person is assumed to be exposed to a constant dose of a specific active ingredient.';
COMMENT ON COLUMN DOSE_ERA.dose_era_id IS 'A unique identifier for each Dose Era.';
COMMENT ON COLUMN 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 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.';
@ -312,6 +334,7 @@ COMMENT ON COLUMN DOSE_ERA.dose_value IS 'The numeric value of the dose.';
COMMENT ON COLUMN 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 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 TABLE DRUG_ERA IS 'A Drug Era is defined as a span of time when the Person is assumed to be exposed to a particular active ingredient. A Drug Era is not the same as a Drug Exposure: Exposures are individual records corresponding to the source when Drug was delivered to the Person, while successive periods of Drug Exposures are combined under certain rules to produce continuous Drug Eras.';
COMMENT ON COLUMN DRUG_ERA.drug_era_id IS 'A unique identifier for each Drug Era.';
COMMENT ON COLUMN 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 DRUG_ERA.drug_concept_id IS 'A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies for the Ingredient Concept.';
@ -323,6 +346,7 @@ COMMENT ON COLUMN DRUG_ERA.gap_days IS 'The number of days that are not covered
--SYSTEM
--
-- CARE_SITE
COMMENT ON TABLE CARE_SITE IS 'The CARE_SITE table contains a list of uniquely identified institutional (physical or organizational) units where healthcare delivery is practiced (offices, wards, hospitals, clinics, etc.).';
COMMENT ON COLUMN CARE_SITE.care_site_id IS 'A unique identifier for each Care Site.';
COMMENT ON COLUMN CARE_SITE.care_site_name IS 'The verbatim description or name of the Care Site as in data source';
COMMENT ON COLUMN CARE_SITE.place_of_service_concept_id IS 'A foreign key that refers to a Place of Service Concept ID in the Standardized Vocabularies.';
@ -330,6 +354,7 @@ COMMENT ON COLUMN CARE_SITE.location_id IS 'A foreign key to the geographic Loca
COMMENT ON COLUMN CARE_SITE.care_site_source_value IS 'The identifier for the Care Site in the source data, stored here for reference.';
COMMENT ON COLUMN 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 TABLE LOCATION IS 'The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Sites.';
COMMENT ON COLUMN LOCATION.location_id IS 'A unique identifier for each geographic location.';
COMMENT ON COLUMN LOCATION.address_1 IS 'The address field 1, typically used for the street address, as it appears in the source data.';
COMMENT ON COLUMN 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.';
@ -339,6 +364,7 @@ COMMENT ON COLUMN LOCATION.zip IS 'The zip or postal code.';
COMMENT ON COLUMN LOCATION.county IS 'The county.';
COMMENT ON COLUMN 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 TABLE PROVIDER IS 'The PROVIDER table contains a list of uniquely identified healthcare providers. These are individuals providing hands-on healthcare to patients, such as physicians, nurses, midwives, physical therapists etc.';
COMMENT ON COLUMN PROVIDER.provider_id IS 'A unique identifier for each Provider.';
COMMENT ON COLUMN PROVIDER.provider_name IS 'A description of the Provider.';
COMMENT ON COLUMN PROVIDER.npi IS 'The National Provider Identifier (NPI) of the provider.';
@ -356,12 +382,14 @@ COMMENT ON COLUMN PROVIDER.gender_source_concept_id IS 'A foreign key to a Conce
--SYSTEM
--
-- ATTRIBUTE_DEFINITION
COMMENT ON TABLE ATTRIBUTE_DEFINITION IS 'The ATTRIBUTE_DEFINITION table contains records defining Attributes, or covariates, to members of a Cohort through an associated description and syntax and upon instantiation (execution of the algorithm) placed into the COHORT_ATTRIBUTE table. Attributes are derived elements that can be selected or calculated for a subject in a Cohort. The ATTRIBUTE_DEFINITION table provides a standardized structure for maintaining the rules governing the calculation of covariates for a subject in a Cohort, and can store operational programming code to instantiate the Attributes for a given Cohort within the OMOP Common Data Model.';
COMMENT ON COLUMN ATTRIBUTE_DEFINITION.attribute_definition_id IS 'A unique identifier for each Attribute.';
COMMENT ON COLUMN ATTRIBUTE_DEFINITION.attribute_name IS 'A short description of the Attribute.';
COMMENT ON COLUMN ATTRIBUTE_DEFINITION.attribute_description IS 'A complete description of the Attribute definition';
COMMENT ON COLUMN 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 ATTRIBUTE_DEFINITION.attribute_syntax IS 'Syntax or code to operationalize the Attribute definition';
-- COHORT_DEFINITION
COMMENT ON TABLE COHORT_DEFINITION IS 'The COHORT_DEFINITION table contains records defining a Cohort derived from the data through the associated description and syntax and upon instantiation (execution of the algorithm) placed into the COHORT table. Cohorts are a set of subjects that satisfy a given combination of inclusion criteria for a duration of time. The COHORT_DEFINITION table provides a standardized structure for maintaining the rules governing the inclusion of a subject into a cohort, and can store operational programming code to instantiate the cohort within the OMOP Common Data Model.';
COMMENT ON COLUMN COHORT_DEFINITION.cohort_definition_id IS 'A unique identifier for each Cohort.';
COMMENT ON COLUMN COHORT_DEFINITION.cohort_definition_name IS 'A short description of the Cohort.';
COMMENT ON COLUMN COHORT_DEFINITION.cohort_definition_description IS 'A complete description of the Cohort definition';
@ -370,15 +398,18 @@ COMMENT ON COLUMN COHORT_DEFINITION.cohort_definition_syntax IS 'Syntax or code
COMMENT ON COLUMN 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 COHORT_DEFINITION.cohort_initiation_date IS 'A date to indicate when the Cohort was initiated in the COHORT table';
-- CONCEPT_ANCESTOR
COMMENT ON TABLE CONCEPT_ANCESTOR IS 'The CONCEPT_ANCESTOR table is designed to simplify observational analysis by providing the complete hierarchical relationships between Concepts. Only direct parent-child relationships between Concepts are stored in the CONCEPT_RELATIONSHIP table. To determine higher level ancestry connections, all individual direct relationships would have to be navigated at analysis time. The CONCEPT_ANCESTOR table includes records for all parent-child relationships, as well as grandparent-grandchild relationships and those of any other level of lineage. Using the CONCEPT_ANCESTOR table allows for querying for all descendants of a hierarchical concept. For example, drug ingredients and drug products are all descendants of a drug class ancestor.';
COMMENT ON COLUMN 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 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 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 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 TABLE CONCEPT_CLASS IS 'The CONCEPT_CLASS table is a reference table, which includes a list of the classifications used to differentiate Concepts within a given Vocabulary. This reference table is populated with a single record for each Concept Class:';
COMMENT ON COLUMN CONCEPT_CLASS.concept_class_id IS 'A unique key for each class.';
COMMENT ON COLUMN CONCEPT_CLASS.concept_class_name IS 'The name describing the Concept Class, e.g. "Clinical Finding", "Ingredient", etc.';
COMMENT ON COLUMN 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 TABLE CONCEPT IS 'The Standardized Vocabularies contains records, or Concepts, that uniquely identify each fundamental unit of meaning used to express clinical information in all domain tables of the CDM. Concepts are derived from vocabularies, which represent clinical information across a domain (e.g. conditions, drugs, procedures) through the use of codes and associated descriptions. Some Concepts are designated Standard Concepts, meaning these Concepts can be used as normative expressions of a clinical entity within the OMOP Common Data Model and within standardized analytics. Each Standard Concept belongs to one domain, which defines the location where the Concept would be expected to occur within data tables of the CDM.';
COMMENT ON COLUMN CONCEPT.concept_id IS 'A unique identifier for each Concept across all domains.';
COMMENT ON COLUMN CONCEPT.concept_name IS 'An unambiguous, meaningful and descriptive name for the Concept.';
COMMENT ON COLUMN CONCEPT.domain_id IS 'A foreign key to the [DOMAIN](https://github.com/OHDSI/CommonDataModel/wiki/DOMAIN) table the Concept belongs to.';
@ -390,6 +421,7 @@ COMMENT ON COLUMN CONCEPT.valid_start_date IS 'The date when the Concept was fir
COMMENT ON COLUMN 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 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 TABLE CONCEPT_RELATIONSHIP IS 'The CONCEPT_RELATIONSHIP table contains records that define direct relationships between any two Concepts and the nature or type of the relationship. Each type of a relationship is defined in the [RELATIONSHIP](https://github.com/OHDSI/CommonDataModel/wiki/RELATIONSHIP) table.';
COMMENT ON COLUMN 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 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 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.';
@ -397,14 +429,17 @@ COMMENT ON COLUMN CONCEPT_RELATIONSHIP.valid_start_date IS 'The date when the in
COMMENT ON COLUMN 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 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 TABLE CONCEPT_SYNONYM IS 'The CONCEPT_SYNONYM table is used to store alternate names and descriptions for Concepts.';
COMMENT ON COLUMN CONCEPT_SYNONYM.concept_id IS 'A foreign key to the Concept in the CONCEPT table.';
COMMENT ON COLUMN CONCEPT_SYNONYM.concept_synonym_name IS 'The alternative name for the Concept.';
COMMENT ON COLUMN CONCEPT_SYNONYM.language_concept_id IS 'A foreign key to a Concept representing the language.';
-- DOMAIN
COMMENT ON TABLE DOMAIN IS 'The DOMAIN table includes a list of OMOP-defined Domains the Concepts of the Standardized Vocabularies can belong to. A Domain defines the set of allowable Concepts for the standardized fields in the CDM tables. For example, the "Condition" Domain contains Concepts that describe a condition of a patient, and these Concepts can only be stored in the condition_concept_id field of the [CONDITION_OCCURRENCE](https://github.com/OHDSI/CommonDataModel/wiki/CONDITION_OCCURRENCE) and [CONDITION_ERA](https://github.com/OHDSI/CommonDataModel/wiki/CONDITION_ERA) tables. This reference table is populated with a single record for each Domain and includes a descriptive name for the Domain.';
COMMENT ON COLUMN DOMAIN.domain_id IS 'A unique key for each domain.';
COMMENT ON COLUMN DOMAIN.domain_name IS 'The name describing the Domain, e.g. "Condition", "Procedure", "Measurement" etc.';
COMMENT ON COLUMN 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 TABLE DRUG_STRENGTH IS 'The DRUG_STRENGTH table contains structured content about the amount or concentration and associated units of a specific ingredient contained within a particular drug product. This table is supplemental information to support standardized analysis of drug utilization.';
COMMENT ON COLUMN 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 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 DRUG_STRENGTH.amount_value IS 'The numeric value associated with the amount of active ingredient contained within the product.';
@ -418,6 +453,7 @@ COMMENT ON COLUMN DRUG_STRENGTH.valid_start_date IS 'The date when the Concept w
COMMENT ON COLUMN 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 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 TABLE RELATIONSHIP IS '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.';
COMMENT ON COLUMN RELATIONSHIP.relationship_id IS 'The type of relationship captured by the relationship record.';
COMMENT ON COLUMN RELATIONSHIP.relationship_name IS 'The text that describes the relationship type.';
COMMENT ON COLUMN RELATIONSHIP.is_hierarchical IS 'Defines whether a relationship defines concepts into classes or hierarchies. Values are 1 for hierarchical relationship or 0 if not.';
@ -425,6 +461,7 @@ COMMENT ON COLUMN RELATIONSHIP.defines_ancestry IS 'Defines whether a hierarchic
COMMENT ON COLUMN RELATIONSHIP.reverse_relationship_id IS 'The identifier for the relationship used to define the reverse relationship between two concepts.';
COMMENT ON COLUMN 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 TABLE SOURCE_TO_CONCEPT_MAP IS 'The source to concept map table is a legacy data structure within the OMOP Common Data Model, recommended for use in ETL processes to maintain local source codes which are not available as Concepts in the Standardized Vocabularies, and to establish mappings for each source code into a Standard Concept as target_concept_ids that can be used to populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table is no longer populated with content within the Standardized Vocabularies published to the OMOP community.';
COMMENT ON COLUMN SOURCE_TO_CONCEPT_MAP.source_code IS 'The source code being translated into a Standard Concept.';
COMMENT ON COLUMN 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 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.';
@ -435,6 +472,7 @@ COMMENT ON COLUMN SOURCE_TO_CONCEPT_MAP.valid_start_date IS 'The date when the m
COMMENT ON COLUMN 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 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 TABLE VOCABULARY IS 'The VOCABULARY table includes a list of the Vocabularies collected from various sources or created de novo by the OMOP community. This reference table is populated with a single record for each Vocabulary source and includes a descriptive name and other associated attributes for the Vocabulary.';
COMMENT ON COLUMN VOCABULARY.vocabulary_id IS 'A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit.';
COMMENT ON COLUMN 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 VOCABULARY.vocabulary_reference IS 'External reference to documentation or available download of the about the vocabulary.';

40
PostgreSQL/extract_comments.sh
View File

@ -1,52 +1,67 @@
#!/bin/bash
#COMMENT ON TABLE mytable IS 'This is my table.';
#
#CLINICAL
#
echo "\n\n--\n--CLINICAL\n--\n" > "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- VISIT_OCCURRENCE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/VISIT_OCCURRENCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE visit_occurrence IS '\1';/g" >> "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 visit_occurrence.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CONDITION_OCCURRENCE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/CONDITION_OCCURRENCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE condition_occurrence IS '\1';/g" >> "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 condition_occurrence.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- DEATH" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/DEATH.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE death IS '\1';/g" >> "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 death.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- DEVICE_EXPOSURE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/DEVICE_EXPOSURE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE device_exposure IS '\1';/g" >> "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 device_exposure.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- DRUG_EXPOSURE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/DRUG_EXPOSURE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE drug_exposure IS '\1';/g" >> "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 drug_exposure.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- FACT_RELATIONSHIP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/FACT_RELATIONSHIP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE FACT_RELATIONSHIP IS '\1';/g" >> "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 FACT_RELATIONSHIP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- MEASUREMENT" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/MEASUREMENT.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE MEASUREMENT IS '\1';/g" >> "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 MEASUREMENT.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- NOTE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/NOTE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE NOTE IS '\1';/g" >> "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 NOTE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- VISIT_DETAIL" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/VISIT_DETAIL.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE VISIT_DETAIL IS '\1';/g" >> "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 VISIT_DETAIL.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- SPECIMEN" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/SPECIMEN.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE SPECIMEN IS '\1';/g" >> "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 SPECIMEN.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- PROCEDURE_OCCURRENCE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/PROCEDURE_OCCURRENCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE PROCEDURE_OCCURRENCE IS '\1';/g" >> "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 PROCEDURE_OCCURRENCE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- PERSON" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/PERSON.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE PERSON IS '\1';/g" >> "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 PERSON.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- OBSERVATION_PERIOD" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/OBSERVATION_PERIOD.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE OBSERVATION_PERIOD IS '\1';/g" >> "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 OBSERVATION_PERIOD.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- OBSERVATION" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/OBSERVATION.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE OBSERVATION IS '\1';/g" >> "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 OBSERVATION.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- NOTE_NLP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/NOTE_NLP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE NOTE_NLP IS '\1';/g" >> "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 NOTE_NLP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
#
@ -54,9 +69,11 @@ grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables
#
echo "\n\n--\n--ECONOMIC\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- COST" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/COST.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE COST IS '\1';/g" >> "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 COST.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- PAYER_PLAN_PERIOD" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE PAYER_PLAN_PERIOD IS '\1';/g" >> "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 PAYER_PLAN_PERIOD.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
#
@ -64,6 +81,7 @@ grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDat
#
echo "\n\n--\n--METADATA\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CDM_SOURCE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedMetadata/CDM_SOURCE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE CDM_SOURCE IS '\1';/g" >> "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 CDM_SOURCE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
@ -72,18 +90,23 @@ grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedMetadata/CDM_SOURC
#
echo "\n\n--\n--DERIVED\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- COHORT_ATTRIBUTE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT_ATTRIBUTE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE COHORT_ATTRIBUTE IS '\1';/g" >> "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 COHORT_ATTRIBUTE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- COHORT" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE COHORT IS '\1';/g" >> "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 COHORT.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CONDITION_ERA" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/CONDITION_ERA.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE CONDITION_ERA IS '\1';/g" >> "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 CONDITION_ERA.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- DOSE_ERA" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/DOSE_ERA.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE DOSE_ERA IS '\1';/g" >> "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 DOSE_ERA.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- DRUG_ERA" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/DRUG_ERA.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE DRUG_ERA IS '\1';/g" >> "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 DRUG_ERA.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
@ -93,12 +116,15 @@ grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/DR
echo "\n\n--\n--SYSTEM\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CARE_SITE" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/CARE_SITE.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE CARE_SITE IS '\1';/g" >> "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 CARE_SITE.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- LOCATION" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/LOCATION.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE LOCATION IS '\1';/g" >> "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 LOCATION.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- PROVIDER" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/PROVIDER.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE PROVIDER IS '\1';/g" >> "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 PROVIDER.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
@ -108,39 +134,51 @@ grep "|" Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTa
echo "\n\n--\n--SYSTEM\n--\n" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- ATTRIBUTE_DEFINITION" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE ATTRIBUTE_DEFINITION IS '\1';/g" >> "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 ATTRIBUTE_DEFINITION.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- COHORT_DEFINITION" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE COHORT_DEFINITION IS '\1';/g" >> "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 COHORT_DEFINITION.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CONCEPT_ANCESTOR" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_ANCESTOR.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE CONCEPT_ANCESTOR IS '\1';/g" >> "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 CONCEPT_ANCESTOR.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CONCEPT_CLASS" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_CLASS.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE CONCEPT_CLASS IS '\1';/g" >> "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 CONCEPT_CLASS.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CONCEPT" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE CONCEPT IS '\1';/g" >> "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 CONCEPT.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CONCEPT_RELATIONSHIP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE CONCEPT_RELATIONSHIP IS '\1';/g" >> "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 CONCEPT_RELATIONSHIP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- CONCEPT_SYNONYM" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE CONCEPT_SYNONYM IS '\1';/g" >> "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 CONCEPT_SYNONYM.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- DOMAIN" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/DOMAIN.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE DOMAIN IS '\1';/g" >> "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 DOMAIN.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- DRUG_STRENGTH" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/DRUG_STRENGTH.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE DRUG_STRENGTH IS '\1';/g" >> "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 DRUG_STRENGTH.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- RELATIONSHIP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/RELATIONSHIP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE RELATIONSHIP IS '\1';/g" >> "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 RELATIONSHIP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- SOURCE_TO_CONCEPT_MAP" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE SOURCE_TO_CONCEPT_MAP IS '\1';/g" >> "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 SOURCE_TO_CONCEPT_MAP.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
echo "\n\n-- VOCABULARY" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
head -1 Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/VOCABULARY.md |sed '/^Field/ d'|sed '/^:--/ d'|sed "s/'/'';/g" |sed "s/\(.*\)/COMMENT ON TABLE VOCABULARY IS '\1';/g" >> "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 VOCABULARY.\1 IS '\2';/g" >> "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"
sed -i '/^--\|^COMMENT/!d' "PostgreSQL/OMOP CDM comments - PostgreSQL.sql"