@@ -543,10 +568,14 @@ PERSON
person_id
-It is assumed that every person with a different unique identifier is in fact a different person and should be treated independently.
+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.
+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
@@ -570,10 +599,17 @@ PERSON
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.
+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
+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
@@ -602,7 +638,10 @@ PERSON
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.
+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
@@ -628,7 +667,8 @@ PERSON
|
|
-For data sources that provide the precise date of birth, the month should be extracted and stored in this field.
+For data sources that provide the precise date of birth, the month
+should be extracted and stored in this field.
|
integer
@@ -654,7 +694,8 @@ PERSON
|
|
-For data sources that provide the precise date of birth, the day should be extracted and stored in this field.
+For data sources that provide the precise date of birth, the day should
+be extracted and stored in this field.
|
integer
@@ -680,7 +721,15 @@ PERSON
|
|
-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).
+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
@@ -707,7 +756,14 @@ PERSON
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.
+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
@@ -733,10 +789,17 @@ PERSON
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.
+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
+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
@@ -762,10 +825,18 @@ PERSON
location_id
|
-The location refers to the physical address of the person. This field should capture the last known location of the person.
+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.
+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
@@ -790,10 +861,14 @@ PERSON
provider_id
|
-The Provider refers to the last known primary care provider (General Practitioner).
+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.
+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
@@ -818,7 +893,8 @@ PERSON
care_site_id
|
-The Care Site refers to where the Provider typically provides the primary care.
+The Care Site refers to where the Provider typically provides the
+primary care.
|
|
@@ -845,10 +921,14 @@ PERSON
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.
+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.
+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)
@@ -872,7 +952,9 @@ PERSON
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.
+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.
@@ -902,7 +984,8 @@ PERSON
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.
+If the source data codes biological sex in a non-standard vocabulary,
+store the concept_id here.
|
integer
@@ -927,7 +1010,8 @@ PERSON
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.
+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.
@@ -957,7 +1041,8 @@ PERSON
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.
+If the source data codes race in an OMOP supported vocabulary store the
+concept_id here.
|
integer
@@ -982,10 +1067,13 @@ PERSON
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.
+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.
+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)
@@ -1012,7 +1100,8 @@ PERSON
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.
+If the source data codes ethnicity in an OMOP supported vocabulary,
+store the concept_id here.
|
integer
@@ -1038,11 +1127,44 @@ PERSON
OBSERVATION_PERIOD
Table Description
- This table contains records which define spans of time during which two conditions are expected to hold: (i) Clinical Events that happened to the Person are recorded in the Event tables, and (ii) absense of records indicate such Events did not occur during this span of time.
+ This table contains records which define spans of time during which
+two conditions are expected to hold: (i) Clinical Events that happened
+to the Person are recorded in the Event tables, and (ii) absense of
+records indicate such Events did not occur during this span of time.
User Guide
- For each Person, one or more OBSERVATION_PERIOD records may be present, but they will not overlap or be back to back to each other. Events may exist outside all of the time spans of the OBSERVATION_PERIOD records for a patient, however, absence of an Event outside these time spans cannot be construed as evidence of absence of an Event. Incidence or prevalence rates should only be calculated for the time of active OBSERVATION_PERIOD records. When constructing cohorts, outside Events can be used for inclusion criteria definition, but without any guarantee for the performance of these criteria. Also, OBSERVATION_PERIOD records can be as short as a single day, greatly disturbing the denominator of any rate calculation as part of cohort characterizations. To avoid that, apply minimal observation time as a requirement for any cohort definition.
+ For each Person, one or more OBSERVATION_PERIOD records may be
+present, but they will not overlap or be back to back to each other.
+Events may exist outside all of the time spans of the OBSERVATION_PERIOD
+records for a patient, however, absence of an Event outside these time
+spans cannot be construed as evidence of absence of an Event. Incidence
+or prevalence rates should only be calculated for the time of active
+OBSERVATION_PERIOD records. When constructing cohorts, outside Events
+can be used for inclusion criteria definition, but without any guarantee
+for the performance of these criteria. Also, OBSERVATION_PERIOD records
+can be as short as a single day, greatly disturbing the denominator of
+any rate calculation as part of cohort characterizations. To avoid that,
+apply minimal observation time as a requirement for any cohort
+definition.
ETL Conventions
- Each Person needs to have at least one OBSERVATION_PERIOD record, which should represent time intervals with a high capture rate of Clinical Events. Some source data have very similar concepts, such as enrollment periods in insurance claims data. In other source data such as most EHR systems these time spans need to be inferred under a set of assumptions. It is the discretion of the ETL developer to define these assumptions. In many ETL solutions the start date of the first occurrence or the first high quality occurrence of a Clinical Event (Condition, Drug, Procedure, Device, Measurement, Visit) is defined as the start of the OBSERVATION_PERIOD record, and the end date of the last occurrence of last high quality occurrence of a Clinical Event, or the end of the database period becomes the end of the OBSERVATOIN_PERIOD for each Person. If a Person only has a single Clinical Event the OBSERVATION_PERIOD record can be as short as one day. Depending on these definitions it is possible that Clinical Events fall outside the time 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.
+ Each Person needs to have at least one OBSERVATION_PERIOD record,
+which should represent time intervals with a high capture rate of
+Clinical Events. Some source data have very similar concepts, such as
+enrollment periods in insurance claims data. In other source data such
+as most EHR systems these time spans need to be inferred under a set of
+assumptions. It is the discretion of the ETL developer to define these
+assumptions. In many ETL solutions the start date of the first
+occurrence or the first high quality occurrence of a Clinical Event
+(Condition, Drug, Procedure, Device, Measurement, Visit) is defined as
+the start of the OBSERVATION_PERIOD record, and the end date of the last
+occurrence of last high quality occurrence of a Clinical Event, or the
+end of the database period becomes the end of the OBSERVATOIN_PERIOD for
+each Person. If a Person only has a single Clinical Event the
+OBSERVATION_PERIOD record can be as short as one day. Depending on these
+definitions it is possible that Clinical Events fall outside the time
+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.
@@ -1081,10 +1203,12 @@ OBSERVATION_PERIOD
observation_period_id
-A Person can have multiple discrete Observation Periods which are identified by the 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.
+Assign a unique observation_period_id to each discrete Observation
+Period for a Person.
|
integer
@@ -1108,7 +1232,8 @@ OBSERVATION_PERIOD
person_id
|
-The Person ID of the PERSON record for which the Observation Period is recorded.
+The Person ID of the PERSON record for which the Observation Period is
+recorded.
|
|
@@ -1138,7 +1263,14 @@ OBSERVATION_PERIOD
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.
+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
@@ -1162,10 +1294,15 @@ OBSERVATION_PERIOD
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.
+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.
+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
@@ -1189,10 +1326,15 @@ OBSERVATION_PERIOD
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.
+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.
+Choose the observation_period_type_concept_id that best represents how
+the period was determined. Accepted
+Concepts.
|
integer
@@ -1219,25 +1361,100 @@ OBSERVATION_PERIOD
VISIT_OCCURRENCE
Table Description
- This table contains Events where Persons engage with the healthcare system for a duration of time. They are often also called “Encounters”. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed.
+ This table contains Events where Persons engage with the healthcare
+system for a duration of time. They are often also called “Encounters”.
+Visits are defined by a configuration of circumstances under which they
+occur, such as (i) whether the patient comes to a healthcare
+institution, the other way around, or the interaction is remote, (ii)
+whether and what kind of trained medical staff is delivering the service
+during the Visit, and (iii) whether the Visit is transient or for a
+longer period involving a stay in bed.
User Guide
- The configuration defining the Visit are described by Concepts in the Visit Domain, which form a hierarchical structure, but rolling up to generally familiar Visits adopted in most healthcare systems worldwide:
+ The configuration defining the Visit are described by Concepts in the
+Visit Domain, which form a hierarchical structure, but rolling up to
+generally familiar Visits adopted in most healthcare systems
+worldwide:
-- Inpatient Visit: Person visiting hospital, at a Care Site, in bed, for duration of more than one day, with physicians and other Providers permanently available to deliver service around the clock
-- Emergency Room Visit: Person visiting dedicated healthcare institution for treating emergencies, at a Care Site, within one day, with physicians and Providers permanently available to deliver service around the clock
-- Emergency Room and Inpatient Visit: Person visiting ER followed by a subsequent Inpatient Visit, where Emergency department is part of hospital, and transition from the ER to other hospital departments is undefined
-- Non-hospital institution Visit: Person visiting dedicated institution for reasons of poor health, at a Care Site, long-term or permanently, with no physician but possibly other Providers permanently available to deliver service around the clock
-- Outpatient Visit: Person visiting dedicated ambulatory healthcare institution, at a Care Site, within one day, without bed, with physicians or medical Providers delivering service during Visit
-- Home Visit: Provider visiting Person, without a Care Site, within one day, delivering service
-- Telehealth Visit: Patient engages with Provider through communication media
-- Pharmacy Visit: Person visiting pharmacy for dispensing of Drug, at a Care Site, within one day
-- Laboratory Visit: Patient visiting dedicated institution, at a Care Site, within one day, for the purpose of a Measurement.
-- Ambulance Visit: Person using transportation service for the purpose of initiating one of the other Visits, without a Care Site, within one day, potentially with Providers accompanying the Visit and delivering service
-- Case Management Visit: Person interacting with healthcare system, without a Care Site, within a day, with no Providers involved, for administrative purposes
+- Inpatient
+Visit: Person visiting hospital, at a Care Site, in bed, for
+duration of more than one day, with physicians and other Providers
+permanently available to deliver service around the clock
+- Emergency
+Room Visit: Person visiting dedicated healthcare institution for
+treating emergencies, at a Care Site, within one day, with physicians
+and Providers permanently available to deliver service around the
+clock
+- Emergency
+Room and Inpatient Visit: Person visiting ER followed by a
+subsequent Inpatient Visit, where Emergency department is part of
+hospital, and transition from the ER to other hospital departments is
+undefined
+- Non-hospital
+institution Visit: Person visiting dedicated institution for reasons
+of poor health, at a Care Site, long-term or permanently, with no
+physician but possibly other Providers permanently available to deliver
+service around the clock
+- Outpatient
+Visit: Person visiting dedicated ambulatory healthcare institution,
+at a Care Site, within one day, without bed, with physicians or medical
+Providers delivering service during Visit
+- Home
+Visit: Provider visiting Person, without a Care Site, within one
+day, delivering service
+- Telehealth
+Visit: Patient engages with Provider through communication
+media
+- Pharmacy
+Visit: Person visiting pharmacy for dispensing of Drug, at a Care
+Site, within one day
+- Laboratory
+Visit: Patient visiting dedicated institution, at a Care Site,
+within one day, for the purpose of a Measurement.
+- Ambulance
+Visit: Person using transportation service for the purpose of
+initiating one of the other Visits, without a Care Site, within one day,
+potentially with Providers accompanying the Visit and delivering
+service
+- Case
+Management Visit: Person interacting with healthcare system, without
+a Care Site, within a day, with no Providers involved, for
+administrative purposes
- The Visit duration, or ‘length of stay’, is defined as VISIT_END_DATE - VISIT_START_DATE. For all Visits this is <1 day, except Inpatient Visits and Non-hospital institution Visits. The CDM also contains the VISIT_DETAIL table where additional information about the Visit is stored, for example, transfers between units during an inpatient Visit.
+ The Visit duration, or ‘length of stay’, is defined as VISIT_END_DATE
+- VISIT_START_DATE. For all Visits this is <1 day, except Inpatient
+Visits and Non-hospital institution Visits. The CDM also contains the
+VISIT_DETAIL table where additional information about the Visit is
+stored, for example, transfers between units during an inpatient
+Visit.
ETL Conventions
- Visits can be derived easily if the source data contain coding systems for Place of Service or Procedures, like CPT codes for well visits. In those cases, the codes can be looked up and mapped to a Standard Visit Concept. Otherwise, Visit Concepts have to be identified in the ETL process. This table will contain 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. Visits can be adjacent to each other, i.e. the end date of one can be identical with the start date of the other. As a consequence, more than one-day Visits or their descendants can be recorded for the same day. Multi-day visits must not overlap, i.e. share days other than start and end days. It is often the case that some logic should be written for how to define visits and how to assign Visit_Concept_Id. For example, in US claims outpatient visits that appear to occur within the time period of an inpatient visit can be rolled into one with the same Visit_Occurrence_Id. In EHR data inpatient visits that are within one day of each other may be strung together to create one visit. It will all depend on the source data and how 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.
+ Visits can be derived easily if the source data contain coding
+systems for Place of Service or Procedures, like CPT codes for well
+visits. In those cases, the codes can be looked up and mapped to a
+Standard Visit Concept. Otherwise, Visit Concepts have to be identified
+in the ETL process. This table will contain 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. Visits can be adjacent to
+each other, i.e. the end date of one can be identical with the start
+date of the other. As a consequence, more than one-day Visits or their
+descendants can be recorded for the same day. Multi-day visits must not
+overlap, i.e. share days other than start and end days. It is often the
+case that some logic should be written for how to define visits and how
+to assign Visit_Concept_Id. For example, in US claims outpatient visits
+that appear to occur within the time period of an inpatient visit can be
+rolled into one with the same Visit_Occurrence_Id. In EHR data inpatient
+visits that are within one day of each other may be strung together to
+create one visit. It will all depend on the source data and how
+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.
@@ -1276,10 +1493,14 @@ VISIT_OCCURRENCE
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.
+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.
+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
@@ -1329,10 +1550,19 @@ VISIT_OCCURRENCE
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.
+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.
+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
@@ -1358,10 +1588,15 @@ VISIT_OCCURRENCE
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.
+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.
+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
@@ -1387,7 +1622,8 @@ VISIT_OCCURRENCE
|
|
-If no time is given for the start date of a visit, set it to midnight (00:00:0000).
+If no time is given for the start date of a visit, set it to midnight
+(00:00:0000).
|
datetime
@@ -1414,7 +1650,20 @@ VISIT_OCCURRENCE
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.
+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
@@ -1440,7 +1689,8 @@ VISIT_OCCURRENCE
|
|
-If no time is given for the end date of a visit, set it to midnight (00:00:0000).
+If no time is given for the end date of a visit, set it to midnight
+(00:00:0000).
|
datetime
@@ -1464,10 +1714,14 @@ VISIT_OCCURRENCE
visit_type_concept_id
|
-Use this field to understand the provenance of the visit record, or where the record comes from.
+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.
+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
@@ -1493,10 +1747,18 @@ VISIT_OCCURRENCE
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.
+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.
+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
@@ -1521,7 +1783,8 @@ VISIT_OCCURRENCE
care_site_id
|
-This field provides information about the Care Site where the Visit took place.
+This field provides information about the Care Site where the Visit took
+place.
|
There should only be one Care Site associated with a Visit.
@@ -1549,10 +1812,16 @@ VISIT_OCCURRENCE
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.)
+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.
+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)
@@ -1578,7 +1847,9 @@ VISIT_OCCURRENCE
|
|
-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.
+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
@@ -1603,10 +1874,15 @@ VISIT_OCCURRENCE
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.
+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 available, map the admitted_from_source_value to a standard concept
+in the visit domain. Accepted
+Concepts.
|
integer
@@ -1634,7 +1910,10 @@ VISIT_OCCURRENCE
|
|
-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.
+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)
@@ -1658,10 +1937,16 @@ VISIT_OCCURRENCE
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.
+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.
+If available, map the discharge_to_source_value to a standard concept in
+the visit domain. Accepted
+Concepts.
|
integer
@@ -1689,7 +1974,11 @@ VISIT_OCCURRENCE
|
|
-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.
+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)
@@ -1713,10 +2002,13 @@ VISIT_OCCURRENCE
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.
+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”.
+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
@@ -1742,11 +2034,38 @@ VISIT_OCCURRENCE
VISIT_DETAIL
Table Description
- The VISIT_DETAIL table is an optional table used to represents details of each record in the parent VISIT_OCCURRENCE table. A good example of this would be the movement between units in a hospital during an inpatient stay or claim lines associated with a one insurance claim. For every record in the VISIT_OCCURRENCE table there may be 0 or more records in the VISIT_DETAIL table with a 1:n relationship where n may be 0. The VISIT_DETAIL table is structurally very similar to VISIT_OCCURRENCE table and belongs to the visit domain.
+ The VISIT_DETAIL table is an optional table used to represents
+details of each record in the parent VISIT_OCCURRENCE table. A good
+example of this would be the movement between units in a hospital during
+an inpatient stay or claim lines associated with a one insurance claim.
+For every record in the VISIT_OCCURRENCE table there may be 0 or more
+records in the VISIT_DETAIL table with a 1:n relationship where n may be
+0. The VISIT_DETAIL table is structurally very similar to
+VISIT_OCCURRENCE table and belongs to the visit domain.
User Guide
- The configuration defining the Visit Detail is described by Concepts in the Visit Domain, which form a hierarchical structure. The Visit Detail record will have an associated to the Visit Occurrence record in two ways:
1. The Visit Detail record will have the VISIT_OCCURRENCE_ID it is associated to 2. The VISIT_DETAIL_CONCEPT_ID will be a descendant of the VISIT_CONCEPT_ID for the Visit.
+ The configuration defining the Visit Detail is described by Concepts
+in the Visit Domain, which form a hierarchical structure. The Visit
+Detail record will have an associated to the Visit Occurrence record in
+two ways:
1. The Visit Detail record will have the
+VISIT_OCCURRENCE_ID it is associated to 2. The VISIT_DETAIL_CONCEPT_ID
+will be a descendant of the VISIT_CONCEPT_ID for the Visit.
ETL Conventions
- It is not mandatory that the VISIT_DETAIL table be filled in, but if you find that the logic to create VISIT_OCCURRENCE records includes the roll-up of multiple smaller records to create one picture of a Visit then it is a good idea to use VISIT_DETAIL. In EHR data, for example, a Person may be in the hospital but instead of one over-arching Visit their encounters are recorded as times they interacted with a health care provider. A Person in the hospital interacts with multiple providers multiple times a day so the encounters must be strung together using some heuristic (defined by the ETL) to identify the entire Visit. In this case the encounters would be considered Visit Details and the entire Visit would be the Visit Occurrence. In this example it is also possible to use the Vocabulary to distinguish Visit Details from a Visit 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.
+ It is not mandatory that the VISIT_DETAIL table be filled in, but if
+you find that the logic to create VISIT_OCCURRENCE records includes the
+roll-up of multiple smaller records to create one picture of a Visit
+then it is a good idea to use VISIT_DETAIL. In EHR data, for example, a
+Person may be in the hospital but instead of one over-arching Visit
+their encounters are recorded as times they interacted with a health
+care provider. A Person in the hospital interacts with multiple
+providers multiple times a day so the encounters must be strung together
+using some heuristic (defined by the ETL) to identify the entire Visit.
+In this case the encounters would be considered Visit Details and the
+entire Visit would be the Visit Occurrence. In this example it is also
+possible to use the Vocabulary to distinguish Visit Details from a Visit
+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.
@@ -1785,10 +2104,14 @@ VISIT_DETAIL
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.
+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.
+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
@@ -1838,10 +2161,19 @@ VISIT_DETAIL
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.
+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.
+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
@@ -1867,10 +2199,13 @@ VISIT_DETAIL
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.
+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.
+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
@@ -1896,7 +2231,8 @@ VISIT_DETAIL
|
|
-If no time is given for the start date of a visit, set it to midnight (00:00:0000).
+If no time is given for the start date of a visit, set it to midnight
+(00:00:0000).
|
datetime
@@ -1923,7 +2259,21 @@ VISIT_DETAIL
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.
+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
@@ -1949,7 +2299,8 @@ VISIT_DETAIL
|
|
-If no time is given for the end date of a visit, set it to midnight (00:00:0000).
+If no time is given for the end date of a visit, set it to midnight
+(00:00:0000).
|
datetime
@@ -1973,10 +2324,14 @@ VISIT_DETAIL
visit_detail_type_concept_id
|
-Use this field to understand the provenance of the visit detail record, or where the record comes from.
+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.
+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
@@ -2002,10 +2357,16 @@ VISIT_DETAIL
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.
+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.
+The additional providers associated to a Visit can be stored in this
+table where each VISIT_DETAIL record represents a different provider.
|
integer
@@ -2030,7 +2391,8 @@ VISIT_DETAIL
care_site_id
|
-This field provides information about the Care Site where the Visit Detail took place.
+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.
@@ -2058,10 +2420,16 @@ VISIT_DETAIL
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.)
+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.
+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)
@@ -2087,7 +2455,9 @@ VISIT_DETAIL
|
|
-If the VISIT_DETAIL_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.
+If 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
@@ -2114,7 +2484,10 @@ VISIT_DETAIL
|
|
-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.
+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)
@@ -2138,10 +2511,15 @@ VISIT_DETAIL
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.
+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 available, map the admitted_from_source_value to a standard concept
+in the visit domain. Accepted
+Concepts.
|
Integer
@@ -2169,7 +2547,11 @@ VISIT_DETAIL
|
|
-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.
+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)
@@ -2193,10 +2575,16 @@ VISIT_DETAIL
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.
+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.
+If available, map the DISCHARGE_TO_SOURCE_VALUE to a Standard Concept in
+the Visit domain. Accepted
+Concepts.
|
integer
@@ -2222,10 +2610,14 @@ VISIT_DETAIL
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.
+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”.
+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
@@ -2250,10 +2642,14 @@ 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.
+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.
+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
@@ -2304,14 +2700,47 @@ VISIT_DETAIL
|
-
+
CONDITION_OCCURRENCE
Table Description
- This table contains records of Events of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign, or a symptom, which is either observed by a Provider or reported by the patient.
+ This table contains records of Events of a Person suggesting the
+presence of a disease or medical condition stated as a diagnosis, a
+sign, or a symptom, which is either observed by a Provider or reported
+by the patient.
User Guide
- Conditions are defined by Concepts from the Condition domain, which form a complex hierarchy. As a result, the same Person with the same disease may have multiple Condition records, which belong to the same hierarchical family. Most Condition records are mapped from diagnostic codes, but recorded signs, symptoms and summary descriptions also contribute to this table. Rule out diagnoses should not be recorded in this table, but in reality their negating nature is not always captured in the source data, and other precautions must be taken when when identifying Persons who should suffer from the recorded Condition. Record all conditions as they exist in the source data. Any decisions about diagnosis/phenotype definitions would be done through cohort specifications. These cohorts can be housed in the COHORT table. Conditions span a time interval from start to end, but are typically recorded as single snapshot records with no end date. The reason is twofold: (i) At the time of the recording the duration is not known and later not recorded, and (ii) the Persons typically cease interacting with the healthcare system when they feel better, which leads to incomplete capture of resolved Conditions. The CONDITION_ERA table addresses this issue. Family history and past diagnoses (‘history of’) are not recorded in this table. Instead, they are listed in the OBSERVATION table. Codes written in the process of establishing the diagnosis, such as ‘question of’ of and ‘rule out’, should not represented here. Instead, they should be recorded in the OBSERVATION table, if they are used for analyses. However, this information is not always available.
+ Conditions are defined by Concepts from the Condition domain, which
+form a complex hierarchy. As a result, the same Person with the same
+disease may have multiple Condition records, which belong to the same
+hierarchical family. Most Condition records are mapped from diagnostic
+codes, but recorded signs, symptoms and summary descriptions also
+contribute to this table. Rule out diagnoses should not be recorded in
+this table, but in reality their negating nature is not always captured
+in the source data, and other precautions must be taken when when
+identifying Persons who should suffer from the recorded Condition.
+Record all conditions as they exist in the source data. Any decisions
+about diagnosis/phenotype definitions would be done through cohort
+specifications. These cohorts can be housed in the COHORT
+table. Conditions span a time interval from start to end, but are
+typically recorded as single snapshot records with no end date. The
+reason is twofold: (i) At the time of the recording the duration is not
+known and later not recorded, and (ii) the Persons typically cease
+interacting with the healthcare system when they feel better, which
+leads to incomplete capture of resolved Conditions. The CONDITION_ERA
+table addresses this issue. Family history and past diagnoses (‘history
+of’) are not recorded in this table. Instead, they are listed in the OBSERVATION
+table. Codes written in the process of establishing the diagnosis, such
+as ‘question of’ of and ‘rule out’, should not represented here.
+Instead, they should be recorded in the OBSERVATION
+table, if they are used for analyses. However, this information is not
+always available.
ETL Conventions
- Source codes and source text fields mapped to Standard Concepts of the Condition Domain have to be recorded here.
+ Source codes and source text fields mapped to Standard Concepts of
+the Condition Domain have to be recorded here.
@@ -2350,10 +2779,16 @@ CONDITION_OCCURRENCE
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.
+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.
+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
@@ -2404,10 +2839,16 @@ CONDITION_OCCURRENCE
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 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.
+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
@@ -2436,7 +2877,10 @@ CONDITION_OCCURRENCE
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.
+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
@@ -2462,7 +2906,8 @@ CONDITION_OCCURRENCE
|
|
-If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)
+If a source does not specify datetime the convention is to set the time
+to midnight (00:00:0000)
|
datetime
@@ -2489,7 +2934,10 @@ CONDITION_OCCURRENCE
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.
+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
@@ -2515,7 +2963,8 @@ CONDITION_OCCURRENCE
|
|
-If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)
+If a source does not specify datetime the convention is to set the time
+to midnight (00:00:0000)
|
datetime
@@ -2539,10 +2988,15 @@ CONDITION_OCCURRENCE
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.
+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.
+Choose the CONDITION_TYPE_CONCEPT_ID that best represents the provenance
+of the record. Accepted
+Concepts.
|
integer
@@ -2568,10 +3022,18 @@ CONDITION_OCCURRENCE
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.
+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.
+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
@@ -2597,10 +3059,13 @@ CONDITION_OCCURRENCE
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.
+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.
+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)
@@ -2624,10 +3089,14 @@ CONDITION_OCCURRENCE
provider_id
|
-The provider associated with condition record, e.g. the provider who made the diagnosis or the provider who recorded the symptom.
+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.
+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
@@ -2655,7 +3124,13 @@ CONDITION_OCCURRENCE
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.
+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
@@ -2680,7 +3155,11 @@ CONDITION_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.
+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.
@@ -2708,10 +3187,13 @@ CONDITION_OCCURRENCE
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 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.
+This code is mapped to a Standard Condition Concept in the Standardized
+Vocabularies and the original code is stored here for reference.
|
varchar(50)
@@ -2735,10 +3217,19 @@ CONDITION_OCCURRENCE
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.
+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.
+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
@@ -2763,10 +3254,15 @@ CONDITION_OCCURRENCE
condition_status_source_value
|
-This field houses the verbatim value from the source data representing the condition status.
+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.
+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)
@@ -2791,11 +3287,34 @@ CONDITION_OCCURRENCE
DRUG_EXPOSURE
Table Description
- This table captures records about the exposure to a Drug ingested or otherwise introduced into the body. A Drug is a biochemical substance formulated in such a way that when administered to a Person it will exert a certain biochemical effect on the metabolism. Drugs include prescription and over-the-counter medicines, vaccines, and large-molecule biologic therapies. Radiological devices ingested or applied locally do not count as Drugs.
+ This table captures records about the exposure to a Drug ingested or
+otherwise introduced into the body. A Drug is a biochemical substance
+formulated in such a way that when administered to a Person it will
+exert a certain biochemical effect on the metabolism. Drugs include
+prescription and over-the-counter medicines, vaccines, and
+large-molecule biologic therapies. Radiological devices ingested or
+applied locally do not count as Drugs.
User Guide
- The purpose of records in this table is to indicate an exposure to a certain drug as best as possible. In this context a drug is defined as an active ingredient. Drug Exposures are defined by Concepts from the Drug domain, which form a complex hierarchy. As a result, one DRUG_SOURCE_CONCEPT_ID may map to multiple standard concept ids if it is a combination product. Records in this table represent prescriptions written, prescriptions dispensed, and drugs administered by a provider to name a few. The DRUG_TYPE_CONCEPT_ID can be used to find and filter on these types. This table includes additional information about the drug products, the quantity given, and route of administration.
+ The purpose of records in this table is to indicate an exposure to a
+certain drug as best as possible. In this context a drug is defined as
+an active ingredient. Drug Exposures are defined by Concepts from the
+Drug domain, which form a complex hierarchy. As a result, one
+DRUG_SOURCE_CONCEPT_ID may map to multiple standard concept ids if it is
+a combination product. Records in this table represent prescriptions
+written, prescriptions dispensed, and drugs administered by a provider
+to name a few. The DRUG_TYPE_CONCEPT_ID can be used to find and filter
+on these types. This table includes additional information about the
+drug products, the quantity given, and route of administration.
ETL Conventions
- Information about quantity and dose is provided in a variety of different ways and it is important for the ETL to provide as much information as possible from the data. Depending on the provenance of the data fields may be captured differently i.e. quantity for drugs administered may have a separate meaning from quantity for prescriptions 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.
+ Information about quantity and dose is provided in a variety of
+different ways and it is important for the ETL to provide as much
+information as possible from the data. Depending on the provenance of
+the data fields may be captured differently i.e. quantity for drugs
+administered may have a separate meaning from quantity for prescriptions
+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.
@@ -2834,10 +3353,17 @@ DRUG_EXPOSURE
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.
+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.
+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
@@ -2861,7 +3387,8 @@ DRUG_EXPOSURE
person_id
|
-The PERSON_ID of the PERSON for whom the drug dispensing or administration is recorded. This may be a system generated code.
+The PERSON_ID of the PERSON for whom the drug dispensing or
+administration is recorded. This may be a system generated code.
|
|
@@ -2888,10 +3415,35 @@ DRUG_EXPOSURE
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 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.
+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
@@ -2920,7 +3472,10 @@ DRUG_EXPOSURE
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.
+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
@@ -2946,7 +3501,8 @@ DRUG_EXPOSURE
|
|
-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)
+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
@@ -2970,10 +3526,27 @@ DRUG_EXPOSURE
drug_exposure_end_date
|
-The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended for the patient.
+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
+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
@@ -2999,7 +3572,8 @@ DRUG_EXPOSURE
|
|
-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)
+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
@@ -3023,10 +3597,12 @@ DRUG_EXPOSURE
verbatim_end_date
|
-This is the end date of the drug exposure as it appears in the source data, if it is given
+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.
+Put the end date or discontinuation date as it appears from the source
+data or leave blank if unavailable.
|
date
@@ -3050,10 +3626,16 @@ DRUG_EXPOSURE
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.
+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.
+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
@@ -3079,10 +3661,13 @@ DRUG_EXPOSURE
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.
+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.
+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)
@@ -3106,7 +3691,9 @@ DRUG_EXPOSURE
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.
+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.
|
|
@@ -3134,7 +3721,22 @@ DRUG_EXPOSURE
|
-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.
+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
@@ -3160,7 +3762,10 @@ DRUG_EXPOSURE
|
|
-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.
+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
@@ -3184,10 +3789,12 @@ DRUG_EXPOSURE
sig
|
-This is the verbatim instruction for the drug as written by the provider.
+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.
+Put the written out instructions for the drug as it is verbatim in the
+source, if available.
|
varchar(MAX)
@@ -3213,7 +3820,8 @@ DRUG_EXPOSURE
|
|
-The standard CONCEPT_ID that the ROUTE_SOURCE_VALUE maps to in the route domain.
+The standard CONCEPT_ID that the ROUTE_SOURCE_VALUE maps to in the route
+domain.
|
integer
@@ -3264,10 +3872,14 @@ DRUG_EXPOSURE
provider_id
|
-The Provider associated with drug record, e.g. the provider who wrote the prescription or the provider who administered the drug.
+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.
+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
@@ -3292,10 +3904,12 @@ DRUG_EXPOSURE
visit_occurrence_id
|
-The Visit during which the drug was prescribed, administered or dispensed.
+The Visit during which the drug was prescribed, administered or
+dispensed.
|
-To populate this field drug exposures must be explicitly initiated in the visit.
+To populate this field drug exposures must be explicitly initiated in
+the visit.
|
integer
@@ -3320,7 +3934,11 @@ DRUG_EXPOSURE
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.
+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.
@@ -3348,10 +3966,13 @@ DRUG_EXPOSURE
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 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.
+This code is mapped to a Standard Drug Concept in the Standardized
+Vocabularies and the original code is stored here for reference.
|
varchar(50)
@@ -3375,10 +3996,19 @@ DRUG_EXPOSURE
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.
+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.
+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
@@ -3403,10 +4033,14 @@ DRUG_EXPOSURE
route_source_value
|
-This field houses the verbatim value from the source data representing the drug route.
+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.
+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)
@@ -3430,10 +4064,14 @@ DRUG_EXPOSURE
dose_unit_source_value
|
-This field houses the verbatim value from the source data representing the dose unit of the drug given.
+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.
+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)
@@ -3455,14 +4093,34 @@ DRUG_EXPOSURE
|
-
+
PROCEDURE_OCCURRENCE
Table Description
- This table contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient with a diagnostic or therapeutic purpose.
+ This table contains records of activities or processes ordered by, or
+carried out by, a healthcare provider on the patient with a diagnostic
+or therapeutic purpose.
User Guide
- Lab tests are not a procedure, if something is observed with an expected resulting amount and unit then it should be a measurement. Phlebotomy is a procedure but so trivial that it tends to be rarely captured. It can be assumed that there is a phlebotomy procedure associated with many lab tests, therefore it is unnecessary to add them as separate procedures. If the user finds the same procedure over concurrent days, it is assumed those records are part of a procedure lasting more than a day. This logic is in lieu of the procedure_end_date, which will be added in a future version of the CDM.
+ Lab tests are not a procedure, if something is observed with an
+expected resulting amount and unit then it should be a measurement.
+Phlebotomy is a procedure but so trivial that it tends to be rarely
+captured. It can be assumed that there is a phlebotomy procedure
+associated with many lab tests, therefore it is unnecessary to add them
+as separate procedures. If the user finds the same procedure over
+concurrent days, it is assumed those records are part of a procedure
+lasting more than a day. This logic is in lieu of the
+procedure_end_date, which will be added in a future version of the
+CDM.
ETL Conventions
- If a procedure lasts more than 24 hours, 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. When dealing with duplicate records, the ETL must determine whether to sum them up into one record or keep them separate. 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.
+ If a procedure lasts more than 24 hours, 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. When dealing with duplicate records, the ETL must
+determine whether to sum them up into one record or keep them separate.
+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.
@@ -3501,10 +4159,16 @@ PROCEDURE_OCCURRENCE
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.
+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.
+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
@@ -3528,7 +4192,8 @@ PROCEDURE_OCCURRENCE
person_id
|
-The PERSON_ID of the PERSON for whom the procedure is recorded. This may be a system generated code.
+The PERSON_ID of the PERSON for whom the procedure is recorded. This may
+be a system generated code.
|
|
@@ -3555,10 +4220,16 @@ PROCEDURE_OCCURRENCE
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 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.
+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
@@ -3587,7 +4258,10 @@ PROCEDURE_OCCURRENCE
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.
+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
@@ -3613,7 +4287,8 @@ PROCEDURE_OCCURRENCE
|
|
-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)
+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
@@ -3637,10 +4312,17 @@ PROCEDURE_OCCURRENCE
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.
+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.
+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
@@ -3666,10 +4348,17 @@ PROCEDURE_OCCURRENCE
modifier_concept_id
|
-The modifiers are intended to give additional information about the procedure but as of now the vocabulary is under review.
+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.
+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
@@ -3697,7 +4386,9 @@ PROCEDURE_OCCURRENCE
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
+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
@@ -3721,10 +4412,14 @@ PROCEDURE_OCCURRENCE
provider_id
|
-The provider associated with the procedure record, e.g. the provider who performed the Procedure.
+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.
+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
@@ -3752,7 +4447,13 @@ PROCEDURE_OCCURRENCE
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.
+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
@@ -3777,7 +4478,11 @@ PROCEDURE_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.
+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.
@@ -3805,10 +4510,13 @@ PROCEDURE_OCCURRENCE
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.
+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.
+Use this value to look up the source concept id and then map the source
+concept id to a standard concept id.
|
varchar(50)
@@ -3832,10 +4540,19 @@ PROCEDURE_OCCURRENCE
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.
+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.
+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
@@ -3887,11 +4604,21 @@ PROCEDURE_OCCURRENCE
DEVICE_EXPOSURE
Table Description
- The Device domain captures information about a person’s exposure to a foreign physical object or instrument which is used for diagnostic or therapeutic purposes through a mechanism beyond chemical action. Devices include implantable objects (e.g. pacemakers, stents, artificial joints), medical equipment and supplies (e.g. bandages, crutches, syringes), other instruments used in medical procedures (e.g. sutures, defibrillators) and material used in clinical care (e.g. adhesives, body material, dental material, surgical material).
+ The Device domain captures information about a person’s exposure to a
+foreign physical object or instrument which is used for diagnostic or
+therapeutic purposes through a mechanism beyond chemical action. Devices
+include implantable objects (e.g. pacemakers, stents, artificial
+joints), medical equipment and supplies (e.g. bandages, crutches,
+syringes), other instruments used in medical procedures (e.g. sutures,
+defibrillators) and material used in clinical care (e.g. adhesives, body
+material, dental material, surgical material).
User Guide
- The distinction between Devices or supplies and Procedures are sometimes blurry, but the former are physical objects while the latter are actions, often to apply a Device or supply.
+ The distinction between Devices or supplies and Procedures are
+sometimes blurry, but the former are physical objects while the latter
+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.
+ Source codes and source text fields mapped to Standard Concepts of
+the Device Domain have to be recorded here.
@@ -3930,10 +4657,12 @@ DEVICE_EXPOSURE
device_exposure_id
-The unique key given to records a person’s exposure to a foreign physical object or instrument.
+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.
+Each instance of an exposure to a foreign object or device present in
+the source data should be assigned this unique key.
|
integer
@@ -3983,7 +4712,10 @@ DEVICE_EXPOSURE
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 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.
@@ -4015,7 +4747,9 @@ DEVICE_EXPOSURE
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.
+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
@@ -4041,7 +4775,8 @@ DEVICE_EXPOSURE
|
|
-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)
+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
@@ -4065,10 +4800,12 @@ DEVICE_EXPOSURE
device_exposure_end_date
|
-The DEVICE_EXPOSURE_END_DATE denotes the day the device exposure ended for the patient, if given.
+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.
+Put the end date or discontinuation date as it appears from the source
+data or leave blank if unavailable.
|
date
@@ -4094,7 +4831,8 @@ DEVICE_EXPOSURE
|
|
-If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)
+If a source does not specify datetime the convention is to set the time
+to midnight (00:00:0000)
|
datetime
@@ -4118,10 +4856,15 @@ DEVICE_EXPOSURE
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.
+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.
+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
@@ -4147,10 +4890,13 @@ DEVICE_EXPOSURE
unique_device_id
|
-This is the Unique Device Identification number for devices regulated by the FDA, if given.
+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.
+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)
@@ -4199,10 +4945,13 @@ DEVICE_EXPOSURE
provider_id
|
-The Provider associated with device record, e.g. the provider who wrote the prescription or the provider who implanted the device.
+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.
+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
@@ -4230,7 +4979,8 @@ DEVICE_EXPOSURE
The Visit during which the device was prescribed or given.
|
-To populate this field device exposures must be explicitly initiated in the visit.
+To populate this field device exposures must be explicitly initiated in
+the visit.
|
integer
@@ -4258,7 +5008,8 @@ DEVICE_EXPOSURE
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.
+To populate this field device exposures must be explicitly initiated in
+the visit detail record.
|
integer
@@ -4283,10 +5034,13 @@ DEVICE_EXPOSURE
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 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.
+This code is mapped to a Standard Device Concept in the Standardized
+Vocabularies and the original code is stored here for reference.
|
varchar(50)
@@ -4310,10 +5064,19 @@ DEVICE_EXPOSURE
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.
+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.
+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
@@ -4339,11 +5102,47 @@ DEVICE_EXPOSURE
MEASUREMENT
Table Description
- The MEASUREMENT table contains records of Measurements, i.e. structured values (numerical or categorical) obtained through systematic and standardized examination or testing of a Person or Person’s sample. The MEASUREMENT table contains both orders and results of such Measurements as laboratory tests, vital signs, quantitative findings from pathology reports, etc. Measurements are stored as attribute value pairs, with the attribute as the Measurement Concept and the value representing the result. The value can be a Concept (stored in VALUE_AS_CONCEPT), or a numerical value (VALUE_AS_NUMBER) with a Unit (UNIT_CONCEPT_ID). The Procedure for obtaining the sample is housed in the PROCEDURE_OCCURRENCE table, though it is unnecessary to create a PROCEDURE_OCCURRENCE record for each measurement if one does not exist in the source data. Measurements differ from Observations in that they require a standardized test or some other activity to generate a quantitative or qualitative result. If there is no result, it is assumed that the lab test was conducted but the result was not captured.
+ The MEASUREMENT table contains records of Measurements,
+i.e. structured values (numerical or categorical) obtained through
+systematic and standardized examination or testing of a Person or
+Person’s sample. The MEASUREMENT table contains both orders and results
+of such Measurements as laboratory tests, vital signs, quantitative
+findings from pathology reports, etc. Measurements are stored as
+attribute value pairs, with the attribute as the Measurement Concept and
+the value representing the result. The value can be a Concept (stored in
+VALUE_AS_CONCEPT), or a numerical value (VALUE_AS_NUMBER) with a Unit
+(UNIT_CONCEPT_ID). The Procedure for obtaining the sample is housed in
+the PROCEDURE_OCCURRENCE table, though it is unnecessary to create a
+PROCEDURE_OCCURRENCE record for each measurement if one does not exist
+in the source data. Measurements differ from Observations in that they
+require a standardized test or some other activity to generate a
+quantitative or qualitative result. If there is no result, it is assumed
+that the lab test was conducted but the result was not captured.
User Guide
- Measurements are predominately lab tests with a few exceptions, like blood pressure or function tests. Results are given in the form of a value and unit combination. When investigating measurements, look for operator_concept_ids (<, >, etc.).
+ Measurements are predominately lab tests with a few exceptions, like
+blood pressure or function tests. Results are given in the form of a
+value and unit combination. When investigating measurements, look for
+operator_concept_ids (<, >, etc.).
ETL Conventions
- Only records where the source value maps to a Concept in the measurement domain should be included in this table. Even though each Measurement always has a result, the fields VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID are not mandatory as often the result is not given in the source data. When the result is not known, the Measurement record represents just the fact that the corresponding Measurement was carried out, which in itself is already useful information for some use cases. For some Measurement Concepts, the result is included in the test. For example, ICD10 CONCEPT_ID 45548980 ‘Abnormal level of unspecified serum enzyme’ indicates a Measurement and the result (abnormal). 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’. In this example, the ‘Maps to’ relationship directs to 4046263 ‘Enzyme measurement’ as well as a ‘Maps to value’ record to 4135493 ‘Abnormal’.
+ Only records where the source value maps to a Concept in the
+measurement domain should be included in this table. Even though each
+Measurement always has a result, the fields VALUE_AS_NUMBER and
+VALUE_AS_CONCEPT_ID are not mandatory as often the result is not given
+in the source data. When the result is not known, the Measurement record
+represents just the fact that the corresponding Measurement was carried
+out, which in itself is already useful information for some use cases.
+For some Measurement Concepts, the result is included in the test. For
+example, ICD10 CONCEPT_ID 45548980
+‘Abnormal level of unspecified serum enzyme’ indicates a Measurement and
+the result (abnormal). 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’. In this example, the ‘Maps
+to’ relationship directs to 4046263
+‘Enzyme measurement’ as well as a ‘Maps to value’ record to 4135493
+‘Abnormal’.
@@ -4382,10 +5181,15 @@ MEASUREMENT
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.
+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.
+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
@@ -4409,7 +5213,8 @@ MEASUREMENT
person_id
|
-The PERSON_ID of the Person for whom the Measurement is recorded. This may be a system generated code.
+The PERSON_ID of the Person for whom the Measurement is recorded. This
+may be a system generated code.
|
|
@@ -4436,10 +5241,13 @@ MEASUREMENT
measurement_concept_id
-The MEASUREMENT_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies.
+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.
+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
@@ -4468,7 +5276,9 @@ MEASUREMENT
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.
+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
@@ -4494,7 +5304,8 @@ MEASUREMENT
|
|
-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)
+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
@@ -4520,7 +5331,8 @@ MEASUREMENT
|
|
-This is present for backwards compatibility and will be deprecated in an upcoming version.
+This is present for backwards compatibility and will be deprecated in an
+upcoming version.
|
varchar(10)
@@ -4544,10 +5356,16 @@ MEASUREMENT
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.
+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.
+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
@@ -4573,10 +5391,18 @@ MEASUREMENT
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 =.
+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.
+Operators are =, > and these concepts belong to the ‘Meas Value
+Operator’ domain. Accepted
+Concepts.
|
integer
@@ -4601,10 +5427,29 @@ MEASUREMENT
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.
+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
+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
@@ -4628,10 +5473,16 @@ MEASUREMENT
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 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.
+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
@@ -4656,10 +5507,16 @@ MEASUREMENT
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 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.
+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
@@ -4685,10 +5542,13 @@ MEASUREMENT
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.
+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.
+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
@@ -4712,10 +5572,13 @@ MEASUREMENT
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.
+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.
+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
@@ -4739,10 +5602,14 @@ MEASUREMENT
provider_id
|
-The provider associated with measurement record, e.g. the provider who ordered the test or the provider who recorded the result.
+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.
+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
@@ -4770,7 +5637,15 @@ MEASUREMENT
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.
+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
@@ -4795,7 +5670,10 @@ MEASUREMENT
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.
+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.
@@ -4823,10 +5701,14 @@ MEASUREMENT
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 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.
+This code is mapped to a Standard Measurement Concept in the
+Standardized Vocabularies and the original code is stored here for
+reference.
|
varchar(50)
@@ -4850,10 +5732,19 @@ MEASUREMENT
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.
+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.
+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
@@ -4878,10 +5769,12 @@ MEASUREMENT
unit_source_value
|
-This field houses the verbatim value from the source data representing the unit of the Measurement that occurred.
+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.
+This code is mapped to a Standard Condition Concept in the Standardized
+Vocabularies and the original code is stored here for reference.
|
varchar(50)
@@ -4905,10 +5798,14 @@ MEASUREMENT
value_source_value
|
-This field houses the verbatim result value of the Measurement from the source data .
+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.
+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)
@@ -4933,11 +5830,35 @@ MEASUREMENT
OBSERVATION
Table Description
- The OBSERVATION table captures clinical facts about a Person obtained in the context of examination, questioning or a procedure. Any data that cannot be represented by any other domains, such as social and lifestyle facts, medical history, family history, etc. are recorded here.
+ The OBSERVATION table captures clinical facts about a Person obtained
+in the context of examination, questioning or a procedure. Any data that
+cannot be represented by any other domains, such as social and lifestyle
+facts, medical history, family history, etc. are recorded here.
User Guide
- Observations differ from Measurements in that they do not require a standardized test or some other activity to generate clinical fact. Typical observations are medical history, family history, the stated need for certain treatment, social circumstances, lifestyle choices, healthcare utilization patterns, etc. If the generation clinical facts requires a standardized testing such as lab testing or imaging and leads to a standardized result, the data item is recorded in the MEASUREMENT table. If the clinical fact observed determines a sign, symptom, diagnosis of a disease or other medical condition, it is recorded in the CONDITION_OCCURRENCE table. Valid Observation Concepts are not enforced to be from any domain though they still should be Standard Concepts.
+ Observations differ from Measurements in that they do not require a
+standardized test or some other activity to generate clinical fact.
+Typical observations are medical history, family history, the stated
+need for certain treatment, social circumstances, lifestyle choices,
+healthcare utilization patterns, etc. If the generation clinical facts
+requires a standardized testing such as lab testing or imaging and leads
+to a standardized result, the data item is recorded in the MEASUREMENT
+table. If the clinical fact observed determines a sign, symptom,
+diagnosis of a disease or other medical condition, it is recorded in the
+CONDITION_OCCURRENCE table. Valid Observation Concepts are not enforced
+to be from any domain though they still should be Standard Concepts.
ETL Conventions
- Records whose Source Values map to any domain besides Condition, Procedure, Drug, Measurement or Device should be stored in the Observation table. Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be a Concept (stored in VALUE_AS_CONCEPT), a numerical value (VALUE_AS_NUMBER), a verbatim string (VALUE_AS_STRING), or a datetime (VALUE_AS_DATETIME). Even though Observations do not have an explicit result, the clinical fact can be 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.
+ Records whose Source Values map to any domain besides Condition,
+Procedure, Drug, Measurement or Device should be stored in the
+Observation table. Observations can be stored as attribute value pairs,
+with the attribute as the Observation Concept and the value representing
+the clinical fact. This fact can be a Concept (stored in
+VALUE_AS_CONCEPT), a numerical value (VALUE_AS_NUMBER), a verbatim
+string (VALUE_AS_STRING), or a datetime (VALUE_AS_DATETIME). Even though
+Observations do not have an explicit result, the clinical fact can be
+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.
@@ -4976,10 +5897,12 @@ OBSERVATION
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.
+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.
+Each instance of an observation present in the source data should be
+assigned this unique key.
|
integer
@@ -5003,7 +5926,8 @@ OBSERVATION
person_id
|
-The PERSON_ID of the Person for whom the Observation is recorded. This may be a system generated code.
+The PERSON_ID of the Person for whom the Observation is recorded. This
+may be a system generated code.
|
|
@@ -5030,10 +5954,14 @@ OBSERVATION
observation_concept_id
-The OBSERVATION_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies.
+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.
+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
@@ -5058,10 +5986,13 @@ OBSERVATION
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.
+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.
+For some observations the ETL may need to make a choice as to which date
+to choose.
|
date
@@ -5111,10 +6042,16 @@ OBSERVATION
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.
+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.
+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
@@ -5140,7 +6077,10 @@ OBSERVATION
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.
+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.
|
|
@@ -5166,7 +6106,8 @@ OBSERVATION
value_as_string
-This is the categorical value of the Result of the Observation, if applicable and available.
+This is the categorical value of the Result of the Observation, if
+applicable and available.
|
|
@@ -5192,10 +6133,29 @@ OBSERVATION
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.
+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’.
+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
@@ -5220,10 +6180,14 @@ OBSERVATION
qualifier_concept_id
|
-This field contains all attributes specifying the clinical fact further, such as as degrees, severities, drug-drug interaction alerts etc.
+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.
+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
@@ -5248,10 +6212,15 @@ OBSERVATION
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 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.
+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
@@ -5277,10 +6246,14 @@ OBSERVATION
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 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.
+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
@@ -5308,7 +6281,15 @@ OBSERVATION
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.
+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
@@ -5333,7 +6314,10 @@ OBSERVATION
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.
+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.
@@ -5361,10 +6345,13 @@ OBSERVATION
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 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.
+This code is mapped to a Standard Concept in the Standardized
+Vocabularies and the original code is stored here for reference.
|
varchar(50)
@@ -5388,10 +6375,19 @@ OBSERVATION
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.
+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.
+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
@@ -5416,10 +6412,12 @@ OBSERVATION
unit_source_value
|
-This field houses the verbatim value from the source data representing the unit of the Observation that occurred.
+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.
+This code is mapped to a Standard Condition Concept in the Standardized
+Vocabularies and the original code is stored here for reference.
|
varchar(50)
@@ -5443,10 +6441,12 @@ OBSERVATION
qualifier_source_value
|
-This field houses the verbatim value from the source data representing the qualifier of the Observation that occurred.
+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.
+This code is mapped to a Standard Condition Concept in the Standardized
+Vocabularies and the original code is stored here for reference.
|
varchar(50)
@@ -5471,7 +6471,11 @@ OBSERVATION
DEATH
Table Description
- The death domain contains the clinical event for how and when a Person dies. A person can have up to one record if the source system contains evidence about the Death, such as: Condition in an administrative claim, status of enrollment into a health plan, or explicit record in EHR data.
+ The death domain contains the clinical event for how and when a
+Person dies. A person can have up to one record if the source system
+contains evidence about the Death, such as: Condition in an
+administrative claim, status of enrollment into a health plan, or
+explicit record in EHR data.
@@ -5539,7 +6543,9 @@ DEATH
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.
+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
@@ -5589,10 +6595,15 @@ DEATH
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.
+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.
+Use the type concept that be reflects the source of the death record. Accepted
+Concepts.
|
integer
@@ -5618,10 +6629,12 @@ DEATH
cause_concept_id
|
-This is the Standard Concept representing the Person’s cause of death, if available.
+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.
+There is no specified domain for this concept, just choose the Standard
+Concept Id that best represents the person’s cause of death.
|
integer
@@ -5674,7 +6687,8 @@ DEATH
|
|
-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.
+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
@@ -5700,17 +6714,38 @@ DEATH
NOTE
Table Description
- The NOTE table captures unstructured information that was recorded by a provider about a patient in free text (in ASCII, or preferably in UTF8 format) notes on a given date. The type of note_text is CLOB or varchar(MAX) depending on RDBMS.
+ The NOTE table captures unstructured information that was recorded by
+a provider about a patient in free text (in ASCII, or preferably in UTF8
+format) notes on a given date. The type of note_text is CLOB or
+varchar(MAX) depending on RDBMS.
ETL Conventions
- HL7/LOINC CDO is a standard for consistent naming of documents to support a range of use cases: retrieval, organization, display, and exchange. It guides the creation of LOINC codes for clinical notes. CDO annotates each document with 5 dimensions:
+ HL7/LOINC CDO is a standard for consistent naming of documents to
+support a range of use cases: retrieval, organization, display, and
+exchange. It guides the creation of LOINC codes for clinical notes. CDO
+annotates each document with 5 dimensions:
-- Kind of Document: Characterizes the general structure of the document at a macro level (e.g. Anesthesia Consent)
-- Type of Service: Characterizes the kind of service or activity (e.g. evaluations, consultations, and summaries). The notion of time sequence, e.g., at the beginning (admission) at the end (discharge) is subsumed in this axis. Example: Discharge Teaching.
-- Setting: Setting is an extension of CMS’s definitions (e.g. Inpatient, Outpatient)
-- Subject Matter Domain (SMD): Characterizes the subject matter domain of a note (e.g. Anesthesiology)
-- Role: Characterizes the training or professional level of the author of the document, but does not break down to specialty or subspecialty (e.g. Physician) Each combination of these 5 dimensions rolls up to a unique LOINC code.
+- Kind of Document: Characterizes the general
+structure of the document at a macro level (e.g. Anesthesia
+Consent)
+- Type of Service: Characterizes the kind of service
+or activity (e.g. evaluations, consultations, and summaries). The notion
+of time sequence, e.g., at the beginning (admission) at the end
+(discharge) is subsumed in this axis. Example: Discharge Teaching.
+- Setting: Setting is an extension of CMS’s
+definitions (e.g. Inpatient, Outpatient)
+- Subject Matter Domain (SMD): Characterizes the
+subject matter domain of a note (e.g. Anesthesiology)
+- Role: Characterizes the training or professional
+level of the author of the document, but does not break down to
+specialty or subspecialty (e.g. Physician) Each combination of these 5
+dimensions rolls up to a unique LOINC code.
- According to CDO requirements, only 2 of the 5 dimensions are required to properly annotate a document; Kind of Document and any one 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.
+ According to CDO requirements, only 2 of the 5 dimensions are
+required to properly annotate a document; Kind of Document and any one
+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.
@@ -5856,7 +6891,9 @@ NOTE
The provenance of the note. Most likely this will be EHR.
-Put the source system of the note, as in EHR record. Accepted Concepts.
+Put the source system of the note, as in EHR record. Accepted
+Concepts.
|
integer
@@ -5882,10 +6919,17 @@ NOTE
note_class_concept_id
|
-A Standard Concept Id representing the HL7 LOINC Document Type Vocabulary classification of the note.
+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).
+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
@@ -5965,7 +7009,10 @@ NOTE
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.
+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
@@ -5993,7 +7040,9 @@ NOTE
The language of the note.
|
-Use Concepts that are descendants of the concept 4182347 (World Languages).
+Use Concepts that are descendants of the concept 4182347
+(World Languages).
|
integer
@@ -6127,7 +7176,8 @@ NOTE
NOTE_NLP
Table Description
- The NOTE_NLP table encodes all output of NLP on clinical notes. Each row represents a single extracted term from a note.
+ The NOTE_NLP table encodes all output of NLP on clinical notes. Each
+row represents a single extracted term from a note.
@@ -6220,7 +7270,12 @@ NOTE_NLP
|
-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.
+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
@@ -6377,7 +7432,8 @@ NOTE_NLP
|
|
-Name and version of the NLP system that extracted the term. Useful for data provenance.
+Name and version of the NLP system that extracted the term. Useful for
+data provenance.
|
varchar(250)
@@ -6455,7 +7511,12 @@ NOTE_NLP
|
|
-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.
+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)
@@ -6481,7 +7542,9 @@ NOTE_NLP
|
|
-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
+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)
@@ -6507,7 +7570,12 @@ NOTE_NLP
|
|
-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.
+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)
@@ -6532,9 +7600,12 @@ NOTE_NLP
SPECIMEN
Table Description
- The specimen domain contains the records identifying biological samples from a person.
+ The specimen domain contains the records identifying biological
+samples from a person.
ETL Conventions
- Anatomic site is coded at the most specific level of granularity possible, such that higher level classifications can be derived using the Standardized Vocabularies.
+ Anatomic site is coded at the most specific level of granularity
+possible, such that higher level classifications can be derived using
+the Standardized Vocabularies.
@@ -6628,7 +7699,10 @@ SPECIMEN
|
-The standard CONCEPT_ID that the SPECIMEN_SOURCE_VALUE maps to in the specimen domain. Accepted Concepts
+The standard CONCEPT_ID that the SPECIMEN_SOURCE_VALUE maps to in the
+specimen domain. Accepted
+Concepts
|
integer
@@ -6655,7 +7729,9 @@ SPECIMEN
|
|
-Put the source of the specimen record, as in an EHR system. Accepted Concepts.
+Put the source of the specimen record, as in an EHR system. Accepted
+Concepts.
|
integer
@@ -6761,7 +7837,9 @@ SPECIMEN
The unit for the quantity of the specimen.
|
-Map the UNIT_SOURCE_VALUE to a Standard Concept in the Unit domain. Accepted Concepts
+Map the UNIT_SOURCE_VALUE to a Standard Concept in the Unit domain. Accepted
+Concepts
|
integer
@@ -6789,7 +7867,11 @@ SPECIMEN
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
+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
@@ -6893,7 +7975,8 @@ SPECIMEN
|
|
-This unit for the quantity of the specimen, as represented in the source.
+This unit for the quantity of the specimen, as represented in the
+source.
|
varchar(50)
@@ -6919,7 +8002,8 @@ SPECIMEN
|
|
-This is the site on the body where the specimen was taken from, as represented in the source.
+This is the site on the body where the specimen was taken from, as
+represented in the source.
|
varchar(50)
@@ -6969,9 +8053,24 @@ SPECIMEN
FACT_RELATIONSHIP
Table Description
- The FACT_RELATIONSHIP table contains records about the relationships between facts stored as records in any table of the CDM. Relationships can be defined between facts from the same domain, or different domains. Examples of Fact Relationships include: Person relationships (parent-child), care site relationships (hierarchical organizational structure of facilities within a health system), indication relationship (between drug exposures and associated conditions), usage relationships (of devices during the course of an associated procedure), or facts derived from one another (measurements derived from an associated specimen).
+ The FACT_RELATIONSHIP table contains records about the relationships
+between facts stored as records in any table of the CDM. Relationships
+can be defined between facts from the same domain, or different domains.
+Examples of Fact Relationships include: Person
+relationships (parent-child), care site relationships (hierarchical
+organizational structure of facilities within a health system),
+indication relationship (between drug exposures and associated
+conditions), usage relationships (of devices during the course of an
+associated procedure), or facts derived from one another (measurements
+derived from an associated specimen).
ETL Conventions
- All relationships are directional, and each relationship is represented twice symmetrically within the FACT_RELATIONSHIP table. For 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
+ All relationships are directional, and each relationship is
+represented twice symmetrically within the FACT_RELATIONSHIP table. For
+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
@@ -7142,9 +8241,14 @@ Health System Data Tables
LOCATION
Table Description
- The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Sites.
+ The LOCATION table represents a generic way to capture physical
+location or address information of Persons and Care Sites.
ETL Conventions
- Each address or Location is unique and is present only once in the 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.
+ Each address or Location is unique and is present only once in the
+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.
@@ -7186,7 +8290,8 @@ LOCATION
The unique key given to a unique Location.
-Each instance of a Location in the source data should be assigned this unique key.
+Each instance of a Location in the source data should be assigned this
+unique key.
|
integer
@@ -7314,7 +8419,12 @@ LOCATION
|
|
-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.
+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)
@@ -7365,7 +8475,8 @@ LOCATION
|
|
-Put the verbatim value for the location here, as it shows up in the source.
+Put the verbatim value for the location here, as it shows up in the
+source.
|
varchar(50)
@@ -7390,9 +8501,23 @@ LOCATION
CARE_SITE
Table Description
- The CARE_SITE table contains a list of uniquely identified institutional (physical or organizational) units where healthcare delivery is practiced (offices, wards, hospitals, clinics, etc.).
+ The CARE_SITE table contains a list of uniquely identified
+institutional (physical or organizational) units where healthcare
+delivery is practiced (offices, wards, hospitals, clinics, etc.).
ETL Conventions
- Care site is a unique combination of location_id and place_of_service_source_value. Care site does not take into account the provider (human) information such a specialty. Many source data do not make a distinction between individual and institutional providers. The CARE_SITE table contains the institutional providers. If the source, instead of uniquely identifying individual Care Sites, only provides limited information such as Place of Service, generic or “pooled” Care Site records are listed in the CARE_SITE table. There can be hierarchical and business relationships between Care Sites. For example, 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.
+ Care site is a unique combination of location_id and
+place_of_service_source_value. Care site does not take into account the
+provider (human) information such a specialty. Many source data do not
+make a distinction between individual and institutional providers. The
+CARE_SITE table contains the institutional providers. If the source,
+instead of uniquely identifying individual Care Sites, only provides
+limited information such as Place of Service, generic or “pooled” Care
+Site records are listed in the CARE_SITE table. There can be
+hierarchical and business relationships between Care Sites. For example,
+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.
@@ -7433,7 +8558,8 @@ CARE_SITE
|
-Assign an id to each unique combination of location_id and place_of_service_source_value
+Assign an id to each unique combination of location_id and
+place_of_service_source_value
|
integer
@@ -7483,10 +8609,18 @@ CARE_SITE
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.
+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.
+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
@@ -7511,7 +8645,8 @@ CARE_SITE
location_id
|
-The location_id from the LOCATION table representing the physical location of the care_site.
+The location_id from the LOCATION table representing the physical
+location of the care_site.
|
|
@@ -7538,7 +8673,8 @@ CARE_SITE
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.
+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.
|
|
@@ -7566,7 +8702,8 @@ CARE_SITE
|
-Put the place of service of the care_site as it appears in the source data.
+Put the place of service of the care_site as it appears in the source
+data.
|
varchar(50)
@@ -7591,9 +8728,16 @@ CARE_SITE
PROVIDER
Table Description
- The PROVIDER table contains a list of uniquely identified healthcare providers. These are individuals providing hands-on healthcare to patients, such as physicians, nurses, midwives, physical therapists etc.
+ The PROVIDER table contains a list of uniquely identified healthcare
+providers. These are individuals providing hands-on healthcare to
+patients, such as physicians, nurses, midwives, physical therapists
+etc.
User Guide
- Many sources do not make a distinction between individual and institutional providers. The PROVIDER table contains the individual providers. If the source, instead of uniquely identifying individual providers, only provides limited information such as specialty, generic or ‘pooled’ Provider records are listed in the PROVIDER table.
+ Many sources do not make a distinction between individual and
+institutional providers. The PROVIDER table contains the individual
+providers. If the source, instead of uniquely identifying individual
+providers, only provides limited information such as specialty, generic
+or ‘pooled’ Provider records are listed in the PROVIDER table.
@@ -7632,10 +8776,12 @@ PROVIDER
provider_id
-It is assumed that every provider with a different unique identifier is in fact a different person and should be treated independently.
+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.
+This identifier can be the original id from the source data provided it
+is an integer, otherwise it can be an autogenerated number.
|
integer
@@ -7661,7 +8807,9 @@ PROVIDER
|
|
-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.
+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)
@@ -7685,7 +8833,8 @@ PROVIDER
npi
|
-This is the National Provider Number issued to health care providers in the US by the Centers for Medicare and Medicaid Services (CMS).
+This is the National Provider Number issued to health care providers in
+the US by the Centers for Medicare and Medicaid Services (CMS).
|
|
@@ -7711,7 +8860,8 @@ PROVIDER
dea
-This is the identifier issued by the DEA, a US federal agency, that allows a provider to write prescriptions for controlled substances.
+This is the identifier issued by the DEA, a US federal agency, that
+allows a provider to write prescriptions for controlled substances.
|
|
@@ -7737,10 +8887,20 @@ PROVIDER
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.
+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.
+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
@@ -7765,10 +8925,12 @@ PROVIDER
care_site_id
|
-This is the CARE_SITE_ID for the location that the provider primarily practices in.
+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.
+If a Provider has more than one Care Site, the main or most often
+exerted CARE_SITE_ID should be recorded.
|
integer
@@ -7818,10 +8980,14 @@ PROVIDER
gender_concept_id
|
-This field represents the recorded gender of the provider in the source data.
+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.
+If given, put a concept from the gender domain representing the recorded
+gender of the provider. Accepted
+Concepts.
|
integer
@@ -7847,10 +9013,13 @@ PROVIDER
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.
+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.
+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)
@@ -7874,10 +9043,15 @@ PROVIDER
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.
+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.
+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)
@@ -7901,10 +9075,12 @@ PROVIDER
specialty_source_concept_id
|
-This is often zero as many sites use proprietary codes to store physician speciality.
+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.
+If the source data codes provider specialty in an OMOP supported
+vocabulary store the concept_id here.
|
integer
@@ -7932,7 +9108,9 @@ PROVIDER
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.
+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)
@@ -7956,10 +9134,12 @@ PROVIDER
gender_source_concept_id
|
-This is often zero as many sites use proprietary codes to store provider gender.
+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.
+If the source data codes provider gender in an OMOP supported vocabulary
+store the concept_id here.
|
integer
@@ -7988,9 +9168,25 @@ Health Economics Data Tables
PAYER_PLAN_PERIOD
Table Description
- The PAYER_PLAN_PERIOD table captures details of the period of time that a Person is continuously enrolled under a specific health Plan benefit structure from a given Payer. Each Person receiving healthcare is typically covered by a health benefit plan, which pays for (fully or partially), or directly provides, the care. These benefit plans are provided by payers, such as health insurances or state or government agencies. In each plan the details of the health benefits are defined for the Person or her family, and the health benefit Plan might change over time typically with increasing utilization (reaching certain cost thresholds such as deductibles), plan availability and purchasing choices of the Person. The unique combinations of Payer organizations, health benefit Plans and time periods in which they are valid for a Person are recorded in this table.
+ The PAYER_PLAN_PERIOD table captures details of the period of time
+that a Person is continuously enrolled under a specific health Plan
+benefit structure from a given Payer. Each Person receiving healthcare
+is typically covered by a health benefit plan, which pays for (fully or
+partially), or directly provides, the care. These benefit plans are
+provided by payers, such as health insurances or state or government
+agencies. In each plan the details of the health benefits are defined
+for the Person or her family, and the health benefit Plan might change
+over time typically with increasing utilization (reaching certain cost
+thresholds such as deductibles), plan availability and purchasing
+choices of the Person. The unique combinations of Payer organizations,
+health benefit Plans and time periods in which they are valid for a
+Person are recorded in this table.
User Guide
- A Person can have multiple, overlapping, Payer_Plan_Periods in this table. For example, medical and drug coverage in the US can be represented by two Payer_Plan_Periods. The details of the benefit structure of the Plan is rarely known, the idea is just to identify that the Plans are different.
+ A Person can have multiple, overlapping, Payer_Plan_Periods in this
+table. For example, medical and drug coverage in the US can be
+represented by two Payer_Plan_Periods. The details of the benefit
+structure of the Plan is rarely known, the idea is just to identify that
+the Plans are different.
@@ -8029,7 +9225,8 @@ PAYER_PLAN_PERIOD
payer_plan_period_id
-A unique identifier for each unique combination of a Person, Payer, Plan, and Period of time.
+A unique identifier for each unique combination of a Person, Payer,
+Plan, and Period of time.
|
|
@@ -8058,7 +9255,8 @@ PAYER_PLAN_PERIOD
The Person covered by the Plan.
-A single Person can have multiple, overlapping, PAYER_PLAN_PERIOD records
+A single Person can have multiple, overlapping, PAYER_PLAN_PERIOD
+records
|
integer
@@ -8135,10 +9333,17 @@ PAYER_PLAN_PERIOD
payer_concept_id
|
-This field represents the organization who reimburses the provider which administers care to the Person.
+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.
+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
@@ -8191,7 +9396,8 @@ PAYER_PLAN_PERIOD
|
|
-If the source data codes the Payer in an OMOP supported vocabulary store the concept_id here.
+If the source data codes the Payer in an OMOP supported vocabulary store
+the concept_id here.
|
integer
@@ -8216,10 +9422,17 @@ PAYER_PLAN_PERIOD
plan_concept_id
|
-This field represents the specific health benefit Plan the Person is enrolled in.
+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.
+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
@@ -8244,7 +9457,8 @@ PAYER_PLAN_PERIOD
plan_source_value
|
-This is the health benefit Plan of the Person as it appears in the source data.
+This is the health benefit Plan of the Person as it appears in the
+source data.
|
|
@@ -8272,7 +9486,8 @@ PAYER_PLAN_PERIOD
|
-If the source data codes the Plan in an OMOP supported vocabulary store the concept_id here.
+If the source data codes the Plan in an OMOP supported vocabulary store
+the concept_id here.
|
integer
@@ -8297,10 +9512,18 @@ PAYER_PLAN_PERIOD
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.
+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.
+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
@@ -8353,7 +9576,8 @@ PAYER_PLAN_PERIOD
|
|
-If the source data codes the sponsor in an OMOP supported vocabulary store the concept_id here.
+If the source data codes the sponsor in an OMOP supported vocabulary
+store the concept_id here.
|
integer
@@ -8378,10 +9602,12 @@ PAYER_PLAN_PERIOD
family_source_value
|
-The common identifier for all people (often a family) that covered by the same policy.
+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.
+Often these are the common digits of the enrollment id of the policy
+members.
|
varchar(50)
@@ -8408,7 +9634,11 @@ PAYER_PLAN_PERIOD
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.
+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
@@ -8461,7 +9691,8 @@ PAYER_PLAN_PERIOD
|
|
-If the source data codes the stop reason in an OMOP supported vocabulary store the concept_id here.
+If the source data codes the stop reason in an OMOP supported vocabulary
+store the concept_id here.
|
integer
@@ -8487,12 +9718,36 @@ PAYER_PLAN_PERIOD
COST
Table Description
- The COST table captures records containing the cost of any medical event recorded in one of the OMOP clinical event tables such as DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, VISIT_OCCURRENCE, VISIT_DETAIL, DEVICE_OCCURRENCE, OBSERVATION or MEASUREMENT.
- Each record in the cost table account for the amount of money transacted for the clinical event. So, the COST table may be used to represent both receivables (charges) and payments (paid), each transaction type represented by its COST_CONCEPT_ID. The COST_TYPE_CONCEPT_ID field will use concepts in the Standardized Vocabularies to designate the source (provenance) of the cost data. A reference to the health plan information in the PAYER_PLAN_PERIOD table is stored in the record for information used for the adjudication system to determine the persons benefit for the clinical event.
+ The COST table captures records containing the cost of any medical
+event recorded in one of the OMOP clinical event tables such as
+DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, VISIT_OCCURRENCE, VISIT_DETAIL,
+DEVICE_OCCURRENCE, OBSERVATION or MEASUREMENT.
+ Each record in the cost table account for the amount of money
+transacted for the clinical event. So, the COST table may be used to
+represent both receivables (charges) and payments (paid), each
+transaction type represented by its COST_CONCEPT_ID. The
+COST_TYPE_CONCEPT_ID field will use concepts in the Standardized
+Vocabularies to designate the source (provenance) of the cost data. A
+reference to the health plan information in the PAYER_PLAN_PERIOD table
+is stored in the record for information used for the adjudication system
+to determine the persons benefit for the clinical event.
User Guide
- When dealing with summary costs, the cost of the goods or services the provider provides is often not known directly, but derived from the hospital charges multiplied by an average cost-to-charge ratio.
+ When dealing with summary costs, the cost of the goods or services
+the provider provides is often not known directly, but derived from the
+hospital charges multiplied by an average cost-to-charge ratio.
ETL Conventions
- One cost record is generated for each response by a payer. In a claims databases, the payment and payment terms reported by the payer for the goods or services billed will generate one cost record. If the source data has payment information for more than one payer (i.e. primary insurance and secondary insurance payment for one entity), then a cost record is created for each reporting payer. Therefore, it is possible for one procedure to have multiple cost records for each payer, but typically it contains one or no record per entity. Payer 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).
+ One cost record is generated for each response by a payer. In a
+claims databases, the payment and payment terms reported by the payer
+for the goods or services billed will generate one cost record. If the
+source data has payment information for more than one payer
+(i.e. primary insurance and secondary insurance payment for one entity),
+then a cost record is created for each reporting payer. Therefore, it is
+possible for one procedure to have multiple cost records for each payer,
+but typically it contains one or no record per entity. Payer
+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).
@@ -9010,7 +10265,8 @@ COST
revenue_code_source_value
-Revenue codes are a method to charge for a class of procedures and conditions in the U.S. hospital system.
+Revenue codes are a method to charge for a class of procedures and
+conditions in the U.S. hospital system.
|
|
@@ -9062,7 +10318,8 @@ COST
drg_source_value
-Diagnosis Related Groups are US codes used to classify hospital cases into one of approximately 500 groups.
+Diagnosis Related Groups are US codes used to classify hospital cases
+into one of approximately 500 groups.
|
|
@@ -9092,9 +10349,15 @@ Standardized Derived Elements
DRUG_ERA
Table Description
- A Drug Era is defined as a span of time when the Person is assumed to be exposed to a particular active ingredient. A Drug Era is not the same as a Drug Exposure: Exposures are individual records corresponding to the source when Drug was delivered to the Person, while successive periods of Drug Exposures are combined under certain rules to produce continuous Drug Eras.
+ A Drug Era is defined as a span of time when the Person is assumed to
+be exposed to a particular active ingredient. A Drug Era is not the same
+as a Drug Exposure: Exposures are individual records corresponding to
+the source when Drug was delivered to the Person, while successive
+periods of Drug Exposures are combined under certain rules to produce
+continuous Drug Eras.
ETL Conventions
- The SQL script for generating DRUG_ERA records can be found here.
+ The SQL script for generating DRUG_ERA records can be found here.
@@ -9214,7 +10477,8 @@ DRUG_ERA
|
-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.
+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
@@ -9240,7 +10504,19 @@ DRUG_ERA
|
|
-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.
+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
@@ -9291,7 +10567,16 @@ DRUG_ERA
|
|
-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.
+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
@@ -9316,9 +10601,15 @@ DRUG_ERA
DOSE_ERA
Table Description
- A Dose Era is defined as a span of time when the Person is assumed to be exposed to a constant dose of a specific active ingredient.
+ A Dose Era is defined as a span of time when the Person is assumed to
+be exposed to a constant dose of a specific active ingredient.
ETL Conventions
- Dose Eras will be derived from records in the DRUG_EXPOSURE table and the Dose information from the DRUG_STRENGTH table using a standardized 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.
+ Dose Eras will be derived from records in the DRUG_EXPOSURE table and
+the Dose information from the DRUG_STRENGTH table using a standardized
+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.
@@ -9490,7 +10781,8 @@ DOSE_ERA
dose_era_start_date
-The date the Person started on the specific dosage, with at least 31 days since any prior exposure.
+The date the Person started on the specific dosage, with at least 31
+days since any prior exposure.
|
|
@@ -9518,7 +10810,9 @@ DOSE_ERA
|
-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.
+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
@@ -9543,13 +10837,39 @@ DOSE_ERA
CONDITION_ERA
Table Description
- A Condition Era is defined as a span of time when the Person is assumed to have a given condition. Similar to Drug Eras, Condition Eras are chronological periods of Condition Occurrence. Combining individual Condition Occurrences into a single Condition Era serves two purposes:
+ A Condition Era is defined as a span of time when the Person is
+assumed to have a given condition. Similar to Drug Eras, Condition Eras
+are chronological periods of Condition Occurrence. Combining individual
+Condition Occurrences into a single Condition Era serves two
+purposes:
-- It allows aggregation of chronic conditions that require frequent ongoing care, instead of treating each Condition Occurrence as an independent event.
-- It allows aggregation of multiple, closely timed doctor visits for the same Condition to avoid double-counting the Condition Occurrences. For example, consider a Person who visits her Primary Care Physician (PCP) and who is referred to a specialist. At a later time, the Person visits the specialist, who confirms the PCP’s original diagnosis and provides the appropriate treatment to resolve the condition. These two independent doctor visits should be aggregated into one Condition Era.
+- It allows aggregation of chronic conditions that require frequent
+ongoing care, instead of treating each Condition Occurrence as an
+independent event.
+- It allows aggregation of multiple, closely timed doctor visits for
+the same Condition to avoid double-counting the Condition Occurrences.
+For example, consider a Person who visits her Primary Care Physician
+(PCP) and who is referred to a specialist. At a later time, the Person
+visits the specialist, who confirms the PCP’s original diagnosis and
+provides the appropriate treatment to resolve the condition. These two
+independent doctor visits should be aggregated into one Condition
+Era.
ETL Conventions
- Each Condition Era corresponds to one or many Condition Occurrence records that form a continuous interval. The condition_concept_id field contains Concepts that are identical to those of the CONDITION_OCCURRENCE table records that make up the Condition Era. In contrast to Drug Eras, Condition Eras are not aggregated to contain Conditions of different hierarchical layers. The SQl Script for generating CONDITION_ERA records can be found here The Condition Era Start Date is the start date of the first Condition Occurrence. The Condition Era End Date is the end date of the last 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.
+ Each Condition Era corresponds to one or many Condition Occurrence
+records that form a continuous interval. The condition_concept_id field
+contains Concepts that are identical to those of the
+CONDITION_OCCURRENCE table records that make up the Condition Era. In
+contrast to Drug Eras, Condition Eras are not aggregated to contain
+Conditions of different hierarchical layers. The SQl Script for
+generating CONDITION_ERA records can be found here
+The Condition Era Start Date is the start date of the first Condition
+Occurrence. The Condition Era End Date is the end date of the last
+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.
@@ -9667,7 +10987,10 @@ CONDITION_ERA
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.
+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.
|
|
@@ -9693,7 +11016,9 @@ CONDITION_ERA
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.
+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.
|
|
@@ -9719,7 +11044,8 @@ CONDITION_ERA
condition_occurrence_count
-The number of individual Condition Occurrences used to construct the condition era.
+The number of individual Condition Occurrences used to construct the
+condition era.
|
|
@@ -9749,7 +11075,8 @@ Metadata Tables
| | | | | | | | | | | | | | | | | |
OMOP CDM Background
-