From 2614905905ca2e43ab79b380e35ce1c93b09a674 Mon Sep 17 00:00:00 2001 From: parisni Date: Sun, 10 Sep 2017 00:16:23 +0200 Subject: [PATCH] comment generator & ddl --- PostgreSQL/OMOP CDM comments - PostgreSQL.sql | 232 ++++++++++++++++++ PostgreSQL/extract_comments.sh | 46 ++++ 2 files changed, 278 insertions(+) create mode 100644 PostgreSQL/OMOP CDM comments - PostgreSQL.sql create mode 100644 PostgreSQL/extract_comments.sh diff --git a/PostgreSQL/OMOP CDM comments - PostgreSQL.sql b/PostgreSQL/OMOP CDM comments - PostgreSQL.sql new file mode 100644 index 0000000..293c867 --- /dev/null +++ b/PostgreSQL/OMOP CDM comments - PostgreSQL.sql @@ -0,0 +1,232 @@ +-- 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.'; +COMMENT ON COLUMN omop.visit_occurence.visit_concept_id IS 'A foreign key that refers to a visit Concept identifier in the Standardized Vocabularies.'; +COMMENT ON COLUMN omop.visit_occurence.visit_start_date IS 'The start date of the visit.'; +COMMENT ON COLUMN omop.visit_occurence.visit_start_datetime IS 'The date and time of the visit started.'; +COMMENT ON COLUMN omop.visit_occurence.visit_end_date IS 'The end date of the visit. If this is a one-day visit the end date should match the start date.'; +COMMENT ON COLUMN omop.visit_occurence.visit_end_datetime IS 'The date and time of the visit end.'; +COMMENT ON COLUMN omop.visit_occurence.visit_type_concept_id IS 'A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the type of source data from which the visit record is derived.'; +COMMENT ON COLUMN omop.visit_occurence.provider_id IS 'A foreign key to the provider in the provider table who was associated with the visit.'; +COMMENT ON COLUMN omop.visit_occurence.care_site_id IS 'A foreign key to the care site in the care site table that was visited.'; +COMMENT ON COLUMN omop.visit_occurence.visit_source_value IS 'The source code for the visit as it appears in the source data.'; +COMMENT ON COLUMN omop.visit_occurence.visit_source_concept_id IS 'A foreign key to a Concept that refers to the code used in the source.'; +COMMENT ON COLUMN omop.visit_occurence.admitting_source_concept_id| IS 'A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the admitting source for a visit.'; +COMMENT ON COLUMN omop.visit_occurence.admitting_source_value IS ' The source code for the admitting source as it appears in the source data.'; +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. '; +COMMENT ON COLUMN omop.condition_occurence. condition_concept_id IS ' A foreign key that refers to a Standard Condition Concept identifier in the Standardized Vocabularies. '; +COMMENT ON COLUMN omop.condition_occurence. condition_start_date IS ' The date when the instance of the Condition is recorded. '; +COMMENT ON COLUMN omop.condition_occurence. condition_start_datetime IS ' The date and time when the instance of the Condition is recorded. '; +COMMENT ON COLUMN omop.condition_occurence. condition_end_date IS ' The date when the instance of the Condition is considered to have ended. '; +COMMENT ON COLUMN omop.condition_occurence. condition_end_datetime IS ' The date when the instance of the Condition is considered to have ended. '; +COMMENT ON COLUMN omop.condition_occurence. condition_type_concept_id IS ' 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. '; +COMMENT ON COLUMN omop.condition_occurence. stop_reason IS ' The reason that the condition was no longer present, as indicated in the source data. '; +COMMENT ON COLUMN omop.condition_occurence. provider_id IS ' A foreign key to the Provider in the PROVIDER table who was responsible for capturing (diagnosing) the Condition. '; +COMMENT ON COLUMN omop.condition_occurence. visit_occurrence_id IS ' A foreign key to the visit in the VISIT_OCCURRENCE table during which the Condition was determined (diagnosed). '; +COMMENT ON COLUMN omop.condition_occurence. visit_detail_id IS ' A foreign key to the visit in the VISIT_DETAIL table during which the Condition was determined (diagnosed). '; +COMMENT ON COLUMN omop.condition_occurence. condition_source_value IS ' 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. '; +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.'; +COMMENT ON COLUMN omop.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.'; +COMMENT ON COLUMN omop.death.death_type_concept_id IS 'A foreign key referring to the predefined concept identifier in the Standardized Vocabularies reflecting how the death was represented in the source data.'; +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.'; +COMMENT ON COLUMN omop.device_exposure.device_concept_id IS 'A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies for the Device concept.'; +COMMENT ON COLUMN omop.device_exposure.device_exposure_start_date IS 'The date the Device or supply was applied or used.'; +COMMENT ON COLUMN omop.device_exposure.device_exposure_start_datetime IS 'The date and time the Device or supply was applied or used.'; +COMMENT ON COLUMN omop.device_exposure.device_exposure_end_date IS 'The date the Device or supply was removed from use.'; +COMMENT ON COLUMN omop.device_exposure.device_exposure_end_datetime IS 'The date and time the Device or supply was removed from use.'; +COMMENT ON COLUMN omop.device_exposure.device_type_concept_id IS 'A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the type of Device Exposure recorded. It indicates how the Device Exposure was represented in the source data.'; +COMMENT ON COLUMN omop.device_exposure.unique_device_id IS 'A UDI or equivalent identifying the instance of the Device used in the Person.'; +COMMENT ON COLUMN omop.device_exposure.quantity IS 'The number of individual Devices used for the exposure.'; +COMMENT ON COLUMN omop.device_exposure.provider_id IS 'A foreign key to the provider in the PROVIDER table who initiated of administered the Device.'; +COMMENT ON COLUMN omop.device_exposure.visit_occurrence_id IS 'A foreign key to the visit in the VISIT table during which the device was used.'; +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.'; +COMMENT ON COLUMN omop.drug_exposure.drug_concept_id IS 'A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies for the Drug concept.'; +COMMENT ON COLUMN omop.drug_exposure.drug_exposure_start_date IS 'The start date for the current instance of Drug utilization. Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration procedure was recorded.'; +COMMENT ON COLUMN omop.drug_exposure.drug_exposure_start_datetime IS 'The start date and time for the current instance of Drug utilization. Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration procedure was recorded.'; +COMMENT ON COLUMN omop.drug_exposure.drug_exposure_end_date IS 'The end date for the current instance of Drug utilization. It is not available from all sources.'; +COMMENT ON COLUMN omop.drug_exposure.drug_exposure_end_datetime IS 'The end date and time for the current instance of Drug utilization. It is not available from all sources.'; +COMMENT ON COLUMN omop.drug_exposure.verbatim_end_date IS 'The known end date of a drug_exposure as provided by the source'; +COMMENT ON COLUMN omop.drug_exposure.drug_type_concept_id IS ' A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the type of Drug Exposure recorded. It indicates how the Drug Exposure was represented in the source data.'; +COMMENT ON COLUMN omop.drug_exposure.stop_reason IS 'The reason the Drug was stopped. Reasons include regimen completed, changed, removed, etc.'; +COMMENT ON COLUMN omop.drug_exposure.refills IS 'The number of refills after the initial prescription. The initial prescription is not counted, values start with 0.'; +COMMENT ON COLUMN omop.drug_exposure.quantity IS 'The quantity of drug as recorded in the original prescription or dispensing record.'; +COMMENT ON COLUMN omop.drug_exposure.days_supply IS 'The number of days of supply of the medication as recorded in the original prescription or dispensing record.'; +COMMENT ON COLUMN omop.drug_exposure.sig IS 'The directions ("signetur") on the Drug prescription as recorded in the original prescription (and printed on the container) or dispensing record.'; +COMMENT ON COLUMN omop.drug_exposure.route_concept_id IS 'A foreign key to a predefined concept in the Standardized Vocabularies reflecting the route of administration.'; +COMMENT ON COLUMN omop.drug_exposure.lot_number IS 'An identifier assigned to a particular quantity or lot of Drug product from the manufacturer.'; +COMMENT ON COLUMN omop.drug_exposure.provider_id IS 'A foreign key to the provider in the provider table who initiated (prescribed or administered) the Drug Exposure.'; +COMMENT ON COLUMN omop.drug_exposure.visit_occurrence_id IS 'A foreign key to the visit in the visit table during which the Drug Exposure was initiated.'; +COMMENT ON COLUMN omop.drug_exposure.drug_source_value IS 'The source code for the Drug as it appears in the source data. This code is mapped to a Standard Drug concept in the Standardized Vocabularies and the original code is, stored here for reference.'; +COMMENT ON COLUMN omop.drug_exposure.drug_source_concept_id IS 'A foreign key to a Drug Concept that refers to the code used in the source.'; +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.'; +COMMENT ON COLUMN omop.MEASUREMENT.measurement_concept_id IS 'A foreign key to the standard measurement concept identifier in the Standardized Vocabularies.'; +COMMENT ON COLUMN omop.MEASUREMENT.measurement_date IS 'The date of the Measurement.'; +COMMENT ON COLUMN omop.MEASUREMENT.measurement_datetime IS 'The date and time of the Measurement. Some database systems don'';t have a datatype of time. To accomodate all temporal analyses, datatype datetime can be used (combining measurement_date and measurement_time [forum discussion](http://forums.ohdsi.org/t/date-time-and-datetime-problem-and-the-world-of-hours-and-1day/314))'; +COMMENT ON COLUMN omop.MEASUREMENT.measurement_type_concept_id IS 'A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the provenance from where the Measurement record was recorded.'; +COMMENT ON COLUMN omop.MEASUREMENT.operator_concept_id IS 'A foreign key identifier to the predefined Concept in the Standardized Vocabularies reflecting the mathematical operator that is applied to the value_as_number. Operators are <, <=, =, >=, >.'; +COMMENT ON COLUMN omop.MEASUREMENT.value_as_number IS 'A Measurement result where the result is expressed as a numeric value.'; +COMMENT ON COLUMN omop.MEASUREMENT.value_as_concept_id IS 'A foreign key to a Measurement result represented as a Concept from the Standardized Vocabularies (e.g., positive/negative, present/absent, low/high, etc.).'; +COMMENT ON COLUMN omop.MEASUREMENT.unit_concept_id IS 'A foreign key to a Standard Concept ID of Measurement Units in the Standardized Vocabularies.'; +COMMENT ON COLUMN omop.MEASUREMENT.range_low IS 'The lower limit of the normal range of the Measurement result. The lower range is assumed to be of the same unit of measure as the Measurement value.'; +COMMENT ON COLUMN omop.MEASUREMENT.range_high IS 'The upper limit of the normal range of the Measurement. The upper range is assumed to be of the same unit of measure as the Measurement value.'; +COMMENT ON COLUMN omop.MEASUREMENT.provider_id IS 'A foreign key to the provider in the PROVIDER table who was responsible for initiating or obtaining the measurement.'; +COMMENT ON COLUMN omop.MEASUREMENT.visit_occurrence_id IS 'A foreign key to the Visit in the VISIT_OCCURRENCE table during which the Measurement was recorded.'; +COMMENT ON COLUMN omop.MEASUREMENT.visit_detail_id IS 'A foreign key to the Visit in the VISIT_DETAIL table during which the Measurement was recorded. '; +COMMENT ON COLUMN omop.MEASUREMENT.measurement_source_value IS 'The Measurement name 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.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.'; +COMMENT ON COLUMN omop.NOTE.note_date IS 'The date the note was recorded.'; +COMMENT ON COLUMN omop.NOTE.note_datetime IS 'The date and time the note was recorded.'; +COMMENT ON COLUMN omop.NOTE.note_type_concept_id IS 'A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the type, origin or provenance of the Note.'; +COMMENT ON COLUMN omop.NOTE.note_class_concept_id IS ' A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the HL7 LOINC Document Type Vocabulary classification of the note.'; +COMMENT ON COLUMN omop.NOTE.note_title IS ' The title of the Note as it appears in the source.'; +COMMENT ON COLUMN omop.NOTE.note_text IS 'The content of the Note.'; +COMMENT ON COLUMN omop.NOTE.encoding_concept_id IS ' A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the note character encoding type'; +COMMENT ON COLUMN omop.NOTE.language_concept_id IS 'A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the language of the note'; +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.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.visit_detail_concept_id IS 'A foreign key that refers to a visit Concept identifier in the Standardized Vocabularies.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.visit_start_date IS 'The start date of the visit.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.visit_start_datetime IS 'The date and time of the visit started.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.visit_end_date IS 'The end date of the visit. If this is a one-day visit the end date should match the start date.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.visit_end_datetime IS 'The date and time of the visit end.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.visit_type_concept_id IS 'A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the type of source data from which the visit record is derived.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.provider_id IS 'A foreign key to the provider in the provider table who was associated with the visit.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.care_site_id IS 'A foreign key to the care site in the care site table that was visited.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.visit_source_value IS 'The source code for the visit as it appears in the source data.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.visit_source_concept_id IS 'A foreign key to a Concept that refers to the code used in the source.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.admitting_source_value IS ' The source code for the admitting source as it appears in the source data.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.admitting_source_concept_id| IS 'A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the admitting source for a visit.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.discharge_to_source_value IS ' The source code for the discharge disposition as it appears in the source data.'; +COMMENT ON COLUMN omop.VISIT_DETAIL.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_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.'; +COMMENT ON COLUMN omop.SPECIMEN.specimen_concept_id IS 'A foreign key referring to a Standard Concept identifier in the Standardized Vocabularies for the Specimen.'; +COMMENT ON COLUMN omop.SPECIMEN.specimen_type_concept_id IS 'A foreign key referring to the Concept identifier in the Standardized Vocabularies reflecting the system of record from which the Specimen was represented in the source data.'; +COMMENT ON COLUMN omop.SPECIMEN.specimen_date IS 'The date the specimen was obtained from the Person.'; +COMMENT ON COLUMN omop.SPECIMEN.specimen_datetime IS 'The date and time on the date when the Specimen was obtained from the person.'; +COMMENT ON COLUMN omop.SPECIMEN.quantity IS 'The amount of specimen collection from the person during the sampling procedure.'; +COMMENT ON COLUMN omop.SPECIMEN.unit_concept_id IS 'A foreign key to a Standard Concept identifier for the Unit associated with the numeric quantity of the Specimen collection.'; +COMMENT ON COLUMN omop.SPECIMEN.anatomic_site_concept_id IS 'A foreign key to a Standard Concept identifier for the anatomic location of specimen collection.'; +COMMENT ON COLUMN omop.SPECIMEN.disease_status_concept_id IS 'A foreign key to a Standard Concept identifier for the Disease Status of specimen collection.'; +COMMENT ON COLUMN omop.SPECIMEN.specimen_source_id IS 'The Specimen identifier as it appears in the source data.'; +COMMENT ON COLUMN omop.SPECIMEN.specimen_source_value IS 'The Specimen value as it appears in the source data. This value is mapped to a Standard Concept in the Standardized Vocabularies and the original code is, stored here for reference.'; +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.'; +COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.procedure_concept_id IS 'A foreign key that refers to a standard procedure Concept identifier in the Standardized Vocabularies.'; +COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.procedure_date IS 'The date on which the Procedure was performed.'; +COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.procedure_datetime IS 'The date and time on which the Procedure was performed.'; +COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.procedure_type_concept_id IS 'A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the type of source data from which the procedure record is derived.'; +COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.modifier_concept_id IS 'A foreign key to a Standard Concept identifier for a modifier to the Procedure (e.g. bilateral)'; +COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.quantity IS 'The quantity of procedures ordered or administered.'; +COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.provider_id IS 'A foreign key to the provider in the provider table who was responsible for carrying out the procedure.'; +COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.visit_occurrence_id IS 'A foreign key to the visit in the visit table during which the Procedure was carried out.'; +COMMENT ON COLUMN omop.PROCEDURE_OCCURRENCE.procedure_source_value IS 'The source code for the Procedure as it appears in the source data. This code is mapped to a standard procedure Concept in the Standardized Vocabularies and the original code is, stored here for reference. Procedure source codes are typically ICD-9-Proc, CPT-4, HCPCS or OPCS-4 codes.'; +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.'; +COMMENT ON COLUMN omop.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.'; +COMMENT ON COLUMN omop.PERSON.month_of_birth IS 'The month of birth of the person. For data sources that provide the precise date of birth, the month is extracted and stored in this field.'; +COMMENT ON COLUMN omop.PERSON.day_of_birth IS 'The day of the month of birth of the person. For data sources that provide the precise date of birth, the day is extracted and stored in this field.'; +COMMENT ON COLUMN omop.PERSON.birth_datetime IS 'The date and time of birth of the person.'; +COMMENT ON COLUMN omop.PERSON.race_concept_id IS 'A foreign key that refers to an identifier in the CONCEPT table for the unique race of the person.'; +COMMENT ON COLUMN omop.PERSON.ethnicity_concept_id IS 'A foreign key that refers to the standard concept identifier in the Standardized Vocabularies for the ethnicity of the person.'; +COMMENT ON COLUMN omop.PERSON.location_id IS 'A foreign key to the place of residency for the person in the location table, where the detailed address information is stored.'; +COMMENT ON COLUMN omop.PERSON.provider_id IS 'A foreign key to the primary care provider the person is seeing in the provider table.'; +COMMENT ON COLUMN omop.PERSON.care_site_id IS 'A foreign key to the site of primary care in the care_site table, where the details of the care site are stored.'; +COMMENT ON COLUMN omop.PERSON.person_source_value IS 'An (encrypted) key derived from the person identifier in the source data. This is necessary when a use case requires a link back to the person data at the source dataset.'; +COMMENT ON COLUMN omop.PERSON.gender_source_value IS 'The source code for the gender of the person as it appears in the source data. The person’s gender is mapped to a standard gender concept in the Standardized Vocabularies; the original value is stored here for reference.'; +COMMENT ON COLUMN omop.PERSON.gender_source_concept_id IS 'A foreign key to the gender concept that refers to the code used in the source.'; +COMMENT ON COLUMN omop.PERSON.race_source_value IS 'The source code for the race of the person as it appears in the source data. The person race is mapped to a standard race concept in the Standardized Vocabularies and the original value is stored here for reference.'; +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.'; +COMMENT ON COLUMN omop.OBSERVATION.observation_concept_id IS 'A foreign key to the standard observation concept identifier in the Standardized Vocabularies.'; +COMMENT ON COLUMN omop.OBSERVATION.observation_date IS 'The date of the observation.'; +COMMENT ON COLUMN omop.OBSERVATION.observation_datetime IS 'The date and time of the observation.'; +COMMENT ON COLUMN omop.OBSERVATION.observation_type_concept_id IS 'A foreign key to the predefined concept identifier in the Standardized Vocabularies reflecting the type of the observation.'; +COMMENT ON COLUMN omop.OBSERVATION.value_as_number IS 'The observation result stored as a number. This is applicable to observations where the result is expressed as a numeric value.'; +COMMENT ON COLUMN omop.OBSERVATION.value_as_string IS 'The observation result stored as a string. This is applicable to observations where the result is expressed as verbatim text.'; +COMMENT ON COLUMN omop.OBSERVATION.value_as_concept_id IS 'A foreign key to an observation result stored as a Concept ID. This is applicable to observations where the result can be expressed as a Standard Concept from the Standardized Vocabularies (e.g., positive/negative, present/absent, low/high, etc.).'; +COMMENT ON COLUMN omop.OBSERVATION.qualifier_concept_id IS 'A foreign key to a Standard Concept ID for a qualifier (e.g., severity of drug-drug interaction alert)'; +COMMENT ON COLUMN omop.OBSERVATION.unit_concept_id IS 'A foreign key to a Standard Concept ID of measurement units in the Standardized Vocabularies.'; +COMMENT ON COLUMN omop.OBSERVATION.provider_id IS 'A foreign key to the provider in the PROVIDER table who was responsible for making the observation.'; +COMMENT ON COLUMN omop.OBSERVATION.visit_occurrence_id IS 'A foreign key to the visit in the VISIT_OCCURRENCE table during which the observation was recorded.'; +COMMENT ON COLUMN omop.OBSERVATION.visit_detail_id IS 'A foreign key to the visit in the VISIT_DETAIL table during which the observation was recorded.'; +COMMENT ON COLUMN omop.OBSERVATION.observation_source_value IS 'The observation code 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.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.'; +COMMENT ON COLUMN omop.NOTE_NLP.section_concept_id IS ' A foreign key to the predefined Concept in the Standardized Vocabularies representing the section of the extracted term.'; +COMMENT ON COLUMN omop.NOTE_NLP.snippet IS ' A small window of text surrounding the term.'; +COMMENT ON COLUMN omop.NOTE_NLP.offset IS ' Character offset of the extracted term in the input note.'; +COMMENT ON COLUMN omop.NOTE_NLP.lexical_variant IS ' Raw text extracted from the NLP tool.'; +COMMENT ON COLUMN omop.NOTE_NLP.note_nlp_concept_id IS ' 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.'; +COMMENT ON COLUMN omop.NOTE_NLP.note_nlp_source_concept_id IS ' A foreign key to a Concept that refers to the code in the source vocabulary used by the NLP system'; +COMMENT ON COLUMN omop.NOTE_NLP.nlp_system IS ' Name and version of the NLP system that extracted the term.Useful for data provenance.'; +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 diff --git a/PostgreSQL/extract_comments.sh b/PostgreSQL/extract_comments.sh new file mode 100644 index 0000000..b90d205 --- /dev/null +++ b/PostgreSQL/extract_comments.sh @@ -0,0 +1,46 @@ +#!/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" + +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 "-- 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 "-- 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 "-- 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 "-- 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 "-- 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 "-- 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 "-- 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 "-- 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 "-- 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 "-- 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 "-- 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 "-- 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 "-- 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"