From ad666fdd9d879e9e6cfac18d466121b134e7ff53 Mon Sep 17 00:00:00 2001 From: Maxim Moinat Date: Thu, 6 Jun 2024 17:31:54 +0200 Subject: [PATCH] remove drug end date convention --- inst/csv/OMOP_CDMv5.3_Field_Level.csv | 242 +++++++++++++------------- inst/csv/OMOP_CDMv5.4_Field_Level.csv | 6 +- 2 files changed, 124 insertions(+), 124 deletions(-) diff --git a/inst/csv/OMOP_CDMv5.3_Field_Level.csv b/inst/csv/OMOP_CDMv5.3_Field_Level.csv index 7f17c1a..3f52888 100644 --- a/inst/csv/OMOP_CDMv5.3_Field_Level.csv +++ b/inst/csv/OMOP_CDMv5.3_Field_Level.csv @@ -27,12 +27,12 @@ visit_occurrence,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA visit_occurrence,visit_concept_id,Yes,integer,"This field contains a concept id representing the kind of visit, like inpatient or outpatient. All concepts in this field should be standard and belong to the Visit domain.","Populate this field based on the kind of visit that took place for the person. For example this could be ""Inpatient Visit"", ""Outpatient Visit"", ""Ambulatory Visit"", etc. This table will contain standard concepts in the Visit domain. These concepts are arranged in a hierarchical structure to facilitate cohort definitions by rolling up to generally familiar Visits adopted in most healthcare systems worldwide. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,NA,NA visit_occurrence,visit_start_date,Yes,date,"For inpatient visits, the start date is typically the admission date. For outpatient visits the start date and end date will be the same.","When populating VISIT_START_DATE, you should think about the patient experience to make decisions on how to define visits. In the case of an inpatient visit this should be the date the patient was admitted to the hospital or institution. In all other cases this should be the date of the patient-provider interaction. If this information is not available the record should be dropped.",No,No,NA,NA,NA,NA,NA visit_occurrence,visit_start_datetime,No,datetime,NA,"If no time is given for the start date of a visit, set it to midnight (00:00:0000).",No,No,NA,NA,NA,NA,NA -visit_occurrence,visit_end_date,Yes,date,For inpatient visits the end date is typically the discharge date.,"Visit end dates are mandatory. If end dates are not provided in the source there are three ways in which to derive them: -- Outpatient Visit: visit_end_datetime = visit_start_datetime -- Emergency Room Visit: visit_end_datetime = visit_start_datetime -- Inpatient Visit: Usually there is information about discharge. If not, you should be able to derive the end date from the sudden decline of activity or from the absence of inpatient procedures/drugs. -- Non-hospital institution Visits: Particularly for claims data, if end dates are not provided assume the visit is for the duration of month that it occurs. -For Inpatient Visits ongoing at the date of ETL, put date of processing the data into visit_end_datetime and visit_type_concept_id with 32220 ""Still patient"" to identify the visit as incomplete. +visit_occurrence,visit_end_date,Yes,date,For inpatient visits the end date is typically the discharge date.,"Visit end dates are mandatory. If end dates are not provided in the source there are three ways in which to derive them: +- Outpatient Visit: visit_end_datetime = visit_start_datetime +- Emergency Room Visit: visit_end_datetime = visit_start_datetime +- Inpatient Visit: Usually there is information about discharge. If not, you should be able to derive the end date from the sudden decline of activity or from the absence of inpatient procedures/drugs. +- Non-hospital institution Visits: Particularly for claims data, if end dates are not provided assume the visit is for the duration of month that it occurs. +For Inpatient Visits ongoing at the date of ETL, put date of processing the data into visit_end_datetime and visit_type_concept_id with 32220 ""Still patient"" to identify the visit as incomplete. - All other Visits: visit_end_datetime = visit_start_datetime. If this is a one-day visit the end date should match the start date.",No,No,NA,NA,NA,NA,NA visit_occurrence,visit_end_datetime,No,datetime,NA,"If no time is given for the end date of a visit, set it to midnight (00:00:0000).",No,No,NA,NA,NA,NA,NA visit_occurrence,visit_type_concept_id,Yes,Integer,"Use this field to understand the provenance of the visit record, or where the record comes from.","Populate this field based on the provenance of the visit record, as in whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA @@ -50,12 +50,12 @@ visit_detail,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA visit_detail,visit_detail_concept_id,Yes,integer,"This field contains a concept id representing the kind of visit detail, like inpatient or outpatient. All concepts in this field should be standard and belong to the Visit domain.","Populate this field based on the kind of visit that took place for the person. For example this could be ""Inpatient Visit"", ""Outpatient Visit"", ""Ambulatory Visit"", etc. This table will contain standard concepts in the Visit domain. These concepts are arranged in a hierarchical structure to facilitate cohort definitions by rolling up to generally familiar Visits adopted in most healthcare systems worldwide. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,NA,NA visit_detail,visit_detail_start_date,Yes,date,This is the date of the start of the encounter. This may or may not be equal to the date of the Visit the Visit Detail is associated with.,"When populating VISIT_DETAIL_START_DATE, you should think about the patient experience to make decisions on how to define visits. Most likely this should be the date of the patient-provider interaction.",No,No,NA,NA,NA,NA,NA visit_detail,visit_detail_start_datetime,No,datetime,NA,"If no time is given for the start date of a visit, set it to midnight (00:00:0000).",No,No,NA,NA,NA,NA,NA -visit_detail,visit_detail_end_date,Yes,date,This the end date of the patient-provider interaction.,"Visit Detail end dates are mandatory. If end dates are not provided in the source there are three ways in which to derive them:
-- Outpatient Visit Detail: visit_detail_end_datetime = visit_detail_start_datetime -- Emergency Room Visit Detail: visit_detail_end_datetime = visit_detail_start_datetime -- Inpatient Visit Detail: Usually there is information about discharge. If not, you should be able to derive the end date from the sudden decline of activity or from the absence of inpatient procedures/drugs. -- Non-hospital institution Visit Details: Particularly for claims data, if end dates are not provided assume the visit is for the duration of month that it occurs.
-For Inpatient Visit Details ongoing at the date of ETL, put date of processing the data into visit_detai_end_datetime and visit_detail_type_concept_id with 32220 ""Still patient"" to identify the visit as incomplete. +visit_detail,visit_detail_end_date,Yes,date,This the end date of the patient-provider interaction.,"Visit Detail end dates are mandatory. If end dates are not provided in the source there are three ways in which to derive them:
+- Outpatient Visit Detail: visit_detail_end_datetime = visit_detail_start_datetime +- Emergency Room Visit Detail: visit_detail_end_datetime = visit_detail_start_datetime +- Inpatient Visit Detail: Usually there is information about discharge. If not, you should be able to derive the end date from the sudden decline of activity or from the absence of inpatient procedures/drugs. +- Non-hospital institution Visit Details: Particularly for claims data, if end dates are not provided assume the visit is for the duration of month that it occurs.
+For Inpatient Visit Details ongoing at the date of ETL, put date of processing the data into visit_detai_end_datetime and visit_detail_type_concept_id with 32220 ""Still patient"" to identify the visit as incomplete. All other Visits Details: visit_detail_end_datetime = visit_detail_start_datetime.",No,No,NA,NA,NA,NA,NA visit_detail,visit_detail_end_datetime,No,datetime,NA,"If no time is given for the end date of a visit, set it to midnight (00:00:0000).",No,No,NA,NA,NA,NA,NA visit_detail,visit_detail_type_concept_id,Yes,integer,"Use this field to understand the provenance of the visit detail record, or where the record comes from.","Populate this field based on the provenance of the visit detail record, as in whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA @@ -88,17 +88,17 @@ condition_occurrence,condition_source_concept_id,No,integer,"This is the concept condition_occurrence,condition_status_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the condition status.,This information may be called something different in the source data but the field is meant to contain a value indicating when and how a diagnosis was given to a patient. This source value is mapped to a standard concept which is stored in the CONDITION_STATUS_CONCEPT_ID field.,No,No,NA,NA,NA,NA,NA drug_exposure,drug_exposure_id,Yes,integer,The unique key given to records of drug dispensings or administrations for a person. Refer to the ETL for how duplicate drugs during the same visit were handled.,"Each instance of a drug dispensing or administration present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same drug within the same visit. It is valid to keep these duplicates and assign them individual, unique, DRUG_EXPOSURE_IDs, though it is up to the ETL how they should be handled.",Yes,No,NA,NA,NA,NA,NA drug_exposure,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the drug dispensing or administration is recorded. This may be a system generated code.,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA -drug_exposure,drug_concept_id,Yes,integer,"The DRUG_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a drug product or molecule otherwise introduced to the body. The drug concepts can have a varying degree of information about drug strength and dose. This information is relevant in the context of quantity and administration information in the subsequent fields plus strength information from the DRUG_STRENGTH table, provided as part of the standard vocabulary download.","The CONCEPT_ID that the DRUG_SOURCE_VALUE maps to. The concept id should be derived either from mapping from the source concept id or by picking the drug concept representing the most amount of detail you have. Records whose source values map to standard concepts with a domain of Drug should go in this table. When the Drug Source Value of the code cannot be translated into Standard Drug Concept IDs, a Drug exposure entry is stored with only the corresponding SOURCE_CONCEPT_ID and DRUG_SOURCE_VALUE and a DRUG_CONCEPT_ID of 0. The Drug Concept with the most detailed content of information is preferred during the mapping process. These are indicated in the CONCEPT_CLASS_ID field of the Concept and are recorded in the following order of precedence: ÒMarketed ProductÓ, ÒBranded PackÓ, ÒClinical PackÓ, ÒBranded DrugÓ, ÒClinical DrugÓ, ÒBranded Drug ComponentÓ, ÒClinical Drug ComponentÓ, ÒBranded Drug FormÓ, ÒClinical Drug FormÓ, and only if no other information is available ÒIngredientÓ. Note: If only the drug class is known, the DRUG_CONCEPT_ID field should contain 0. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Drug&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Drug,NA,NA +drug_exposure,drug_concept_id,Yes,integer,"The DRUG_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a drug product or molecule otherwise introduced to the body. The drug concepts can have a varying degree of information about drug strength and dose. This information is relevant in the context of quantity and administration information in the subsequent fields plus strength information from the DRUG_STRENGTH table, provided as part of the standard vocabulary download.","The CONCEPT_ID that the DRUG_SOURCE_VALUE maps to. The concept id should be derived either from mapping from the source concept id or by picking the drug concept representing the most amount of detail you have. Records whose source values map to standard concepts with a domain of Drug should go in this table. When the Drug Source Value of the code cannot be translated into Standard Drug Concept IDs, a Drug exposure entry is stored with only the corresponding SOURCE_CONCEPT_ID and DRUG_SOURCE_VALUE and a DRUG_CONCEPT_ID of 0. The Drug Concept with the most detailed content of information is preferred during the mapping process. These are indicated in the CONCEPT_CLASS_ID field of the Concept and are recorded in the following order of precedence: �Marketed Product�, �Branded Pack�, �Clinical Pack�, �Branded Drug�, �Clinical Drug�, �Branded Drug Component�, �Clinical Drug Component�, �Branded Drug Form�, �Clinical Drug Form�, and only if no other information is available �Ingredient�. Note: If only the drug class is known, the DRUG_CONCEPT_ID field should contain 0. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Drug&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Drug,NA,NA drug_exposure,drug_exposure_start_date,Yes,date,Use this date to determine the start date of the drug record.,"Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration was recorded. It is a valid ETL choice to use the date the drug was ordered as the DRUG_EXPOSURE_START_DATE.",No,No,NA,NA,NA,NA,NA drug_exposure,drug_exposure_start_datetime,No,datetime,NA,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,NA,NA,NA,NA,NA -drug_exposure,drug_exposure_end_date,Yes,date,The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended for the patient.,"If this information is not explicitly available in the data, infer the end date using the following methods:

1. Start first with duration or days supply using the calculation drug start date + days supply -1 day. 2. Use quantity divided by daily dose that you may obtain from the sig or a source field (or assumed daily dose of 1) for solid, indivisibile, drug products. If quantity represents ingredient amount, quantity divided by daily dose * concentration (from drug_strength) drug concept id tells you the dose form. 3. If it is an administration record, set drug end date equal to drug start date. If the record is a written prescription then set end date to start date + 29. If the record is a mail-order prescription set end date to start date + 89. The end date must be equal to or greater than the start date. Ibuprofen 20mg/mL oral solution concept tells us this is oral solution. Calculate duration as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL) 200*5/20 = 50 days. [Examples by dose form](https://ohdsi.github.io/CommonDataModel/drug_dose.html)

For detailed conventions for how to populate this field, please see the [THEMIS repository](https://ohdsi.github.io/Themis/tag_drug_exposure.html).",No,No,NA,NA,NA,NA,NA +drug_exposure,drug_exposure_end_date,Yes,date,The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended for the patient.,"If this information is not explicitly available in the data, infer the end date from start date and duration.
For detailed conventions for how to populate this field, please see the [THEMIS repository](https://ohdsi.github.io/Themis/tag_drug_exposure.html).",No,No,NA,NA,NA,NA,NA drug_exposure,drug_exposure_end_datetime,No,datetime,NA,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,NA,NA,NA,NA,NA drug_exposure,verbatim_end_date,No,date,"This is the end date of the drug exposure as it appears in the source data, if it is given",Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable.,No,No,NA,NA,NA,NA,NA drug_exposure,drug_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to delineate between prescriptions written vs. prescriptions dispensed vs. medication history vs. patient-reported exposure, etc.","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA drug_exposure,stop_reason,No,varchar(20),"The reason a person stopped a medication as it is represented in the source. Reasons include regimen completed, changed, removed, etc. This field will be retired in v6.0.",This information is often not populated in source data and it is a valid etl choice to leave it blank if the information does not exist.,No,No,NA,NA,NA,NA,NA drug_exposure,refills,No,integer,This is only filled in when the record is coming from a prescription written this field is meant to represent intended refills at time of the prescription.,NA,No,No,NA,NA,NA,NA,NA -drug_exposure,quantity,No,float,NA,"To find the dose form of a drug the RELATIONSHIP table can be used where the relationship_id is 'Has dose form'. If liquid, quantity stands for the total amount dispensed or ordered of ingredient in the units given by the drug_strength table. If the unit from the source data does not align with the unit in the DRUG_STRENGTH table the quantity should be converted to the correct unit given in DRUG_STRENGTH. For clinical drugs with fixed dose forms (tablets etc.) the quantity is the number of units/tablets/capsules prescribed or dispensed (can be partial, but then only 1/2 or 1/3, not 0.01). Clinical drugs with divisible dose forms (injections) the quantity is the amount of ingredient the patient got. For example, if the injection is 2mg/mL but the patient got 80mL then quantity is reported as 160. -Quantified clinical drugs with divisible dose forms (prefilled syringes), the quantity is the amount of ingredient similar to clinical drugs. Please see [how to calculate drug dose](https://ohdsi.github.io/CommonDataModel/drug_dose.html) for more information. +drug_exposure,quantity,No,float,NA,"To find the dose form of a drug the RELATIONSHIP table can be used where the relationship_id is 'Has dose form'. If liquid, quantity stands for the total amount dispensed or ordered of ingredient in the units given by the drug_strength table. If the unit from the source data does not align with the unit in the DRUG_STRENGTH table the quantity should be converted to the correct unit given in DRUG_STRENGTH. For clinical drugs with fixed dose forms (tablets etc.) the quantity is the number of units/tablets/capsules prescribed or dispensed (can be partial, but then only 1/2 or 1/3, not 0.01). Clinical drugs with divisible dose forms (injections) the quantity is the amount of ingredient the patient got. For example, if the injection is 2mg/mL but the patient got 80mL then quantity is reported as 160. +Quantified clinical drugs with divisible dose forms (prefilled syringes), the quantity is the amount of ingredient similar to clinical drugs. Please see [how to calculate drug dose](https://ohdsi.github.io/CommonDataModel/drug_dose.html) for more information. ",No,No,NA,NA,NA,NA,NA drug_exposure,days_supply,No,integer,The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure).,"The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields.

Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible: 1) record is not trustworthy and we remove the record entirely. 2) we trust the record and leave days_supply empty or 3) record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras.",No,No,NA,NA,NA,NA,NA drug_exposure,sig,No,varchar(MAX),This is the verbatim instruction for the drug as written by the provider.,"Put the written out instructions for the drug as it is verbatim in the source, if available.",No,No,NA,NA,NA,NA,NA @@ -142,7 +142,7 @@ device_exposure,device_source_value,No,varchar(50),"This field houses the verbat device_exposure,device_source_concept_id,No,integer,"This is the concept representing the device source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Device necessary for a given analytic use case. Consider using DEVICE_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the DEVICE_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA measurement,measurement_id,Yes,integer,The unique key given to a Measurement record for a Person. Refer to the ETL for how duplicate Measurements during the same Visit were handled.,"Each instance of a measurement present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same measurement within the same visit. It is valid to keep these duplicates and assign them individual, unique, MEASUREMENT_IDs, though it is up to the ETL how they should be handled.",Yes,No,NA,NA,NA,NA,NA measurement,person_id,Yes,integer,The PERSON_ID of the Person for whom the Measurement is recorded. This may be a system generated code.,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA -measurement,measurement_concept_id,Yes,integer,"The MEASUREMENT_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source value which represents a measurement.",The CONCEPT_ID that the MEASUREMENT_SOURCE_VALUE maps to. Only records whose source values map to concepts with a domain of ÒMeasurementÓ should go in this table.,No,Yes,CONCEPT,CONCEPT_ID,Measurement,NA,NA +measurement,measurement_concept_id,Yes,integer,"The MEASUREMENT_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source value which represents a measurement.",The CONCEPT_ID that the MEASUREMENT_SOURCE_VALUE maps to. Only records whose source values map to concepts with a domain of �Measurement� should go in this table.,No,Yes,CONCEPT,CONCEPT_ID,Measurement,NA,NA measurement,measurement_date,Yes,date,Use this date to determine the date of the measurement.,"If there are multiple dates in the source data associated with a record such as order_date, draw_date, and result_date, choose the one that is closest to the date the sample was drawn from the patient.",No,No,NA,NA,NA,NA,NA measurement,measurement_datetime,No,datetime,NA,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,NA,NA,NA,NA,NA measurement,measurement_time,No,varchar(10),NA,This is present for backwards compatibility and will be deprecated in an upcoming version.,No,No,NA,NA,NA,NA,NA @@ -190,7 +190,7 @@ note,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA note,note_date,Yes,date,The date the note was recorded.,NA,No,No,NA,NA,NA,NA,NA note,note_datetime,No,datetime,NA,If time is not given set the time to midnight.,No,No,NA,NA,NA,NA,NA note,note_type_concept_id,Yes,integer,The provenance of the note. Most likely this will be EHR.,"Put the source system of the note, as in EHR record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA -note,note_class_concept_id,Yes,integer,"A Standard Concept Id representing the HL7 LOINC +note,note_class_concept_id,Yes,integer,"A Standard Concept Id representing the HL7 LOINC Document Type Vocabulary classification of the note.",Map the note classification to a Standard Concept. For more information see the ETL Conventions in the description of the NOTE table. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&conceptClass=Doc+Kind&conceptClass=Doc+Role&conceptClass=Doc+Setting&conceptClass=Doc+Subject+Matter&conceptClass=Doc+Type+of+Service&domain=Meas+Value&page=1&pageSize=15&query=). This Concept can alternatively be represented by concepts with the relationship 'Kind of (LOINC)' to [706391](https://athena.ohdsi.org/search-terms/terms/706391) (Note).,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA note,note_title,No,varchar(250),The title of the note.,NA,No,No,NA,NA,NA,NA,NA note,note_text,Yes,varchar(MAX),The content of the note.,NA,No,No,NA,NA,NA,NA,NA @@ -211,22 +211,22 @@ note_nlp,note_nlp_source_concept_id,No,integer,NA,NA,No,Yes,CONCEPT,CONCEPT_ID,N note_nlp,nlp_system,No,varchar(250),NA,Name and version of the NLP system that extracted the term. Useful for data provenance.,No,No,NA,NA,NA,NA,NA note_nlp,nlp_date,Yes,date,The date of the note processing.,NA,No,No,NA,NA,NA,NA,NA note_nlp,nlp_datetime,No,datetime,The date and time of the note processing.,NA,No,No,NA,NA,NA,NA,NA -note_nlp,term_exists,No,varchar(1),NA,"Term_exists is defined as a flag that indicates if the patient actually has or had the condition. Any of the following modifiers would make Term_exists false: -Negation = true -Subject = [anything other than the patient] -Conditional = true/li> -Rule_out = true -Uncertain = very low certainty or any lower certainties -A complete lack of modifiers would make Term_exists true. +note_nlp,term_exists,No,varchar(1),NA,"Term_exists is defined as a flag that indicates if the patient actually has or had the condition. Any of the following modifiers would make Term_exists false: +Negation = true +Subject = [anything other than the patient] +Conditional = true/li> +Rule_out = true +Uncertain = very low certainty or any lower certainties +A complete lack of modifiers would make Term_exists true. ",No,No,NA,NA,NA,NA,NA -note_nlp,term_temporal,No,varchar(50),NA,"Term_temporal is to indicate if a condition is present or just in the past. The following would be past:

-- History = true +note_nlp,term_temporal,No,varchar(50),NA,"Term_temporal is to indicate if a condition is present or just in the past. The following would be past:

+- History = true - Concept_date = anything before the time of the report",No,No,NA,NA,NA,NA,NA -note_nlp,term_modifiers,No,varchar(2000),NA,"For the modifiers that are there, they would have to have these values:

-- Negation = false -- Subject = patient -- Conditional = false -- Rule_out = false +note_nlp,term_modifiers,No,varchar(2000),NA,"For the modifiers that are there, they would have to have these values:

+- Negation = false +- Subject = patient +- Conditional = false +- Rule_out = false - Uncertain = true or high or moderate or even low (could argue about low). Term_modifiers will concatenate all modifiers for different types of entities (conditions, drugs, labs etc) into one string. Lab values will be saved as one of the modifiers.",No,No,NA,NA,NA,NA,NA specimen,specimen_id,Yes,integer,Unique identifier for each specimen.,NA,Yes,No,NA,NA,NA,NA,NA specimen,person_id,Yes,integer,The person from whom the specimen is collected.,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA @@ -318,9 +318,9 @@ drug_era,drug_era_id,Yes,integer,NA,NA,Yes,No,NA,NA,NA,NA,NA drug_era,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA drug_era,drug_concept_id,Yes,integer,The drug_concept_id should conform to the concept class 'ingredient' as the drug_era is an era of time where a person is exposed to a particular drug ingredient.,NA,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient,NA drug_era,drug_era_start_date,Yes,date,NA,"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,NA,NA,NA,NA,NA -drug_era,drug_era_end_date,Yes,date,NA,"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). +drug_era,drug_era_end_date,Yes,date,NA,"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,NA,NA,NA,NA,NA drug_era,drug_exposure_count,No,integer,The count of grouped DRUG_EXPOSURE records that were included in the DRUG_ERA row,NA,No,No,NA,NA,NA,NA,NA drug_era,gap_days,No,integer,NA,"The Gap Days determine how many total drug-free days are observed between all Drug Exposure events that contribute to a DRUG_ERA record. It is assumed that the drugs are ""not stockpiled"" by the patient, i.e. that if a new drug prescription or refill is observed (a new DRUG_EXPOSURE record is written), the remaining supply from the previous events is abandoned. The difference between Persistence Window and Gap Days is that the former is the maximum drug-free time allowed between two subsequent DRUG_EXPOSURE records, while the latter is the sum of actual drug-free days for the given Drug Era under the above assumption of non-stockpiling.",No,No,NA,NA,NA,NA,NA @@ -334,20 +334,20 @@ dose_era,dose_era_end_date,Yes,date,NA,The date the Person was no longer exposed condition_era,condition_era_id,Yes,integer,NA,NA,Yes,No,NA,NA,NA,NA,NA condition_era,person_id,Yes,integer,NA,NA,No,No,PERSON,PERSON_ID,NA,NA,NA condition_era,condition_concept_id,Yes,integer,The Concept Id representing the Condition.,NA,No,Yes,CONCEPT,CONCEPT_ID,Condition,NA,NA -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 +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.",NA,No,No,NA,NA,NA,NA,NA -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 -continuously recorded instance of the +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 +continuously recorded instance of the Condition.",NA,No,No,NA,NA,NA,NA,NA -condition_era,condition_occurrence_count,No,integer,"The number of individual Condition -Occurrences used to construct the +condition_era,condition_occurrence_count,No,integer,"The number of individual Condition +Occurrences used to construct the condition era.",NA,No,No,NA,NA,NA,NA,NA metadata,metadata_concept_id,Yes,integer,NA,NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA metadata,metadata_type_concept_id,Yes,integer,NA,NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA @@ -369,57 +369,57 @@ cdm_source,vocabulary_version,No,varchar(20),NA,NA,No,No,NA,NA,NA,NA,NA concept,concept_id,Yes,integer,A unique identifier for each Concept across all domains.,NA,Yes,No,NA,NA,NA,NA,NA concept,concept_name,Yes,varchar(255),"An unambiguous, meaningful and descriptive name for the Concept.",NA,No,No,NA,NA,NA,NA,NA 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.,NA,No,Yes,DOMAIN,DOMAIN_ID,NA,NA,NA -concept,vocabulary_id,Yes,varchar(20),"A foreign key to the [VOCABULARY](https://ohdsi.github.io/CommonDataModel/cdm531.html#vocabulary) -table indicating from which source the +concept,vocabulary_id,Yes,varchar(20),"A foreign key to the [VOCABULARY](https://ohdsi.github.io/CommonDataModel/cdm531.html#vocabulary) +table indicating from which source the Concept has been adapted.",NA,No,Yes,VOCABULARY,VOCABULARY_ID,NA,NA,NA -concept,concept_class_id,Yes,varchar(20),"The attribute or concept class of the -Concept. Examples are 'Clinical Drug', +concept,concept_class_id,Yes,varchar(20),"The attribute or concept class of the +Concept. Examples are 'Clinical Drug', 'Ingredient', 'Clinical Finding' etc.",NA,No,Yes,CONCEPT_CLASS,CONCEPT_CLASS_ID,NA,NA,NA -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,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.",NA,No,No,NA,NA,NA,NA,NA -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 +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.",NA,No,No,NA,NA,NA,NA,NA -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 +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.",NA,No,No,NA,NA,NA,NA,NA -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 +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.",NA,No,No,NA,NA,NA,NA,NA -concept,invalid_reason,No,varchar(1),"Reason the Concept was invalidated. -Possible values are D (deleted), U -(replaced with an update) or NULL when +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.",NA,No,No,NA,NA,NA,NA,NA -vocabulary,vocabulary_id,Yes,varchar(20),"A unique identifier for each Vocabulary, such +vocabulary,vocabulary_id,Yes,varchar(20),"A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit.",NA,Yes,No,NA,NA,NA,NA,NA -vocabulary,vocabulary_name,Yes,varchar(255),"The name describing the vocabulary, for -example, International Classification of -Diseases, Ninth Revision, Clinical +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.",NA,No,No,NA,NA,NA,NA,NA -vocabulary,vocabulary_reference,Yes,varchar(255),"External reference to documentation or -available download of the about the +vocabulary,vocabulary_reference,Yes,varchar(255),"External reference to documentation or +available download of the about the vocabulary.",NA,No,No,NA,NA,NA,NA,NA -vocabulary,vocabulary_version,No,varchar(255),"Version of the Vocabulary as indicated in +vocabulary,vocabulary_version,No,varchar(255),"Version of the Vocabulary as indicated in the source.",NA,No,No,NA,NA,NA,NA,NA vocabulary,vocabulary_concept_id,Yes,integer,A Concept that represents the Vocabulary the VOCABULARY record belongs to.,NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA domain,domain_id,Yes,varchar(20),A unique key for each domain.,NA,Yes,No,NA,NA,NA,NA,NA -domain,domain_name,Yes,varchar(255),"The name describing the Domain, e.g. -Condition, Procedure, Measurement +domain,domain_name,Yes,varchar(255),"The name describing the Domain, e.g. +Condition, Procedure, Measurement etc.",NA,No,No,NA,NA,NA,NA,NA domain,domain_concept_id,Yes,integer,A Concept representing the Domain Concept the DOMAIN record belongs to.,NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA concept_class,concept_class_id,Yes,varchar(20),A unique key for each class.,NA,Yes,No,NA,NA,NA,NA,NA -concept_class,concept_class_name,Yes,varchar(255),"The name describing the Concept Class, e.g. +concept_class,concept_class_name,Yes,varchar(255),"The name describing the Concept Class, e.g. Clinical Finding, Ingredient, etc.",NA,No,No,NA,NA,NA,NA,NA concept_class,concept_class_concept_id,Yes,integer,A Concept that represents the Concept Class.,NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA concept_relationship,concept_id_1,Yes,integer,NA,NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA @@ -428,63 +428,63 @@ concept_relationship,relationship_id,Yes,varchar(20),The relationship between CO concept_relationship,valid_start_date,Yes,date,The date when the relationship is first recorded.,NA,No,No,NA,NA,NA,NA,NA concept_relationship,valid_end_date,Yes,date,The date when the relationship is invalidated.,NA,No,No,NA,NA,NA,NA,NA concept_relationship,invalid_reason,No,varchar(1),"Reason the relationship was invalidated. Possible values are 'D' (deleted), 'U' (updated) or NULL.",NA,No,No,NA,NA,NA,NA,NA -relationship,relationship_id,Yes,varchar(20),"The type of relationship captured by the +relationship,relationship_id,Yes,varchar(20),"The type of relationship captured by the relationship record.",NA,Yes,No,NA,NA,NA,NA,NA relationship,relationship_name,Yes,varchar(255),NA,NA,No,No,NA,NA,NA,NA,NA -relationship,is_hierarchical,Yes,varchar(1),"Defines whether a relationship defines -concepts into classes or hierarchies. Values +relationship,is_hierarchical,Yes,varchar(1),"Defines whether a relationship defines +concepts into classes or hierarchies. Values are 1 for hierarchical relationship or 0 if not.",NA,No,No,NA,NA,NA,NA,NA -relationship,defines_ancestry,Yes,varchar(1),"Defines whether a hierarchical relationship -contributes to the concept_ancestor table. -These are subsets of the hierarchical +relationship,defines_ancestry,Yes,varchar(1),"Defines whether a hierarchical relationship +contributes to the concept_ancestor table. +These are subsets of the hierarchical relationships. Valid values are 1 or 0.",NA,No,No,NA,NA,NA,NA,NA -relationship,reverse_relationship_id,Yes,varchar(20),"The identifier for the relationship used to -define the reverse relationship between two +relationship,reverse_relationship_id,Yes,varchar(20),"The identifier for the relationship used to +define the reverse relationship between two concepts.",NA,No,No,NA,NA,NA,NA,NA -relationship,relationship_concept_id,Yes,integer,"A foreign key that refers to an identifier in -the [CONCEPT](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept) table for the unique +relationship,relationship_concept_id,Yes,integer,"A foreign key that refers to an identifier in +the [CONCEPT](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept) table for the unique relationship concept.",NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA concept_synonym,concept_id,Yes,integer,NA,NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA concept_synonym,concept_synonym_name,Yes,varchar(1000),NA,NA,No,No,NA,NA,NA,NA,NA concept_synonym,language_concept_id,Yes,integer,NA,NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA -concept_ancestor,ancestor_concept_id,Yes,integer,"The Concept Id for the higher-level concept +concept_ancestor,ancestor_concept_id,Yes,integer,"The Concept Id for the higher-level concept that forms the ancestor in the relationship.",NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA -concept_ancestor,descendant_concept_id,Yes,integer,"The Concept Id for the lower-level concept -that forms the descendant in the +concept_ancestor,descendant_concept_id,Yes,integer,"The Concept Id for the lower-level concept +that forms the descendant in the relationship.",NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA -concept_ancestor,min_levels_of_separation,Yes,integer,"The minimum separation in number of -levels of hierarchy between ancestor and -descendant concepts. This is an attribute +concept_ancestor,min_levels_of_separation,Yes,integer,"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.",NA,No,No,NA,NA,NA,NA,NA -concept_ancestor,max_levels_of_separation,Yes,integer,"The maximum separation in number of -levels of hierarchy between ancestor and -descendant concepts. This is an attribute +concept_ancestor,max_levels_of_separation,Yes,integer,"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.",NA,No,No,NA,NA,NA,NA,NA -source_to_concept_map,source_code,Yes,varchar(50),"The source code being translated +source_to_concept_map,source_code,Yes,varchar(50),"The source code being translated into a Standard Concept.",NA,No,No,NA,NA,NA,NA,NA -source_to_concept_map,source_concept_id,Yes,integer,"A foreign key to the Source -Concept that is being translated +source_to_concept_map,source_concept_id,Yes,integer,"A foreign key to the Source +Concept that is being translated into a Standard Concept.","This is either 0 or should be a number above 2 billion, which are the Concepts reserved for site-specific codes and mappings.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA -source_to_concept_map,source_vocabulary_id,Yes,varchar(20),"A foreign key to the -VOCABULARY table defining the -vocabulary of the source code that -is being translated to a Standard +source_to_concept_map,source_vocabulary_id,Yes,varchar(20),"A foreign key to the +VOCABULARY table defining the +vocabulary of the source code that +is being translated to a Standard Concept.",NA,No,No,NA,NA,NA,NA,NA -source_to_concept_map,source_code_description,No,varchar(255),"An optional description for the -source code. This is included as a -convenience to compare the -description of the source code to +source_to_concept_map,source_code_description,No,varchar(255),"An optional description for the +source code. This is included as a +convenience to compare the +description of the source code to the name of the concept.",NA,No,No,NA,NA,NA,NA,NA -source_to_concept_map,target_concept_id,Yes,integer,"The target Concept -to which the source code is being +source_to_concept_map,target_concept_id,Yes,integer,"The target Concept +to which the source code is being mapped.",NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA source_to_concept_map,target_vocabulary_id,Yes,varchar(20),The Vocabulary of the target Concept.,NA,No,Yes,VOCABULARY,VOCABULARY_ID,NA,NA,NA -source_to_concept_map,valid_start_date,Yes,date,"The date when the mapping +source_to_concept_map,valid_start_date,Yes,date,"The date when the mapping instance was first recorded.",NA,No,No,NA,NA,NA,NA,NA -source_to_concept_map,valid_end_date,Yes,date,"The date when the mapping -instance became invalid because it -was deleted or superseded -(updated) by a new relationship. +source_to_concept_map,valid_end_date,Yes,date,"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.",NA,No,No,NA,NA,NA,NA,NA source_to_concept_map,invalid_reason,No,varchar(1),"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.",NA,No,No,NA,NA,NA,NA,NA drug_strength,drug_concept_id,Yes,integer,The Concept representing the Branded Drug or Clinical Drug Product.,NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA @@ -496,8 +496,8 @@ drug_strength,numerator_unit_concept_id,No,integer,The Concept representing the drug_strength,denominator_value,No,float,"The amount of total liquid (or other divisible product, such as ointment, gel, spray, etc.).",NA,No,No,NA,NA,NA,NA,NA drug_strength,denominator_unit_concept_id,No,integer,The Concept representing the denominator unit for the concentration of active ingredient.,NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA drug_strength,box_size,No,integer,The number of units of Clinical Branded Drug or Quantified Clinical or Branded Drug contained in a box as dispensed to the patient.,NA,No,No,NA,NA,NA,NA,NA -drug_strength,valid_start_date,Yes,date,"The date when the Concept was first -recorded. The default value is +drug_strength,valid_start_date,Yes,date,"The date when the Concept was first +recorded. The default value is 1-Jan-1970.",NA,No,No,NA,NA,NA,NA,NA drug_strength,valid_end_date,Yes,date,The date when then Concept became invalid.,NA,No,No,NA,NA,NA,NA,NA drug_strength,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.",NA,No,No,NA,NA,NA,NA,NA diff --git a/inst/csv/OMOP_CDMv5.4_Field_Level.csv b/inst/csv/OMOP_CDMv5.4_Field_Level.csv index 9c061b8..7817bb9 100644 --- a/inst/csv/OMOP_CDMv5.4_Field_Level.csv +++ b/inst/csv/OMOP_CDMv5.4_Field_Level.csv @@ -88,10 +88,10 @@ condition_occurrence,condition_source_concept_id,No,integer,"This is the concept condition_occurrence,condition_status_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the condition status.,This information may be called something different in the source data but the field is meant to contain a value indicating when and how a diagnosis was given to a patient. This source value is mapped to a standard concept which is stored in the CONDITION_STATUS_CONCEPT_ID field.,No,No,NA,NA,NA,NA,NA drug_exposure,drug_exposure_id,Yes,integer,The unique key given to records of drug dispensings or administrations for a person. Refer to the ETL for how duplicate drugs during the same visit were handled.,"Each instance of a drug dispensing or administration present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same drug within the same visit. It is valid to keep these duplicates and assign them individual, unique, DRUG_EXPOSURE_IDs, though it is up to the ETL how they should be handled.",Yes,No,NA,NA,NA,NA,NA drug_exposure,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the drug dispensing or administration is recorded. This may be a system generated code.,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA -drug_exposure,drug_concept_id,Yes,integer,"The DRUG_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a drug product or molecule otherwise introduced to the body. The drug concepts can have a varying degree of information about drug strength and dose. This information is relevant in the context of quantity and administration information in the subsequent fields plus strength information from the DRUG_STRENGTH table, provided as part of the standard vocabulary download.","The CONCEPT_ID that the DRUG_SOURCE_VALUE maps to. The concept id should be derived either from mapping from the source concept id or by picking the drug concept representing the most amount of detail you have. Records whose source values map to standard concepts with a domain of Drug should go in this table. When the Drug Source Value of the code cannot be translated into Standard Drug Concept IDs, a Drug exposure entry is stored with only the corresponding SOURCE_CONCEPT_ID and DRUG_SOURCE_VALUE and a DRUG_CONCEPT_ID of 0. The Drug Concept with the most detailed content of information is preferred during the mapping process. These are indicated in the CONCEPT_CLASS_ID field of the Concept and are recorded in the following order of precedence: ÒMarketed ProductÓ, ÒBranded PackÓ, ÒClinical PackÓ, ÒBranded DrugÓ, ÒClinical DrugÓ, ÒBranded Drug ComponentÓ, ÒClinical Drug ComponentÓ, ÒBranded Drug FormÓ, ÒClinical Drug FormÓ, and only if no other information is available ÒIngredientÓ. Note: If only the drug class is known, the DRUG_CONCEPT_ID field should contain 0. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Drug&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Drug,NA,NA +drug_exposure,drug_concept_id,Yes,integer,"The DRUG_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a drug product or molecule otherwise introduced to the body. The drug concepts can have a varying degree of information about drug strength and dose. This information is relevant in the context of quantity and administration information in the subsequent fields plus strength information from the DRUG_STRENGTH table, provided as part of the standard vocabulary download.","The CONCEPT_ID that the DRUG_SOURCE_VALUE maps to. The concept id should be derived either from mapping from the source concept id or by picking the drug concept representing the most amount of detail you have. Records whose source values map to standard concepts with a domain of Drug should go in this table. When the Drug Source Value of the code cannot be translated into Standard Drug Concept IDs, a Drug exposure entry is stored with only the corresponding SOURCE_CONCEPT_ID and DRUG_SOURCE_VALUE and a DRUG_CONCEPT_ID of 0. The Drug Concept with the most detailed content of information is preferred during the mapping process. These are indicated in the CONCEPT_CLASS_ID field of the Concept and are recorded in the following order of precedence: �Marketed Product�, �Branded Pack�, �Clinical Pack�, �Branded Drug�, �Clinical Drug�, �Branded Drug Component�, �Clinical Drug Component�, �Branded Drug Form�, �Clinical Drug Form�, and only if no other information is available �Ingredient�. Note: If only the drug class is known, the DRUG_CONCEPT_ID field should contain 0. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Drug&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Drug,NA,NA drug_exposure,drug_exposure_start_date,Yes,date,Use this date to determine the start date of the drug record.,"Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration was recorded. It is a valid ETL choice to use the date the drug was ordered as the DRUG_EXPOSURE_START_DATE.",No,No,NA,NA,NA,NA,NA drug_exposure,drug_exposure_start_datetime,No,datetime,NA,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,NA,NA,NA,NA,NA -drug_exposure,drug_exposure_end_date,Yes,date,The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended for the patient.,"If this information is not explicitly available in the data, infer the end date using the following methods:

1. Start first with duration or days supply using the calculation drug start date + days supply -1 day. 2. Use quantity divided by daily dose that you may obtain from the sig or a source field (or assumed daily dose of 1) for solid, indivisibile, drug products. If quantity represents ingredient amount, quantity divided by daily dose * concentration (from drug_strength) drug concept id tells you the dose form. 3. If it is an administration record, set drug end date equal to drug start date. If the record is a written prescription then set end date to start date + 29. If the record is a mail-order prescription set end date to start date + 89. The end date must be equal to or greater than the start date. Ibuprofen 20mg/mL oral solution concept tells us this is oral solution. Calculate duration as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL) 200*5/20 = 50 days. [Examples by dose form](https://ohdsi.github.io/CommonDataModel/drug_dose.html)

For detailed conventions for how to populate this field, please see the [THEMIS repository](https://ohdsi.github.io/Themis/tag_drug_exposure.html).",No,No,NA,NA,NA,NA,NA +drug_exposure,drug_exposure_end_date,Yes,date,The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended for the patient.,"If this information is not explicitly available in the data, infer the end date from start date and duration.
For detailed conventions for how to populate this field, please see the [THEMIS repository](https://ohdsi.github.io/Themis/tag_drug_exposure.html).",No,No,NA,NA,NA,NA,NA drug_exposure,drug_exposure_end_datetime,No,datetime,NA,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,NA,NA,NA,NA,NA drug_exposure,verbatim_end_date,No,date,"This is the end date of the drug exposure as it appears in the source data, if it is given",Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable.,No,No,NA,NA,NA,NA,NA drug_exposure,drug_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to delineate between prescriptions written vs. prescriptions dispensed vs. medication history vs. patient-reported exposure, etc.","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA @@ -148,7 +148,7 @@ device_exposure,unit_source_value,No,varchar(50),"This field houses the verbatim device_exposure,unit_source_concept_id,No,integer,"This is the concept representing the UNIT_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Unit necessary for a given analytic use case. Consider using UNIT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the UNIT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA measurement,measurement_id,Yes,integer,The unique key given to a Measurement record for a Person. Refer to the ETL for how duplicate Measurements during the same Visit were handled.,"Each instance of a measurement present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same measurement within the same visit. It is valid to keep these duplicates and assign them individual, unique, MEASUREMENT_IDs, though it is up to the ETL how they should be handled.",Yes,No,NA,NA,NA,NA,NA measurement,person_id,Yes,integer,The PERSON_ID of the Person for whom the Measurement is recorded. This may be a system generated code.,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA -measurement,measurement_concept_id,Yes,integer,"The MEASUREMENT_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source value which represents a measurement.",The CONCEPT_ID that the MEASUREMENT_SOURCE_VALUE maps to. Only records whose source values map to concepts with a domain of ÒMeasurementÓ should go in this table.,No,Yes,CONCEPT,CONCEPT_ID,Measurement,NA,NA +measurement,measurement_concept_id,Yes,integer,"The MEASUREMENT_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source value which represents a measurement.",The CONCEPT_ID that the MEASUREMENT_SOURCE_VALUE maps to. Only records whose source values map to concepts with a domain of �Measurement� should go in this table.,No,Yes,CONCEPT,CONCEPT_ID,Measurement,NA,NA measurement,measurement_date,Yes,date,Use this date to determine the date of the measurement.,"If there are multiple dates in the source data associated with a record such as order_date, draw_date, and result_date, choose the one that is closest to the date the sample was drawn from the patient.",No,No,NA,NA,NA,NA,NA measurement,measurement_datetime,No,datetime,NA,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,NA,NA,NA,NA,NA measurement,measurement_time,No,varchar(10),NA,This is present for backwards compatibility and will be deprecated in an upcoming version.,No,No,NA,NA,NA,NA,NA