From 2188e7e014b2e9f39de1883d5ba2ef31dad9224b Mon Sep 17 00:00:00 2001 From: Clair Blacketer Date: Tue, 13 Feb 2024 08:26:11 -0500 Subject: [PATCH] Adding documentation back --- docs/cdm53.html | 12803 ++++++++++++++++++++++++++++++++++++++++++ docs/cdm54.html | 14046 +++++++++++++++++++++++++++++++++++++++++++++- rmd/cdm54.Rmd | 18 +- 3 files changed, 26840 insertions(+), 27 deletions(-) diff --git a/docs/cdm53.html b/docs/cdm53.html index b58bdc4..331dfeb 100644 --- a/docs/cdm53.html +++ b/docs/cdm53.html @@ -524,6 +524,599 @@ contributes Events to the database, Persons must be reconciled, if possible, across the sources to create one single record per Person. The content of the BIRTH_DATETIME must be equivalent to the content of BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+person_id + +It is assumed that every person with a different unique identifier is in +fact a different person and should be treated independently. + +Any person linkage that needs to occur to uniquely identify Persons +ought to be done prior to writing this table. This identifier can be the +original id from the source data provided if it is an integer, otherwise +it can be an autogenerated number. + +integer + +Yes + +Yes + +No + + +
+gender_concept_id + +This field is meant to capture the biological sex at birth of the +Person. This field should not be used to study gender identity issues. + +Use the gender or sex value present in the data under the assumption +that it is the biological sex at birth. If the source data captures +gender identity it should be stored in the OBSERVATION +table. Accepted +gender concepts + +integer + +Yes + +No + +Yes + +CONCEPT + +Gender +
+year_of_birth + +Compute age using year_of_birth. + +For data sources with date of birth, the year should be extracted. For +data sources where the year of birth is not available, the approximate +year of birth could be derived based on age group categorization, if +available. + +integer + +Yes + +No + +No + + +
+month_of_birth + + +For data sources that provide the precise date of birth, the month +should be extracted and stored in this field. + +integer + +No + +No + +No + + +
+day_of_birth + + +For data sources that provide the precise date of birth, the day should +be extracted and stored in this field. + +integer + +No + +No + +No + + +
+birth_datetime + + +This field is not required but highly encouraged. For data sources that +provide the precise datetime of birth, that value should be stored in +this field. If birth_datetime is not provided in the source, use the +following logic to infer the date: If day_of_birth is null and +month_of_birth is not null then use the first of the month in that year. +If month_of_birth is null or if day_of_birth AND month_of_birth are both +null and the person has records during their year of birth then use the +date of the earliest record, otherwise use the 15th of June of that +year. If time of birth is not given use midnight (00:00:0000). + +datetime + +No + +No + +No + + +
+race_concept_id + +This field captures race or ethnic background of the person. + +Only use this field if you have information about race or ethnic +background. The Vocabulary contains Concepts about the main races and +ethnic backgrounds in a hierarchical system. Due to the imprecise nature +of human races and ethnic backgrounds, this is not a perfect system. +Mixed races are not supported. If a clear race or ethnic background +cannot be established, use Concept_Id 0. Accepted +Race Concepts. + +integer + +Yes + +No + +Yes + +CONCEPT + +Race +
+ethnicity_concept_id + +This field captures Ethnicity as defined by the Office of Management and +Budget (OMB) of the US Government: it distinguishes only between +“Hispanic” and “Not Hispanic”. Races and ethnic backgrounds are not +stored here. + +Only use this field if you have US-based data and a source of this +information. Do not attempt to infer Ethnicity from the race or ethnic +background of the Person. Accepted +ethnicity concepts + +integer + +Yes + +No + +Yes + +CONCEPT + +Ethnicity +
+location_id + +The location refers to the physical address of the person. This field +should capture the last known location of the person. + +Put the location_id from the LOCATION +table here that represents the most granular location information for +the person. This could represent anything from postal code or parts +thereof, state, or county for example. Since many databases contain +deidentified data, it is common that the precision of the location is +reduced to prevent re-identification. This field should capture the last +known location. + +integer + +No + +No + +Yes + +LOCATION + +
+provider_id + +The Provider refers to the last known primary care provider (General +Practitioner). + +Put the provider_id from the PROVIDER +table of the last known general practitioner of the person. If there are +multiple providers, it is up to the ETL to decide which to put here. + +integer + +No + +No + +Yes + +PROVIDER + +
+care_site_id + +The Care Site refers to where the Provider typically provides the +primary care. + + +integer + +No + +No + +Yes + +CARE_SITE + +
+person_source_value + +Use this field to link back to persons in the source data. This is +typically used for error checking of ETL logic. + +Some use cases require the ability to link back to persons in the source +data. This field allows for the storing of the person value as it +appears in the source. This field is not required but strongly +recommended. + +varchar(50) + +No + +No + +No + + +
+gender_source_value + +This field is used to store the biological sex of the person from the +source data. It is not intended for use in standard analytics but for +reference only. + +Put the biological sex of the person as it appears in the source data. + +varchar(50) + +No + +No + +No + + +
+gender_source_concept_id + +Due to the small number of options, this tends to be zero. + +If the source data codes biological sex in a non-standard vocabulary, +store the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +
+race_source_value + +This field is used to store the race of the person from the source data. +It is not intended for use in standard analytics but for reference only. + +Put the race of the person as it appears in the source data. + +varchar(50) + +No + +No + +No + + +
+race_source_concept_id + +Due to the small number of options, this tends to be zero. + +If the source data codes race in an OMOP supported vocabulary store the +concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +
+ethnicity_source_value + +This field is used to store the ethnicity of the person from the source +data. It is not intended for use in standard analytics but for reference +only. + +If the person has an ethnicity other than the OMB standard of “Hispanic” +or “Not Hispanic” store that value from the source data here. + +varchar(50) + +No + +No + +No + + +
+ethnicity_source_concept_id + +Due to the small number of options, this tends to be zero. + +If the source data codes ethnicity in an OMOP supported vocabulary, +store the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +

observation_period

@@ -566,6 +1159,198 @@ spans defined by OBSERVATION_PERIOD records. Family history or history of Clinical Events generally are not used to generate OBSERVATION_PERIOD records around the time they are referring to. Any two overlapping or adjacent OBSERVATION_PERIOD records have to be merged into one.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+observation_period_id + +A Person can have multiple discrete Observation Periods which are +identified by the Observation_Period_Id. + +Assign a unique observation_period_id to each discrete Observation +Period for a Person. + +integer + +Yes + +Yes + +No + + +
+person_id + +The Person ID of the PERSON record for which the Observation Period is +recorded. + + +integer + +Yes + +No + +Yes + +PERSON + +
+observation_period_start_date + +Use this date to determine the start date of the Observation Period. + +It is often the case that the idea of Observation Periods does not exist +in source data. In those cases, the observation_period_start_date can be +inferred as the earliest Event date available for the Person. In +insurance claim data, the Observation Period can be considered as the +time period the Person is enrolled with a payer. If a Person switches +plans but stays with the same payer, and therefore capturing of data +continues, that change would be captured in PAYER_PLAN_PERIOD. + +date + +Yes + +No + +No + + +
+observation_period_end_date + +Use this date to determine the end date of the period for which we can +assume that all events for a Person are recorded. + +It is often the case that the idea of Observation Periods does not exist +in source data. In those cases, the observation_period_end_date can be +inferred as the last Event date available for the Person. In insurance +claim data, the Observation Period can be considered as the time period +the Person is enrolled with a payer. + +date + +Yes + +No + +No + + +
+period_type_concept_id + +This field can be used to determine the provenance of the Observation +Period as in whether the period was determined from an insurance +enrollment file, EHR healthcare encounters, or other sources. + +Choose the observation_period_type_concept_id that best represents how +the period was determined. Accepted +Concepts. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +

visit_occurrence

@@ -664,6 +1449,581 @@ encounter records should be translated to visit occurrences. Providers can be associated with a Visit through the PROVIDER_ID field, or indirectly through PROCEDURE_OCCURRENCE records linked both to the VISIT and PROVIDER tables.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+visit_occurrence_id + +Use this to identify unique interactions between a person and the health +care system. This identifier links across the other CDM event tables to +associate events with a visit. + +This should be populated by creating a unique identifier for each unique +interaction between a person and the healthcare system where the person +receives a medical good or service over a span of time. + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+visit_concept_id + +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. + +integer + +Yes + +No + +Yes + +CONCEPT + +Visit +
+visit_start_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. + +date + +Yes + +No + +No + + +
+visit_start_datetime + + +If no time is given for the start date of a visit, set it to midnight +(00:00:0000). + +datetime + +No + +No + +No + + +
+visit_end_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. + +date + +Yes + +No + +No + + +
+visit_end_datetime + + +If no time is given for the end date of a visit, set it to midnight +(00:00:0000). + +datetime + +No + +No + +No + + +
+visit_type_concept_id + +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. + +Integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+provider_id + +There will only be one provider per visit record and the ETL document +should clearly state how they were chosen (attending, admitting, etc.). +If there are multiple providers associated with a visit in the source, +this can be reflected in the event tables (CONDITION_OCCURRENCE, +PROCEDURE_OCCURRENCE, etc.) or in the VISIT_DETAIL table. + +If there are multiple providers associated with a visit, you will need +to choose which one to put here. The additional providers can be stored +in the VISIT_DETAIL +table. + +integer + +No + +No + +Yes + +PROVIDER + +
+care_site_id + +This field provides information about the Care Site where the Visit took +place. + +There should only be one Care Site associated with a Visit. + +integer + +No + +No + +Yes + +CARE_SITE + +
+visit_source_value + +This field houses the verbatim value from the source data representing +the kind of visit that took place (inpatient, outpatient, emergency, +etc.) + +If there is information about the kind of visit 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 source value, +such as IP -> ER-> OP. This should line up with the logic chosen +to determine how visits are created. + +varchar(50) + +No + +No + +No + + +
+visit_source_concept_id + + +If the visit source value is coded in the source data using an OMOP +supported vocabulary put the concept id representing the source value +here. + +integer + +No + +No + +Yes + +CONCEPT + +
+admitting_source_concept_id + +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. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +Visit +
+admitting_source_value + + +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. + +varchar(50) + +No + +No + +No + + +
+discharge_to_concept_id + +Use this field to determine where the patient was discharged to after a +visit. 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. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +Visit +
+discharge_to_source_value + + +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. + +varchar(50) + +No + +No + +No + + +
+preceding_visit_occurrence_id + +Use this field to find the visit that occurred for the person prior to +the given visit. There could be a few days or a few years in between. + +This field can be used to link a visit immediately preceding the current +visit. Note this is not symmetrical, and there is no such thing as a +“following_visit_id”. + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +

visit_detail

@@ -700,6 +2060,639 @@ Occurrence by setting the VISIT_CONCEPT_ID to 9201 and the VISIT_DETAIL_CONCEPT_IDs either to 9201 or its children to indicate where the patient was in the hospital at the time of care.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+visit_detail_id + +Use this to identify unique interactions between a person and the health +care system. This identifier links across the other CDM event tables to +associate events with a visit detail. + +This should be populated by creating a unique identifier for each unique +interaction between a person and the healthcare system where the person +receives a medical good or service over a span of time. + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+visit_detail_concept_id + +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. + +integer + +Yes + +No + +Yes + +CONCEPT + +Visit +
+visit_detail_start_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. + +date + +Yes + +No + +No + + +
+visit_detail_start_datetime + + +If no time is given for the start date of a visit, set it to midnight +(00:00:0000). + +datetime + +No + +No + +No + + +
+visit_detail_end_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. +		 +date + +Yes + +No + +No + + +
+visit_detail_end_datetime + + +If no time is given for the end date of a visit, set it to midnight +(00:00:0000). + +datetime + +No + +No + +No + + +
+visit_detail_type_concept_id + +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. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+provider_id + +There will only be one provider per visit record and +the ETL document should clearly state how they were chosen (attending, +admitting, etc.). This is a typical reason for leveraging the +VISIT_DETAIL table as even though each VISIT_DETAIL record can only have +one provider, there is no limit to the number of VISIT_DETAIL records +that can be associated to a VISIT_OCCURRENCE record. + +The additional providers associated to a Visit can be stored in this +table where each VISIT_DETAIL record represents a different provider. + +integer + +No + +No + +Yes + +PROVIDER + +
+care_site_id + +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. + +integer + +No + +No + +Yes + +CARE_SITE + +
+visit_detail_source_value + +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. + +varchar(50) + +No + +No + +No + + +
+visit_detail_source_concept_id + + +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. + +Integer + +No + +No + +Yes + +CONCEPT + +
+admitting_source_value + + +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. + +Varchar(50) + +No + +No + +No + + +
+admitting_source_concept_id + +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. Accepted +Concepts. + +Integer + +No + +No + +Yes + +CONCEPT + +Visit +
+discharge_to_source_value + + +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. + +Varchar(50) + +No + +No + +No + + +
+discharge_to_concept_id + +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. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +Visit +
+preceding_visit_detail_id + +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”. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+visit_detail_parent_id + +Use this field to find the visit detail that subsumes the given visit +detail record. This is used in the case that a visit detail record needs +to be nested beyond the VISIT_OCCURRENCE/VISIT_DETAIL relationship. + +If there are multiple nested levels to how Visits are represented in the +source, the VISIT_DETAIL_PARENT_ID can be used to record this +relationship. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+visit_occurrence_id + +Use this field to link the VISIT_DETAIL record to its VISIT_OCCURRENCE. + +Put the VISIT_OCCURRENCE_ID that subsumes the VISIT_DETAIL record here. + +integer + +Yes + +No + +Yes + +VISIT_OCCURRENCE + +
@@ -742,6 +2735,548 @@ always available.

ETL Conventions

Source codes and source text fields mapped to Standard Concepts of the Condition Domain have to be recorded here.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+condition_occurrence_id + +The unique key given to a condition record for a person. Refer to the +ETL for how duplicate conditions during the same visit were handled. + +Each instance of a condition present in the source data should be +assigned this unique key. In some cases, a person can have multiple +records of the same condition within the same visit. It is valid to keep +these duplicates and assign them individual, unique, +CONDITION_OCCURRENCE_IDs, though it is up to the ETL how they should be +handled. + +integer + +Yes + +Yes + +No + + +
+person_id + +The PERSON_ID of the PERSON for whom the condition is recorded. + + +integer + +Yes + +No + +Yes + +PERSON + +
+condition_concept_id + +The CONDITION_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 condition + +The CONCEPT_ID that the CONDITION_SOURCE_VALUE maps to. Only records +whose source values map to concepts with a domain of “Condition” should +go in this table. Accepted +Concepts. + +integer + +Yes + +No + +Yes + +CONCEPT + +Condition +
+condition_start_date + +Use this date to determine the start date of the condition + +Most often data sources do not have the idea of a start date for a +condition. Rather, if a source only has one date associated with a +condition record it is acceptable to use that date for both the +CONDITION_START_DATE and the CONDITION_END_DATE. + +date + +Yes + +No + +No + + +
+condition_start_datetime + + +If a source does not specify datetime the convention is to set the time +to midnight (00:00:0000) + +datetime + +No + +No + +No + + +
+condition_end_date + +Use this date to determine the end date of the condition + +Most often data sources do not have the idea of a start date for a +condition. Rather, if a source only has one date associated with a +condition record it is acceptable to use that date for both the +CONDITION_START_DATE and the CONDITION_END_DATE. + +date + +No + +No + +No + + +
+condition_end_datetime + + +If a source does not specify datetime the convention is to set the time +to midnight (00:00:0000) + +datetime + +No + +No + +No + + +
+condition_type_concept_id + +This field can be used to determine the provenance of the Condition +record, as in whether the condition was from an EHR system, insurance +claim, registry, or other sources. + +Choose the CONDITION_TYPE_CONCEPT_ID that best represents the provenance +of the record. Accepted +Concepts. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+condition_status_concept_id + +This concept represents the point during the visit the diagnosis was +given (admitting diagnosis, final diagnosis), whether the diagnosis was +determined due to laboratory findings, if the diagnosis was +exclusionary, or if it was a preliminary diagnosis, among others. + +Choose the Concept in the Condition Status domain that best represents +the point during the visit when the diagnosis was given. These can +include admitting diagnosis, principal diagnosis, and secondary +diagnosis. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +Condition Status +
+stop_reason + +The Stop Reason indicates why a Condition is no longer valid with +respect to the purpose within the source data. Note that a Stop Reason +does not necessarily imply that the condition is no longer occurring. + +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. + +varchar(20) + +No + +No + +No + + +
+provider_id + +The provider associated with condition record, e.g. the provider who +made the diagnosis or the provider who recorded the symptom. + +The ETL may need to make a choice as to which PROVIDER_ID to put here. +Based on what is available this may or may not be different than the +provider associated with the overall VISIT_OCCURRENCE record, for +example the admitting vs attending physician on an EHR record. + +integer + +No + +No + +Yes + +PROVIDER + +
+visit_occurrence_id + +The visit during which the condition occurred. + +Depending on the structure of the source data, this may have to be +determined based on dates. If a CONDITION_START_DATE occurs within the +start and end date of a Visit it is a valid ETL choice to choose the +VISIT_OCCURRENCE_ID from the Visit that subsumes it, even if not +explicitly stated in the data. While not required, an attempt should be +made to locate the VISIT_OCCURRENCE_ID of the CONDITION_OCCURRENCE +record. + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +
+visit_detail_id + +The VISIT_DETAIL record during which the condition occurred. For +example, if the person was in the ICU at the time of the diagnosis the +VISIT_OCCURRENCE record would reflect the overall hospital stay and the +VISIT_DETAIL record would reflect the ICU stay during the hospital +visit. + +Same rules apply as for the VISIT_OCCURRENCE_ID. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+condition_source_value + +This field houses the verbatim value from the source data representing +the condition that occurred. For example, this could be an ICD10 or Read +code. + +This code is mapped to a Standard Condition Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +
+condition_source_concept_id + +This is the concept representing the condition 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 Condition +necessary for a given analytic use case. Consider using +CONDITION_CONCEPT_ID instead to enable standardized analytics that can +be consistent across the network. + +If the CONDITION_SOURCE_VALUE is coded in the source data using an OMOP +supported vocabulary put the concept id representing the source value +here. + +integer + +No + +No + +Yes + +CONCEPT + +
+condition_status_source_value + +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. + +varchar(50) + +No + +No + +No + + +

drug_exposure

@@ -774,6 +3309,783 @@ dispensed. If a patient has multiple records on the same day for the same drug or procedures the ETL should not de-dupe them unless there is probable reason to believe the item is a true data duplicate. Take note on how to handle refills for prescriptions written.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+drug_exposure_id + +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. + +integer + +Yes + +Yes + +No + + +
+person_id + +The PERSON_ID of the PERSON for whom the drug dispensing or +administration is recorded. This may be a system generated code. + + +integer + +Yes + +No + +Yes + +PERSON + +
+drug_concept_id + +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: ‘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. + +integer + +Yes + +No + +Yes + +CONCEPT + +Drug +
+drug_exposure_start_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. + +date + +Yes + +No + +No + + +
+drug_exposure_start_datetime + + +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) + +datetime + +No + +No + +No + + +
+drug_exposure_end_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 +		 +date + +Yes + +No + +No + + +
+drug_exposure_end_datetime + + +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) + +datetime + +No + +No + +No + + +
+verbatim_end_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. + +date + +No + +No + +No + + +
+drug_type_concept_id + +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. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+stop_reason + +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. + +varchar(20) + +No + +No + +No + + +
+refills + +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. + + +integer + +No + +No + +No + + +
+quantity + + +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 for more information. + +float + +No + +No + +No + + +
+days_supply + + +Days supply of the drug. This should be the verbatim days_supply as +given on the prescription. If the drug is physician administered use +duration end date if given or set to 1 as default if duration is not +available. + +integer + +No + +No + +No + + +
+sig + +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. + +varchar(MAX) + +No + +No + +No + + +
+route_concept_id + + +The standard CONCEPT_ID that the ROUTE_SOURCE_VALUE maps to in the route +domain. + +integer + +No + +No + +Yes + +CONCEPT + +Route +
+lot_number + + + +varchar(50) + +No + +No + +No + + +
+provider_id + +The Provider associated with drug record, e.g. the provider who wrote +the prescription or the provider who administered the drug. + +The ETL may need to make a choice as to which PROVIDER_ID to put here. +Based on what is available this may or may not be different than the +provider associated with the overall VISIT_OCCURRENCE record, for +example the ordering vs administering physician on an EHR record. + +integer + +No + +No + +Yes + +PROVIDER + +
+visit_occurrence_id + +The Visit during which the drug was prescribed, administered or +dispensed. + +To populate this field drug exposures must be explicitly initiated in +the visit. + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +
+visit_detail_id + +The VISIT_DETAIL record during which the drug exposure occurred. For +example, if the person was in the ICU at the time of the drug +administration the VISIT_OCCURRENCE record would reflect the overall +hospital stay and the VISIT_DETAIL record would reflect the ICU stay +during the hospital visit. + +Same rules apply as for the VISIT_OCCURRENCE_ID. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+drug_source_value + +This field houses the verbatim value from the source data representing +the drug exposure that occurred. For example, this could be an NDC or +Gemscript code. + +This code is mapped to a Standard Drug Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +
+drug_source_concept_id + +This is the concept representing the drug 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 Drug +necessary for a given analytic use case. Consider using DRUG_CONCEPT_ID +instead to enable standardized analytics that can be consistent across +the network. + +If the DRUG_SOURCE_VALUE is coded in the source data using an OMOP +supported vocabulary put the concept id representing the source value +here. + +integer + +No + +No + +Yes + +CONCEPT + +
+route_source_value + +This field houses the verbatim value from the source data representing +the drug route. + +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 drug +was given to a patient. This source value is mapped to a standard +concept which is stored in the ROUTE_CONCEPT_ID field. + +varchar(50) + +No + +No + +No + + +
+dose_unit_source_value + +This field houses the verbatim value from the source data representing +the dose unit of the drug given. + +This information may be called something different in the source data +but the field is meant to contain a value indicating the unit of dosage +of drug given to the patient. This is an older column and will be +deprecated in an upcoming version. + +varchar(50) + +No + +No + +No + + +
@@ -803,6 +4115,485 @@ Things to consider are: - Same Procedure - Same PROCEDURE_DATETIME - Same Visit Occurrence or Visit Detail - Same Provider - Same Modifier for Procedures. Source codes and source text fields mapped to Standard Concepts of the Procedure Domain have to be recorded here.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+procedure_occurrence_id + +The unique key given to a procedure record for a person. Refer to the +ETL for how duplicate procedures during the same visit were handled. + +Each instance of a procedure occurrence in the source data should be +assigned this unique key. In some cases, a person can have multiple +records of the same procedure within the same visit. It is valid to keep +these duplicates and assign them individual, unique, +PROCEDURE_OCCURRENCE_IDs, though it is up to the ETL how they should be +handled. + +integer + +Yes + +Yes + +No + + +
+person_id + +The PERSON_ID of the PERSON for whom the procedure is recorded. This may +be a system generated code. + + +integer + +Yes + +No + +Yes + +PERSON + +
+procedure_concept_id + +The PROCEDURE_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 procedure + +The CONCEPT_ID that the PROCEDURE_SOURCE_VALUE maps to. Only records +whose source values map to standard concepts with a domain of +“Procedure” should go in this table. Accepted +Concepts. + +integer + +Yes + +No + +Yes + +CONCEPT + +Procedure +
+procedure_date + +Use this date to determine the date the procedure occurred. + +If a procedure lasts more than a day, then it should be recorded as a +separate record for each day the procedure occurred, this logic is in +lieu of the procedure_end_date, which will be added in a future version +of the CDM. + +date + +Yes + +No + +No + + +
+procedure_datetime + + +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) + +datetime + +No + +No + +No + + +
+procedure_type_concept_id + +This field can be used to determine the provenance of the Procedure +record, as in whether the procedure was from an EHR system, insurance +claim, registry, or other sources. + +Choose the PROCEDURE_TYPE_CONCEPT_ID that best represents the provenance +of the record, for example whether it came from an EHR record or billing +claim. If a procedure is recorded as an EHR encounter, the +PROCEDURE_TYPE_CONCEPT would be ‘EHR encounter record’. Accepted +Concepts. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+modifier_concept_id + +The modifiers are intended to give additional information about the +procedure but as of now the vocabulary is under review. + +It is up to the ETL to choose how to map modifiers if they exist in +source data. These concepts are typically distinguished by ‘Modifier’ +concept classes (e.g., ‘CPT4 Modifier’ as part of the ‘CPT4’ +vocabulary). If there is more than one modifier on a record, one should +be chosen that pertains to the procedure rather than provider. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+quantity + +If the quantity value is omitted, a single procedure is assumed. + +If a Procedure has a quantity of ‘0’ in the source, this should default +to ‘1’ in the ETL. If there is a record in the source it can be assumed +the exposure occurred at least once + +integer + +No + +No + +No + + +
+provider_id + +The provider associated with the procedure record, e.g. the provider who +performed the Procedure. + +The ETL may need to make a choice as to which PROVIDER_ID to put here. +Based on what is available this may or may not be different than the +provider associated with the overall VISIT_OCCURRENCE record, for +example the admitting vs attending physician on an EHR record. + +integer + +No + +No + +No + +PROVIDER + +
+visit_occurrence_id + +The visit during which the procedure occurred. + +Depending on the structure of the source data, this may have to be +determined based on dates. If a PROCEDURE_DATE occurs within the start +and end date of a Visit it is a valid ETL choice to choose the +VISIT_OCCURRENCE_ID from the Visit that subsumes it, even if not +explicitly stated in the data. While not required, an attempt should be +made to locate the VISIT_OCCURRENCE_ID of the PROCEDURE_OCCURRENCE +record. + +integer + +No + +No + +No + +VISIT_OCCURRENCE + +
+visit_detail_id + +The VISIT_DETAIL record during which the Procedure occurred. For +example, if the Person was in the ICU at the time of the Procedure the +VISIT_OCCURRENCE record would reflect the overall hospital stay and the +VISIT_DETAIL record would reflect the ICU stay during the hospital +visit. + +Same rules apply as for the VISIT_OCCURRENCE_ID. + +integer + +No + +No + +No + +VISIT_DETAIL + +
+procedure_source_value + +This field houses the verbatim value from the source data representing +the procedure that occurred. For example, this could be an CPT4 or OPCS4 +code. + +Use this value to look up the source concept id and then map the source +concept id to a standard concept id. + +varchar(50) + +No + +No + +No + + +
+procedure_source_concept_id + +This is the concept representing the procedure 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 Procedure +necessary for a given analytic use case. Consider using +PROCEDURE_CONCEPT_ID instead to enable standardized analytics that can +be consistent across the network. + +If the PROCEDURE_SOURCE_VALUE is coded in the source data using an OMOP +supported vocabulary put the concept id representing the source value +here. + +integer + +No + +No + +No + +CONCEPT + +
+modifier_source_value + + +The original modifier code from the source is stored here for reference. + +varchar(50) + +No + +No + +No + + +

device_exposure

@@ -822,6 +4613,485 @@ are actions, often to apply a Device or supply.

ETL Conventions

Source codes and source text fields mapped to Standard Concepts of the Device Domain have to be recorded here.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+device_exposure_id + +The unique key given to records a person’s exposure to a foreign +physical object or instrument. + +Each instance of an exposure to a foreign object or device present in +the source data should be assigned this unique key. + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+device_concept_id + +The DEVICE_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 foreign object or +instrument the person was exposed to. + +The CONCEPT_ID that the DEVICE_SOURCE_VALUE maps to. + +integer + +Yes + +No + +Yes + +CONCEPT + +Device +
+device_exposure_start_date + +Use this date to determine the start date of the device record. + +Valid entries include a start date of a procedure to implant a device, +the date of a prescription for a device, or the date of device +administration. + +date + +Yes + +No + +No + + +
+device_exposure_start_datetime + + +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) + +datetime + +No + +No + +No + + +
+device_exposure_end_date + +The DEVICE_EXPOSURE_END_DATE denotes the day the device exposure ended +for the patient, if given. + +Put the end date or discontinuation date as it appears from the source +data or leave blank if unavailable. + +date + +No + +No + +No + + +
+device_exposure_end_datetime + + +If a source does not specify datetime the convention is to set the time +to midnight (00:00:0000) + +datetime + +No + +No + +No + + +
+device_type_concept_id + +You can use the TYPE_CONCEPT_ID to denote the provenance of the record, +as in whether the record is from administrative claims or EHR. + +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. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+unique_device_id + +This is the Unique Device Identification number for devices regulated by +the FDA, if given. + +For medical devices that are regulated by the FDA, a Unique Device +Identification (UDI) is provided if available in the data source and is +recorded in the UNIQUE_DEVICE_ID field. + +varchar(50) + +No + +No + +No + + +
+quantity + + + +integer + +No + +No + +No + + +
+provider_id + +The Provider associated with device record, e.g. the provider who wrote +the prescription or the provider who implanted the device. + +The ETL may need to make a choice as to which PROVIDER_ID to put here. +Based on what is available this may or may not be different than the +provider associated with the overall VISIT_OCCURRENCE record. + +integer + +No + +No + +Yes + +PROVIDER + +
+visit_occurrence_id + +The Visit during which the device was prescribed or given. + +To populate this field device exposures must be explicitly initiated in +the visit. + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +
+visit_detail_id + +The Visit Detail during which the device was prescribed or given. + +To populate this field device exposures must be explicitly initiated in +the visit detail record. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+device_source_value + +This field houses the verbatim value from the source data representing +the device exposure that occurred. For example, this could be an NDC or +Gemscript code. + +This code is mapped to a Standard Device Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +
+device_source_concept_id + +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. + +integer + +No + +No + +Yes + +CONCEPT + +

measurement

@@ -867,6 +5137,689 @@ href="https://athena.ohdsi.org/search-terms/terms/4046263">4046263 ‘Enzyme measurement’ as well as a ‘Maps to value’ record to 4135493 ‘Abnormal’.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+measurement_id + +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. + +integer + +Yes + +Yes + +No + + +
+person_id + +The PERSON_ID of the Person for whom the Measurement is recorded. This +may be a system generated code. + + +integer + +Yes + +No + +Yes + +PERSON + +
+measurement_concept_id + +The MEASUREMENT_CONCEPT_ID field is recommended for primary use in +analyses, and must be used for network studies. + +The CONCEPT_ID that the MEASUREMENT_SOURCE_CONCEPT_ID maps to. Only +records whose SOURCE_CONCEPT_IDs map to Standard Concepts with a domain +of “Measurement” should go in this table. + +integer + +Yes + +No + +Yes + +CONCEPT + +Measurement +
+measurement_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. + +date + +Yes + +No + +No + + +
+measurement_datetime + + +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) + +datetime + +No + +No + +No + + +
+measurement_time + + +This is present for backwards compatibility and will be deprecated in an +upcoming version. + +varchar(10) + +No + +No + +No + + +
+measurement_type_concept_id + +This field can be used to determine the provenance of the Measurement +record, as in whether the measurement was from an EHR system, insurance +claim, registry, or other sources. + +Choose the MEASUREMENT_TYPE_CONCEPT_ID that best represents the +provenance of the record, for example whether it came from an EHR record +or billing claim. Accepted +Concepts. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+operator_concept_id + +The meaning of Concept 4172703 +for ‘=’ is identical to omission of a OPERATOR_CONCEPT_ID value. Since +the use of this field is rare, it’s important when devising analyses to +not to forget testing for the content of this field for values different +from =. + +Operators are =, > and these concepts belong to the ‘Meas Value +Operator’ domain. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+value_as_number + +This is the numerical value of the Result of the Measurement, if +available. Note that measurements such as blood pressures will be split +into their component parts i.e. one record for systolic, one record for +diastolic. + +If there is a negative value coming from the source, set the +VALUE_AS_NUMBER to NULL, with the exception of the following +Measurements (listed as LOINC codes):
- 1925-7 +Base excess in Arterial blood by calculation - 1927-3 +Base excess in Venous blood by calculation - 8632-2 +QRS-Axis - 11555-0 +Base excess in Blood by calculation - 1926-5 +Base excess in Capillary blood by calculation - 28638-5 +Base excess in Arterial cord blood by calculation 28639-3 +Base excess in Venous cord blood by calculation +		 +float + +No + +No + +No + + +
+value_as_concept_id + +If the raw data gives a categorial result for measurements those values +are captured and mapped to standard concepts in the ‘Meas Value’ domain. + +If the raw data provides categorial results as well as continuous +results for measurements, it is a valid ETL choice to preserve both +values. The continuous value should go in the VALUE_AS_NUMBER field and +the categorical value should be mapped to a standard concept in the +‘Meas Value’ domain and put in the VALUE_AS_CONCEPT_ID field. This is +also the destination for the ‘Maps to value’ relationship. + +integer + +No + +No + +Yes + +CONCEPT + +
+unit_concept_id + +There is currently no recommended unit for individual measurements, +i.e. it is not mandatory to represent Hemoglobin a1C measurements as a +percentage. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in +the Unit domain that best represents the unit as given in the source +data. + +There is no standardization requirement for units associated with +MEASUREMENT_CONCEPT_IDs, however, it is the responsibility of the ETL to +choose the most plausible unit. + +integer + +No + +No + +Yes + +CONCEPT + +Unit +
+range_low + +Ranges have the same unit as the VALUE_AS_NUMBER. These ranges are +provided by the source and should remain NULL if not given. + +If reference ranges for upper and lower limit of normal as provided +(typically by a laboratory) these are stored in the RANGE_HIGH and +RANGE_LOW fields. This should be set to NULL if not provided. + +float + +No + +No + +No + + +
+range_high + +Ranges have the same unit as the VALUE_AS_NUMBER. These ranges are +provided by the source and should remain NULL if not given. + +If reference ranges for upper and lower limit of normal as provided +(typically by a laboratory) these are stored in the RANGE_HIGH and +RANGE_LOW fields. This should be set to NULL if not provided. + +float + +No + +No + +No + + +
+provider_id + +The provider associated with measurement record, e.g. the provider who +ordered the test or the provider who recorded the result. + +The ETL may need to make a choice as to which PROVIDER_ID to put here. +Based on what is available this may or may not be different than the +provider associated with the overall VISIT_OCCURRENCE record. For +example the admitting vs attending physician on an EHR record. + +integer + +No + +No + +Yes + +PROVIDER + +
+visit_occurrence_id + +The visit during which the Measurement occurred. + +Depending on the structure of the source data, this may have to be +determined based on dates. If a MEASUREMENT_DATE occurs within the start +and end date of a Visit it is a valid ETL choice to choose the +VISIT_OCCURRENCE_ID from the visit that subsumes it, even if not +explicitly stated in the data. While not required, an attempt should be +made to locate the VISIT_OCCURRENCE_ID of the measurement record. If a +measurement is related to a visit explicitly in the source data, it is +possible that the result date of the Measurement falls outside of the +bounds of the Visit dates. + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +
+visit_detail_id + +The VISIT_DETAIL record during which the Measurement occurred. For +example, if the Person was in the ICU at the time the VISIT_OCCURRENCE +record would reflect the overall hospital stay and the VISIT_DETAIL +record would reflect the ICU stay during the hospital visit. + +Same rules apply as for the VISIT_OCCURRENCE_ID. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+measurement_source_value + +This field houses the verbatim value from the source data representing +the Measurement that occurred. For example, this could be an ICD10 or +Read code. + +This code is mapped to a Standard Measurement Concept in the +Standardized Vocabularies and the original code is stored here for +reference. + +varchar(50) + +No + +No + +No + + +
+measurement_source_concept_id + +This is the concept representing the MEASUREMENT_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 +Measurement necessary for a given analytic use case. Consider using +MEASUREMENT_CONCEPT_ID instead to enable standardized analytics that can +be consistent across the network. + +If the MEASUREMENT_SOURCE_VALUE is coded in the source data using an +OMOP supported vocabulary put the concept id representing the source +value here. + +integer + +No + +No + +Yes + +CONCEPT + +
+unit_source_value + +This field houses the verbatim value from the source data representing +the unit of the Measurement that occurred. + +This code is mapped to a Standard Condition Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +
+value_source_value + +This field houses the verbatim result value of the Measurement from the +source data . + +If both a continuous and categorical result are given in the source data +such that both VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID are both +included, store the verbatim value that was mapped to +VALUE_AS_CONCEPT_ID here. + +varchar(50) + +No + +No + +No + + +

observation

@@ -900,6 +5853,614 @@ stated separately from the type of Observation in the VALUE_AS_* fields. It is recommended for Observations that are suggestive statements of positive assertion should have a value of ‘Yes’ (concept_id=4188539), recorded, even though the null value is the equivalent.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+observation_id + +The unique key given to an Observation record for a Person. Refer to the +ETL for how duplicate Observations during the same Visit were handled. + +Each instance of an observation present in the source data should be +assigned this unique key. + +integer + +Yes + +Yes + +No + + +
+person_id + +The PERSON_ID of the Person for whom the Observation is recorded. This +may be a system generated code. + + +integer + +Yes + +No + +Yes + +PERSON + +
+observation_concept_id + +The OBSERVATION_CONCEPT_ID field is recommended for primary use in +analyses, and must be used for network studies. + +The CONCEPT_ID that the OBSERVATION_SOURCE_CONCEPT_ID maps to. There is +no specified domain that the Concepts in this table must adhere to. The +only rule is that records with Concepts in the Condition, Procedure, +Drug, Measurement, or Device domains MUST go to the corresponding table. + +integer + +Yes + +No + +Yes + +CONCEPT + +
+observation_date + +The date of the Observation. Depending on what the Observation +represents this could be the date of a lab test, the date of a survey, +or the date a patient’s family history was taken. + +For some observations the ETL may need to make a choice as to which date +to choose. + +date + +Yes + +No + +No + + +
+observation_datetime + + +If no time is given set to midnight (00:00:00). + +datetime + +No + +No + +No + + +
+observation_type_concept_id + +This field can be used to determine the provenance of the Observation +record, as in whether the measurement was from an EHR system, insurance +claim, registry, or other sources. + +Choose the OBSERVATION_TYPE_CONCEPT_ID that best represents the +provenance of the record, for example whether it came from an EHR record +or billing claim. Accepted +Concepts. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+value_as_number + +This is the numerical value of the Result of the Observation, if +applicable and available. It is not expected that all Observations will +have numeric results, rather, this field is here to house values should +they exist. + + +float + +No + +No + +No + + +
+value_as_string + +This is the categorical value of the Result of the Observation, if +applicable and available. + + +varchar(60) + +No + +No + +No + + +
+value_as_concept_id + +It is possible that some records destined for the Observation table have +two clinical ideas represented in one source code. This is common with +ICD10 codes that describe a family history of some Condition, for +example. In OMOP the Vocabulary breaks these two clinical ideas into two +codes; one becomes the OBSERVATION_CONCEPT_ID and the other becomes the +VALUE_AS_CONCEPT_ID. It is important when using the Observation table to +keep this possibility in mind and to examine the VALUE_AS_CONCEPT_ID +field for relevant information. + +Note that the value of VALUE_AS_CONCEPT_ID may be provided through +mapping from a source Concept which contains the content of the +Observation. In those situations, the CONCEPT_RELATIONSHIP table in +addition to the ‘Maps to’ record contains a second record with the +relationship_id set to ‘Maps to value’. For example, ICD10 Z82.4 +‘Family history of ischaemic heart disease and other diseases of the +circulatory system’ has a ‘Maps to’ relationship to 4167217 +‘Family history of clinical finding’ as well as a ‘Maps to value’ record +to 134057 +‘Disorder of cardiovascular system’. + +Integer + +No + +No + +Yes + +CONCEPT + +
+qualifier_concept_id + +This field contains all attributes specifying the clinical fact further, +such as as degrees, severities, drug-drug interaction alerts etc. + +Use your best judgement as to what Concepts to use here and if they are +necessary to accurately represent the clinical record. There is no +restriction on the domain of these Concepts, they just need to be +Standard. + +integer + +No + +No + +Yes + +CONCEPT + +
+unit_concept_id + +There is currently no recommended unit for individual observation +concepts. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in +the Unit domain that best represents the unit as given in the source +data. + +There is no standardization requirement for units associated with +OBSERVATION_CONCEPT_IDs, however, it is the responsibility of the ETL to +choose the most plausible unit. + +integer + +No + +No + +Yes + +CONCEPT + +Unit +
+provider_id + +The provider associated with the observation record, e.g. the provider +who ordered the test or the provider who recorded the result. + +The ETL may need to make a choice as to which PROVIDER_ID to put here. +Based on what is available this may or may not be different than the +provider associated with the overall VISIT_OCCURRENCE record. For +example the admitting vs attending physician on an EHR record. + +integer + +No + +No + +Yes + +PROVIDER + +
+visit_occurrence_id + +The visit during which the Observation occurred. + +Depending on the structure of the source data, this may have to be +determined based on dates. If an OBSERVATION_DATE occurs within the +start and end date of a Visit it is a valid ETL choice to choose the +VISIT_OCCURRENCE_ID from the visit that subsumes it, even if not +explicitly stated in the data. While not required, an attempt should be +made to locate the VISIT_OCCURRENCE_ID of the observation record. If an +observation is related to a visit explicitly in the source data, it is +possible that the result date of the Observation falls outside of the +bounds of the Visit dates. + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +
+visit_detail_id + +The VISIT_DETAIL record during which the Observation occurred. For +example, if the Person was in the ICU at the time the VISIT_OCCURRENCE +record would reflect the overall hospital stay and the VISIT_DETAIL +record would reflect the ICU stay during the hospital visit. + +Same rules apply as for the VISIT_OCCURRENCE_ID. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+observation_source_value + +This field houses the verbatim value from the source data representing +the Observation that occurred. For example, this could be an ICD10 or +Read code. + +This code is mapped to a Standard Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +
+observation_source_concept_id + +This is the concept representing the OBSERVATION_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 +Observation necessary for a given analytic use case. Consider using +OBSERVATION_CONCEPT_ID instead to enable standardized analytics that can +be consistent across the network. + +If the OBSERVATION_SOURCE_VALUE is coded in the source data using an +OMOP supported vocabulary put the concept id representing the source +value here. + +integer + +No + +No + +Yes + +CONCEPT + +
+unit_source_value + +This field houses the verbatim value from the source data representing +the unit of the Observation that occurred. + +This code is mapped to a Standard Condition Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +
+qualifier_source_value + +This field houses the verbatim value from the source data representing +the qualifier of the Observation that occurred. + +This code is mapped to a Standard Condition Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +

death

@@ -913,6 +6474,240 @@ explicit record in EHR data.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+death_date + +The date the person was deceased. + +If the precise date include day or month is not known or not allowed, +December is used as the default month, and the last day of the month the +default day. + +date + +Yes + +No + +No + + +
+death_datetime + + +If not available set time to midnight (00:00:00) + +datetime + +No + +No + +No + + +
+death_type_concept_id + +This is the provenance of the death record, i.e., where it came from. It +is possible that an administrative claims database would source death +information from a government file so do not assume the Death Type is +the same as the Visit Type, etc. + +Use the type concept that be reflects the source of the death record. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +Type Concept +
+cause_concept_id + +This is the Standard Concept representing the Person’s cause of death, +if available. + +There is no specified domain for this concept, just choose the Standard +Concept Id that best represents the person’s cause of death. + +integer + +No + +No + +Yes + +CONCEPT + +
+cause_source_value + + +If available, put the source code representing the cause of death here. + +varchar(50) + +No + +No + +No + + +
+cause_source_concept_id + + +If the cause of death was coded using a Vocabulary present in the OMOP +Vocabularies put the CONCEPT_ID representing the cause of death here. + +integer + +No + +No + +Yes + +CONCEPT + +

note

@@ -951,6 +6746,432 @@ of the other 4 dimensions. However, not all the permutations of the CDO dimensions will necessarily yield an existing LOINC code. Each of these dimensions are contained in the OMOP Vocabulary under the domain of ‘Meas Value’ with each dimension represented as a Concept Class.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+note_id + +A unique identifier for each note. + + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+note_date + +The date the note was recorded. + + +date + +Yes + +No + +No + + +
+note_datetime + + +If time is not given set the time to midnight. + +datetime + +No + +No + +No + + +
+note_type_concept_id + +The provenance of the note. Most likely this will be EHR. + +Put the source system of the note, as in EHR record. Accepted +Concepts. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+note_class_concept_id + +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. This Concept can alternatively be represented by concepts +with the relationship ‘Kind of (LOINC)’ to 706391 +(Note). + +integer + +Yes + +No + +Yes + +CONCEPT + +
+note_title + +The title of the note. + + +varchar(250) + +No + +No + +No + + +
+note_text + +The content of the note. + + +varchar(MAX) + +Yes + +No + +No + + +
+encoding_concept_id + +This is the Concept representing the character encoding type. + +Put the Concept Id that represents the encoding character type here. +Currently the only option is UTF-8 (32678). It +the note is encoded in any other type, like ASCII then put 0. + +integer + +Yes + +No + +Yes + +CONCEPT + +
+language_concept_id + +The language of the note. + +Use Concepts that are descendants of the concept 4182347 +(World Languages). + +integer + +Yes + +No + +Yes + +CONCEPT + +
+provider_id + +The Provider who wrote the note. + +The ETL may need to make a determination on which provider to put here. + +integer + +No + +No + +Yes + +PROVIDER + +
+visit_occurrence_id + +The Visit during which the note was written. + + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +
+visit_detail_id + +The Visit Detail during which the note was written. + + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+note_source_value + + +The source value mapped to the NOTE_CLASS_CONCEPT_ID. + +varchar(50) + +No + +No + +No + + +

note_nlp

@@ -961,6 +7182,424 @@ row represents a single extracted term from a note.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+note_nlp_id + +A unique identifier for the NLP record. + + +integer + +Yes + +Yes + +No + + +
+note_id + +This is the NOTE_ID for the NOTE record the NLP record is associated to. + + +integer + +Yes + +No + +No + + +
+section_concept_id + + +The SECTION_CONCEPT_ID should be used to represent the note section +contained in the NOTE_NLP record. These concepts can be found as parts +of document panels and are based on the type of note written, i.e. a +discharge summary. These panels can be found as concepts with the +relationship ‘Subsumes’ to CONCEPT_ID 45875957. + +integer + +No + +No + +Yes + +CONCEPT + +
+snippet + +A small window of text surrounding the term + + +varchar(250) + +No + +No + +No + + +
+“offset” + +Character offset of the extracted term in the input note + + +varchar(50) + +No + +No + +No + + +
+lexical_variant + +Raw text extracted from the NLP tool. + + +varchar(250) + +Yes + +No + +No + + +
+note_nlp_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+note_nlp_source_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+nlp_system + + +Name and version of the NLP system that extracted the term. Useful for +data provenance. + +varchar(250) + +No + +No + +No + + +
+nlp_date + +The date of the note processing. + + +date + +Yes + +No + +No + + +
+nlp_datetime + +The date and time of the note processing. + + +datetime + +No + +No + +No + + +
+term_exists + + +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. + +varchar(1) + +No + +No + +No + + +
+term_temporal + + +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 +		 +varchar(50) + +No + +No + +No + + +
+term_modifiers + + +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. +		 +varchar(2000) + +No + +No + +No + + +

specimen

@@ -973,6 +7612,449 @@ samples from a person.

Anatomic site is coded at the most specific level of granularity possible, such that higher level classifications can be derived using the Standardized Vocabularies.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+specimen_id + +Unique identifier for each specimen. + + +integer + +Yes + +Yes + +No + + +
+person_id + +The person from whom the specimen is collected. + + +integer + +Yes + +No + +Yes + +PERSON + +
+specimen_concept_id + + +The standard CONCEPT_ID that the SPECIMEN_SOURCE_VALUE maps to in the +specimen domain. Accepted +Concepts + +integer + +Yes + +No + +Yes + +CONCEPT + +
+specimen_type_concept_id + + +Put the source of the specimen record, as in an EHR system. Accepted +Concepts. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+specimen_date + +The date the specimen was collected. + + +date + +Yes + +No + +No + + +
+specimen_datetime + + + +datetime + +No + +No + +No + + +
+quantity + +The amount of specimen collected from the person. + + +float + +No + +No + +No + + +
+unit_concept_id + +The unit for the quantity of the specimen. + +Map the UNIT_SOURCE_VALUE to a Standard Concept in the Unit domain. Accepted +Concepts + +integer + +No + +No + +Yes + +CONCEPT + +
+anatomic_site_concept_id + +This is the site on the body where the specimen is from. + +Map the ANATOMIC_SITE_SOURCE_VALUE to a Standard Concept in the Spec +Anatomic Site domain. This should be coded at the lowest level of +granularity Accepted +Concepts + +integer + +No + +No + +Yes + +CONCEPT + +
+disease_status_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+specimen_source_id + +This is the identifier for the specimen from the source system. + + +varchar(50) + +No + +No + +No + + +
+specimen_source_value + + + +varchar(50) + +No + +No + +No + + +
+unit_source_value + + +This unit for the quantity of the specimen, as represented in the +source. + +varchar(50) + +No + +No + +No + + +
+anatomic_site_source_value + + +This is the site on the body where the specimen was taken from, as +represented in the source. + +varchar(50) + +No + +No + +No + + +
+disease_status_source_value + + + +varchar(50) + +No + +No + +No + + +

fact_relationship

@@ -997,6 +8079,169 @@ example, two persons if person_id = 1 is the mother of person_id = 2 two records are in the FACT_RELATIONSHIP table (all strings in fact concept_id records in the Concept table: - Person, 1, Person, 2, parent of - Person, 2, Person, 1, child of

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+domain_concept_id_1 + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+fact_id_1 + + + +integer + +Yes + +No + +No + + +
+domain_concept_id_2 + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+fact_id_2 + + + +integer + +Yes + +No + +No + + +
+relationship_concept_id + + + +integer + +Yes + +No + +Yes + +CONCEPT + +

location

@@ -1011,6 +8256,254 @@ table. Locations do not contain names, such as the name of a hospital. In order to construct a full address that can be used in the postal service, the address information from the Location needs to be combined with information from the Care Site.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+location_id + +The unique key given to a unique Location. + +Each instance of a Location in the source data should be assigned this +unique key. + +integer + +Yes + +Yes + +No + + +
+address_1 + +This is the first line of the address. + + +varchar(50) + +No + +No + +No + + +
+address_2 + +This is the second line of the address + + +varchar(50) + +No + +No + +No + + +
+city + + + +varchar(50) + +No + +No + +No + + +
+state + + + +varchar(2) + +No + +No + +No + + +
+zip + + +Zip codes are handled as strings of up to 9 characters length. For US +addresses, these represent either a 3-digit abbreviated Zip code as +provided by many sources for patient protection reasons, the full +5-digit Zip or the 9-digit (ZIP + 4) codes. Unless for specific reasons +analytical methods should expect and utilize only the first 3 digits. +For international addresses, different rules apply. + +varchar(9) + +No + +No + +No + + +
+county + + + +varchar(20) + +No + +No + +No + + +
+location_source_value + + +Put the verbatim value for the location here, as it shows up in the +source. + +varchar(50) + +No + +No + +No + + +

care_site

@@ -1034,6 +8527,212 @@ wards can belong to clinics or departments, which can in turn belong to hospitals, which in turn can belong to hospital systems, which in turn can belong to HMOs.The relationships between Care Sites are defined in the FACT_RELATIONSHIP table.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+care_site_id + + +Assign an id to each unique combination of location_id and +place_of_service_source_value + +integer + +Yes + +Yes + +No + + +
+care_site_name + +The name of the care_site as it appears in the source data + + +varchar(255) + +No + +No + +No + + +
+place_of_service_concept_id + +This is a high-level way of characterizing a Care Site. Typically, +however, Care Sites can provide care in multiple settings (inpatient, +outpatient, etc.) and this granularity should be reflected in the visit. + +Choose the concept in the visit domain that best represents the setting +in which healthcare is provided in the Care Site. If most visits in a +Care Site are Inpatient, then the place_of_service_concept_id should +represent Inpatient. If information is present about a unique Care Site +(e.g. Pharmacy) then a Care Site record should be created. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+location_id + +The location_id from the LOCATION table representing the physical +location of the care_site. + + +integer + +No + +No + +Yes + +LOCATION + +
+care_site_source_value + +The identifier of the care_site as it appears in the source data. This +could be an identifier separate from the name of the care_site. + + +varchar(50) + +No + +No + +No + + +
+place_of_service_source_value + + +Put the place of service of the care_site as it appears in the source +data. + +varchar(50) + +No + +No + +No + + +

provider

@@ -1050,6 +8749,429 @@ providers, only provides limited information such as specialty, generic or ‘pooled’ Provider records are listed in the PROVIDER table.

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+provider_id + +It is assumed that every provider with a different unique identifier is +in fact a different person and should be treated independently. + +This identifier can be the original id from the source data provided it +is an integer, otherwise it can be an autogenerated number. + +integer + +Yes + +Yes + +No + + +
+provider_name + + +This field is not necessary as it is not necessary to have the actual +identity of the Provider. Rather, the idea is to uniquely and +anonymously identify providers of care across the database. + +varchar(255) + +No + +No + +No + + +
+npi + +This is the National Provider Number issued to health care providers in +the US by the Centers for Medicare and Medicaid Services (CMS). + + +varchar(20) + +No + +No + +No + + +
+dea + +This is the identifier issued by the DEA, a US federal agency, that +allows a provider to write prescriptions for controlled substances. + + +varchar(20) + +No + +No + +No + + +
+specialty_concept_id + +This field either represents the most common specialty that occurs in +the data or the most specific concept that represents all specialties +listed, should the provider have more than one. This includes physician +specialties such as internal medicine, emergency medicine, etc. and +allied health professionals such as nurses, midwives, and pharmacists. + +If a Provider has more than one Specialty, there are two options: 1. +Choose a concept_id which is a common ancestor to the multiple +specialties, or, 2. Choose the specialty that occurs most often for the +provider. Concepts in this field should be Standard with a domain of +Provider. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+care_site_id + +This is the CARE_SITE_ID for the location that the provider primarily +practices in. + +If a Provider has more than one Care Site, the main or most often +exerted CARE_SITE_ID should be recorded. + +integer + +No + +No + +Yes + +CARE_SITE + +
+year_of_birth + + + +integer + +No + +No + +No + + +
+gender_concept_id + +This field represents the recorded gender of the provider in the source +data. + +If given, put a concept from the gender domain representing the recorded +gender of the provider. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +Gender +
+provider_source_value + +Use this field to link back to providers in the source data. This is +typically used for error checking of ETL logic. + +Some use cases require the ability to link back to providers in the +source data. This field allows for the storing of the provider +identifier as it appears in the source. + +varchar(50) + +No + +No + +No + + +
+specialty_source_value + +This is the kind of provider or specialty as it appears in the source +data. This includes physician specialties such as internal medicine, +emergency medicine, etc. and allied health professionals such as nurses, +midwives, and pharmacists. + +Put the kind of provider as it appears in the source data. This field is +up to the discretion of the ETL-er as to whether this should be the +coded value from the source or the text description of the lookup value. + +varchar(50) + +No + +No + +No + + +
+specialty_source_concept_id + +This is often zero as many sites use proprietary codes to store +physician speciality. + +If the source data codes provider specialty in an OMOP supported +vocabulary store the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +
+gender_source_value + +This is provider’s gender as it appears in the source data. + +Put the provider’s gender as it appears in the source data. This field +is up to the discretion of the ETL-er as to whether this should be the +coded value from the source or the text description of the lookup value. + +varchar(50) + +No + +No + +No + + +
+gender_source_concept_id + +This is often zero as many sites use proprietary codes to store provider +gender. + +If the source data codes provider gender in an OMOP supported vocabulary +store the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +

payer_plan_period

@@ -1075,6 +9197,533 @@ structure of the Plan is rarely known, the idea is just to identify that the Plans are different.

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+payer_plan_period_id + +A unique identifier for each unique combination of a Person, Payer, +Plan, and Period of time. + + +integer + +Yes + +Yes + +No + + +
+person_id + +The Person covered by the Plan. + +A single Person can have multiple, overlapping, PAYER_PLAN_PERIOD +records + +integer + +Yes + +No + +Yes + +PERSON + +
+payer_plan_period_start_date + +Start date of Plan coverage. + + +date + +Yes + +No + +No + + +
+payer_plan_period_end_date + +End date of Plan coverage. + + +date + +Yes + +No + +No + + +
+payer_concept_id + +This field represents the organization who reimburses the provider which +administers care to the Person. + +Map the Payer directly to a standard CONCEPT_ID. If one does not exists +please contact the vocabulary team. There is no global controlled +vocabulary available for this information. The point is to stratify on +this information and identify if Persons have the same payer, though the +name of the Payer is not necessary. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+payer_source_value + +This is the Payer as it appears in the source data. + + +varchar(50) + +No + +No + +No + + +
+payer_source_concept_id + + +If the source data codes the Payer in an OMOP supported vocabulary store +the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +
+plan_concept_id + +This field represents the specific health benefit Plan the Person is +enrolled in. + +Map the Plan directly to a standard CONCEPT_ID. If one does not exists +please contact the vocabulary team. There is no global controlled +vocabulary available for this information. The point is to stratify on +this information and identify if Persons have the same health benefit +Plan though the name of the Plan is not necessary. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+plan_source_value + +This is the health benefit Plan of the Person as it appears in the +source data. + + +varchar(50) + +No + +No + +No + + +
+plan_source_concept_id + + +If the source data codes the Plan in an OMOP supported vocabulary store +the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +
+sponsor_concept_id + +This field represents the sponsor of the Plan who finances the Plan. +This includes self-insured, small group health plan and large group +health plan. + +Map the sponsor directly to a standard CONCEPT_ID. If one does not +exists please contact the vocabulary team. There is no global controlled +vocabulary available for this information. The point is to stratify on +this information and identify if Persons have the same sponsor though +the name of the sponsor is not necessary. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+sponsor_source_value + +The Plan sponsor as it appears in the source data. + + +varchar(50) + +No + +No + +No + + +
+sponsor_source_concept_id + + +If the source data codes the sponsor in an OMOP supported vocabulary +store the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +
+family_source_value + +The common identifier for all people (often a family) that covered by +the same policy. + +Often these are the common digits of the enrollment id of the policy +members. + +varchar(50) + +No + +No + +No + + +
+stop_reason_concept_id + +This field represents the reason the Person left the Plan, if known. + +Map the stop reason directly to a standard CONCEPT_ID. If one does not +exists please contact the vocabulary team. There is no global controlled +vocabulary available for this information. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+stop_reason_source_value + +The Plan stop reason as it appears in the source data. + + +varchar(50) + +No + +No + +No + + +
+stop_reason_source_concept_id + + +If the source data codes the stop reason in an OMOP supported vocabulary +store the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +

cost

@@ -1109,6 +9758,600 @@ reimbursement cost records will be identified by using the PAYER_PLAN_ID field. Drug costs are composed of ingredient cost (the amount charged by the wholesale distributor or manufacturer), the dispensing fee (the amount charged by the pharmacy and the sales tax).

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+cost_id + + + +integer + +Yes + +Yes + +No + + +
+cost_event_id + + + +integer + +Yes + +No + +No + + +
+cost_domain_id + + + +varchar(20) + +Yes + +No + +Yes + +DOMAIN + +
+cost_type_concept_id + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+currency_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+total_charge + + + +float + +No + +No + +No + + +
+total_cost + + + +float + +No + +No + +No + + +
+total_paid + + + +float + +No + +No + +No + + +
+paid_by_payer + + + +float + +No + +No + +No + + +
+paid_by_patient + + + +float + +No + +No + +No + + +
+paid_patient_copay + + + +float + +No + +No + +No + + +
+paid_patient_coinsurance + + + +float + +No + +No + +No + + +
+paid_patient_deductible + + + +float + +No + +No + +No + + +
+paid_by_primary + + + +float + +No + +No + +No + + +
+paid_ingredient_cost + + + +float + +No + +No + +No + + +
+paid_dispensing_fee + + + +float + +No + +No + +No + + +
+payer_plan_period_id + + + +integer + +No + +No + +No + + +
+amount_allowed + + + +float + +No + +No + +No + + +
+revenue_code_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+revenue_code_source_value + +Revenue codes are a method to charge for a class of procedures and +conditions in the U.S. hospital system. + + +varchar(50) + +No + +No + +No + + +
+drg_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+drg_source_value + +Diagnosis Related Groups are US codes used to classify hospital cases +into one of approximately 500 groups. + + +varchar(3) + +No + +No + +No + + +

drug_era

@@ -1124,6 +10367,245 @@ continuous Drug Eras.

ETL Conventions

The SQL script for generating DRUG_ERA records can be found here.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+drug_era_id + + + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+drug_concept_id + +The Concept Id representing the specific drug ingredient. + + +integer + +Yes + +No + +Yes + +CONCEPT + +Drug +
+drug_era_start_date + + +The Drug Era Start Date is the start date of the first Drug Exposure for +a given ingredient, with at least 31 days since the previous exposure. + +date + +Yes + +No + +No + + +
+drug_era_end_date + + +The Drug Era End Date is the end date of the last Drug Exposure. The End +Date of each Drug Exposure is either taken from the field +drug_exposure_end_date or, as it is typically not available, inferred +using the following rules: For pharmacy prescription data, the date when +the drug was dispensed plus the number of days of supply are used to +extrapolate the End Date for the Drug Exposure. Depending on the +country-specific healthcare system, this supply information is either +explicitly provided in the day_supply field or inferred from package +size or similar information. For Procedure Drugs, usually the drug is +administered on a single date (i.e., the administration date). A +standard Persistence Window of 30 days (gap, slack) is permitted between +two subsequent such extrapolated DRUG_EXPOSURE records to be considered +to be merged into a single Drug Era. + +date + +Yes + +No + +No + + +
+drug_exposure_count + + + +integer + +No + +No + +No + + +
+gap_days + + +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. + +integer + +No + +No + +No + + +

dose_era

@@ -1139,6 +10621,229 @@ algorithm. Dose Form information is not taken into account. So, if the patient changes between different formulations, or different manufacturers with the same formulation, the Dose Era is still spanning the entire time of exposure to the Ingredient.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+dose_era_id + + + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+drug_concept_id + +The Concept Id representing the specific drug ingredient. + + +integer + +Yes + +No + +Yes + +CONCEPT + +Drug +
+unit_concept_id + +The Concept Id representing the unit of the specific drug ingredient. + + +integer + +Yes + +No + +Yes + +CONCEPT + +Unit +
+dose_value + +The numeric value of the dosage of the drug_ingredient. + + +float + +Yes + +No + +No + + +
+dose_era_start_date + +The date the Person started on the specific dosage, with at least 31 +days since any prior exposure. + + +date + +Yes + +No + +No + + +
+dose_era_end_date + + +The date the Person was no longer exposed to the dosage of the specific +drug ingredient. An era is ended if there are 31 days or more between +dosage records. + +date + +Yes + +No + +No + + +

condition_era

@@ -1178,6 +10883,204 @@ Condition Occurrence. Condition Eras are built with a Persistence Window of 30 days, meaning, if no occurrence of the same condition_concept_id happens within 30 days of any one occurrence, it will be considered the condition_era_end_date.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+condition_era_id + + + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +No + +PERSON + +
+condition_concept_id + +The Concept Id representing the Condition. + + +integer + +Yes + +No + +Yes + +CONCEPT + +Condition +
+condition_era_start_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. + + +date + +Yes + +No + +No + + +
+condition_era_end_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. + + +date + +Yes + +No + +No + + +
+condition_occurrence_count + +The number of individual Condition Occurrences used to construct the +condition era. + + +integer + +No + +No + +No + + +

metadata

@@ -1188,6 +11091,219 @@ has been transformed to the OMOP Common Data Model.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+metadata_concept_id + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+metadata_type_concept_id + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+name + + + +varchar(250) + +Yes + +No + +No + + +
+value_as_string + + + +varchar(250) + +No + +No + +No + + +
+value_as_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+metadata_date + + + +date + +No + +No + +No + + +
+metadata_datetime + + + +datetime + +No + +No + +No + + +

cdm_source

@@ -1199,6 +11315,298 @@ Model.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+cdm_source_name + +The name of the CDM instance. + + +varchar(255) + +Yes + +No + +No + + +
+cdm_source_abbreviation + +The abbreviation of the CDM instance. + + +varchar(25) + +No + +No + +No + + +
+cdm_holder + +The holder of the CDM instance. + + +varchar(255) + +No + +No + +No + + +
+source_description + +The description of the CDM instance. + + +varchar(MAX) + +No + +No + +No + + +
+source_documentation_reference + + + +varchar(255) + +No + +No + +No + + +
+cdm_etl_reference + + +Put the link to the CDM version used. + +varchar(255) + +No + +No + +No + + +
+source_release_date + +The release date of the source data. + + +date + +No + +No + +No + + +
+cdm_release_date + +The release data of the CDM instance. + + +date + +No + +No + +No + + +
+cdm_version + + + +varchar(10) + +No + +No + +No + + +
+vocabulary_version + + + +varchar(20) + +No + +No + +No + + +

concept

@@ -1227,6 +11635,319 @@ observational data analysis.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+concept_id + +A unique identifier for each Concept across all domains. + + +integer + +Yes + +Yes + +No + + +
+concept_name + +An unambiguous, meaningful and descriptive name for the Concept. + + +varchar(255) + +Yes + +No + +No + + +
+domain_id + +A foreign key to the DOMAIN +table the Concept belongs to. + + +varchar(20) + +Yes + +No + +Yes + +DOMAIN + +
+vocabulary_id + +A foreign key to the VOCABULARY +table indicating from which source the Concept has been adapted. + + +varchar(20) + +Yes + +No + +Yes + +VOCABULARY + +
+concept_class_id + +The attribute or concept class of the Concept. Examples are ‘Clinical +Drug’, ‘Ingredient’, ‘Clinical Finding’ etc. + + +varchar(20) + +Yes + +No + +Yes + +CONCEPT_CLASS + +
+standard_concept + +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. + + +varchar(1) + +No + +No + +No + + +
+concept_code + +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. + + +varchar(50) + +Yes + +No + +No + + +
+valid_start_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. + + +date + +Yes + +No + +No + + +
+valid_end_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. + + +date + +Yes + +No + +No + + +
+invalid_reason + +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. + + +varchar(1) + +No + +No + +No + + +

vocabulary

@@ -1240,6 +11961,176 @@ for the Vocabulary.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+vocabulary_id + +A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit. + + +varchar(20) + +Yes + +Yes + +No + + +
+vocabulary_name + +The name describing the vocabulary, for example, International +Classification of Diseases, Ninth Revision, Clinical Modification, +Volume 1 and 2 (NCHS) etc. + + +varchar(255) + +Yes + +No + +No + + +
+vocabulary_reference + +External reference to documentation or available download of the about +the vocabulary. + + +varchar(255) + +Yes + +No + +No + + +
+vocabulary_version + +Version of the Vocabulary as indicated in the source. + + +varchar(255) + +No + +No + +No + + +
+vocabulary_concept_id + +A Concept that represents the Vocabulary the VOCABULARY record belongs +to. + + +integer + +Yes + +No + +Yes + +CONCEPT + +

domain

@@ -1256,6 +12147,121 @@ Domain and includes a descriptive name for the Domain.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+domain_id + +A unique key for each domain. + + +varchar(20) + +Yes + +Yes + +No + + +
+domain_name + +The name describing the Domain, e.g. Condition, Procedure, Measurement +etc. + + +varchar(255) + +Yes + +No + +No + + +
+domain_concept_id + +A Concept representing the Domain Concept the DOMAIN record belongs to. + + +integer + +Yes + +No + +Yes + +CONCEPT + +

concept_class

@@ -1268,6 +12274,121 @@ each Concept Class.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+concept_class_id + +A unique key for each class. + + +varchar(20) + +Yes + +Yes + +No + + +
+concept_class_name + +The name describing the Concept Class, e.g. Clinical Finding, +Ingredient, etc. + + +varchar(255) + +Yes + +No + +No + + +
+concept_class_concept_id + +A Concept that represents the Concept Class. + + +integer + +Yes + +No + +Yes + +CONCEPT + +
@@ -1281,6 +12402,202 @@ table.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+concept_id_1 + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+concept_id_2 + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+relationship_id + +The relationship between CONCEPT_ID_1 and CONCEPT_ID_2. Please see the +Vocabulary +Conventions. for more information. + + +varchar(20) + +Yes + +No + +Yes + +RELATIONSHIP + +
+valid_start_date + +The date when the relationship is first recorded. + + +date + +Yes + +No + +No + + +
+valid_end_date + +The date when the relationship is invalidated. + + +date + +Yes + +No + +No + + +
+invalid_reason + +Reason the relationship was invalidated. Possible values are ‘D’ +(deleted), ‘U’ (updated) or NULL. + + +varchar(1) + +No + +No + +No + + +

relationship

@@ -1292,6 +12609,203 @@ CONCEPT_RELATIONSHP table.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+relationship_id + +The type of relationship captured by the relationship record. + + +varchar(20) + +Yes + +Yes + +No + + +
+relationship_name + + + +varchar(255) + +Yes + +No + +No + + +
+is_hierarchical + +Defines whether a relationship defines concepts into classes or +hierarchies. Values are 1 for hierarchical relationship or 0 if not. + + +varchar(1) + +Yes + +No + +No + + +
+defines_ancestry + +Defines whether a hierarchical relationship contributes to the +concept_ancestor table. These are subsets of the hierarchical +relationships. Valid values are 1 or 0. + + +varchar(1) + +Yes + +No + +No + + +
+reverse_relationship_id + +The identifier for the relationship used to define the reverse +relationship between two concepts. + + +varchar(20) + +Yes + +No + +No + + +
+relationship_concept_id + +A foreign key that refers to an identifier in the CONCEPT +table for the unique relationship concept. + + +integer + +Yes + +No + +Yes + +CONCEPT + +

concept_synonym

@@ -1302,6 +12816,118 @@ descriptions for Concepts.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+concept_id + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+concept_synonym_name + + + +varchar(1000) + +Yes + +No + +No + + +
+language_concept_id + + + +integer + +Yes + +No + +Yes + +CONCEPT + +

concept_ancestor

@@ -1323,6 +12949,153 @@ and RELATIONSHIP tables.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+ancestor_concept_id + +The Concept Id for the higher-level concept that forms the ancestor in +the relationship. + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+descendant_concept_id + +The Concept Id for the lower-level concept that forms the descendant in +the relationship. + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+min_levels_of_separation + +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. + + +integer + +Yes + +No + +No + + +
+max_levels_of_separation + +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. + + +integer + +Yes + +No + +No + + +
@@ -1340,6 +13113,288 @@ published to the OMOP community.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+source_code + +The source code being translated into a Standard Concept. + + +varchar(50) + +Yes + +No + +No + + +
+source_concept_id + +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. + +integer + +Yes + +No + +Yes + +CONCEPT + +
+source_vocabulary_id + +A foreign key to the VOCABULARY table defining the vocabulary of the +source code that is being translated to a Standard Concept. + + +varchar(20) + +Yes + +No + +No + + +
+source_code_description + +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. + + +varchar(255) + +No + +No + +No + + +
+target_concept_id + +The target Concept to which the source code is being mapped. + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+target_vocabulary_id + +The Vocabulary of the target Concept. + + +varchar(20) + +Yes + +No + +Yes + +VOCABULARY + +
+valid_start_date + +The date when the mapping instance was first recorded. + + +date + +Yes + +No + +No + + +
+valid_end_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. + + +date + +Yes + +No + +No + + +
+invalid_reason + +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. + + +varchar(1) + +No + +No + +No + + +

drug_strength

@@ -1352,6 +13407,371 @@ to support standardized analysis of drug utilization.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+drug_concept_id + +The Concept representing the Branded Drug or Clinical Drug Product. + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+ingredient_concept_id + +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. + +integer + +Yes + +No + +Yes + +CONCEPT + +
+amount_value + +The numeric value or the amount of active ingredient contained within +the drug product. + + +float + +No + +No + +No + + +
+amount_unit_concept_id + +The Concept representing the Unit of measure for the amount of active +ingredient contained within the drug product. + + +integer + +No + +No + +Yes + +CONCEPT + +
+numerator_value + +The concentration of the active ingredient contained within the drug +product. + + +float + +No + +No + +No + + +
+numerator_unit_concept_id + +The Concept representing the Unit of measure for the concentration of +active ingredient. + + +integer + +No + +No + +Yes + +CONCEPT + +
+denominator_value + +The amount of total liquid (or other divisible product, such as +ointment, gel, spray, etc.). + + +float + +No + +No + +No + + +
+denominator_unit_concept_id + +The Concept representing the denominator unit for the concentration of +active ingredient. + + +integer + +No + +No + +Yes + +CONCEPT + +
+box_size + +The number of units of Clinical Branded Drug or Quantified Clinical or +Branded Drug contained in a box as dispensed to the patient. + + +integer + +No + +No + +No + + +
+valid_start_date + +The date when the Concept was first recorded. The default value is +1-Jan-1970. + + +date + +Yes + +No + +No + + +
+valid_end_date + +The date when then Concept became invalid. + + +date + +Yes + +No + +No + + +
+invalid_reason + +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. + + +varchar(1) + +No + +No + +No + + +

cohort_definition

@@ -1369,6 +13789,228 @@ Model.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+cohort_definition_id + +This is the identifier given to the cohort, usually by the ATLAS +application + + +integer + +Yes + +No + +No + + +
+cohort_definition_name + +A short description of the cohort + + +varchar(255) + +Yes + +No + +No + + +
+cohort_definition_description + +A complete description of the cohort. + + +varchar(MAX) + +No + +No + +No + + +
+definition_type_concept_id + +Type defining what kind of Cohort Definition the record represents and +how the syntax may be executed. + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+cohort_definition_syntax + +Syntax or code to operationalize the Cohort Definition. + + +varchar(MAX) + +No + +No + +No + + +
+subject_concept_id + +This field contains a Concept that represents the domain of the subjects +that are members of the cohort (e.g., Person, Provider, Visit). + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+cohort_initiation_date + +A date to indicate when the Cohort was initiated in the COHORT table. + + +date + +No + +No + +No + + +
@@ -1386,6 +14028,167 @@ the OMOP Common Data Model.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+attribute_definition_id + + + +integer + +Yes + +No + +No + + +
+attribute_name + + + +varchar(255) + +Yes + +No + +No + + +
+attribute_description + + + +varchar(MAX) + +No + +No + +No + + +
+attribute_type_concept_id + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+attribute_syntax + + + +varchar(MAX) + +No + +No + +No + + +
diff --git a/docs/cdm54.html b/docs/cdm54.html index 1f11baf..95a1f3b 100644 --- a/docs/cdm54.html +++ b/docs/cdm54.html @@ -508,9 +508,9 @@ page.

two levels of support: legacy support means that the tool supports all tables and fields that were present in CDM v5.3 and feature support indicates that the tool supports any new tables and fields in CDM v5.4 -that were not present in CDM v5.3. A green check ✅ indicates that the +that were not present in CDM v5.3. A green check ✔️ indicates that the support level for the listed tool is in place, has been tested, and -released. A warning sign ⚠️ indicates that the support level for the +released. A warning sign ❗ indicates that the support level for the listed tool has been initiated but has not yet been tested and released.

@@ -535,8 +535,8 @@ listed tool has been initiated but has not yet been tested and released. href="https://github.com/OHDSI/CommonDataModel/">https://github.com/OHDSI/CommonDataModel/. It functions to dynamically create the OMOP CDM documentation and DDL scripts to instantiate the CDM tables. - - + + @@ -545,8 +545,8 @@ href="https://github.com/OHDSI/DataQualityDashboard">https://github.com/OHDSI/Da It runs a set of > 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study. - - + + @@ -554,8 +554,8 @@ participating in an OHDSI network research study. href="https://github.com/OHDSI/Achilles">https://github.com/OHDSI/Achilles, performing a set of broad database characterizations agains an OMOP CDM instance. - - + + @@ -564,16 +564,16 @@ href="https://github.com/OHDSI/Ares">https://github.com/OHDSI/Ares and is designed to display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research. - - + + - - + + @@ -582,8 +582,8 @@ href="https://github.com/OHDSI/WhiteRabbit">https://github.com/OHDSI/WhiteRabbit and is an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit. - - + + @@ -591,16 +591,16 @@ White Rabbit. href="https://github.com/OHDSI/FeatureExtraction">https://github.com/OHDSI/FeatureExtraction. It is designed to generate features (covariates) for a cohort generated using the OMOP CDM. - - + + - - + +
✅✅✔️✔️
Data Quality Dashboard✅⚠️✔️❗
Achilles✅⚠️✔️❗
ARES✅⚠️✔️❗
ATLAS ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. Demo✅⚠️✔️❗
Rabbit-In-A-Hat✅✅✔️✔️
Feature Extraction✅✅*✔️✔️*
Cohort Diagnostics This package can be downloaded from https://github.com/OHDSI/CohortDiagnostics and is used to critically evaluate cohort phenotypes.✅⚠️✔️❗
@@ -630,6 +630,599 @@ contributes Events to the database, Persons must be reconciled, if possible, across the sources to create one single record per Person. The content of the BIRTH_DATETIME must be equivalent to the content of BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+person_id + +It is assumed that every person with a different unique identifier is in +fact a different person and should be treated independently. + +Any person linkage that needs to occur to uniquely identify Persons +ought to be done prior to writing this table. This identifier can be the +original id from the source data provided if it is an integer, otherwise +it can be an autogenerated number. + +integer + +Yes + +Yes + +No + + +
+gender_concept_id + +This field is meant to capture the biological sex at birth of the +Person. This field should not be used to study gender identity issues. + +Use the gender or sex value present in the data under the assumption +that it is the biological sex at birth. If the source data captures +gender identity it should be stored in the OBSERVATION +table. Accepted +gender concepts + +integer + +Yes + +No + +Yes + +CONCEPT + +Gender +
+year_of_birth + +Compute age using year_of_birth. + +For data sources with date of birth, the year should be extracted. For +data sources where the year of birth is not available, the approximate +year of birth could be derived based on age group categorization, if +available. + +integer + +Yes + +No + +No + + +
+month_of_birth + + +For data sources that provide the precise date of birth, the month +should be extracted and stored in this field. + +integer + +No + +No + +No + + +
+day_of_birth + + +For data sources that provide the precise date of birth, the day should +be extracted and stored in this field. + +integer + +No + +No + +No + + +
+birth_datetime + + +This field is not required but highly encouraged. For data sources that +provide the precise datetime of birth, that value should be stored in +this field. If birth_datetime is not provided in the source, use the +following logic to infer the date: If day_of_birth is null and +month_of_birth is not null then use the first of the month in that year. +If month_of_birth is null or if day_of_birth AND month_of_birth are both +null and the person has records during their year of birth then use the +date of the earliest record, otherwise use the 15th of June of that +year. If time of birth is not given use midnight (00:00:0000). + +datetime + +No + +No + +No + + +
+race_concept_id + +This field captures race or ethnic background of the person. + +Only use this field if you have information about race or ethnic +background. The Vocabulary contains Concepts about the main races and +ethnic backgrounds in a hierarchical system. Due to the imprecise nature +of human races and ethnic backgrounds, this is not a perfect system. +Mixed races are not supported. If a clear race or ethnic background +cannot be established, use Concept_Id 0. Accepted +Race Concepts. + +integer + +Yes + +No + +Yes + +CONCEPT + +Race +
+ethnicity_concept_id + +This field captures Ethnicity as defined by the Office of Management and +Budget (OMB) of the US Government: it distinguishes only between +“Hispanic” and “Not Hispanic”. Races and ethnic backgrounds are not +stored here. + +Only use this field if you have US-based data and a source of this +information. Do not attempt to infer Ethnicity from the race or ethnic +background of the Person. Accepted +ethnicity concepts + +integer + +Yes + +No + +Yes + +CONCEPT + +Ethnicity +
+location_id + +The location refers to the physical address of the person. This field +should capture the last known location of the person. + +Put the location_id from the LOCATION +table here that represents the most granular location information for +the person. This could represent anything from postal code or parts +thereof, state, or county for example. Since many databases contain +deidentified data, it is common that the precision of the location is +reduced to prevent re-identification. This field should capture the last +known location. + +integer + +No + +No + +Yes + +LOCATION + +
+provider_id + +The Provider refers to the last known primary care provider (General +Practitioner). + +Put the provider_id from the PROVIDER +table of the last known general practitioner of the person. If there are +multiple providers, it is up to the ETL to decide which to put here. + +integer + +No + +No + +Yes + +PROVIDER + +
+care_site_id + +The Care Site refers to where the Provider typically provides the +primary care. + + +integer + +No + +No + +Yes + +CARE_SITE + +
+person_source_value + +Use this field to link back to persons in the source data. This is +typically used for error checking of ETL logic. + +Some use cases require the ability to link back to persons in the source +data. This field allows for the storing of the person value as it +appears in the source. This field is not required but strongly +recommended. + +varchar(50) + +No + +No + +No + + +
+gender_source_value + +This field is used to store the biological sex of the person from the +source data. It is not intended for use in standard analytics but for +reference only. + +Put the biological sex of the person as it appears in the source data. + +varchar(50) + +No + +No + +No + + +
+gender_source_concept_id + +Due to the small number of options, this tends to be zero. + +If the source data codes biological sex in a non-standard vocabulary, +store the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +
+race_source_value + +This field is used to store the race of the person from the source data. +It is not intended for use in standard analytics but for reference only. + +Put the race of the person as it appears in the source data. + +varchar(50) + +No + +No + +No + + +
+race_source_concept_id + +Due to the small number of options, this tends to be zero. + +If the source data codes race in an OMOP supported vocabulary store the +concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +
+ethnicity_source_value + +This field is used to store the ethnicity of the person from the source +data. It is not intended for use in standard analytics but for reference +only. + +If the person has an ethnicity other than the OMB standard of “Hispanic” +or “Not Hispanic” store that value from the source data here. + +varchar(50) + +No + +No + +No + + +
+ethnicity_source_concept_id + +Due to the small number of options, this tends to be zero. + +If the source data codes ethnicity in an OMOP supported vocabulary, +store the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +

observation_period

@@ -672,6 +1265,201 @@ spans defined by OBSERVATION_PERIOD records. Family history or history of Clinical Events generally are not used to generate OBSERVATION_PERIOD records around the time they are referring to. Any two overlapping or adjacent OBSERVATION_PERIOD records have to be merged into one.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+observation_period_id + +A Person can have multiple discrete Observation Periods which are +identified by the Observation_Period_Id. + +Assign a unique observation_period_id to each discrete Observation +Period for a Person. + +integer + +Yes + +Yes + +No + + +
+person_id + +The Person ID of the PERSON record for which the Observation Period is +recorded. + + +integer + +Yes + +No + +Yes + +PERSON + +
+observation_period_start_date + +Use this date to determine the start date of the Observation Period. + +It is often the case that the idea of Observation Periods does not exist +in source data. In those cases, the observation_period_start_date can be +inferred as the earliest Event date available for the Person. In +insurance claim data, the Observation Period can be considered as the +time period the Person is enrolled with a payer. If a Person switches +plans but stays with the same payer, and therefore capturing of data +continues, that change would be captured in PAYER_PLAN_PERIOD. + +date + +Yes + +No + +No + + +
+observation_period_end_date + +Use this date to determine the end date of the period for which we can +assume that all events for a Person are recorded. + +It is often the case that the idea of Observation Periods does not exist +in source data. In those cases, the observation_period_end_date can be +inferred as the last Event date available for the Person. In insurance +claim data, the Observation Period can be considered as the time period +the Person is enrolled with a payer. + +date + +Yes + +No + +No + + +
+period_type_concept_id + +This field can be used to determine the provenance of the Observation +Period as in whether the period was determined from an insurance +enrollment file, EHR healthcare encounters, or other sources. + +Choose the observation_period_type_concept_id that best represents how +the period was determined. Accepted +Concepts. A more detailed explanation of each Type Concept can be +found on the vocabulary +wiki. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +

visit_occurrence

@@ -770,6 +1558,592 @@ encounter records should be translated to visit occurrences. Providers can be associated with a Visit through the PROVIDER_ID field, or indirectly through PROCEDURE_OCCURRENCE records linked both to the VISIT and PROVIDER tables.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+visit_occurrence_id + +Use this to identify unique interactions between a person and the health +care system. This identifier links across the other CDM event tables to +associate events with a visit. + +This should be populated by creating a unique identifier for each unique +interaction between a person and the healthcare system where the person +receives a medical good or service over a span of time. + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+visit_concept_id + +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. + +integer + +Yes + +No + +Yes + +CONCEPT + +Visit +
+visit_start_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. + +date + +Yes + +No + +No + + +
+visit_start_datetime + + +If no time is given for the start date of a visit, set it to midnight +(00:00:0000). + +datetime + +No + +No + +No + + +
+visit_end_date + +For inpatient visits the end date is typically the discharge date. If a +Person is still an inpatient in the hospital at the time of the data +extract and does not have a visit_end_date, then set the visit_end_date +to the date of the data pull. + +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. + +date + +Yes + +No + +No + + +
+visit_end_datetime + +If a Person is still an inpatient in the hospital at the time of the +data extract and does not have a visit_end_datetime, then set the +visit_end_datetime to the datetime of the data pull. + +If no time is given for the end date of a visit, set it to midnight +(00:00:0000). + +datetime + +No + +No + +No + + +
+visit_type_concept_id + +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. A more detailed explanation of each Type Concept can be +found on the vocabulary +wiki. + +Integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+provider_id + +There will only be one provider per visit record and the ETL document +should clearly state how they were chosen (attending, admitting, etc.). +If there are multiple providers associated with a visit in the source, +this can be reflected in the event tables (CONDITION_OCCURRENCE, +PROCEDURE_OCCURRENCE, etc.) or in the VISIT_DETAIL table. + +If there are multiple providers associated with a visit, you will need +to choose which one to put here. The additional providers can be stored +in the VISIT_DETAIL +table. + +integer + +No + +No + +Yes + +PROVIDER + +
+care_site_id + +This field provides information about the Care Site where the Visit took +place. + +There should only be one Care Site associated with a Visit. + +integer + +No + +No + +Yes + +CARE_SITE + +
+visit_source_value + +This field houses the verbatim value from the source data representing +the kind of visit that took place (inpatient, outpatient, emergency, +etc.) + +If there is information about the kind of visit 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 source value, +such as IP -> ER-> OP. This should line up with the logic chosen +to determine how visits are created. + +varchar(50) + +No + +No + +No + + +
+visit_source_concept_id + + +If the visit source value is coded in the source data using an OMOP +supported vocabulary put the concept id representing the source value +here. + +integer + +No + +No + +Yes + +CONCEPT + +
+admitted_from_concept_id + +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. Accepted +Concepts. If a person was admitted from home, set this to 0. + +integer + +No + +No + +Yes + +CONCEPT + +Visit +
+admitted_from_source_value + + +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. + +varchar(50) + +No + +No + +No + + +
+discharged_to_concept_id + +Use this field to determine where the patient was discharged to after a +visit. This concept is part of the visit domain and can indicate if a +patient was transferred to another hospital or sent to a long-term care +facility, for example. It is assumed that a person is discharged to home +therefore there is not a standard concept id for “home”. Use concept id += 0 when a person is discharged to home. + +If available, map the discharged_to_source_value to a standard concept +in the visit domain. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +Visit +
+discharged_to_source_value + + +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. + +varchar(50) + +No + +No + +No + + +
+preceding_visit_occurrence_id + +Use this field to find the visit that occurred for the person prior to +the given visit. There could be a few days or a few years in between. + +This field can be used to link a visit immediately preceding the current +visit. Note this is not symmetrical, and there is no such thing as a +“following_visit_id”. + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +

visit_detail

@@ -806,6 +2180,650 @@ Occurrence by setting the VISIT_CONCEPT_ID to 9201 and the VISIT_DETAIL_CONCEPT_IDs either to 9201 or its children to indicate where the patient was in the hospital at the time of care.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+visit_detail_id + +Use this to identify unique interactions between a person and the health +care system. This identifier links across the other CDM event tables to +associate events with a visit detail. + +This should be populated by creating a unique identifier for each unique +interaction between a person and the healthcare system where the person +receives a medical good or service over a span of time. + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+visit_detail_concept_id + +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. + +integer + +Yes + +No + +Yes + +CONCEPT + +Visit +
+visit_detail_start_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. + +date + +Yes + +No + +No + + +
+visit_detail_start_datetime + + +If no time is given for the start date of a visit, set it to midnight +(00:00:0000). + +datetime + +No + +No + +No + + +
+visit_detail_end_date + +This the end date of the patient-provider interaction. If a Person is +still an inpatient in the hospital at the time of the data extract and +does not have a visit_end_date, then set the visit_end_date to the date +of the data pull. + +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. +		 +date + +Yes + +No + +No + + +
+visit_detail_end_datetime + +If a Person is still an inpatient in the hospital at the time of the +data extract and does not have a visit_end_datetime, then set the +visit_end_datetime to the datetime of the data pull. + +If no time is given for the end date of a visit, set it to midnight +(00:00:0000). + +datetime + +No + +No + +No + + +
+visit_detail_type_concept_id + +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. A more detailed explanation of each Type Concept can be +found on the vocabulary +wiki. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+provider_id + +There will only be one provider per visit record and +the ETL document should clearly state how they were chosen (attending, +admitting, etc.). This is a typical reason for leveraging the +VISIT_DETAIL table as even though each VISIT_DETAIL record can only have +one provider, there is no limit to the number of VISIT_DETAIL records +that can be associated to a VISIT_OCCURRENCE record. + +The additional providers associated to a Visit can be stored in this +table where each VISIT_DETAIL record represents a different provider. + +integer + +No + +No + +Yes + +PROVIDER + +
+care_site_id + +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. + +integer + +No + +No + +Yes + +CARE_SITE + +
+visit_detail_source_value + +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. + +varchar(50) + +No + +No + +No + + +
+visit_detail_source_concept_id + + +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. + +Integer + +No + +No + +Yes + +CONCEPT + +
+admitted_from_concept_id + +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. Accepted +Concepts. If the person was admitted from home, set this to 0. + +Integer + +No + +No + +Yes + +CONCEPT + +Visit +
+admitted_from_source_value + + +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. + +varchar(50) + +No + +No + +No + + +
+discharged_to_source_value + + +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. + +varchar(50) + +No + +No + +No + + +
+discharged_to_concept_id + +Use this field to determine where the patient was discharged to after a +visit. This concept is part of the visit domain and can indicate if a +patient was transferred to another hospital or sent to a long-term care +facility, for example. It is assumed that a person is discharged to home +therefore there is not a standard concept id for “home”. Use concept id += 0 when a person is discharged to home. + +If available, map the DISCHARGE_TO_SOURCE_VALUE to a Standard Concept in +the Visit domain. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +Visit +
+preceding_visit_detail_id + +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”. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+parent_visit_detail_id + +Use this field to find the visit detail that subsumes the given visit +detail record. This is used in the case that a visit detail record needs +to be nested beyond the VISIT_OCCURRENCE/VISIT_DETAIL relationship. + +If there are multiple nested levels to how Visits are represented in the +source, the VISIT_DETAIL_PARENT_ID can be used to record this +relationship. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+visit_occurrence_id + +Use this field to link the VISIT_DETAIL record to its VISIT_OCCURRENCE. + +Put the VISIT_OCCURRENCE_ID that subsumes the VISIT_DETAIL record here. + +integer + +Yes + +No + +Yes + +VISIT_OCCURRENCE + +
@@ -848,6 +2866,551 @@ always available.

ETL Conventions

Source codes and source text fields mapped to Standard Concepts of the Condition Domain have to be recorded here.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+condition_occurrence_id + +The unique key given to a condition record for a person. Refer to the +ETL for how duplicate conditions during the same visit were handled. + +Each instance of a condition present in the source data should be +assigned this unique key. In some cases, a person can have multiple +records of the same condition within the same visit. It is valid to keep +these duplicates and assign them individual, unique, +CONDITION_OCCURRENCE_IDs, though it is up to the ETL how they should be +handled. + +integer + +Yes + +Yes + +No + + +
+person_id + +The PERSON_ID of the PERSON for whom the condition is recorded. + + +integer + +Yes + +No + +Yes + +PERSON + +
+condition_concept_id + +The CONDITION_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 condition + +The CONCEPT_ID that the CONDITION_SOURCE_VALUE maps to. Only records +whose source values map to concepts with a domain of “Condition” should +go in this table. Accepted +Concepts. + +integer + +Yes + +No + +Yes + +CONCEPT + +Condition +
+condition_start_date + +Use this date to determine the start date of the condition + +Most often data sources do not have the idea of a start date for a +condition. Rather, if a source only has one date associated with a +condition record it is acceptable to use that date for both the +CONDITION_START_DATE and the CONDITION_END_DATE. + +date + +Yes + +No + +No + + +
+condition_start_datetime + + +If a source does not specify datetime the convention is to set the time +to midnight (00:00:0000) + +datetime + +No + +No + +No + + +
+condition_end_date + +Use this date to determine the end date of the condition + +Most often data sources do not have the idea of a start date for a +condition. Rather, if a source only has one date associated with a +condition record it is acceptable to use that date for both the +CONDITION_START_DATE and the CONDITION_END_DATE. + +date + +No + +No + +No + + +
+condition_end_datetime + + +If a source does not specify datetime the convention is to set the time +to midnight (00:00:0000) + +datetime + +No + +No + +No + + +
+condition_type_concept_id + +This field can be used to determine the provenance of the Condition +record, as in whether the condition was from an EHR system, insurance +claim, registry, or other sources. + +Choose the CONDITION_TYPE_CONCEPT_ID that best represents the provenance +of the record. Accepted +Concepts. A more detailed explanation of each Type Concept can be +found on the vocabulary +wiki. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+condition_status_concept_id + +This concept represents the point during the visit the diagnosis was +given (admitting diagnosis, final diagnosis), whether the diagnosis was +determined due to laboratory findings, if the diagnosis was +exclusionary, or if it was a preliminary diagnosis, among others. + +Choose the Concept in the Condition Status domain that best represents +the point during the visit when the diagnosis was given. These can +include admitting diagnosis, principal diagnosis, and secondary +diagnosis. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +Condition Status +
+stop_reason + +The Stop Reason indicates why a Condition is no longer valid with +respect to the purpose within the source data. Note that a Stop Reason +does not necessarily imply that the condition is no longer occurring. + +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. + +varchar(20) + +No + +No + +No + + +
+provider_id + +The provider associated with condition record, e.g. the provider who +made the diagnosis or the provider who recorded the symptom. + +The ETL may need to make a choice as to which PROVIDER_ID to put here. +Based on what is available this may or may not be different than the +provider associated with the overall VISIT_OCCURRENCE record, for +example the admitting vs attending physician on an EHR record. + +integer + +No + +No + +Yes + +PROVIDER + +
+visit_occurrence_id + +The visit during which the condition occurred. + +Depending on the structure of the source data, this may have to be +determined based on dates. If a CONDITION_START_DATE occurs within the +start and end date of a Visit it is a valid ETL choice to choose the +VISIT_OCCURRENCE_ID from the Visit that subsumes it, even if not +explicitly stated in the data. While not required, an attempt should be +made to locate the VISIT_OCCURRENCE_ID of the CONDITION_OCCURRENCE +record. + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +
+visit_detail_id + +The VISIT_DETAIL record during which the condition occurred. For +example, if the person was in the ICU at the time of the diagnosis the +VISIT_OCCURRENCE record would reflect the overall hospital stay and the +VISIT_DETAIL record would reflect the ICU stay during the hospital +visit. + +Same rules apply as for the VISIT_OCCURRENCE_ID. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+condition_source_value + +This field houses the verbatim value from the source data representing +the condition that occurred. For example, this could be an ICD10 or Read +code. + +This code is mapped to a Standard Condition Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +
+condition_source_concept_id + +This is the concept representing the condition 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 Condition +necessary for a given analytic use case. Consider using +CONDITION_CONCEPT_ID instead to enable standardized analytics that can +be consistent across the network. + +If the CONDITION_SOURCE_VALUE is coded in the source data using an OMOP +supported vocabulary put the concept id representing the source value +here. + +integer + +No + +No + +Yes + +CONCEPT + +
+condition_status_source_value + +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. + +varchar(50) + +No + +No + +No + + +

drug_exposure

@@ -880,6 +3443,786 @@ dispensed. If a patient has multiple records on the same day for the same drug or procedures the ETL should not de-dupe them unless there is probable reason to believe the item is a true data duplicate. Take note on how to handle refills for prescriptions written.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+drug_exposure_id + +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. + +integer + +Yes + +Yes + +No + + +
+person_id + +The PERSON_ID of the PERSON for whom the drug dispensing or +administration is recorded. This may be a system generated code. + + +integer + +Yes + +No + +Yes + +PERSON + +
+drug_concept_id + +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: ‘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. + +integer + +Yes + +No + +Yes + +CONCEPT + +Drug +
+drug_exposure_start_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. + +date + +Yes + +No + +No + + +
+drug_exposure_start_datetime + + +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) + +datetime + +No + +No + +No + + +
+drug_exposure_end_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 +		 +date + +Yes + +No + +No + + +
+drug_exposure_end_datetime + + +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) + +datetime + +No + +No + +No + + +
+verbatim_end_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. + +date + +No + +No + +No + + +
+drug_type_concept_id + +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. A more detailed explanation of each Type Concept can be +found on the vocabulary +wiki. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+stop_reason + +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. + +varchar(20) + +No + +No + +No + + +
+refills + +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. + + +integer + +No + +No + +No + + +
+quantity + + +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 for more information. + +float + +No + +No + +No + + +
+days_supply + + +Days supply of the drug. This should be the verbatim days_supply as +given on the prescription. If the drug is physician administered use +duration end date if given or set to 1 as default if duration is not +available. + +integer + +No + +No + +No + + +
+sig + +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. + +varchar(MAX) + +No + +No + +No + + +
+route_concept_id + + +The standard CONCEPT_ID that the ROUTE_SOURCE_VALUE maps to in the route +domain. + +integer + +No + +No + +Yes + +CONCEPT + +Route +
+lot_number + + + +varchar(50) + +No + +No + +No + + +
+provider_id + +The Provider associated with drug record, e.g. the provider who wrote +the prescription or the provider who administered the drug. + +The ETL may need to make a choice as to which PROVIDER_ID to put here. +Based on what is available this may or may not be different than the +provider associated with the overall VISIT_OCCURRENCE record, for +example the ordering vs administering physician on an EHR record. + +integer + +No + +No + +Yes + +PROVIDER + +
+visit_occurrence_id + +The Visit during which the drug was prescribed, administered or +dispensed. + +To populate this field drug exposures must be explicitly initiated in +the visit. + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +
+visit_detail_id + +The VISIT_DETAIL record during which the drug exposure occurred. For +example, if the person was in the ICU at the time of the drug +administration the VISIT_OCCURRENCE record would reflect the overall +hospital stay and the VISIT_DETAIL record would reflect the ICU stay +during the hospital visit. + +Same rules apply as for the VISIT_OCCURRENCE_ID. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+drug_source_value + +This field houses the verbatim value from the source data representing +the drug exposure that occurred. For example, this could be an NDC or +Gemscript code. + +This code is mapped to a Standard Drug Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +
+drug_source_concept_id + +This is the concept representing the drug 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 Drug +necessary for a given analytic use case. Consider using DRUG_CONCEPT_ID +instead to enable standardized analytics that can be consistent across +the network. + +If the DRUG_SOURCE_VALUE is coded in the source data using an OMOP +supported vocabulary put the concept id representing the source value +here. + +integer + +No + +No + +Yes + +CONCEPT + +
+route_source_value + +This field houses the verbatim value from the source data representing +the drug route. + +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 drug +was given to a patient. This source value is mapped to a standard +concept which is stored in the ROUTE_CONCEPT_ID field. + +varchar(50) + +No + +No + +No + + +
+dose_unit_source_value + +This field houses the verbatim value from the source data representing +the dose unit of the drug given. + +This information may be called something different in the source data +but the field is meant to contain a value indicating the unit of dosage +of drug given to the patient. This is an older column and will +be deprecated in an upcoming version. + +varchar(50) + +No + +No + +No + + +
@@ -906,6 +4249,545 @@ are: - Same Procedure - Same PROCEDURE_DATETIME - Same Visit Occurrence or Visit Detail - Same Provider - Same Modifier for Procedures. Source codes and source text fields mapped to Standard Concepts of the Procedure Domain have to be recorded here.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+procedure_occurrence_id + +The unique key given to a procedure record for a person. Refer to the +ETL for how duplicate procedures during the same visit were handled. + +Each instance of a procedure occurrence in the source data should be +assigned this unique key. In some cases, a person can have multiple +records of the same procedure within the same visit. It is valid to keep +these duplicates and assign them individual, unique, +PROCEDURE_OCCURRENCE_IDs, though it is up to the ETL how they should be +handled. + +integer + +Yes + +Yes + +No + + +
+person_id + +The PERSON_ID of the PERSON for whom the procedure is recorded. This may +be a system generated code. + + +integer + +Yes + +No + +Yes + +PERSON + +
+procedure_concept_id + +The PROCEDURE_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 procedure + +The CONCEPT_ID that the PROCEDURE_SOURCE_VALUE maps to. Only records +whose source values map to standard concepts with a domain of +“Procedure” should go in this table. Accepted +Concepts. + +integer + +Yes + +No + +Yes + +CONCEPT + +Procedure +
+procedure_date + +Use this date to determine the date the procedure started. + +This is meant to be the start date of the procedure. It +will be renamed in a future version to +PROCEDURE_START_DATE. + +date + +Yes + +No + +No + + +
+procedure_datetime + + +If the procedure has a start time in the native date, use this field to +house that information. This will be renamed in a future version to +PROCEDURE_START_DATETIME. + +datetime + +No + +No + +No + + +
+procedure_end_date + +Use this field to house the date that the procedure ended. + +This is meant to be the end date of the procedure. It is not required +and for most cases will be the same as the PROCEDURE_START_DATE. + +date + +No + +No + +No + + +
+procedure_end_datetime + +Use this field to house the datetime that the procedure ended. + +This is meant to house the end datetime of the procedure and will most +often be used in conjunction with the procedure_start_datetime to +determine the length of the procedure. + +datetime + +No + +No + +No + + +
+procedure_type_concept_id + +This field can be used to determine the provenance of the Procedure +record, as in whether the procedure was from an EHR system, insurance +claim, registry, or other sources. + +Choose the PROCEDURE_TYPE_CONCEPT_ID that best represents the provenance +of the record, for example whether it came from an EHR record or billing +claim. If a procedure is recorded as an EHR encounter, the +PROCEDURE_TYPE_CONCEPT would be ‘EHR encounter record’. Accepted +Concepts. A more detailed explanation of each Type Concept can be +found on the vocabulary +wiki. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+modifier_concept_id + +The modifiers are intended to give additional information about the +procedure but as of now the vocabulary is under review. + +It is up to the ETL to choose how to map modifiers if they exist in +source data. These concepts are typically distinguished by ‘Modifier’ +concept classes (e.g., ‘CPT4 Modifier’ as part of the ‘CPT4’ +vocabulary). If there is more than one modifier on a record, one should +be chosen that pertains to the procedure rather than provider. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+quantity + +If the quantity value is omitted, a single procedure is assumed. + +If a Procedure has a quantity of ‘0’ in the source, this should default +to ‘1’ in the ETL. If there is a record in the source it can be assumed +the exposure occurred at least once + +integer + +No + +No + +No + + +
+provider_id + +The provider associated with the procedure record, e.g. the provider who +performed the Procedure. + +The ETL may need to make a choice as to which PROVIDER_ID to put here. +Based on what is available this may or may not be different than the +provider associated with the overall VISIT_OCCURRENCE record, for +example the admitting vs attending physician on an EHR record. + +integer + +No + +No + +Yes + +PROVIDER + +
+visit_occurrence_id + +The visit during which the procedure occurred. + +Depending on the structure of the source data, this may have to be +determined based on dates. If a PROCEDURE_DATE occurs within the start +and end date of a Visit it is a valid ETL choice to choose the +VISIT_OCCURRENCE_ID from the Visit that subsumes it, even if not +explicitly stated in the data. While not required, an attempt should be +made to locate the VISIT_OCCURRENCE_ID of the PROCEDURE_OCCURRENCE +record. + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +
+visit_detail_id + +The VISIT_DETAIL record during which the Procedure occurred. For +example, if the Person was in the ICU at the time of the Procedure the +VISIT_OCCURRENCE record would reflect the overall hospital stay and the +VISIT_DETAIL record would reflect the ICU stay during the hospital +visit. + +Same rules apply as for the VISIT_OCCURRENCE_ID. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+procedure_source_value + +This field houses the verbatim value from the source data representing +the procedure that occurred. For example, this could be an CPT4 or OPCS4 +code. + +Use this value to look up the source concept id and then map the source +concept id to a standard concept id. + +varchar(50) + +No + +No + +No + + +
+procedure_source_concept_id + +This is the concept representing the procedure 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 Procedure +necessary for a given analytic use case. Consider using +PROCEDURE_CONCEPT_ID instead to enable standardized analytics that can +be consistent across the network. + +If the PROCEDURE_SOURCE_VALUE is coded in the source data using an OMOP +supported vocabulary put the concept id representing the source value +here. + +integer + +No + +No + +Yes + +CONCEPT + +
+modifier_source_value + + +The original modifier code from the source is stored here for reference. + +varchar(50) + +No + +No + +No + + +

device_exposure

@@ -925,6 +4807,618 @@ are actions, often to apply a Device or supply.

ETL Conventions

Source codes and source text fields mapped to Standard Concepts of the Device Domain have to be recorded here.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+device_exposure_id + +The unique key given to records a person’s exposure to a foreign +physical object or instrument. + +Each instance of an exposure to a foreign object or device present in +the source data should be assigned this unique key. + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+device_concept_id + +The DEVICE_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 foreign object or +instrument the person was exposed to. + +The CONCEPT_ID that the DEVICE_SOURCE_VALUE maps to. + +integer + +Yes + +No + +Yes + +CONCEPT + +Device +
+device_exposure_start_date + +Use this date to determine the start date of the device record. + +Valid entries include a start date of a procedure to implant a device, +the date of a prescription for a device, or the date of device +administration. + +date + +Yes + +No + +No + + +
+device_exposure_start_datetime + + +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) + +datetime + +No + +No + +No + + +
+device_exposure_end_date + +The DEVICE_EXPOSURE_END_DATE denotes the day the device exposure ended +for the patient, if given. + +Put the end date or discontinuation date as it appears from the source +data or leave blank if unavailable. + +date + +No + +No + +No + + +
+device_exposure_end_datetime + + +If a source does not specify datetime the convention is to set the time +to midnight (00:00:0000) + +datetime + +No + +No + +No + + +
+device_type_concept_id + +You can use the TYPE_CONCEPT_ID to denote the provenance of the record, +as in whether the record is from administrative claims or EHR. + +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. A more detailed explanation of each Type Concept can be +found on the vocabulary +wiki. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+unique_device_id + +This is the Unique Device Identification (UDI-DI) number for devices +regulated by the FDA, if given. + +For medical devices that are regulated by the FDA, a Unique Device +Identification (UDI) is provided if available in the data source and is +recorded in the UNIQUE_DEVICE_ID field. + +varchar(255) + +No + +No + +No + + +
+production_id + +This is the Production Identifier (UDI-PI) portion of the Unique Device +Identification. + + +varchar(255) + +No + +No + +No + + +
+quantity + + + +integer + +No + +No + +No + + +
+provider_id + +The Provider associated with device record, e.g. the provider who wrote +the prescription or the provider who implanted the device. + +The ETL may need to make a choice as to which PROVIDER_ID to put here. +Based on what is available this may or may not be different than the +provider associated with the overall VISIT_OCCURRENCE record. + +integer + +No + +No + +Yes + +PROVIDER + +
+visit_occurrence_id + +The Visit during which the device was prescribed or given. + +To populate this field device exposures must be explicitly initiated in +the visit. + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +
+visit_detail_id + +The Visit Detail during which the device was prescribed or given. + +To populate this field device exposures must be explicitly initiated in +the visit detail record. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+device_source_value + +This field houses the verbatim value from the source data representing +the device exposure that occurred. For example, this could be an NDC or +Gemscript code. + +This code is mapped to a Standard Device Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +
+device_source_concept_id + +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. + +integer + +No + +No + +Yes + +CONCEPT + +
+unit_concept_id + +UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit +domain that best represents the unit as given in the source data. + +There is no standardization requirement for units associated with +DEVICE_CONCEPT_IDs, however, it is the responsibility of the ETL to +choose the most plausible unit. If there is no unit associated with a +Device record, set to NULL. + +integer + +No + +No + +Yes + +CONCEPT + +Unit +
+unit_source_value + +This field houses the verbatim value from the source data representing +the unit of the Device. For example, blood transfusions are considered +devices and can be given in mL quantities. + +This code is mapped to a Standard Condition Concept in the Standardized +Vocabularies and the original code is stored here for reference. Using +the blood transfusion example, blood transfusion is represented by the +DEVICE_CONCEPT_ID and the unit (mL) would be housed in the +UNIT_SOURCE_VALUE and mapped to a standard concept in the unit domain. + +varchar(50) + +No + +No + +No + + +
+unit_source_concept_id + +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. + +integer + +No + +No + +Yes + +CONCEPT + +

measurement

@@ -970,6 +5464,788 @@ href="https://athena.ohdsi.org/search-terms/terms/4046263">4046263 ‘Enzyme measurement’ as well as a ‘Maps to value’ record to 4135493 ‘Abnormal’.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+measurement_id + +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. + +integer + +Yes + +Yes + +No + + +
+person_id + +The PERSON_ID of the Person for whom the Measurement is recorded. This +may be a system generated code. + + +integer + +Yes + +No + +Yes + +PERSON + +
+measurement_concept_id + +The MEASUREMENT_CONCEPT_ID field is recommended for primary use in +analyses, and must be used for network studies. + +The CONCEPT_ID that the MEASUREMENT_SOURCE_CONCEPT_ID maps to. Only +records whose SOURCE_CONCEPT_IDs map to Standard Concepts with a domain +of “Measurement” should go in this table. + +integer + +Yes + +No + +Yes + +CONCEPT + +Measurement +
+measurement_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. + +date + +Yes + +No + +No + + +
+measurement_datetime + + +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) + +datetime + +No + +No + +No + + +
+measurement_time + + +This is present for backwards compatibility and will be deprecated in an +upcoming version. + +varchar(10) + +No + +No + +No + + +
+measurement_type_concept_id + +This field can be used to determine the provenance of the Measurement +record, as in whether the measurement was from an EHR system, insurance +claim, registry, or other sources. + +Choose the MEASUREMENT_TYPE_CONCEPT_ID that best represents the +provenance of the record, for example whether it came from an EHR record +or billing claim. Accepted +Concepts. A more detailed explanation of each Type Concept can be +found on the vocabulary +wiki. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+operator_concept_id + +The meaning of Concept 4172703 +for ‘=’ is identical to omission of a OPERATOR_CONCEPT_ID value. Since +the use of this field is rare, it’s important when devising analyses to +not to forget testing for the content of this field for values different +from =. + +Operators are =, > and these concepts belong to the ‘Meas Value +Operator’ domain. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+value_as_number + +This is the numerical value of the Result of the Measurement, if +available. Note that measurements such as blood pressures will be split +into their component parts i.e. one record for systolic, one record for +diastolic. + +If there is a negative value coming from the source, set the +VALUE_AS_NUMBER to NULL, with the exception of the following +Measurements (listed as LOINC codes):
- 1925-7 +Base excess in Arterial blood by calculation - 1927-3 +Base excess in Venous blood by calculation - 8632-2 +QRS-Axis - 11555-0 +Base excess in Blood by calculation - 1926-5 +Base excess in Capillary blood by calculation - 28638-5 +Base excess in Arterial cord blood by calculation 28639-3 +Base excess in Venous cord blood by calculation +		 +float + +No + +No + +No + + +
+value_as_concept_id + +If the raw data gives a categorial result for measurements those values +are captured and mapped to standard concepts in the ‘Meas Value’ domain. + +If the raw data provides categorial results as well as continuous +results for measurements, it is a valid ETL choice to preserve both +values. The continuous value should go in the VALUE_AS_NUMBER field and +the categorical value should be mapped to a standard concept in the +‘Meas Value’ domain and put in the VALUE_AS_CONCEPT_ID field. This is +also the destination for the ‘Maps to value’ relationship. + +integer + +No + +No + +Yes + +CONCEPT + +
+unit_concept_id + +There is currently no recommended unit for individual measurements, +i.e. it is not mandatory to represent Hemoglobin a1C measurements as a +percentage. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in +the Unit domain that best represents the unit as given in the source +data. + +There is no standardization requirement for units associated with +MEASUREMENT_CONCEPT_IDs, however, it is the responsibility of the ETL to +choose the most plausible unit. + +integer + +No + +No + +Yes + +CONCEPT + +Unit +
+range_low + +Ranges have the same unit as the VALUE_AS_NUMBER. These ranges are +provided by the source and should remain NULL if not given. + +If reference ranges for upper and lower limit of normal as provided +(typically by a laboratory) these are stored in the RANGE_HIGH and +RANGE_LOW fields. This should be set to NULL if not provided. + +float + +No + +No + +No + + +
+range_high + +Ranges have the same unit as the VALUE_AS_NUMBER. These ranges are +provided by the source and should remain NULL if not given. + +If reference ranges for upper and lower limit of normal as provided +(typically by a laboratory) these are stored in the RANGE_HIGH and +RANGE_LOW fields. This should be set to NULL if not provided. + +float + +No + +No + +No + + +
+provider_id + +The provider associated with measurement record, e.g. the provider who +ordered the test or the provider who recorded the result. + +The ETL may need to make a choice as to which PROVIDER_ID to put here. +Based on what is available this may or may not be different than the +provider associated with the overall VISIT_OCCURRENCE record. For +example the admitting vs attending physician on an EHR record. + +integer + +No + +No + +Yes + +PROVIDER + +
+visit_occurrence_id + +The visit during which the Measurement occurred. + +Depending on the structure of the source data, this may have to be +determined based on dates. If a MEASUREMENT_DATE occurs within the start +and end date of a Visit it is a valid ETL choice to choose the +VISIT_OCCURRENCE_ID from the visit that subsumes it, even if not +explicitly stated in the data. While not required, an attempt should be +made to locate the VISIT_OCCURRENCE_ID of the measurement record. If a +measurement is related to a visit explicitly in the source data, it is +possible that the result date of the Measurement falls outside of the +bounds of the Visit dates. + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +
+visit_detail_id + +The VISIT_DETAIL record during which the Measurement occurred. For +example, if the Person was in the ICU at the time the VISIT_OCCURRENCE +record would reflect the overall hospital stay and the VISIT_DETAIL +record would reflect the ICU stay during the hospital visit. + +Same rules apply as for the VISIT_OCCURRENCE_ID. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+measurement_source_value + +This field houses the verbatim value from the source data representing +the Measurement that occurred. For example, this could be an ICD10 or +Read code. + +This code is mapped to a Standard Measurement Concept in the +Standardized Vocabularies and the original code is stored here for +reference. + +varchar(50) + +No + +No + +No + + +
+measurement_source_concept_id + +This is the concept representing the MEASUREMENT_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 +Measurement necessary for a given analytic use case. Consider using +MEASUREMENT_CONCEPT_ID instead to enable standardized analytics that can +be consistent across the network. + +If the MEASUREMENT_SOURCE_VALUE is coded in the source data using an +OMOP supported vocabulary put the concept id representing the source +value here. + +integer + +No + +No + +Yes + +CONCEPT + +
+unit_source_value + +This field houses the verbatim value from the source data representing +the unit of the Measurement that occurred. + +This code is mapped to a Standard Condition Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +
+unit_source_concept_id + +“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 +Measurement 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. + +integer + +No + +No + +Yes + +CONCEPT + +
+value_source_value + +This field houses the verbatim result value of the Measurement from the +source data . + +If both a continuous and categorical result are given in the source data +such that both VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID are both +included, store the verbatim value that was mapped to +VALUE_AS_CONCEPT_ID here. + +varchar(50) + +No + +No + +No + + +
+measurement_event_id + +If the Measurement record is related to another record in the database, +this field is the primary key of the linked record. + +Put the primary key of the linked record, if applicable, here. + +integer + +No + +No + +No + + +
+meas_event_field_concept_id + +If the Measurement record is related to another record in the database, +this field is the CONCEPT_ID that identifies which table the primary key +of the linked record came from. + +Put the CONCEPT_ID that identifies which table and field the +MEASUREMENT_EVENT_ID came from. + +integer + +No + +No + +Yes + +CONCEPT + +

observation

@@ -1003,6 +6279,713 @@ stated separately from the type of Observation in the VALUE_AS_* fields. It is recommended for Observations that are suggestive statements of positive assertion should have a value of ‘Yes’ (concept_id=4188539), recorded, even though the null value is the equivalent.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+observation_id + +The unique key given to an Observation record for a Person. Refer to the +ETL for how duplicate Observations during the same Visit were handled. + +Each instance of an observation present in the source data should be +assigned this unique key. + +integer + +Yes + +Yes + +No + + +
+person_id + +The PERSON_ID of the Person for whom the Observation is recorded. This +may be a system generated code. + + +integer + +Yes + +No + +Yes + +PERSON + +
+observation_concept_id + +The OBSERVATION_CONCEPT_ID field is recommended for primary use in +analyses, and must be used for network studies. + +The CONCEPT_ID that the OBSERVATION_SOURCE_CONCEPT_ID maps to. There is +no specified domain that the Concepts in this table must adhere to. The +only rule is that records with Concepts in the Condition, Procedure, +Drug, Measurement, or Device domains MUST go to the corresponding table. + +integer + +Yes + +No + +Yes + +CONCEPT + +
+observation_date + +The date of the Observation. Depending on what the Observation +represents this could be the date of a lab test, the date of a survey, +or the date a patient’s family history was taken. + +For some observations the ETL may need to make a choice as to which date +to choose. + +date + +Yes + +No + +No + + +
+observation_datetime + + +If no time is given set to midnight (00:00:00). + +datetime + +No + +No + +No + + +
+observation_type_concept_id + +This field can be used to determine the provenance of the Observation +record, as in whether the measurement was from an EHR system, insurance +claim, registry, or other sources. + +Choose the OBSERVATION_TYPE_CONCEPT_ID that best represents the +provenance of the record, for example whether it came from an EHR record +or billing claim. Accepted +Concepts. A more detailed explanation of each Type Concept can be +found on the vocabulary +wiki. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+value_as_number + +This is the numerical value of the Result of the Observation, if +applicable and available. It is not expected that all Observations will +have numeric results, rather, this field is here to house values should +they exist. + + +float + +No + +No + +No + + +
+value_as_string + +This is the categorical value of the Result of the Observation, if +applicable and available. + + +varchar(60) + +No + +No + +No + + +
+value_as_concept_id + +It is possible that some records destined for the Observation table have +two clinical ideas represented in one source code. This is common with +ICD10 codes that describe a family history of some Condition, for +example. In OMOP the Vocabulary breaks these two clinical ideas into two +codes; one becomes the OBSERVATION_CONCEPT_ID and the other becomes the +VALUE_AS_CONCEPT_ID. It is important when using the Observation table to +keep this possibility in mind and to examine the VALUE_AS_CONCEPT_ID +field for relevant information. + +Note that the value of VALUE_AS_CONCEPT_ID may be provided through +mapping from a source Concept which contains the content of the +Observation. In those situations, the CONCEPT_RELATIONSHIP table in +addition to the ‘Maps to’ record contains a second record with the +relationship_id set to ‘Maps to value’. For example, ICD10 Z82.4 +‘Family history of ischaemic heart disease and other diseases of the +circulatory system’ has a ‘Maps to’ relationship to 4167217 +‘Family history of clinical finding’ as well as a ‘Maps to value’ record +to 134057 +‘Disorder of cardiovascular system’. + +Integer + +No + +No + +Yes + +CONCEPT + +
+qualifier_concept_id + +This field contains all attributes specifying the clinical fact further, +such as as degrees, severities, drug-drug interaction alerts etc. + +Use your best judgement as to what Concepts to use here and if they are +necessary to accurately represent the clinical record. There is no +restriction on the domain of these Concepts, they just need to be +Standard. + +integer + +No + +No + +Yes + +CONCEPT + +
+unit_concept_id + +There is currently no recommended unit for individual observation +concepts. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in +the Unit domain that best represents the unit as given in the source +data. + +There is no standardization requirement for units associated with +OBSERVATION_CONCEPT_IDs, however, it is the responsibility of the ETL to +choose the most plausible unit. + +integer + +No + +No + +Yes + +CONCEPT + +Unit +
+provider_id + +The provider associated with the observation record, e.g. the provider +who ordered the test or the provider who recorded the result. + +The ETL may need to make a choice as to which PROVIDER_ID to put here. +Based on what is available this may or may not be different than the +provider associated with the overall VISIT_OCCURRENCE record. For +example the admitting vs attending physician on an EHR record. + +integer + +No + +No + +Yes + +PROVIDER + +
+visit_occurrence_id + +The visit during which the Observation occurred. + +Depending on the structure of the source data, this may have to be +determined based on dates. If an OBSERVATION_DATE occurs within the +start and end date of a Visit it is a valid ETL choice to choose the +VISIT_OCCURRENCE_ID from the visit that subsumes it, even if not +explicitly stated in the data. While not required, an attempt should be +made to locate the VISIT_OCCURRENCE_ID of the observation record. If an +observation is related to a visit explicitly in the source data, it is +possible that the result date of the Observation falls outside of the +bounds of the Visit dates. + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +
+visit_detail_id + +The VISIT_DETAIL record during which the Observation occurred. For +example, if the Person was in the ICU at the time the VISIT_OCCURRENCE +record would reflect the overall hospital stay and the VISIT_DETAIL +record would reflect the ICU stay during the hospital visit. + +Same rules apply as for the VISIT_OCCURRENCE_ID. + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+observation_source_value + +This field houses the verbatim value from the source data representing +the Observation that occurred. For example, this could be an ICD10 or +Read code. + +This code is mapped to a Standard Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +
+observation_source_concept_id + +This is the concept representing the OBSERVATION_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 +Observation necessary for a given analytic use case. Consider using +OBSERVATION_CONCEPT_ID instead to enable standardized analytics that can +be consistent across the network. + +If the OBSERVATION_SOURCE_VALUE is coded in the source data using an +OMOP supported vocabulary put the concept id representing the source +value here. + +integer + +No + +No + +Yes + +CONCEPT + +
+unit_source_value + +This field houses the verbatim value from the source data representing +the unit of the Observation that occurred. + +This code is mapped to a Standard Condition Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +
+qualifier_source_value + +This field houses the verbatim value from the source data representing +the qualifier of the Observation that occurred. + +This code is mapped to a Standard Condition Concept in the Standardized +Vocabularies and the original code is stored here for reference. + +varchar(50) + +No + +No + +No + + +
+value_source_value + +This field houses the verbatim result value of the Observation from the +source data. Do not get confused with the Observation_source_value which +captures source value of the observation mapped to +observation_concept_id. This field is the observation result value from +the source. + +If the observation_source_value was a question, for example, or an +observation that requires a result then this field is the answer/ result +from the source data. Store the verbatim value that represents the +result of the observation_source_value. + +varchar(50) + +No + +No + +No + + +
+observation_event_id + +If the Observation record is related to another record in the database, +this field is the primary key of the linked record. + +Put the primary key of the linked record, if applicable, here. See the +ETL +Conventions for the OBSERVATION table for more details. + +integer + +No + +No + +No + + +
+obs_event_field_concept_id + +If the Observation record is related to another record in the database, +this field is the CONCEPT_ID that identifies which table the primary key +of the linked record came from. + +Put the CONCEPT_ID that identifies which table and field the +OBSERVATION_EVENT_ID came from. + +integer + +No + +No + +Yes + +CONCEPT + +

death

@@ -1016,6 +6999,243 @@ explicit record in EHR data.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+death_date + +The date the person was deceased. + +If the precise date include day or month is not known or not allowed, +December is used as the default month, and the last day of the month the +default day. + +date + +Yes + +No + +No + + +
+death_datetime + + +If not available set time to midnight (00:00:00) + +datetime + +No + +No + +No + + +
+death_type_concept_id + +This is the provenance of the death record, i.e., where it came from. It +is possible that an administrative claims database would source death +information from a government file so do not assume the Death Type is +the same as the Visit Type, etc. + +Use the type concept that be reflects the source of the death record. Accepted +Concepts. A more detailed explanation of each Type Concept can be +found on the vocabulary +wiki. + +integer + +No + +No + +Yes + +CONCEPT + +Type Concept +
+cause_concept_id + +This is the Standard Concept representing the Person’s cause of death, +if available. + +There is no specified domain for this concept, just choose the Standard +Concept Id that best represents the person’s cause of death. + +integer + +No + +No + +Yes + +CONCEPT + +
+cause_source_value + + +If available, put the source code representing the cause of death here. + +varchar(50) + +No + +No + +No + + +
+cause_source_concept_id + + +If the cause of death was coded using a Vocabulary present in the OMOP +Vocabularies put the CONCEPT_ID representing the cause of death here. + +integer + +No + +No + +Yes + +CONCEPT + +

note

@@ -1054,6 +7274,494 @@ of the other 4 dimensions. However, not all the permutations of the CDO dimensions will necessarily yield an existing LOINC code. Each of these dimensions are contained in the OMOP Vocabulary under the domain of ‘Meas Value’ with each dimension represented as a Concept Class.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+note_id + +A unique identifier for each note. + + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+note_date + +The date the note was recorded. + + +date + +Yes + +No + +No + + +
+note_datetime + + +If time is not given set the time to midnight. + +datetime + +No + +No + +No + + +
+note_type_concept_id + +The provenance of the note. Most likely this will be EHR. + +Put the source system of the note, as in EHR record. Accepted +Concepts. A more detailed explanation of each Type Concept can be +found on the vocabulary +wiki. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+note_class_concept_id + +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. This Concept can alternatively be represented by concepts +with the relationship ‘Kind of (LOINC)’ to 706391 +(Note). + +integer + +Yes + +No + +Yes + +CONCEPT + +
+note_title + +The title of the note. + + +varchar(250) + +No + +No + +No + + +
+note_text + +The content of the note. + + +varchar(MAX) + +Yes + +No + +No + + +
+encoding_concept_id + +This is the Concept representing the character encoding type. + +Put the Concept Id that represents the encoding character type here. +Currently the only option is UTF-8 (32678). It +the note is encoded in any other type, like ASCII then put 0. + +integer + +Yes + +No + +Yes + +CONCEPT + +
+language_concept_id + +The language of the note. + +Use Concepts that are descendants of the concept 4182347 +(World Languages). + +integer + +Yes + +No + +Yes + +CONCEPT + +
+provider_id + +The Provider who wrote the note. + +The ETL may need to make a determination on which provider to put here. + +integer + +No + +No + +Yes + +PROVIDER + +
+visit_occurrence_id + +The Visit during which the note was written. + + +integer + +No + +No + +Yes + +VISIT_OCCURRENCE + +
+visit_detail_id + +The Visit Detail during which the note was written. + + +integer + +No + +No + +Yes + +VISIT_DETAIL + +
+note_source_value + + +The source value mapped to the NOTE_CLASS_CONCEPT_ID. + +varchar(50) + +No + +No + +No + + +
+note_event_id + +If the Note record is related to another record in the database, this +field is the primary key of the linked record. + +Put the primary key of the linked record, if applicable, here. + +integer + +No + +No + +No + + +
+note_event_field_concept_id + +If the Note record is related to another record in the database, this +field is the CONCEPT_ID that identifies which table the primary key of +the linked record came from. + +Put the CONCEPT_ID that identifies which table and field the +NOTE_EVENT_ID came from. + +integer + +No + +No + +Yes + +CONCEPT + +

note_nlp

@@ -1064,6 +7772,424 @@ row represents a single extracted term from a note.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+note_nlp_id + +A unique identifier for the NLP record. + + +integer + +Yes + +Yes + +No + + +
+note_id + +This is the NOTE_ID for the NOTE record the NLP record is associated to. + + +integer + +Yes + +No + +No + + +
+section_concept_id + + +The SECTION_CONCEPT_ID should be used to represent the note section +contained in the NOTE_NLP record. These concepts can be found as parts +of document panels and are based on the type of note written, i.e. a +discharge summary. These panels can be found as concepts with the +relationship ‘Subsumes’ to CONCEPT_ID 45875957. + +integer + +No + +No + +Yes + +CONCEPT + +
+snippet + +A small window of text surrounding the term + + +varchar(250) + +No + +No + +No + + +
+“offset” + +Character offset of the extracted term in the input note + + +varchar(50) + +No + +No + +No + + +
+lexical_variant + +Raw text extracted from the NLP tool. + + +varchar(250) + +Yes + +No + +No + + +
+note_nlp_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+note_nlp_source_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+nlp_system + + +Name and version of the NLP system that extracted the term. Useful for +data provenance. + +varchar(250) + +No + +No + +No + + +
+nlp_date + +The date of the note processing. + + +date + +Yes + +No + +No + + +
+nlp_datetime + +The date and time of the note processing. + + +datetime + +No + +No + +No + + +
+term_exists + + +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. + +varchar(1) + +No + +No + +No + + +
+term_temporal + + +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 +		 +varchar(50) + +No + +No + +No + + +
+term_modifiers + + +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. +		 +varchar(2000) + +No + +No + +No + + +

specimen

@@ -1076,6 +8202,452 @@ samples from a person.

Anatomic site is coded at the most specific level of granularity possible, such that higher level classifications can be derived using the Standardized Vocabularies.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+specimen_id + +Unique identifier for each specimen. + + +integer + +Yes + +Yes + +No + + +
+person_id + +The person from whom the specimen is collected. + + +integer + +Yes + +No + +Yes + +PERSON + +
+specimen_concept_id + + +The standard CONCEPT_ID that the SPECIMEN_SOURCE_VALUE maps to in the +specimen domain. Accepted +Concepts + +integer + +Yes + +No + +Yes + +CONCEPT + +
+specimen_type_concept_id + + +Put the source of the specimen record, as in an EHR system. Accepted +Concepts. A more detailed explanation of each Type Concept can be +found on the vocabulary +wiki. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+specimen_date + +The date the specimen was collected. + + +date + +Yes + +No + +No + + +
+specimen_datetime + + + +datetime + +No + +No + +No + + +
+quantity + +The amount of specimen collected from the person. + + +float + +No + +No + +No + + +
+unit_concept_id + +The unit for the quantity of the specimen. + +Map the UNIT_SOURCE_VALUE to a Standard Concept in the Unit domain. Accepted +Concepts + +integer + +No + +No + +Yes + +CONCEPT + +
+anatomic_site_concept_id + +This is the site on the body where the specimen is from. + +Map the ANATOMIC_SITE_SOURCE_VALUE to a Standard Concept in the Spec +Anatomic Site domain. This should be coded at the lowest level of +granularity Accepted +Concepts + +integer + +No + +No + +Yes + +CONCEPT + +
+disease_status_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+specimen_source_id + +This is the identifier for the specimen from the source system. + + +varchar(50) + +No + +No + +No + + +
+specimen_source_value + + + +varchar(50) + +No + +No + +No + + +
+unit_source_value + + +This unit for the quantity of the specimen, as represented in the +source. + +varchar(50) + +No + +No + +No + + +
+anatomic_site_source_value + + +This is the site on the body where the specimen was taken from, as +represented in the source. + +varchar(50) + +No + +No + +No + + +
+disease_status_source_value + + + +varchar(50) + +No + +No + +No + + +

fact_relationship

@@ -1100,6 +8672,169 @@ example, two persons if person_id = 1 is the mother of person_id = 2 two records are in the FACT_RELATIONSHIP table (all strings in fact concept_id records in the Concept table: - Person, 1, Person, 2, parent of - Person, 2, Person, 1, child of

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+domain_concept_id_1 + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+fact_id_1 + + + +integer + +Yes + +No + +No + + +
+domain_concept_id_2 + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+fact_id_2 + + + +integer + +Yes + +No + +No + + +
+relationship_concept_id + + + +integer + +Yes + +No + +Yes + +CONCEPT + +

location

@@ -1118,6 +8853,361 @@ table. Locations do not contain names, such as the name of a hospital. In order to construct a full address that can be used in the postal service, the address information from the Location needs to be combined with information from the Care Site.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+location_id + +The unique key given to a unique Location. + +Each instance of a Location in the source data should be assigned this +unique key. + +integer + +Yes + +Yes + +No + + +
+address_1 + +This is the first line of the address. + + +varchar(50) + +No + +No + +No + + +
+address_2 + +This is the second line of the address + + +varchar(50) + +No + +No + +No + + +
+city + + + +varchar(50) + +No + +No + +No + + +
+state + + + +varchar(2) + +No + +No + +No + + +
+zip + + +Zip codes are handled as strings of up to 9 characters length. For US +addresses, these represent either a 3-digit abbreviated Zip code as +provided by many sources for patient protection reasons, the full +5-digit Zip or the 9-digit (ZIP + 4) codes. Unless for specific reasons +analytical methods should expect and utilize only the first 3 digits. +For international addresses, different rules apply. + +varchar(9) + +No + +No + +No + + +
+county + + + +varchar(20) + +No + +No + +No + + +
+location_source_value + + +Put the verbatim value for the location here, as it shows up in the +source. + +varchar(50) + +No + +No + +No + + +
+country_concept_id + +The Concept Id representing the country. Values should conform to the Geography +domain. + + +integer + +No + +No + +Yes + +CONCEPT + +
+country_source_value + +The name of the country. + + +varchar(80) + +No + +No + +No + + +
+latitude + + +Must be between -90 and 90. + +float + +No + +No + +No + + +
+longitude + + +Must be between -180 and 180. + +float + +No + +No + +No + + +

care_site

@@ -1141,6 +9231,213 @@ wards can belong to clinics or departments, which can in turn belong to hospitals, which in turn can belong to hospital systems, which in turn can belong to HMOs.The relationships between Care Sites are defined in the FACT_RELATIONSHIP table.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+care_site_id + + +Assign an ID to each combination of a location and nature of the site - +the latter could be the Place of Service, name or another characteristic +in your source data. + +integer + +Yes + +Yes + +No + + +
+care_site_name + +The name of the care_site as it appears in the source data + + +varchar(255) + +No + +No + +No + + +
+place_of_service_concept_id + +This is a high-level way of characterizing a Care Site. Typically, +however, Care Sites can provide care in multiple settings (inpatient, +outpatient, etc.) and this granularity should be reflected in the visit. + +Choose the concept in the visit domain that best represents the setting +in which healthcare is provided in the Care Site. If most visits in a +Care Site are Inpatient, then the place_of_service_concept_id should +represent Inpatient. If information is present about a unique Care Site +(e.g. Pharmacy) then a Care Site record should be created. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+location_id + +The location_id from the LOCATION table representing the physical +location of the care_site. + + +integer + +No + +No + +Yes + +LOCATION + +
+care_site_source_value + +The identifier of the care_site as it appears in the source data. This +could be an identifier separate from the name of the care_site. + + +varchar(50) + +No + +No + +No + + +
+place_of_service_source_value + + +Put the place of service of the care_site as it appears in the source +data. + +varchar(50) + +No + +No + +No + + +

provider

@@ -1157,6 +9454,429 @@ providers, only provides limited information such as specialty, generic or ‘pooled’ Provider records are listed in the PROVIDER table.

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+provider_id + +It is assumed that every provider with a different unique identifier is +in fact a different person and should be treated independently. + +This identifier can be the original id from the source data provided it +is an integer, otherwise it can be an autogenerated number. + +integer + +Yes + +Yes + +No + + +
+provider_name + + +This field is not necessary as it is not necessary to have the actual +identity of the Provider. Rather, the idea is to uniquely and +anonymously identify providers of care across the database. + +varchar(255) + +No + +No + +No + + +
+npi + +This is the National Provider Number issued to health care providers in +the US by the Centers for Medicare and Medicaid Services (CMS). + + +varchar(20) + +No + +No + +No + + +
+dea + +This is the identifier issued by the DEA, a US federal agency, that +allows a provider to write prescriptions for controlled substances. + + +varchar(20) + +No + +No + +No + + +
+specialty_concept_id + +This field either represents the most common specialty that occurs in +the data or the most specific concept that represents all specialties +listed, should the provider have more than one. This includes physician +specialties such as internal medicine, emergency medicine, etc. and +allied health professionals such as nurses, midwives, and pharmacists. + +If a Provider has more than one Specialty, there are two options: 1. +Choose a concept_id which is a common ancestor to the multiple +specialties, or, 2. Choose the specialty that occurs most often for the +provider. Concepts in this field should be Standard with a domain of +Provider. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+care_site_id + +This is the CARE_SITE_ID for the location that the provider primarily +practices in. + +If a Provider has more than one Care Site, the main or most often +exerted CARE_SITE_ID should be recorded. + +integer + +No + +No + +Yes + +CARE_SITE + +
+year_of_birth + + + +integer + +No + +No + +No + + +
+gender_concept_id + +This field represents the recorded gender of the provider in the source +data. + +If given, put a concept from the gender domain representing the recorded +gender of the provider. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +Gender +
+provider_source_value + +Use this field to link back to providers in the source data. This is +typically used for error checking of ETL logic. + +Some use cases require the ability to link back to providers in the +source data. This field allows for the storing of the provider +identifier as it appears in the source. + +varchar(50) + +No + +No + +No + + +
+specialty_source_value + +This is the kind of provider or specialty as it appears in the source +data. This includes physician specialties such as internal medicine, +emergency medicine, etc. and allied health professionals such as nurses, +midwives, and pharmacists. + +Put the kind of provider as it appears in the source data. This field is +up to the discretion of the ETL-er as to whether this should be the +coded value from the source or the text description of the lookup value. + +varchar(50) + +No + +No + +No + + +
+specialty_source_concept_id + +This is often zero as many sites use proprietary codes to store +physician speciality. + +If the source data codes provider specialty in an OMOP supported +vocabulary store the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +
+gender_source_value + +This is provider’s gender as it appears in the source data. + +Put the provider’s gender as it appears in the source data. This field +is up to the discretion of the ETL-er as to whether this should be the +coded value from the source or the text description of the lookup value. + +varchar(50) + +No + +No + +No + + +
+gender_source_concept_id + +This is often zero as many sites use proprietary codes to store provider +gender. + +If the source data codes provider gender in an OMOP supported vocabulary +store the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +

payer_plan_period

@@ -1182,6 +9902,533 @@ structure of the Plan is rarely known, the idea is just to identify that the Plans are different.

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+payer_plan_period_id + +A unique identifier for each unique combination of a Person, Payer, +Plan, and Period of time. + + +integer + +Yes + +Yes + +No + + +
+person_id + +The Person covered by the Plan. + +A single Person can have multiple, overlapping, PAYER_PLAN_PERIOD +records + +integer + +Yes + +No + +Yes + +PERSON + +
+payer_plan_period_start_date + +Start date of Plan coverage. + + +date + +Yes + +No + +No + + +
+payer_plan_period_end_date + +End date of Plan coverage. + + +date + +Yes + +No + +No + + +
+payer_concept_id + +This field represents the organization who reimburses the provider which +administers care to the Person. + +Map the Payer directly to a standard CONCEPT_ID. If one does not exists +please contact the vocabulary team. There is no global controlled +vocabulary available for this information. The point is to stratify on +this information and identify if Persons have the same payer, though the +name of the Payer is not necessary. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+payer_source_value + +This is the Payer as it appears in the source data. + + +varchar(50) + +No + +No + +No + + +
+payer_source_concept_id + + +If the source data codes the Payer in an OMOP supported vocabulary store +the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +
+plan_concept_id + +This field represents the specific health benefit Plan the Person is +enrolled in. + +Map the Plan directly to a standard CONCEPT_ID. If one does not exists +please contact the vocabulary team. There is no global controlled +vocabulary available for this information. The point is to stratify on +this information and identify if Persons have the same health benefit +Plan though the name of the Plan is not necessary. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+plan_source_value + +This is the health benefit Plan of the Person as it appears in the +source data. + + +varchar(50) + +No + +No + +No + + +
+plan_source_concept_id + + +If the source data codes the Plan in an OMOP supported vocabulary store +the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +
+sponsor_concept_id + +This field represents the sponsor of the Plan who finances the Plan. +This includes self-insured, small group health plan and large group +health plan. + +Map the sponsor directly to a standard CONCEPT_ID. If one does not +exists please contact the vocabulary team. There is no global controlled +vocabulary available for this information. The point is to stratify on +this information and identify if Persons have the same sponsor though +the name of the sponsor is not necessary. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+sponsor_source_value + +The Plan sponsor as it appears in the source data. + + +varchar(50) + +No + +No + +No + + +
+sponsor_source_concept_id + + +If the source data codes the sponsor in an OMOP supported vocabulary +store the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +
+family_source_value + +The common identifier for all people (often a family) that covered by +the same policy. + +Often these are the common digits of the enrollment id of the policy +members. + +varchar(50) + +No + +No + +No + + +
+stop_reason_concept_id + +This field represents the reason the Person left the Plan, if known. + +Map the stop reason directly to a standard CONCEPT_ID. If one does not +exists please contact the vocabulary team. There is no global controlled +vocabulary available for this information. Accepted +Concepts. + +integer + +No + +No + +Yes + +CONCEPT + +
+stop_reason_source_value + +The Plan stop reason as it appears in the source data. + + +varchar(50) + +No + +No + +No + + +
+stop_reason_source_concept_id + + +If the source data codes the stop reason in an OMOP supported vocabulary +store the concept_id here. + +integer + +No + +No + +Yes + +CONCEPT + +

cost

@@ -1216,6 +10463,600 @@ reimbursement cost records will be identified by using the PAYER_PLAN_ID field. Drug costs are composed of ingredient cost (the amount charged by the wholesale distributor or manufacturer), the dispensing fee (the amount charged by the pharmacy and the sales tax).

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+cost_id + + + +integer + +Yes + +Yes + +No + + +
+cost_event_id + + + +integer + +Yes + +No + +No + + +
+cost_domain_id + + + +varchar(20) + +Yes + +No + +Yes + +DOMAIN + +
+cost_type_concept_id + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+currency_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+total_charge + + + +float + +No + +No + +No + + +
+total_cost + + + +float + +No + +No + +No + + +
+total_paid + + + +float + +No + +No + +No + + +
+paid_by_payer + + + +float + +No + +No + +No + + +
+paid_by_patient + + + +float + +No + +No + +No + + +
+paid_patient_copay + + + +float + +No + +No + +No + + +
+paid_patient_coinsurance + + + +float + +No + +No + +No + + +
+paid_patient_deductible + + + +float + +No + +No + +No + + +
+paid_by_primary + + + +float + +No + +No + +No + + +
+paid_ingredient_cost + + + +float + +No + +No + +No + + +
+paid_dispensing_fee + + + +float + +No + +No + +No + + +
+payer_plan_period_id + + + +integer + +No + +No + +No + + +
+amount_allowed + + + +float + +No + +No + +No + + +
+revenue_code_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+revenue_code_source_value + +Revenue codes are a method to charge for a class of procedures and +conditions in the U.S. hospital system. + + +varchar(50) + +No + +No + +No + + +
+drg_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+drg_source_value + +Diagnosis Related Groups are US codes used to classify hospital cases +into one of approximately 500 groups. + + +varchar(3) + +No + +No + +No + + +

drug_era

@@ -1231,6 +11072,245 @@ continuous Drug Eras.

ETL Conventions

The SQL script for generating DRUG_ERA records can be found here.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+drug_era_id + + + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+drug_concept_id + +The Concept Id representing the specific drug ingredient. + + +integer + +Yes + +No + +Yes + +CONCEPT + +Drug +
+drug_era_start_date + + +The Drug Era Start Date is the start date of the first Drug Exposure for +a given ingredient, with at least 31 days since the previous exposure. + +date + +Yes + +No + +No + + +
+drug_era_end_date + + +The Drug Era End Date is the end date of the last Drug Exposure. The End +Date of each Drug Exposure is either taken from the field +drug_exposure_end_date or, as it is typically not available, inferred +using the following rules: For pharmacy prescription data, the date when +the drug was dispensed plus the number of days of supply are used to +extrapolate the End Date for the Drug Exposure. Depending on the +country-specific healthcare system, this supply information is either +explicitly provided in the day_supply field or inferred from package +size or similar information. For Procedure Drugs, usually the drug is +administered on a single date (i.e., the administration date). A +standard Persistence Window of 30 days (gap, slack) is permitted between +two subsequent such extrapolated DRUG_EXPOSURE records to be considered +to be merged into a single Drug Era. + +date + +Yes + +No + +No + + +
+drug_exposure_count + + + +integer + +No + +No + +No + + +
+gap_days + + +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. + +integer + +No + +No + +No + + +

dose_era

@@ -1246,6 +11326,229 @@ algorithm. Dose Form information is not taken into account. So, if the patient changes between different formulations, or different manufacturers with the same formulation, the Dose Era is still spanning the entire time of exposure to the Ingredient.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+dose_era_id + + + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+drug_concept_id + +The Concept Id representing the specific drug ingredient. + + +integer + +Yes + +No + +Yes + +CONCEPT + +Drug +
+unit_concept_id + +The Concept Id representing the unit of the specific drug ingredient. + + +integer + +Yes + +No + +Yes + +CONCEPT + +Unit +
+dose_value + +The numeric value of the dosage of the drug_ingredient. + + +float + +Yes + +No + +No + + +
+dose_era_start_date + +The date the Person started on the specific dosage, with at least 31 +days since any prior exposure. + + +date + +Yes + +No + +No + + +
+dose_era_end_date + + +The date the Person was no longer exposed to the dosage of the specific +drug ingredient. An era is ended if there are 31 days or more between +dosage records. + +date + +Yes + +No + +No + + +

condition_era

@@ -1285,6 +11588,204 @@ Condition Occurrence. Condition Eras are built with a Persistence Window of 30 days, meaning, if no occurrence of the same condition_concept_id happens within 30 days of any one occurrence, it will be considered the condition_era_end_date.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+condition_era_id + + + +integer + +Yes + +Yes + +No + + +
+person_id + + + +integer + +Yes + +No + +Yes + +PERSON + +
+condition_concept_id + +The Concept Id representing the Condition. + + +integer + +Yes + +No + +Yes + +CONCEPT + +Condition +
+condition_era_start_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. + + +date + +Yes + +No + +No + + +
+condition_era_end_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. + + +date + +Yes + +No + +No + + +
+condition_occurrence_count + +The number of individual Condition Occurrences used to construct the +condition era. + + +integer + +No + +No + +No + + +

episode

@@ -1306,6 +11807,429 @@ from the data. It is understood that that table is not currently expected to be comprehensive.

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+episode_id + +A unique identifier for each Episode. + + +integer + +Yes + +Yes + +No + + +
+person_id + +The PERSON_ID of the PERSON for whom the episode is recorded. + + +integer + +Yes + +No + +Yes + +PERSON + +
+episode_concept_id + +The EPISODE_CONCEPT_ID represents the kind abstraction related to the +disease phase, outcome or treatment. + +Choose a concept in the Episode domain that best represents the ongoing +disease phase, outcome, or treatment. Please see [article] for cancers +and [article] for non-cancers describing how these are defined. Accepted +Concepts + +integer + +Yes + +No + +Yes + +CONCEPT + +Episode +
+episode_start_date + +The date when the Episode beings. + +Please see [article] for how to define an Episode start date. + +date + +Yes + +No + +No + + +
+episode_start_datetime + +The date and time when the Episode begins. + + +datetime + +No + +No + +No + + +
+episode_end_date + +The date when the instance of the Episode is considered to have ended. + +Please see [article] for how to define an Episode end date. + +date + +No + +No + +No + + +
+episode_end_datetime + +The date when the instance of the Episode is considered to have ended. + + +datetime + +No + +No + +No + + +
+episode_parent_id + +Use this field to find the Episode that subsumes the given Episode +record. This is used in the case that an Episode are nested into each +other. + +If there are multiple nested levels to how Episodes are represented, the +EPISODE_PARENT_ID can be used to record this relationship. + +integer + +No + +No + +No + + +
+episode_number + +For sequences of episodes, this is used to indicate the order the +episodes occurred. For example, lines of treatment could be indicated +here. + +Please see [article] for the details of how to count episodes. + +integer + +No + +No + +No + + +
+episode_object_concept_id + +A Standard Concept representing the disease phase, outcome, or other +abstraction of which the episode consists. For example, if the +EPISODE_CONCEPT_ID is treatment +regimen then the EPISODE_OBJECT_CONCEPT_ID should contain the +chemotherapy regimen concept, like Afatinib +monotherapy. + +Episode entries from the ‘Disease Episode’ concept class should have an +episode_object_concept_id that comes from the Condition domain. Episode +entries from the ‘Treatment Episode’ concept class should have an +episode_object_concept_id that scome from the ‘Procedure’ domain or +‘Regimen’ concept class. + +integer + +Yes + +No + +Yes + +CONCEPT + +Procedure, Regimen +
+episode_type_concept_id + +This field can be used to determine the provenance of the Episode +record, as in whether the episode was from an EHR system, insurance +claim, registry, or other sources. + +Choose the EPISODE_TYPE_CONCEPT_ID that best represents the provenance +of the record. Accepted +Concepts. A more detailed explanation of each Type Concept can be +found on the vocabulary +wiki. + +integer + +Yes + +No + +Yes + +CONCEPT + +Type Concept +
+episode_source_value + +The source code for the Episdoe as it appears in the source data. This +code is mapped to a Standard Condition Concept in the Standardized +Vocabularies and the original code is stored here for reference. + + +varchar(50) + +No + +No + +No + + +
+episode_source_concept_id + +A foreign key to a Episode Concept that refers to the code used in the +source. + +Given that the Episodes are user-defined it is unlikely that there will +be a Source Concept available. If that is the case then set this field +to zero. + +integer + +No + +No + +Yes + +CONCEPT + +

episode_event

@@ -1321,6 +12245,131 @@ for linking low-level events to abstracted Episodes.

ETL Conventions

Some episodes may not have links to any underlying clinical events. For such episodes, the EPISODE_EVENT table is not populated.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+episode_id + +Use this field to link the EPISODE_EVENT record to its EPISODE. + +Put the EPISODE_ID that subsumes the EPISODE_EVENT record here. + +integer + +Yes + +No + +Yes + +EPISODE + +
+event_id + +This field is the primary key of the linked record in the database. For +example, if the Episode Event is a Condition Occurrence, then the +CONDITION_OCCURRENCE_ID of the linked record goes in this field. + +Put the primary key of the linked record here. + +integer + +Yes + +No + +No + + +
+episode_event_field_concept_id + +This field is the CONCEPT_ID that identifies which table the primary key +of the linked record came from. + +Put the CONCEPT_ID that identifies which table and field the EVENT_ID +came from. Accepted +Concepts + +integer + +Yes + +No + +Yes + +CONCEPT + +Metadata +

metadata

@@ -1331,6 +12380,274 @@ has been transformed to the OMOP Common Data Model.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+metadata_id + +The unique key given to a Metadata record. + +Attribute value is auto-generated + +integer + +Yes + +Yes + +No + + +
+metadata_concept_id + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+metadata_type_concept_id + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+name + + + +varchar(250) + +Yes + +No + +No + + +
+value_as_string + + + +varchar(250) + +No + +No + +No + + +
+value_as_concept_id + + + +integer + +No + +No + +Yes + +CONCEPT + +
+value_as_number + +This is the numerical value of the result of the Metadata, if applicable +and available. It is not expected that all Metadata will have numeric +results, rather, this field is here to house values should they exist. + + +float + +No + +No + +No + + +
+metadata_date + + + +date + +No + +No + +No + + +
+metadata_datetime + + + +datetime + +No + +No + +No + + +

cdm_source

@@ -1342,6 +12659,330 @@ Model.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+cdm_source_name + +The name of the CDM instance. + + +varchar(255) + +Yes + +No + +No + + +
+cdm_source_abbreviation + +The abbreviation of the CDM instance. + + +varchar(25) + +Yes + +No + +No + + +
+cdm_holder + +The holder of the CDM instance. + + +varchar(255) + +Yes + +No + +No + + +
+source_description + +The description of the CDM instance. + + +varchar(MAX) + +No + +No + +No + + +
+source_documentation_reference + + + +varchar(255) + +No + +No + +No + + +
+cdm_etl_reference + + +Put the link to the CDM version used. + +varchar(255) + +No + +No + +No + + +
+source_release_date + +The release date of the source data. + + +date + +Yes + +No + +No + + +
+cdm_release_date + +The release data of the CDM instance. + + +date + +Yes + +No + +No + + +
+cdm_version + + + +varchar(10) + +No + +No + +No + + +
+cdm_version_concept_id + +The Concept Id representing the version of the CDM. + +You can find all concepts that represent the CDM versions using the +query: SELECT * FROM CONCEPT WHERE VOCABULARY_ID = ‘CDM’ AND +CONCEPT_CLASS = ‘CDM’ + +integer + +Yes + +No + +Yes + +CONCEPT + +
+vocabulary_version + + +You can find the version of your Vocabulary using the query: SELECT +vocabulary_version from vocabulary where vocabulary_id = ‘None’ + +varchar(20) + +Yes + +No + +No + + +

concept

@@ -1370,6 +13011,319 @@ observational data analysis.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+concept_id + +A unique identifier for each Concept across all domains. + + +integer + +Yes + +Yes + +No + + +
+concept_name + +An unambiguous, meaningful and descriptive name for the Concept. + + +varchar(255) + +Yes + +No + +No + + +
+domain_id + +A foreign key to the DOMAIN +table the Concept belongs to. + + +varchar(20) + +Yes + +No + +Yes + +DOMAIN + +
+vocabulary_id + +A foreign key to the VOCABULARY +table indicating from which source the Concept has been adapted. + + +varchar(20) + +Yes + +No + +Yes + +VOCABULARY + +
+concept_class_id + +The attribute or concept class of the Concept. Examples are ‘Clinical +Drug’, ‘Ingredient’, ‘Clinical Finding’ etc. + + +varchar(20) + +Yes + +No + +Yes + +CONCEPT_CLASS + +
+standard_concept + +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. + + +varchar(1) + +No + +No + +No + + +
+concept_code + +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. + + +varchar(50) + +Yes + +No + +No + + +
+valid_start_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. + + +date + +Yes + +No + +No + + +
+valid_end_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. + + +date + +Yes + +No + +No + + +
+invalid_reason + +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. + + +varchar(1) + +No + +No + +No + + +

vocabulary

@@ -1383,6 +13337,176 @@ for the Vocabulary.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+vocabulary_id + +A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit. + + +varchar(20) + +Yes + +Yes + +No + + +
+vocabulary_name + +The name describing the vocabulary, for example, International +Classification of Diseases, Ninth Revision, Clinical Modification, +Volume 1 and 2 (NCHS) etc. + + +varchar(255) + +Yes + +No + +No + + +
+vocabulary_reference + +External reference to documentation or available download of the about +the vocabulary. + + +varchar(255) + +No + +No + +No + + +
+vocabulary_version + +Version of the Vocabulary as indicated in the source. + + +varchar(255) + +No + +No + +No + + +
+vocabulary_concept_id + +A Concept that represents the Vocabulary the VOCABULARY record belongs +to. + + +integer + +Yes + +No + +Yes + +CONCEPT + +

domain

@@ -1399,6 +13523,121 @@ Domain and includes a descriptive name for the Domain.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+domain_id + +A unique key for each domain. + + +varchar(20) + +Yes + +Yes + +No + + +
+domain_name + +The name describing the Domain, e.g. Condition, Procedure, Measurement +etc. + + +varchar(255) + +Yes + +No + +No + + +
+domain_concept_id + +A Concept representing the Domain Concept the DOMAIN record belongs to. + + +integer + +Yes + +No + +Yes + +CONCEPT + +

concept_class

@@ -1411,6 +13650,121 @@ each Concept Class.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+concept_class_id + +A unique key for each class. + + +varchar(20) + +Yes + +Yes + +No + + +
+concept_class_name + +The name describing the Concept Class, e.g. Clinical Finding, +Ingredient, etc. + + +varchar(255) + +Yes + +No + +No + + +
+concept_class_concept_id + +A Concept that represents the Concept Class. + + +integer + +Yes + +No + +Yes + +CONCEPT + +
@@ -1424,6 +13778,202 @@ table.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+concept_id_1 + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+concept_id_2 + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+relationship_id + +The relationship between CONCEPT_ID_1 and CONCEPT_ID_2. Please see the +Vocabulary +Conventions. for more information. + + +varchar(20) + +Yes + +No + +Yes + +RELATIONSHIP + +
+valid_start_date + +The date when the relationship is first recorded. + + +date + +Yes + +No + +No + + +
+valid_end_date + +The date when the relationship is invalidated. + + +date + +Yes + +No + +No + + +
+invalid_reason + +Reason the relationship was invalidated. Possible values are ‘D’ +(deleted), ‘U’ (updated) or NULL. + + +varchar(1) + +No + +No + +No + + +

relationship

@@ -1435,6 +13985,203 @@ CONCEPT_RELATIONSHP table.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+relationship_id + +The type of relationship captured by the relationship record. + + +varchar(20) + +Yes + +Yes + +No + + +
+relationship_name + + + +varchar(255) + +Yes + +No + +No + + +
+is_hierarchical + +Defines whether a relationship defines concepts into classes or +hierarchies. Values are 1 for hierarchical relationship or 0 if not. + + +varchar(1) + +Yes + +No + +No + + +
+defines_ancestry + +Defines whether a hierarchical relationship contributes to the +concept_ancestor table. These are subsets of the hierarchical +relationships. Valid values are 1 or 0. + + +varchar(1) + +Yes + +No + +No + + +
+reverse_relationship_id + +The identifier for the relationship used to define the reverse +relationship between two concepts. + + +varchar(20) + +Yes + +No + +No + + +
+relationship_concept_id + +A foreign key that refers to an identifier in the CONCEPT +table for the unique relationship concept. + + +integer + +Yes + +No + +Yes + +CONCEPT + +

concept_synonym

@@ -1445,6 +14192,118 @@ descriptions for Concepts.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+concept_id + + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+concept_synonym_name + + + +varchar(1000) + +Yes + +No + +No + + +
+language_concept_id + + + +integer + +Yes + +No + +Yes + +CONCEPT + +

concept_ancestor

@@ -1466,6 +14325,153 @@ and RELATIONSHIP tables.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+ancestor_concept_id + +The Concept Id for the higher-level concept that forms the ancestor in +the relationship. + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+descendant_concept_id + +The Concept Id for the lower-level concept that forms the descendant in +the relationship. + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+min_levels_of_separation + +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. + + +integer + +Yes + +No + +No + + +
+max_levels_of_separation + +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. + + +integer + +Yes + +No + +No + + +
@@ -1483,6 +14489,288 @@ published to the OMOP community.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+source_code + +The source code being translated into a Standard Concept. + + +varchar(50) + +Yes + +No + +No + + +
+source_concept_id + +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. + +integer + +Yes + +No + +Yes + +CONCEPT + +
+source_vocabulary_id + +A foreign key to the VOCABULARY table defining the vocabulary of the +source code that is being translated to a Standard Concept. + + +varchar(20) + +Yes + +No + +No + + +
+source_code_description + +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. + + +varchar(255) + +No + +No + +No + + +
+target_concept_id + +The target Concept to which the source code is being mapped. + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+target_vocabulary_id + +The Vocabulary of the target Concept. + + +varchar(20) + +Yes + +No + +Yes + +VOCABULARY + +
+valid_start_date + +The date when the mapping instance was first recorded. + + +date + +Yes + +No + +No + + +
+valid_end_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. + + +date + +Yes + +No + +No + + +
+invalid_reason + +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. + + +varchar(1) + +No + +No + +No + + +

drug_strength

@@ -1495,6 +14783,371 @@ to support standardized analysis of drug utilization.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+drug_concept_id + +The Concept representing the Branded Drug or Clinical Drug Product. + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+ingredient_concept_id + +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. + +integer + +Yes + +No + +Yes + +CONCEPT + +
+amount_value + +The numeric value or the amount of active ingredient contained within +the drug product. + + +float + +No + +No + +No + + +
+amount_unit_concept_id + +The Concept representing the Unit of measure for the amount of active +ingredient contained within the drug product. + + +integer + +No + +No + +Yes + +CONCEPT + +
+numerator_value + +The concentration of the active ingredient contained within the drug +product. + + +float + +No + +No + +No + + +
+numerator_unit_concept_id + +The Concept representing the Unit of measure for the concentration of +active ingredient. + + +integer + +No + +No + +Yes + +CONCEPT + +
+denominator_value + +The amount of total liquid (or other divisible product, such as +ointment, gel, spray, etc.). + + +float + +No + +No + +No + + +
+denominator_unit_concept_id + +The Concept representing the denominator unit for the concentration of +active ingredient. + + +integer + +No + +No + +Yes + +CONCEPT + +
+box_size + +The number of units of Clinical Branded Drug or Quantified Clinical or +Branded Drug contained in a box as dispensed to the patient. + + +integer + +No + +No + +No + + +
+valid_start_date + +The date when the Concept was first recorded. The default value is +1-Jan-1970. + + +date + +Yes + +No + +No + + +
+valid_end_date + +The date when then Concept became invalid. + + +date + +Yes + +No + +No + + +
+invalid_reason + +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. + + +varchar(1) + +No + +No + +No + + +

cohort

@@ -1523,6 +15176,141 @@ a cohort at any moment in time. A subject can only have one record in the cohort table for any moment of time, i.e. it is not possible for a person to contain multiple records indicating cohort membership that are overlapping in time

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+cohort_definition_id + + + +integer + +Yes + +No + +No + + +
+subject_id + + + +integer + +Yes + +No + +No + + +
+cohort_start_date + + + +date + +Yes + +No + +No + + +
+cohort_end_date + + + +date + +Yes + +No + +No + + +

cohort_definition

@@ -1540,6 +15328,228 @@ Model.

NA

ETL Conventions

NA

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+CDM Field + +User Guide + +ETL Conventions + +Datatype + +Required + +Primary Key + +Foreign Key + +FK Table + +FK Domain +
+cohort_definition_id + +This is the identifier given to the cohort, usually by the ATLAS +application + + +integer + +Yes + +No + +No + + +
+cohort_definition_name + +A short description of the cohort + + +varchar(255) + +Yes + +No + +No + + +
+cohort_definition_description + +A complete description of the cohort. + + +varchar(MAX) + +No + +No + +No + + +
+definition_type_concept_id + +Type defining what kind of Cohort Definition the record represents and +how the syntax may be executed. + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+cohort_definition_syntax + +Syntax or code to operationalize the Cohort Definition. + + +varchar(MAX) + +No + +No + +No + + +
+subject_concept_id + +This field contains a Concept that represents the domain of the subjects +that are members of the cohort (e.g., Person, Provider, Visit). + + +integer + +Yes + +No + +Yes + +CONCEPT + +
+cohort_initiation_date + +A date to indicate when the Cohort was initiated in the COHORT table. + + +date + +No + +No + +No + + +
diff --git a/rmd/cdm54.Rmd b/rmd/cdm54.Rmd index 87e5b38..69318ee 100644 --- a/rmd/cdm54.Rmd +++ b/rmd/cdm54.Rmd @@ -23,20 +23,20 @@ This is the specification document for the OMOP Common Data Model, v5.4. **This ### Current Support for CDM v5.4 -The table below details which OHDSI tools support CDM v5.4. There are two levels of support: legacy support means that the tool supports all tables and fields that were present in CDM v5.3 and feature support indicates that the tool supports any new tables and fields in CDM v5.4 that were not present in CDM v5.3. A green check `r emo::ji("white heavy check mark")` indicates that the support level for the listed tool is in place, has been tested, and released. A warning sign `r emo::ji("warning")` indicates that the support level for the listed tool has been initiated but has not yet been tested and released. +The table below details which OHDSI tools support CDM v5.4. There are two levels of support: legacy support means that the tool supports all tables and fields that were present in CDM v5.3 and feature support indicates that the tool supports any new tables and fields in CDM v5.4 that were not present in CDM v5.3. A green check `r emoji::emoji("heavy_check_mark")` indicates that the support level for the listed tool is in place, has been tested, and released. A warning sign `r emoji::emoji("exclamation")` indicates that the support level for the listed tool has been initiated but has not yet been tested and released.
|**Tool**|**Description**|**Legacy Support**|**Feature Support**| |--|--|--|--| -|**CDM R package**|This package can be downloaded from [https://github.com/OHDSI/CommonDataModel/](https://github.com/OHDSI/CommonDataModel/). It functions to dynamically create the OMOP CDM documentation and DDL scripts to instantiate the CDM tables. |`r emo::ji("white heavy check mark")`|`r emo::ji("white heavy check mark")` -|**Data Quality Dashboard**|This package can be downloaded from [https://github.com/OHDSI/DataQualityDashboard](https://github.com/OHDSI/DataQualityDashboard). It runs a set of > 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study.|`r emo::ji("white heavy check mark")`| `r emo::ji("warning")` -|**Achilles**|This package can be downloaded from [https://github.com/OHDSI/Achilles](https://github.com/OHDSI/Achilles), performing a set of broad database characterizations agains an OMOP CDM instance. |`r emo::ji("white heavy check mark")`|`r emo::ji("warning")` -|**ARES**|This package can be downloaded from [https://github.com/OHDSI/Ares](https://github.com/OHDSI/Ares) and is designed to display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research.|`r emo::ji("white heavy check mark")`|`r emo::ji("warning")` -|**ATLAS**|ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. [Demo](http://atlas-demo.ohdsi.org/) |`r emo::ji("white heavy check mark")`|`r emo::ji("warning")` -|**Rabbit-In-A-Hat**|This package can be downloaded from [https://github.com/OHDSI/WhiteRabbit](https://github.com/OHDSI/WhiteRabbit) and is an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.|`r emo::ji("white heavy check mark")`|`r emo::ji("white heavy check mark")` -|**Feature Extraction**|This package can be downloaded from [https://github.com/OHDSI/FeatureExtraction](https://github.com/OHDSI/FeatureExtraction). It is designed to generate features (covariates) for a cohort generated using the OMOP CDM. |`r emo::ji("white heavy check mark")`|`r emo::ji("white heavy check mark")`* -|**Cohort Diagnostics**|This package can be downloaded from [https://github.com/OHDSI/CohortDiagnostics](https://github.com/OHDSI/CohortDiagnostics) and is used to critically evaluate cohort phenotypes. |`r emo::ji("white heavy check mark")`|`r emo::ji("warning")` +|**CDM R package**|This package can be downloaded from [https://github.com/OHDSI/CommonDataModel/](https://github.com/OHDSI/CommonDataModel/). It functions to dynamically create the OMOP CDM documentation and DDL scripts to instantiate the CDM tables. |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("heavy_check_mark")` +|**Data Quality Dashboard**|This package can be downloaded from [https://github.com/OHDSI/DataQualityDashboard](https://github.com/OHDSI/DataQualityDashboard). It runs a set of > 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study.|`r emoji::emoji("heavy_check_mark")`| `r emoji::emoji("exclamation")` +|**Achilles**|This package can be downloaded from [https://github.com/OHDSI/Achilles](https://github.com/OHDSI/Achilles), performing a set of broad database characterizations agains an OMOP CDM instance. |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")` +|**ARES**|This package can be downloaded from [https://github.com/OHDSI/Ares](https://github.com/OHDSI/Ares) and is designed to display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research.|`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")` +|**ATLAS**|ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. [Demo](http://atlas-demo.ohdsi.org/) |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")` +|**Rabbit-In-A-Hat**|This package can be downloaded from [https://github.com/OHDSI/WhiteRabbit](https://github.com/OHDSI/WhiteRabbit) and is an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.|`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("heavy_check_mark")` +|**Feature Extraction**|This package can be downloaded from [https://github.com/OHDSI/FeatureExtraction](https://github.com/OHDSI/FeatureExtraction). It is designed to generate features (covariates) for a cohort generated using the OMOP CDM. |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("heavy_check_mark")`* +|**Cohort Diagnostics**|This package can be downloaded from [https://github.com/OHDSI/CohortDiagnostics](https://github.com/OHDSI/CohortDiagnostics) and is used to critically evaluate cohort phenotypes. |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")`
\* The **Feature Extraction** package supports all relevant new features in CDM v5.4. For example, it was decided that, from a methodological perspective, the EPISODE and EPISODE_EVENT tables should not be included to define cohort covariates because the events that make up episodes are already pulled in as potential covariates.