From 6ec05635ceea987a76897a4ab89ff4db68de0923 Mon Sep 17 00:00:00 2001 From: Florian Katsch Date: Wed, 12 Jun 2024 11:40:17 +0200 Subject: [PATCH] fix admitted_from_concept_id / source_value mix up --- inst/csv/OMOP_CDMv6.0_Field_Level.csv | 230 +++++++++++++------------- 1 file changed, 115 insertions(+), 115 deletions(-) diff --git a/inst/csv/OMOP_CDMv6.0_Field_Level.csv b/inst/csv/OMOP_CDMv6.0_Field_Level.csv index a5c2708b..ba6a97c8 100644 --- a/inst/csv/OMOP_CDMv6.0_Field_Level.csv +++ b/inst/csv/OMOP_CDMv6.0_Field_Level.csv @@ -28,12 +28,12 @@ visit_occurrence,person_id,Yes,bigint,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.",No,Yes,CONCEPT,CONCEPT_ID,Visit,NA,NA visit_occurrence,visit_start_date,No,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.",No,No,NA,NA,NA,NA,NA visit_occurrence,visit_start_datetime,Yes,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,No,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,No,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,Yes,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.",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA @@ -51,12 +51,12 @@ visit_detail,person_id,Yes,bigint,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_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=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA @@ -64,8 +64,8 @@ visit_detail,provider_id,No,bigint,"There will only be one provider per **visit visit_detail,care_site_id,No,bigint,This field provides information about the Care Site where the Visit Detail took place.,There should only be one Care Site associated with a Visit Detail.,No,Yes,CARE_SITE,CARE_SITE_ID,NA,NA,NA visit_detail,visit_detail_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the kind of visit detail that took place (inpatient, outpatient, emergency, etc.)","If there is information about the kind of visit detail in the source data that value should be stored here. If a visit is an amalgamation of visits from the source then use a hierarchy to choose the VISIT_DETAIL_SOURCE_VALUE, such as IP -> ER-> OP. This should line up with the logic chosen to determine how visits are created.",No,No,NA,NA,NA,NA,NA visit_detail,visit_detail_source_concept_id,Yes,integer,NA,"If the VISIT_DETAIL_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. If not available, map to 0.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA -visit_detail,admitted_from_concept_id,No,varchar(50),NA,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was admitted from. Typically this applies only to visits that have a length of stay, like inpatient visits or long-term care visits.",No,No,NA,NA,NA,NA,NA -visit_detail,admitted_from_source_value,Yes,integer,"Use this field to determine where the patient was admitted from. This concept is part of the visit domain and can indicate if a patient was admitted to the hospital from a long-term care facility, for example.","If available, map the admitted_from_source_value to a standard concept in the visit domain. If not available, map to 0. [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,admitted_from_source_value,No,varchar(50),NA,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was admitted from. Typically this applies only to visits that have a length of stay, like inpatient visits or long-term care visits.",No,No,NA,NA,NA,NA,NA +visit_detail,admitted_from_concept_id,Yes,integer,"Use this field to determine where the patient was admitted from. This concept is part of the visit domain and can indicate if a patient was admitted to the hospital from a long-term care facility, for example.","If available, map the admitted_from_source_value to a standard concept in the visit domain. If not available, map to 0. [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,discharge_to_source_value,No,varchar(50),NA,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was discharged to after a visit, as in they went home or were moved to long-term care. Typically this applies only to visits that have a length of stay of a day or more.",No,No,NA,NA,NA,NA,NA visit_detail,discharge_to_concept_id,Yes,integer,"Use this field to determine where the patient was discharged to after a visit detail record. This concept is part of the visit domain and can indicate if a patient was discharged to home or sent to a long-term care facility, for example.","If available, map the DISCHARGE_TO_SOURCE_VALUE to a Standard Concept in the Visit domain. If not available, set to 0. [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,preceding_visit_detail_id,No,bigint,Use this field to find the visit detail that occurred for the person prior to the given visit detail record. There could be a few days or a few years in between.,"The PRECEDING_VISIT_DETAIL_ID can be used to link a visit immediately preceding the current Visit Detail. Note this is not symmetrical, and there is no such thing as a ""following_visit_id"".",No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,NA,NA,NA @@ -98,8 +98,8 @@ drug_exposure,verbatim_end_date,No,date,"This is the end date of the drug exposu 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=).",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. 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 @@ -196,7 +196,7 @@ note,note_event_field_concept_id,No,integer,NA,NA,No,Yes,CONCEPT,CONCEPT_ID,NA,N 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=).",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. [AcceptedConcepts](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 @@ -217,22 +217,22 @@ 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,bigint,Unique identifier for each specimen.,NA,Yes,No,NA,NA,NA,NA,NA specimen,person_id,Yes,bigint,The person from whom the specimen is collected.,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA @@ -356,9 +356,9 @@ drug_era,drug_era_id,Yes,bigint,NA,NA,Yes,No,NA,NA,NA,NA,NA drug_era,person_id,Yes,bigint,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA drug_era,drug_concept_id,Yes,integer,The Concept Id representing the specific drug ingredient.,NA,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient,NA drug_era,drug_era_start_datetime,Yes,datetime,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_datetime,Yes,datetime,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_datetime,Yes,datetime,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 @@ -372,20 +372,20 @@ dose_era,dose_era_end_datetime,Yes,datetime,NA,The date the Person was no longer condition_era,condition_era_id,Yes,bigint,NA,NA,Yes,No,NA,NA,NA,NA,NA condition_era,person_id,Yes,bigint,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_datetime,Yes,datetime,"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_datetime,Yes,datetime,"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_datetime,Yes,datetime,"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_datetime,Yes,datetime,"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 @@ -407,57 +407,57 @@ 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 @@ -475,50 +475,50 @@ relationship,relationship_concept_id,Yes,integer,NA,NA,No,Yes,CONCEPT,CONCEPT_ID 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 +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 drug_strength,ingredient_concept_id,Yes,integer,The Concept representing the active ingredient contained within the drug product.,"Combination Drugs will have more than one record in this table, one for each active Ingredient.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA @@ -529,8 +529,8 @@ 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