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Merge pull request #460 from flying-burrito/era-dates 

Update v5.3 / v5.4 docs for Era tables: use date type for *_date fields
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clairblacketer 2022-01-13 12:15:43 -05:00 committed by GitHub
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2 changed files with 12 additions and 12 deletions
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12
inst/csv/OMOP_CDMv5.3_Field_Level.csv
View File

@ -317,8 +317,8 @@ COST,drg_source_value,No,varchar(3),Diagnosis Related Groups are US codes used t
DRUG_ERA,drug_era_id,Yes,integer,,,Yes,No,,,,,
DRUG_ERA,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,,
DRUG_ERA,drug_concept_id,Yes,integer,The Concept Id representing the specific drug ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient,
DRUG_ERA,drug_era_start_date,Yes,datetime,,"The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient, with at least 31 days since the previous exposure. ",No,No,,,,,
DRUG_ERA,drug_era_end_date,Yes,datetime,,"The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules:
DRUG_ERA,drug_era_start_date,Yes,date,,"The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient, with at least 31 days since the previous exposure. ",No,No,,,,,
DRUG_ERA,drug_era_end_date,Yes,date,,"The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules:
For pharmacy prescription data, the date when the drug was dispensed plus the number of days of supply are used to extrapolate the End Date for the Drug Exposure. Depending on the country-specific healthcare system, this supply information is either explicitly provided in the day_supply field or inferred from package size or similar information.
For Procedure Drugs, usually the drug is administered on a single date (i.e., the administration date).
A standard Persistence Window of 30 days (gap, slack) is permitted between two subsequent such extrapolated DRUG_EXPOSURE records to be considered to be merged into a single Drug Era.",No,No,,,,,
@ -329,18 +329,18 @@ DOSE_ERA,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,,
DOSE_ERA,drug_concept_id,Yes,integer,The Concept Id representing the specific drug ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient,
DOSE_ERA,unit_concept_id,Yes,integer,The Concept Id representing the unit of the specific drug ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,Unit,,
DOSE_ERA,dose_value,Yes,float,The numeric value of the dosage of the drug_ingredient.,,No,No,,,,,
DOSE_ERA,dose_era_start_date,Yes,datetime,"The date the Person started on the specific dosage, with at least 31 days since any prior exposure.",,No,No,,,,,
DOSE_ERA,dose_era_end_date,Yes,datetime,,The date the Person was no longer exposed to the dosage of the specific drug ingredient. An era is ended if there are 31 days or more between dosage records.,No,No,,,,,
DOSE_ERA,dose_era_start_date,Yes,date,"The date the Person started on the specific dosage, with at least 31 days since any prior exposure.",,No,No,,,,,
DOSE_ERA,dose_era_end_date,Yes,date,,The date the Person was no longer exposed to the dosage of the specific drug ingredient. An era is ended if there are 31 days or more between dosage records.,No,No,,,,,
CONDITION_ERA,condition_era_id,Yes,integer,,,Yes,No,,,,,
CONDITION_ERA,person_id,Yes,integer,,,No,No,PERSON,PERSON_ID,,,
CONDITION_ERA,condition_concept_id,Yes,integer,The Concept Id representing the Condition.,,No,Yes,CONCEPT,CONCEPT_ID,Condition,,
CONDITION_ERA,condition_era_start_date,Yes,datetime,"The start date for the Condition Era
CONDITION_ERA,condition_era_start_date,Yes,date,"The start date for the Condition Era
constructed from the individual
instances of Condition Occurrences.
It is the start date of the very first
chronologically recorded instance of
the condition with at least 31 days since any prior record of the same Condition. ",,No,No,,,,,
CONDITION_ERA,condition_era_end_date,Yes,datetime,"The end date for the Condition Era
CONDITION_ERA,condition_era_end_date,Yes,date,"The end date for the Condition Era
constructed from the individual
instances of Condition Occurrences.
It is the end date of the final

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
317 CDM_SOURCE cdm_holder No varchar(255) The holder of the CDM instance. No No
318 CDM_SOURCE source_description No varchar(MAX) The description of the CDM instance. No No
319 CDM_SOURCE source_documentation_reference No varchar(255) No No
320 CDM_SOURCE cdm_etl_reference No varchar(255) Put the link to the CDM version used. No No
321 CDM_SOURCE source_release_date No date The release date of the source data. No No
322 CDM_SOURCE cdm_release_date No date The release data of the CDM instance. No No
323 CDM_SOURCE cdm_version No varchar(10) No No
324 CDM_SOURCE vocabulary_version No varchar(20) No No
329 CONCEPT concept_class_id Yes varchar(20) The attribute or concept class of the Concept. Examples are 'Clinical Drug', 'Ingredient', 'Clinical Finding' etc. No Yes CONCEPT_CLASS CONCEPT_CLASS_ID
330 CONCEPT standard_concept No varchar(1) This flag determines where a Concept is a Standard Concept, i.e. is used in the data, a Classification Concept, or a non-standard Source Concept. The allowable values are 'S' (Standard Concept) and 'C' (Classification Concept), otherwise the content is NULL. No No
331 CONCEPT concept_code Yes varchar(50) The concept code represents the identifier of the Concept in the source vocabulary, such as SNOMED-CT concept IDs, RxNorm RXCUIs etc. Note that concept codes are not unique across vocabularies. No No
332 CONCEPT valid_start_date Yes date The date when the Concept was first recorded. The default value is 1-Jan-1970, meaning, the Concept has no (known) date of inception. No No
333 CONCEPT valid_end_date Yes date 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. No No
334 CONCEPT invalid_reason No varchar(1) 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. No No
335 VOCABULARY vocabulary_id Yes varchar(20) A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit. Yes No
336 VOCABULARY vocabulary_name Yes varchar(255) The name describing the vocabulary, for example, International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS) etc. No No
337 VOCABULARY vocabulary_reference Yes varchar(255) External reference to documentation or available download of the about the vocabulary. No No
338 VOCABULARY vocabulary_version No varchar(255) Version of the Vocabulary as indicated in the source. No No
339 VOCABULARY vocabulary_concept_id Yes integer A Concept that represents the Vocabulary the VOCABULARY record belongs to. No Yes CONCEPT CONCEPT_ID
340 DOMAIN domain_id Yes varchar(20) A unique key for each domain. Yes No
341 DOMAIN domain_name Yes varchar(255) The name describing the Domain, e.g. Condition, Procedure, Measurement etc. No No
342 DOMAIN domain_concept_id Yes integer A Concept representing the Domain Concept the DOMAIN record belongs to. No Yes CONCEPT CONCEPT_ID
343 CONCEPT_CLASS concept_class_id Yes varchar(20) A unique key for each class. Yes No
344 CONCEPT_CLASS concept_class_name Yes varchar(255) The name describing the Concept Class, e.g. Clinical Finding, Ingredient, etc. No No
345 CONCEPT_CLASS concept_class_concept_id Yes integer A Concept that represents the Concept Class. No Yes CONCEPT CONCEPT_ID
346 CONCEPT_RELATIONSHIP concept_id_1 Yes integer No Yes CONCEPT CONCEPT_ID

12
inst/csv/OMOP_CDMv5.4_Field_Level.csv
View File

@ -335,8 +335,8 @@ COST,drg_source_value,No,varchar(3),Diagnosis Related Groups are US codes used t
DRUG_ERA,drug_era_id,Yes,integer,,,Yes,No,,,,,
DRUG_ERA,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,,
DRUG_ERA,drug_concept_id,Yes,integer,The Concept Id representing the specific drug ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient,
DRUG_ERA,drug_era_start_date,Yes,datetime,,"The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient, with at least 31 days since the previous exposure. ",No,No,,,,,
DRUG_ERA,drug_era_end_date,Yes,datetime,,"The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules:
DRUG_ERA,drug_era_start_date,Yes,date,,"The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient, with at least 31 days since the previous exposure. ",No,No,,,,,
DRUG_ERA,drug_era_end_date,Yes,date,,"The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules:
For pharmacy prescription data, the date when the drug was dispensed plus the number of days of supply are used to extrapolate the End Date for the Drug Exposure. Depending on the country-specific healthcare system, this supply information is either explicitly provided in the day_supply field or inferred from package size or similar information.
For Procedure Drugs, usually the drug is administered on a single date (i.e., the administration date).
A standard Persistence Window of 30 days (gap, slack) is permitted between two subsequent such extrapolated DRUG_EXPOSURE records to be considered to be merged into a single Drug Era.",No,No,,,,,
@ -347,18 +347,18 @@ DOSE_ERA,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,,
DOSE_ERA,drug_concept_id,Yes,integer,The Concept Id representing the specific drug ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient,
DOSE_ERA,unit_concept_id,Yes,integer,The Concept Id representing the unit of the specific drug ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,Unit,,
DOSE_ERA,dose_value,Yes,float,The numeric value of the dosage of the drug_ingredient.,,No,No,,,,,
DOSE_ERA,dose_era_start_date,Yes,datetime,"The date the Person started on the specific dosage, with at least 31 days since any prior exposure.",,No,No,,,,,
DOSE_ERA,dose_era_end_date,Yes,datetime,,The date the Person was no longer exposed to the dosage of the specific drug ingredient. An era is ended if there are 31 days or more between dosage records.,No,No,,,,,
DOSE_ERA,dose_era_start_date,Yes,date,"The date the Person started on the specific dosage, with at least 31 days since any prior exposure.",,No,No,,,,,
DOSE_ERA,dose_era_end_date,Yes,date,,The date the Person was no longer exposed to the dosage of the specific drug ingredient. An era is ended if there are 31 days or more between dosage records.,No,No,,,,,
CONDITION_ERA,condition_era_id,Yes,integer,,,Yes,No,,,,,
CONDITION_ERA,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,,
CONDITION_ERA,condition_concept_id,Yes,integer,The Concept Id representing the Condition.,,No,Yes,CONCEPT,CONCEPT_ID,Condition,,
CONDITION_ERA,condition_era_start_date,Yes,datetime,"The start date for the Condition Era
CONDITION_ERA,condition_era_start_date,Yes,date,"The start date for the Condition Era
constructed from the individual
instances of Condition Occurrences.
It is the start date of the very first
chronologically recorded instance of
the condition with at least 31 days since any prior record of the same Condition. ",,No,No,,,,,
CONDITION_ERA,condition_era_end_date,Yes,datetime,"The end date for the Condition Era
CONDITION_ERA,condition_era_end_date,Yes,date,"The end date for the Condition Era
constructed from the individual
instances of Condition Occurrences.
It is the end date of the final

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
335 EPISODE episode_object_concept_id Yes integer A Standard Concept representing the disease phase, outcome, or other abstraction of which the episode consists. For example, if the EPISODE_CONCEPT_ID is [treatment regimen](https://athena.ohdsi.org/search-terms/terms/32531) then the EPISODE_OBJECT_CONCEPT_ID should contain the chemotherapy regimen concept, like [Afatinib monotherapy](https://athena.ohdsi.org/search-terms/terms/35804392). Episode entries from the 'Disease Episode' concept class should have an episode_object_concept_id that comes from the Condition domain. Episode entries from the 'Treatment Episode' concept class should have an episode_object_concept_id that scome from the 'Procedure' domain or 'Regimen' concept class. No Yes CONCEPT CONCEPT_ID Procedure, Regimen
336 EPISODE episode_type_concept_id Yes integer This field can be used to determine the provenance of the Episode record, as in whether the episode was from an EHR system, insurance claim, registry, or other sources. Choose the EPISODE_TYPE_CONCEPT_ID that best represents the provenance of the record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID Type Concept
337 EPISODE episode_source_value No varchar(50) The source code for the Episdoe 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. No No
338 EPISODE episode_source_concept_id No integer A foreign key to a Episode Concept that refers to the code used in the source. Given that the Episodes are user-defined it is unlikely that there will be a Source Concept available. If that is the case then set this field to zero. No Yes CONCEPT CONCEPT_ID
339 EPISODE_EVENT episode_id Yes bigint Use this field to link the EPISODE_EVENT record to its EPISODE. Put the EPISODE_ID that subsumes the EPISODE_EVENT record here. No Yes EPISODE EPISODE_ID
340 EPISODE_EVENT event_id Yes bigint This field is the primary key of the linked record in the database. For example, if the Episode Event is a Condition Occurrence, then the CONDITION_OCCURRENCE_ID of the linked record goes in this field. Put the primary key of the linked record here. No No
341 EPISODE_EVENT episode_event_field_concept_id Yes integer This field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. Put the CONCEPT_ID that identifies which table and field the EVENT_ID came from. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?vocabulary=CDM&conceptClass=Field&page=1&pageSize=15&query=) No Yes CONCEPT CONCEPT_ID Metadata
342 METADATA metadata_id Yes integer The unique key given to a Metadata record. Attribute value is auto-generated Yes No
347 METADATA value_as_concept_id No integer No Yes CONCEPT CONCEPT_ID
348 METADATA value_as_number No float This is the numerical value of the result of the Metadata, if applicable and available. It is not expected that all Metadata will have numeric results, rather, this field is here to house values should they exist. No No
349 METADATA metadata_date No date No No
350 METADATA metadata_datetime No datetime No No
351 CDM_SOURCE cdm_source_name Yes varchar(255) The name of the CDM instance. No No
352 CDM_SOURCE cdm_source_abbreviation Yes varchar(25) The abbreviation of the CDM instance. No No
353 CDM_SOURCE cdm_holder Yes varchar(255) The holder of the CDM instance. No No
354 CDM_SOURCE source_description No varchar(MAX) The description of the CDM instance. No No
355 CDM_SOURCE source_documentation_reference No varchar(255) No No
356 CDM_SOURCE cdm_etl_reference No varchar(255) Put the link to the CDM version used. No No
357 CDM_SOURCE source_release_date Yes date The release date of the source data. No No
358 CDM_SOURCE cdm_release_date Yes date The release data of the CDM instance. No No
359 CDM_SOURCE cdm_version No varchar(10) No No
360 CDM_SOURCE cdm_version_concept_id Yes integer The Concept Id representing the version of the CDM. No Yes CONCEPT CONCEPT_ID
361 CDM_SOURCE vocabulary_version Yes varchar(20) No No
362 CONCEPT concept_id Yes integer A unique identifier for each Concept across all domains. Yes No
363 CONCEPT concept_name Yes varchar(255) An unambiguous, meaningful and descriptive name for the Concept. No No
364 CONCEPT domain_id Yes varchar(20) A foreign key to the [DOMAIN](https://ohdsi.github.io/CommonDataModel/cdm531.html#domain) table the Concept belongs to. No Yes DOMAIN DOMAIN_ID