Please be aware that v6.0 of the OMOP CDM is not fully supported by the OHDSI suite of tools and methods. The major difference in CDM v5.3 and CDM v6.0 involves switching the *_datetime fields to mandatory rather than optional. This switch radically changes the assumptions related to exposure and outcome timing. Rather than move forward with v6.0, CDM v5.4 was designed with additions to the model that have been requested by the community while retaining the date structure of medical events in v5.3. Please see our the specifications for CDM v5.4 and detailed changes from CDM v5.3. For new collaborators to OHDSI, please transform your data to CDM v5.4 until such time that the v6 series of the CDM is ready for mainstream use.
Below is the specification document for the OMOP Common Data Model, v6.0. Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the forums or the github issue page.
–after regeneration of DDLs link to csv of cdm link to pdf of cdm documentation link to forum on doc page
Table Description
This table serves as the central identity management for all Persons in the database. It contains records that uniquely identify each person or patient, and some demographic information.
User Guide
All records in this table are independent Persons.
ETL Conventions
All Persons in a database needs one record in this table, unless they fail data quality requirements specified in the ETL. Persons with no Events should have a record nonetheless. If more than one data source contributes Events to the database, Persons must be reconciled, if possible, across the sources to create one single record per Person. The BIRTH_DATETIME must be equivalent to the content of BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR. There is a helpful rule listed in table below for how to derive BIRTH_DATETIME if it is not available in the source. New to CDM v6.0 The person’s death date is now stored in this table instead of the separate DEATH table. In the case that multiple dates of death are given in the source data the ETL should make a choice as to which death date to put in the PERSON table. Any additional dates can be stored in the OBSERVATION table using the concept 4265167 which stands for ‘Date of death’ . Similarly, the cause of death is stored in the CONDITION_OCCURRENCE table using the CONDITION_STATUS_CONCEPT_ID 32891 for ‘Cause of death’.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| person_id | It is assumed that every person with a different unique identifier is in fact a different person and should be treated independently. | Any person linkage that needs to occur to uniquely identify Persons ought to be done prior to writing this table. This identifier can be the original id from the source data provided if it is an integer, otherwise it can be an autogenerated number. | bigint | Yes | Yes | No | ||
| gender_concept_id | This field is meant to capture the biological sex at birth of the Person. This field should not be used to study gender identity issues. | Use the gender or sex value present in the data under the assumption that it is the biological sex at birth. If the source data captures gender identity it should be stored in the OBSERVATION table. Accepted gender concepts | integer | Yes | No | Yes | CONCEPT | Gender |
| year_of_birth | Compute age using year_of_birth. | For data sources with date of birth, the year should be extracted. For data sources where the year of birth is not available, the approximate year of birth could be derived based on age group categorization, if available. | integer | Yes | No | No | ||
| month_of_birth | For data sources that provide the precise date of birth, the month should be extracted and stored in this field. | integer | No | No | No | |||
| day_of_birth | For data sources that provide the precise date of birth, the day should be extracted and stored in this field. | integer | No | No | No | |||
| birth_datetime | This field is not required but highly encouraged. For data sources that provide the precise datetime of birth, that value should be stored in this field. If birth_datetime is not provided in the source, use the following logic to infer the date: If day_of_birth is null and month_of_birth is not null then use the first of the month in that year. If month_of_birth is null or if day_of_birth AND month_of_birth are both null and the person has records during their year of birth then use the date of the earliest record, otherwise use the 15th of June of that year. If time of birth is not given use midnight (00:00:0000). | datetime | No | No | No | |||
| death_datetime | This field is the death date to be used in analysis, as determined by the ETL logic. Any additional information about a Person’s death is stored in the OBSERVATION table with the concept_id 4306655 or in the CONDITION_OCCURRENCE . | If there are multiple dates of death given for a Person, choose the one that is deemed most reliable. This may be a discharge from the hospital where the Person is listed as deceased or it could be latest death date provided. If a patient has clinical activity more than 60 days after the death date given in the source, it is a viable option to drop the death record as it may have been falsely reported. Similarly, if the death record is from a reputable source (e.g. government provided information) it is also a viable option to remove event records that occur in the data > 60 days after death. | datetime | No | ||||
| race_concept_id | This field captures race or ethnic background of the person. | Only use this field if you have information about race or ethnic background. The Vocabulary contains Concepts about the main races and ethnic backgrounds in a hierarchical system. Due to the imprecise nature of human races and ethnic backgrounds, this is not a perfect system. Mixed races are not supported. If a clear race or ethnic background cannot be established, use Concept_Id 0. Accepted Race Concepts. | integer | Yes | No | Yes | CONCEPT | Race |
| ethnicity_concept_id | This field captures Ethnicity as defined by the Office of Management and Budget (OMB) of the US Government: it distinguishes only between “Hispanic” and “Not Hispanic”. Races and ethnic backgrounds are not stored here. | Only use this field if you have US-based data and a source of this information. Do not attempt to infer Ethnicity from the race or ethnic background of the Person. Accepted ethnicity concepts | integer | Yes | No | Yes | CONCEPT | Ethnicity |
| location_id | The location refers to the physical address of the person. This field should capture the last known location of the person. Any prior locations are captured in the LOCATION_HISTORY table. | 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. Any prior locations are captured in the LOCATION_HISTORY table. | bigint | No | No | Yes | LOCATION | |
| provider_id | The Provider refers to the last known primary care provider (General Practitioner). | Put the provider_id from the PROVIDER table of the last known general practitioner of the person. If there are multiple providers, it is up to the ETL to decide which to put here. | bigint | No | No | Yes | PROVIDER | |
| care_site_id | The Care Site refers to where the Provider typically provides the primary care. | bigint | No | No | Yes | CARE_SITE | ||
| person_source_value | Use this field to link back to persons in the source data. This is typically used for error checking of ETL logic. | Some use cases require the ability to link back to persons in the source data. This field allows for the storing of the person value as it appears in the source. This field is not required but strongly recommended. | varchar(50) | No | No | No | ||
| gender_source_value | This field is used to store the biological sex of the person from the source data. It is not intended for use in standard analytics but for reference only. | Put the biological sex of the person as it appears in the source data. | varchar(50) | No | No | No | ||
| gender_source_concept_id | Due to the small number of options, this tends to be zero. | If the source data codes biological sex in a non-standard vocabulary, store the concept_id here, otherwise set to 0. | integer | Yes | No | Yes | CONCEPT | |
| race_source_value | This field is used to store the race of the person from the source data. It is not intended for use in standard analytics but for reference only. | Put the race of the person as it appears in the source data. | varchar(50) | No | No | No | ||
| race_source_concept_id | Due to the small number of options, this tends to be zero. | If the source data codes race in an OMOP supported vocabulary store the concept_id here, otherwise set to 0. | integer | Yes | No | Yes | CONCEPT | |
| ethnicity_source_value | This field is used to store the ethnicity of the person from the source data. It is not intended for use in standard analytics but for reference only. | If the person has an ethnicity other than the OMB standard of “Hispanic” or “Not Hispanic” store that value from the source data here. | varchar(50) | No | No | No | ||
| ethnicity_source_concept_id | Due to the small number of options, this tends to be zero. | If the source data codes ethnicity in an OMOP supported vocabulary, store the concept_id here, otherwise set to 0. | integer | Yes | No | Yes | CONCEPT |
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.
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.
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.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| observation_period_id | A Person can have multiple discrete Observation Periods which are identified by the Observation_Period_Id. | Assign a unique observation_period_id to each discrete Observation Period for a Person. | bigint | Yes | Yes | No | ||
| person_id | The Person ID of the PERSON record for which the Observation Period is recorded. | bigint | Yes | No | Yes | PERSON | ||
| observation_period_start_date | Use this date to determine the start date of the Observation Period | It is often the case that the idea of Observation Periods does not exist in source data. In those cases, the observation_period_start_date can be inferred as the earliest Event date available for the Person. In insurance claim data, the Observation Period can be considered as the time period the Person is enrolled with a payer. If a Person switches plans but stays with the same payer, and therefore capturing of data continues, that change would be captured in PAYER_PLAN_PERIOD. | date | Yes | No | No | ||
| observation_period_end_date | Use this date to determine the end date of the period for which we can assume that all events for a Person are recorded. | It is often the case that the idea of Observation Periods does not exist in source data. In those cases, the observation_period_end_date can be inferred as the last Event date available for the Person. In insurance claim data, the Observation Period can be considered as the time period the Person is enrolled with a payer. | date | Yes | No | No | ||
| period_type_concept_id | This field can be used to determine the provenance of the Observation Period as in whether the period was determined from an insurance enrollment file, EHR healthcare encounters, or other sources. | Choose the observation_period_type_concept_id that best represents how the period was determined. Accepted Concepts. | Integer | Yes | No | Yes | CONCEPT | Type Concept |
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.
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 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.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| visit_occurrence_id | Use this to identify unique interactions between a person and the health care system. This identifier links across the other CDM event tables to associate events with a visit. | This should be populated by creating a unique identifier for each unique interaction between a person and the healthcare system where the person receives a medical good or service over a span of time. | bigint | Yes | Yes | No | ||
| person_id | bigint | Yes | No | Yes | PERSON | |||
| visit_concept_id | This field contains a concept id representing the kind of visit, like inpatient or outpatient. All concepts in this field should be standard and belong to the Visit domain. | Populate this field based on the kind of visit that took place for the person. For example this could be “Inpatient Visit”, “Outpatient Visit”, “Ambulatory Visit”, etc. This table will contain standard concepts in the Visit domain. These concepts are arranged in a hierarchical structure to facilitate cohort definitions by rolling up to generally familiar Visits adopted in most healthcare systems worldwide. | integer | Yes | No | Yes | CONCEPT | Visit |
| visit_start_date | For inpatient visits, the start date is typically the admission date. For outpatient visits the start date and end date will be the same. | When populating visit_start_date, you should think about the patient experience to make decisions on how to define visits. In the case of an inpatient visit this should be the date the patient was admitted to the hospital or institution. In all other cases this should be the date of the patient-provider interaction. | date | No | No | No | ||
| visit_start_datetime | If no time is given for the start date of a visit, set it to midnight (00:00:0000). | datetime | Yes | No | No | |||
| visit_end_date | For inpatient visits the end date is typically the discharge date. | Visit end dates are mandatory. If end dates are not provided in the source there are three ways in which to derive them: Outpatient Visit: visit_end_datetime = visit_start_datetime Emergency Room Visit: visit_end_datetime = visit_start_datetime Inpatient Visit: Usually there is information about discharge. If not, you should be able to derive the end date from the sudden decline of activity or from the absence of inpatient procedures/drugs. Non-hospital institution Visits: Particularly for claims data, if end dates are not provided assume the visit is for the duration of month that it occurs. For Inpatient Visits ongoing at the date of ETL, put date of processing the data into visit_end_datetime and visit_type_concept_id with 32220 “Still patient” to identify the visit as incomplete. All other Visits: visit_end_datetime = visit_start_datetime. If this is a one-day visit the end date should match the start date. | date | No | No | No | ||
| visit_end_datetime | If no time is given for the end date of a visit, set it to midnight (00:00:0000). | datetime | Yes | No | No | |||
| visit_type_concept_id | Use this field to understand the provenance of the visit record, or where the record comes from. | Populate this field based on the provenance of the visit record, as in whether it came from an EHR record or billing claim. | Integer | Yes | No | Yes | CONCEPT | Type Concept |
| provider_id | There will only be one provider per visit record and the ETL document should clearly state how they were chosen (attending, admitting, etc.). If there are multiple providers associated with a visit in the source, this can be reflected in the event tables (CONDITION_OCCURRENCE, PROCEDURE_OCCURRENCE, etc.) or in the VISIT_DETAIL table. | If there are multiple providers associated with a visit, you will need to choose which one to put here. The additional providers can be stored in the visit_detail table. | bigint | No | No | Yes | PROVIDER | |
| care_site_id | This field provides information about the care site where the visit took place. | There should only be one care site associated with a visit. | bigint | No | No | Yes | CARE_SITE | |
| visit_source_value | This field houses the verbatim value from the source data representing the kind of visit that took place (inpatient, outpatient, emergency, etc.) | If there is information about the kind of visit in the source data that value should be stored here. If a visit is an amalgamation of visits from the source then use a hierarchy to choose the visit source value, such as IP -> ER-> OP. This should line up with the logic chosen to determine how visits are created. | varchar(50) | No | No | No | ||
| visit_source_concept_id | If the visit source value is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. If not available set to 0. | integer | Yes | No | Yes | CONCEPT | ||
| admitted_from_concept_id | Use this field to determine where the patient was admitted from. This concept is part of the visit domain and can indicate if a patient was admitted to the hospital from a long-term care facility, for example. | If available, map the admitted_from_source_value to a standard concept in the visit domain. If not available set to 0. | integer | Yes | No | Yes | CONCEPT | Visit |
| admitted_from_source_value | This information may be called something different in the source data but the field is meant to contain a value indicating where a person was admitted from. Typically this applies only to visits that have a length of stay, like inpatient visits or long-term care visits. | varchar(50) | No | No | No | |||
| discharge_to_concept_id | Use this field to determine where the patient was discharged to after a visit. This concept is part of the visit domain and can indicate if a patient was discharged to home or sent to a long-term care facility, for example. | If available, map the discharge_to_source_value to a standard concept in the visit domain. If not available set to 0. | integer | Yes | No | Yes | CONCEPT | Visit |
| discharge_to_source_value | This information may be called something different in the source data but the field is meant to contain a value indicating where a person was discharged to after a visit, as in they went home or were moved to long-term care. Typically this applies only to visits that have a length of stay of a day or more. | varchar(50) | No | No | No | |||
| preceding_visit_occurrence_id | Use this field to find the visit that occurred for the person prior to the given visit. There could be a few days or a few years in between. | The preceding_visit_id 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”. | bigint | No | No | Yes | VISIT_OCCURRENCE |
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.
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.
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.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| visit_detail_id | Use this to identify unique interactions between a person and the health care system. This identifier links across the other CDM event tables to associate events with a visit detail. | This should be populated by creating a unique identifier for each unique interaction between a person and the healthcare system where the person receives a medical good or service over a span of time. | bigint | Yes | Yes | No | ||
| person_id | bigint | Yes | No | Yes | PERSON | |||
| visit_detail_concept_id | This field contains a concept id representing the kind of visit detail, like inpatient or outpatient. All concepts in this field should be standard and belong to the Visit domain. | Populate this field based on the kind of visit that took place for the person. For example this could be “Inpatient Visit”, “Outpatient Visit”, “Ambulatory Visit”, etc. This table will contain standard concepts in the Visit domain. These concepts are arranged in a hierarchical structure to facilitate cohort definitions by rolling up to generally familiar Visits adopted in most healthcare systems worldwide. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Visit |
| visit_detail_start_date | This is the date of the start of the encounter. This may or may not be equal to the date of the Visit the Visit Detail is associated with. | When populating visit_start_date, you should think about the patient experience to make decisions on how to define visits. Most likely this should be the date of the patient-provider interaction. | date | Yes | No | No | ||
| visit_detail_start_datetime | If no time is given for the start date of a visit, set it to midnight (00:00:0000). | datetime | No | No | No | |||
| visit_detail_end_date | This the end date of the patient-provider interaction. | Visit Detail end dates are mandatory. If end dates are not provided in the source there are three ways in which to derive them:<br> - 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.<br> For Inpatient Visit Details ongoing at the date of ETL, put date of processing the data into visit_detai_end_datetime and visit_detail_type_concept_id with 32220 “Still patient” to identify the visit as incomplete. All other Visits Details: visit_detail_end_datetime = visit_detail_start_datetime. | date | Yes | No | No | ||
| visit_detail_end_datetime | If no time is given for the end date of a visit, set it to midnight (00:00:0000). | datetime | No | No | No | |||
| visit_detail_type_concept_id | Use this field to understand the provenance of the visit detail record, or where the record comes from. | Populate this field based on the provenance of the visit detail record, as in whether it came from an EHR record or billing claim. Accepted Concepts. | Integer | Yes | No | Yes | CONCEPT | Type Concept |
| provider_id | There will only be one provider per visit record and the ETL document should clearly state how they were chosen (attending, admitting, etc.). This is a typical reason for leveraging the VISIT_DETAIL table as even though each VISIT_DETAIL record can only have one provider, there is no limit to the number of VISIT_DETAIL records that can be associated to a VISIT_OCCURRENCE record. | The additional providers associated to a Visit can be stored in this table where each VISIT_DETAIL record represents a different provider. | bigint | No | No | Yes | PROVIDER | |
| care_site_id | This field provides information about the Care Site where the Visit Detail took place. | There should only be one Care Site associated with a Visit Detail. | bigint | No | No | Yes | CARE_SITE | |
| visit_detail_source_value | This field houses the verbatim value from the source data representing the kind of visit detail that took place (inpatient, outpatient, emergency, etc.) | If there is information about the kind of visit detail in the source data that value should be stored here. If a visit is an amalgamation of visits from the source then use a hierarchy to choose the VISIT_DETAIL_SOURCE_VALUE, such as IP -> ER-> OP. This should line up with the logic chosen to determine how visits are created. | varchar(50) | No | No | No | ||
| visit_detail_source_concept_id | If the VISIT_DETAIL_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. If not available, map to 0. | integer | Yes | No | Yes | CONCEPT | ||
| admitted_from_concept_id | This information may be called something different in the source data but the field is meant to contain a value indicating where a person was admitted from. Typically this applies only to visits that have a length of stay, like inpatient visits or long-term care visits. | varchar(50) | No | No | No | |||
| admitted_from_source_value | Use this field to determine where the patient was admitted from. This concept is part of the visit domain and can indicate if a patient was admitted to the hospital from a long-term care facility, for example. | If available, map the admitted_from_source_value to a standard concept in the visit domain. If not available, map to 0. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Visit |
| discharge_to_source_value | This information may be called something different in the source data but the field is meant to contain a value indicating where a person was discharged to after a visit, as in they went home or were moved to long-term care. Typically this applies only to visits that have a length of stay of a day or more. | varchar(50) | No | No | No | |||
| discharge_to_concept_id | Use this field to determine where the patient was discharged to after a visit detail record. This concept is part of the visit domain and can indicate if a patient was discharged to home or sent to a long-term care facility, for example. | If available, map the DISCHARGE_TO_SOURCE_VALUE to a Standard Concept in the Visit domain. If not available, set to 0. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Visit |
| preceding_visit_detail_id | Use this field to find the visit detail that occurred for the person prior to the given visit detail record. There could be a few days or a few years in between. | The PRECEDING_VISIT_DETAIL_ID can be used to link a visit immediately preceding the current Visit Detail. Note this is not symmetrical, and there is no such thing as a “following_visit_id”. | bigint | No | No | Yes | VISIT_DETAIL | |
| visit_detail_parent_id | Use this field to find the visit detail that subsumes the given visit detail record. This is used in the case that a visit detail record needs to be nested beyond the VISIT_OCCURRENCE/VISIT_DETAIL relationship. | If there are multiple nested levels to how Visits are represented in the source, the VISIT_DETAIL_PARENT_ID can be used to record this relationship. | bigint | No | No | Yes | VISIT_DETAIL | |
| visit_occurrence_id | Use this field to link the VISIT_DETAIL record to its VISIT_OCCURRENCE. | Put the VISIT_OCCURRENCE_ID that subsumes the VISIT_DETAIL record here. | bigint | Yes | No | Yes | VISIT_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.
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.
ETL Conventions
Source codes and source text fields mapped to Standard Concepts of the Condition Domain have to be recorded here.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| condition_occurrence_id | The unique key given to a condition record for a person. Refer to the ETL for how duplicate conditions during the same visit were handled. | Each instance of a condition present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same condition within the same visit. It is valid to keep these duplicates and assign them individual, unique, CONDITION_OCCURRENCE_IDs, though it is up to the ETL how they should be handled. | bigint | Yes | Yes | No | ||
| person_id | The PERSON_ID of the PERSON for whom the condition is recorded. | bigint | Yes | No | Yes | PERSON | ||
| condition_concept_id | The CONDITION_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source value which represents a condition | The CONCEPT_ID that the CONDITION_SOURCE_VALUE maps to. Only records whose source values map to concepts with a domain of “Condition” should go in this table. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Condition |
| condition_start_date | Use this date to determine the start date of the condition | Most often data sources do not have the idea of a start date for a condition. Rather, if a source only has one date associated with a condition record it is acceptable to use that date for both the CONDITION_START_DATE and the CONDITION_END_DATE. | date | Yes | No | No | ||
| condition_start_datetime | If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) | datetime | No | No | No | |||
| condition_end_date | Use this date to determine the end date of the condition | Most often data sources do not have the idea of a start date for a condition. Rather, if a source only has one date associated with a condition record it is acceptable to use that date for both the CONDITION_START_DATE and the CONDITION_END_DATE. | date | No | No | No | ||
| condition_end_datetime | If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) | datetime | No | No | No | |||
| condition_type_concept_id | This field can be used to determine the provenance of the Condition record, as in whether the condition was from an EHR system, insurance claim, registry, or other sources. | Choose the condition_type_concept_id that best represents the provenance of the record. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Type Concept |
| condition_status_concept_id | This concept represents the point during the visit the diagnosis was given (admitting diagnosis, final diagnosis), whether the diagnosis was determined due to laboratory findings, if the diagnosis was exclusionary, or if it was a preliminary diagnosis, among others. | Choose the Concept in the Condition Status domain that best represents the point during the visit when the diagnosis was given. These can include admitting diagnosis, principal diagnosis, and secondary diagnosis. If not available, set to 0. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | |
| stop_reason | The Stop Reason indicates why a Condition is no longer valid with respect to the purpose within the source data. Note that a Stop Reason does not necessarily imply that the condition is no longer occurring. | This information is often not populated in source data and it is a valid etl choice to leave it blank if the information does not exist. | varchar(20) | No | No | No | ||
| provider_id | The provider associated with condition record, e.g. the provider who made the diagnosis or the provider who recorded the symptom. | The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record, for example the admitting vs attending physician on an EHR record. | bigint | No | No | Yes | PROVIDER | |
| visit_occurrence_id | The visit during which the condition occurred. | Depending on the structure of the source data, this may have to be determined based on dates. If a CONDITION_START_DATE occurs within the start and end date of a Visit it is a valid ETL choice to choose the VISIT_OCCURRENCE_ID from the Visit that subsumes it, even if not explicitly stated in the data. While not required, an attempt should be made to locate the VISIT_OCCURRENCE_ID of the CONDITION_OCCURRENCE record. | bigint | No | No | Yes | VISIT_OCCURRENCE | |
| visit_detail_id | The VISIT_DETAIL record during which the condition occurred. For example, if the person was in the ICU at the time of the diagnosis the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit. | Same rules apply as for the VISIT_OCCURRENCE_ID. | bigint | No | No | Yes | VISIT_DETAIL | |
| condition_source_value | This field houses the verbatim value from the source data representing the condition that occurred. For example, this could be an ICD10 or Read code. | This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference. | varchar(50) | No | No | No | ||
| condition_source_concept_id | This is the concept representing the condition source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Condition necessary for a given analytic use case. Consider using CONDITION_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. | If the CONDITION_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. If not available, set to 0. | integer | Yes | No | Yes | CONCEPT | |
| condition_status_source_value | This field houses the verbatim value from the source data representing the condition status. | This information may be called something different in the source data but the field is meant to contain a value indicating when and how a diagnosis was given to a patient. This source value is mapped to a standard concept which is stored in the CONDITION_STATUS_CONCEPT_ID field. | varchar(50) | No | No | No |
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.
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.
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.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| drug_exposure_id | The unique key given to records of drug dispensings or administrations for a person. Refer to the ETL for how duplicate drugs during the same visit were handled. | Each instance of a drug dispensing or administration present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same drug within the same visit. It is valid to keep these duplicates and assign them individual, unique, DRUG_EXPOSURE_IDs, though it is up to the ETL how they should be handled. | bigint | Yes | Yes | No | ||
| person_id | The PERSON_ID of the PERSON for whom the drug dispensing or administration is recorded. This may be a system generated code. | bigint | Yes | No | Yes | PERSON | ||
| drug_concept_id | The DRUG_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a drug product or molecule otherwise introduced to the body. The drug concepts can have a varying degree of information about drug strength and dose. This information is relevant in the context of quantity and administration information in the subsequent fields plus strength information from the DRUG_STRENGTH table, provided as part of the standard vocabulary download. | The CONCEPT_ID that the DRUG_SOURCE_VALUE maps to. The concept id should be derived either from mapping from the source concept id or by picking the drug concept representing the most amount of detail you have. Records whose source values map to standard concepts with a domain of Drug should go in this table. When the Drug Source Value of the code cannot be translated into Standard Drug Concept IDs, a Drug exposure entry is stored with only the corresponding SOURCE_CONCEPT_ID and DRUG_SOURCE_VALUE and a DRUG_CONCEPT_ID of 0. The Drug Concept with the most detailed content of information is preferred during the mapping process. These are indicated in the CONCEPT_CLASS_ID field of the Concept and are recorded in the following order of precedence: ‘Branded Pack’, ‘Clinical Pack’, ‘Branded Drug’, ‘Clinical Drug’, ‘Branded Drug Component’, ‘Clinical Drug Component’, ‘Branded Drug Form’, ‘Clinical Drug Form’, and only if no other information is available ‘Ingredient’. Note: If only the drug class is known, the DRUG_CONCEPT_ID field should contain 0. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Drug |
| drug_exposure_start_date | Use this date to determine the start date of the drug record. | Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration was recorded. It is a valid ETL choice to use the date the drug was ordered as the DRUG_EXPOSURE_START_DATE. | date | Yes | No | No | ||
| drug_exposure_start_datetime | This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) | datetime | No | No | No | |||
| drug_exposure_end_date | The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended for the patient. | If this information is not explicitly available in the data, infer the end date using the following methods:/n/n 1. Start first with duration or days supply using the calculation drug start date + days supply -1 day. 2. Use quantity divided by daily dose that you may obtain from the sig or a source field (or assumed daily dose of 1) for solid, indivisibile, drug products. If quantity represents ingredient amount, quantity divided by daily dose * concentration (from drug_strength) drug concept id tells you the dose form. 3. If it is an administration record, set drug end date equal to drug start date. If the record is a written prescription then set end date to start date + 29. If the record is a mail-order prescription set end date to start date + 89. The end date must be equal to or greater than the start date. Ibuprofen 20mg/mL oral solution concept tells us this is oral solution. Calculate duration as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL) 200*5/20 = 50 days. Examples by dose form | date | Yes | No | No | ||
| drug_exposure_end_datetime | This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) | datetime | No | No | No | |||
| verbatim_end_date | This is the end date of the drug exposure as it appears in the source data, if it is given | Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable. | date | No | No | No | ||
| drug_type_concept_id | You can use the TYPE_CONCEPT_ID to delineate between prescriptions written vs. prescriptions dispensed vs. medication history vs. patient-reported exposure, etc. | Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Type Concept |
| stop_reason | The reason a person stopped a medication as it is represented in the source. Reasons include regimen completed, changed, removed, etc. This field will be retired in v6.0. | This information is often not populated in source data and it is a valid etl choice to leave it blank if the information does not exist. | varchar(20) | No | No | No | ||
| refills | This is only filled in when the record is coming from a prescription written this field is meant to represent intended refills at time of the prescription. | integer | No | No | No | |||
| quantity | To find the dose form of a drug the RELATIONSHIP table can be used where the relationship_id is ‘Has dose form’. If liquid, quantity stands for the total amount dispensed or ordered of ingredient in the units given by the drug_strength table. If the unit from the source data does not align with the unit in the DRUG_STRENGTH table the quantity should be converted to the correct unit given in DRUG_STRENGTH. For clinical drugs with fixed dose forms (tablets etc.) the quantity is the number of units/tablets/capsules prescribed or dispensed (can be partial, but then only 1/2 or 1/3, not 0.01). Clinical drugs with divisible dose forms (injections) the quantity is the amount of ingredient the patient got. For example, if the injection is 2mg/mL but the patient got 80mL then quantity is reported as 160. Quantified clinical drugs with divisible dose forms (prefilled syringes), the quantity is the amount of ingredient similar to clinical drugs. Please see how to calculate drug dose for more information. | float | No | No | No | |||
| days_supply | Days supply of the drug. This should be the verbatim days_supply as given on the prescription. If the drug is physician administered use duration end date if given or set to 1 as default if duration is not available. | integer | No | No | No | |||
| sig | This is the verbatim instruction for the drug as written by the provider. | Put the written out instructions for the drug as it is verbatim in the source, if available. | varchar(MAX) | No | No | No | ||
| route_concept_id | The standard CONCEPT_ID that the ROUTE_SOURCE_VALUE maps to in the route domain. | integer | No | No | Yes | CONCEPT | Route | |
| lot_number | varchar(50) | No | No | No | ||||
| provider_id | The Provider associated with drug record, e.g. the provider who wrote the prescription or the provider who administered the drug. | The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record, for example the ordering vs administering physician on an EHR record. | bigint | No | No | Yes | PROVIDER | |
| visit_occurrence_id | The Visit during which the drug was prescribed, administered or dispensed. | To populate this field drug exposures must be explicitly initiated in the visit. | bigint | No | No | Yes | VISIT_OCCURRENCE | |
| visit_detail_id | The VISIT_DETAIL record during which the drug exposure occurred. For example, if the person was in the ICU at the time of the drug administration the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit. | Same rules apply as for the VISIT_OCCURRENCE_ID. | bigint | No | No | Yes | VISIT_DETAIL | |
| drug_source_value | This field houses the verbatim value from the source data representing the drug exposure that occurred. For example, this could be an NDC or Gemscript code. | This code is mapped to a Standard Drug Concept in the Standardized Vocabularies and the original code is stored here for reference. | varchar(50) | No | No | No | ||
| drug_source_concept_id | This is the concept representing the drug source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Drug necessary for a given analytic use case. Consider using DRUG_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. | If the DRUG_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. If unavailable, set to 0. | integer | Yes | No | Yes | CONCEPT | |
| route_source_value | This field houses the verbatim value from the source data representing the drug route. | This information may be called something different in the source data but the field is meant to contain a value indicating when and how a drug was given to a patient. This source value is mapped to a standard concept which is stored in the ROUTE_CONCEPT_ID field. | varchar(50) | No | No | No | ||
| dose_unit_source_value | This field houses the verbatim value from the source data representing the dose unit of the drug given. | This information may be called something different in the source data but the field is meant to contain a value indicating the unit of dosage of drug given to the patient. This is an older column and will be deprecated in an upcoming version. | varchar(50) | No | No | No |
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.
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.
ETL Conventions
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. 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.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| procedure_occurrence_id | The unique key given to a procedure record for a person. Refer to the ETL for how duplicate procedures during the same visit were handled. | Each instance of a procedure occurrence in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same procedure within the same visit. It is valid to keep these duplicates and assign them individual, unique, PROCEDURE_OCCURRENCE_IDs, though it is up to the ETL how they should be handled. | bigint | Yes | Yes | No | ||
| person_id | The PERSON_ID of the PERSON for whom the procedure is recorded. This may be a system generated code. | bigint | Yes | No | Yes | PERSON | ||
| procedure_concept_id | The PROCEDURE_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source value which represents a procedure | The CONCEPT_ID that the PROCEDURE_SOURCE_VALUE maps to. Only records whose source values map to standard concepts with a domain of “Procedure” should go in this table. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Procedure |
| procedure_date | Use this date to determine the date the procedure occurred. | If a procedure lasts more than a day, then it should be recorded as a separate record for each day the procedure occurred, this logic is in lieu of the procedure_end_date, which will be added in a future version of the CDM. | date | No | No | No | ||
| procedure_datetime | This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) | datetime | Yes | No | No | |||
| procedure_type_concept_id | This field can be used to determine the provenance of the Procedure record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources. | Choose the PROCEDURE_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. If a procedure is recorded as an EHR encounter, the PROCEDURE_TYPE_CONCEPT would be ‘EHR encounter record’. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Type Concept |
| modifier_concept_id | The modifiers are intended to give additional information about the procedure but as of now the vocabulary is under review. | It is up to the ETL to choose how to map modifiers if they exist in source data. These concepts are typically distinguished by ‘Modifier’ concept classes (e.g., ‘CPT4 Modifier’ as part of the ‘CPT4’ vocabulary). If there is more than one modifier on a record, one should be chosen that pertains to the procedure rather than provider. If not available, set to 0. Accepted Concepts. | integer | No | No | Yes | CONCEPT | |
| quantity | If the quantity value is omitted, a single procedure is assumed. | If a Procedure has a quantity of ‘0’ in the source, this should default to ‘1’ in the ETL. If there is a record in the source it can be assumed the exposure occurred at least once | integer | No | No | No | ||
| provider_id | The provider associated with the procedure record, e.g. the provider who performed the Procedure. | The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record, for example the admitting vs attending physician on an EHR record. | bigint | No | No | No | PROVIDER | |
| visit_occurrence_id | The visit during which the procedure occurred. | Depending on the structure of the source data, this may have to be determined based on dates. If a PROCEDURE_DATE occurs within the start and end date of a Visit it is a valid ETL choice to choose the VISIT_OCCURRENCE_ID from the Visit that subsumes it, even if not explicitly stated in the data. While not required, an attempt should be made to locate the VISIT_OCCURRENCE_ID of the PROCEDURE_OCCURRENCE record. | bigint | No | No | No | VISIT_OCCURRENCE | |
| visit_detail_id | The VISIT_DETAIL record during which the Procedure occurred. For example, if the Person was in the ICU at the time of the Procedure the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit. | Same rules apply as for the VISIT_OCCURRENCE_ID. | bigint | No | No | No | VISIT_DETAIL | |
| procedure_source_value | This field houses the verbatim value from the source data representing the procedure that occurred. For example, this could be an CPT4 or OPCS4 code. | Use this value to look up the source concept id and then map the source concept id to a standard concept id. | varchar(50) | No | No | No | ||
| procedure_source_concept_id | This is the concept representing the procedure source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Procedure necessary for a given analytic use case. Consider using PROCEDURE_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. | If the PROCEDURE_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. If not available, set to 0. | integer | Yes | No | No | CONCEPT | |
| modifier_source_value | The original modifier code from the source is stored here for reference. | varchar(50) | No | No | No |
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).
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.
ETL Conventions
Source codes and source text fields mapped to Standard Concepts of the Device Domain have to be recorded here.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| device_exposure_id | The unique key given to records a person’s exposure to a foreign physical object or instrument. | Each instance of an exposure to a foreign object or device present in the source data should be assigned this unique key. | bigint | Yes | Yes | No | ||
| person_id | bigint | Yes | No | Yes | PERSON | |||
| device_concept_id | The DEVICE_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a foreign object or instrument the person was exposed to. | The CONCEPT_ID that the DEVICE_SOURCE_VALUE maps to. | integer | Yes | No | Yes | CONCEPT | Device |
| device_exposure_start_date | Use this date to determine the start date of the device record. | Valid entries include a start date of a procedure to implant a device, the date of a prescription for a device, or the date of device administration. | date | Yes | No | No | ||
| device_exposure_start_datetime | This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) | datetime | No | No | No | |||
| device_exposure_end_date | The DEVICE_EXPOSURE_END_DATE denotes the day the device exposure ended for the patient, if given. | Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable. | date | No | No | No | ||
| device_exposure_end_datetime | If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) | datetime | No | No | No | |||
| device_type_concept_id | You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR. 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. | integer | Yes | No | Yes | CONCEPT | Type Concept |
| unique_device_id | This is the Unique Device Identification number for devices regulated by the FDA, if given. | For medical devices that are regulated by the FDA, a Unique Device Identification (UDI) is provided if available in the data source and is recorded in the UNIQUE_DEVICE_ID field. | varchar(50) | No | No | No | ||
| quantity | integer | No | No | No | ||||
| provider_id | The Provider associated with device record, e.g. the provider who wrote the prescription or the provider who implanted the device. | The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record. | bigint | No | No | Yes | PROVIDER | |
| visit_occurrence_id | The Visit during which the device was prescribed or given. | To populate this field device exposures must be explicitly initiated in the visit. | bigint | No | No | Yes | VISIT_OCCURRENCE | |
| visit_detail_id | The Visit Detail during which the device was prescribed or given. | To populate this field device exposures must be explicitly initiated in the visit detail record. | bigint | No | No | Yes | VISIT_DETAIL | |
| device_source_value | This field houses the verbatim value from the source data representing the device exposure that occurred. For example, this could be an NDC or Gemscript code. | This code is mapped to a Standard Device Concept in the Standardized Vocabularies and the original code is stored here for reference. | varchar(50) | No | No | No | ||
| device_source_concept_id | This is the concept representing the device source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Device necessary for a given analytic use case. Consider using DEVICE_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. | If the DEVICE_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. If unavailable, set to 0. | integer | Yes | No | Yes | CONCEPT |
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.
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.).
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’.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| measurement_id | The unique key given to a Measurement record for a Person. Refer to the ETL for how duplicate Measurements during the same Visit were handled. | Each instance of a measurement present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same measurement within the same visit. It is valid to keep these duplicates and assign them individual, unique, MEASUREMENT_IDs, though it is up to the ETL how they should be handled. | bigint | Yes | Yes | No | ||
| person_id | The PERSON_ID of the PERSON for whom the measurement is recorded. This may be a system generated code. | bigint | Yes | No | Yes | PERSON | ||
| measurement_concept_id | The MEASUREMENT_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. | The CONCEPT_ID that the MEASUREMENT_SOURCE_CONCEPT_ID maps to. Only records whose SOURCE_CONCEPT_IDs map to Standard Concepts with a domain of “Measurement” should go in this table. | integer | Yes | No | Yes | CONCEPT | Measurement |
| measurement_date | Use this date to determine the date of the measurement. | If there are multiple dates in the source data associated with a record such as order_date, draw_date, and result_date, choose the one that is closest to the date the sample was drawn from the patient. | date | Yes | No | No | ||
| measurement_datetime | This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) | datetime | No | No | No | |||
| measurement_time | This is present for backwards compatibility and will be deprecated in an upcoming version. | varchar(10) | No | No | No | |||
| measurement_type_concept_id | This field can be used to determine the provenance of the Measurement record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources. | Choose the MEASUREMENT_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Type Concept |
| operator_concept_id | The meaning of Concept 4172703 for ‘=’ is identical to omission of a OPERATOR_CONCEPT_ID value. Since the use of this field is rare, it’s important when devising analyses to not to forget testing for the content of this field for values different from =. | Operators are <, <=, =, >=, > and these concepts belong to the ‘Meas Value Operator’ domain. Accepted Concepts. | integer | No | No | Yes | CONCEPT | |
| value_as_number | This is the numerical value of the Result of the Measurement, if available. Note that measurements such as blood pressures will be split into their component parts i.e. one record for systolic, one record for diastolic. | If there is a negative value coming from the source, set the VALUE_AS_NUMBER to NULL, with the exception of the following Measurements (listed as LOINC codes):<br>- 1925-7 Base excess in Arterial blood by calculation - 1927-3 Base excess in Venous blood by calculation - 8632-2 QRS-Axis - 11555-0 Base excess in Blood by calculation - 1926-5 Base excess in Capillary blood by calculation - 28638-5 Base excess in Arterial cord blood by calculation 28639-3 Base excess in Venous cord blood by calculation | float | No | No | No | ||
| value_as_concept_id | If the raw data gives a categorial result for measurements those values are captured and mapped to standard concepts in the ‘Meas Value’ domain. | If the raw data provides categorial results as well as continuous results for measurements, it is a valid ETL choice to preserve both values. The continuous value should go in the VALUE_AS_NUMBER field and the categorical value should be mapped to a standard concept in the ‘Meas Value’ domain and put in the VALUE_AS_CONCEPT_ID field. This is also the destination for the ‘Maps to value’ relationship. | integer | No | No | Yes | CONCEPT | |
| unit_concept_id | There is currently no recommended unit for individual measurements, i.e. it is not mandatory to represent Hemoglobin a1C measurements as a percentage. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data. | There is no standardization requirement for units associated with MEASUREMENT_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. | integer | No | No | Yes | CONCEPT | Unit |
| range_low | Ranges have the same unit as the VALUE_AS_NUMBER. These ranges are provided by the source and should remain NULL if not given. | If reference ranges for upper and lower limit of normal as provided (typically by a laboratory) these are stored in the RANGE_HIGH and RANGE_LOW fields. This should be set to NULL if not provided. | float | No | No | No | ||
| range_high | Ranges have the same unit as the VALUE_AS_NUMBER. These ranges are provided by the source and should remain NULL if not given. | If reference ranges for upper and lower limit of normal as provided (typically by a laboratory) these are stored in the RANGE_HIGH and RANGE_LOW fields. This should be set to NULL if not provided. | float | No | No | No | ||
| provider_id | The provider associated with measurement record, e.g. the provider who ordered the test or the provider who recorded the result. | The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record. For example the admitting vs attending physician on an EHR record. | bigint | No | No | Yes | PROVIDER | |
| visit_occurrence_id | The visit during which the Measurement occurred. | Depending on the structure of the source data, this may have to be determined based on dates. If a MEASUREMENT_DATE occurs within the start and end date of a Visit it is a valid ETL choice to choose the VISIT_OCCURRENCE_ID from the visit that subsumes it, even if not explicitly stated in the data. While not required, an attempt should be made to locate the VISIT_OCCURRENCE_ID of the measurement record. If a measurement is related to a visit explicitly in the source data, it is possible that the result date of the Measurement falls outside of the bounds of the Visit dates. | bigint | No | No | Yes | VISIT_OCCURRENCE | |
| visit_detail_id | The VISIT_DETAIL record during which the Measurement occurred. For example, if the Person was in the ICU at the time the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit. | Same rules apply as for the VISIT_OCCURRENCE_ID. | bigint | No | No | Yes | VISIT_DETAIL | |
| measurement_source_value | This field houses the verbatim value from the source data representing the Measurement that occurred. For example, this could be an ICD10 or Read code. | This code is mapped to a Standard Measurement Concept in the Standardized Vocabularies and the original code is stored here for reference. | varchar(50) | No | No | No | ||
| measurement_source_concept_id | This is the concept representing the MEASUREMENT_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Measurement necessary for a given analytic use case. Consider using MEASUREMENT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. | If the MEASUREMENT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. If not available, set to 0. | integer | Yes | No | Yes | CONCEPT | |
| unit_source_value | This field houses the verbatim value from the source data representing the unit of the Measurement that occurred. | This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference. | varchar(50) | No | No | No | ||
| value_source_value | This field houses the verbatim result value of the Measurement from the source data . | If both a continuous and categorical result are given in the source data such that both VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID are both included, store the verbatim value that was mapped to VALUE_AS_CONCEPT_ID here. | varchar(50) | No | No | No |
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. New to CDM v6.0 An Observation can now be linked to other records in the CDM instance using the fields OBSERVATION_EVENT_ID and OBS_EVENT_FIELD_CONCEPT_ID. To link another record to an Observation, the primary key goes in OBSERVATION_EVENT_ID (CONDITION_OCCURRENCE_ID, DRUG_EXPOSURE_ID, etc.) and the Concept representing the field where the OBSERVATION_EVENT_ID was taken from go in the OBS_EVENT_FIELD_CONCEPT_ID. For example, a CONDITION_OCCURRENCE of Asthma might be linked to an Observation of a family history of Asthma. In this case the CONDITION_OCCURRENCE_ID of the Asthma record would go in OBSERVATION_EVENT_ID of the family history record and the CONCEPT_ID 1147127 would go in OBS_EVENT_FIELD_CONCEPT_ID to denote that the OBSERVATION_EVENT_ID represents a CONDITION_OCCURRENCE_ID.
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.
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.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| observation_id | The unique key given to an Observation record for a Person. Refer to the ETL for how duplicate Observations during the same Visit were handled. | Each instance of an observation present in the source data should be assigned this unique key. | bigint | Yes | Yes | No | ||
| person_id | The PERSON_ID of the Person for whom the Observation is recorded. This may be a system generated code. | bigint | Yes | No | Yes | PERSON | ||
| observation_concept_id | The OBSERVATION_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. | The CONCEPT_ID that the OBSERVATION_SOURCE_CONCEPT_ID maps to. There is no specified domain that the Concepts in this table must adhere to. The only rule is that records with Concepts in the Condition, Procedure, Drug, Measurement, or Device domains MUST go to the corresponding table. | integer | Yes | No | Yes | CONCEPT | |
| observation_date | The date of the Observation. Depending on what the Observation represents this could be the date of a lab test, the date of a survey, or the date a patient’s family history was taken. | For some observations the ETL may need to make a choice as to which date to choose. | date | No | No | No | ||
| observation_datetime | If no time is given set to midnight (00:00:00). | datetime | Yes | No | No | |||
| observation_type_concept_id | This field can be used to determine the provenance of the Observation record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources. | Choose the OBSERVATION_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Type Concept |
| value_as_number | This is the numerical value of the Result of the Observation, if applicable and available. It is not expected that all Observations will have numeric results, rather, this field is here to house values should they exist. | float | No | No | No | |||
| value_as_string | This is the categorical value of the Result of the Observation, if applicable and available. | varchar(60) | No | No | No | |||
| value_as_concept_id | It is possible that some records destined for the Observation table have two clinical ideas represented in one source code. This is common with ICD10 codes that describe a family history of some Condition, for example. In OMOP the Vocabulary breaks these two clinical ideas into two codes; one becomes the OBSERVATION_CONCEPT_ID and the other becomes the VALUE_AS_CONCEPT_ID. It is important when using the Observation table to keep this possibility in mind and to examine the VALUE_AS_CONCEPT_ID field for relevant information. | Note that the value of VALUE_AS_CONCEPT_ID may be provided through mapping from a source Concept which contains the content of the Observation. In those situations, the CONCEPT_RELATIONSHIP table in addition to the ‘Maps to’ record contains a second record with the relationship_id set to ‘Maps to value’. For example, ICD10 Z82.4 ‘Family history of ischaemic heart disease and other diseases of the circulatory system’ has a ‘Maps to’ relationship to 4167217 ‘Family history of clinical finding’ as well as a ‘Maps to value’ record to 134057 ‘Disorder of cardiovascular system’. | Integer | No | No | Yes | CONCEPT | |
| qualifier_concept_id | This field contains all attributes specifying the clinical fact further, such as as degrees, severities, drug-drug interaction alerts etc. | Use your best judgement as to what Concepts to use here and if they are necessary to accurately represent the clinical record. There is no restriction on the domain of these Concepts, they just need to be Standard. | integer | No | No | Yes | CONCEPT | |
| unit_concept_id | There is currently no recommended unit for individual observation concepts. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data. | There is no standardization requirement for units associated with OBSERVATION_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. | integer | No | No | Yes | CONCEPT | Unit |
| provider_id | The provider associated with the observation record, e.g. the provider who ordered the test or the provider who recorded the result. | The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record. For example the admitting vs attending physician on an EHR record. | bigint | No | No | Yes | PROVIDER | |
| visit_occurrence_id | The visit during which the Observation occurred. | Depending on the structure of the source data, this may have to be determined based on dates. If an OBSERVATION_DATE occurs within the start and end date of a Visit it is a valid ETL choice to choose the VISIT_OCCURRENCE_ID from the visit that subsumes it, even if not explicitly stated in the data. While not required, an attempt should be made to locate the VISIT_OCCURRENCE_ID of the observation record. If an observation is related to a visit explicitly in the source data, it is possible that the result date of the Observation falls outside of the bounds of the Visit dates. | bigint | No | No | Yes | VISIT_OCCURRENCE | |
| visit_detail_id | The VISIT_DETAIL record during which the Observation occurred. For example, if the Person was in the ICU at the time the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit. | Same rules apply as for the VISIT_OCCURRENCE_ID. | bigint | No | No | Yes | VISIT_DETAIL | |
| observation_source_value | This field houses the verbatim value from the source data representing the Observation that occurred. For example, this could be an ICD10 or Read code. | This code is mapped to a Standard Concept in the Standardized Vocabularies and the original code is stored here for reference. | varchar(50) | No | No | No | ||
| observation_source_concept_id | This is the concept representing the OBSERVATION_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Observation necessary for a given analytic use case. Consider using OBSERVATION_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. | If the OBSERVATION_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. If not available, set to 0. | integer | Yes | No | Yes | CONCEPT | |
| unit_source_value | This field houses the verbatim value from the source data representing the unit of the Observation that occurred. | This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference. | varchar(50) | No | No | No | ||
| qualifier_source_value | This field houses the verbatim value from the source data representing the qualifier of the Observation that occurred. | This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference. | varchar(50) | No | No | No | ||
| observation_event_id | If the Observation record is related to another record in the database, this field is the primary key of the linked record. | Put the primary key of the linked record, if applicable, here. See the ETL Conventions for the OBSERVATION table for more details. | bigint | No | No | No | ||
| obs_event_field_concept_id | If the Observation record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. | Put the CONCEPT_ID that identifies which table and field the OBSERVATION_EVENT_ID came from. | integer | No | No | Yes | CONCEPT | |
| value_as_datetime | It is possible that some Observation records might store a result as a date value. | datetime | No | No | No |
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.
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:
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.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| note_id | A unique identifier for each note. | integer | Yes | Yes | No | |||
| person_id | bigint | Yes | No | Yes | PERSON | |||
| note_event_id | bigint | No | No | No | ||||
| note_event_field_concept_id | integer | No | No | Yes | CONCEPT | |||
| note_date | The date the note was recorded. | date | Yes | No | No | |||
| note_datetime | If time is not given set the time to midnight. | datetime | No | No | No | |||
| note_type_concept_id | The provenance of the note. Most likely this will be EHR. | Put the source system of the note, as in EHR record. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Type Concept |
| note_class_concept_id | A Standard Concept Id representing the HL7 LOINC Document Type Vocabulary classification of the note. | Map the note classification to a Standard Concept. For more information see the ETL Conventions in the description of the NOTE table. AcceptedConcepts. This Concept can alternatively be represented by concepts with the relationship ‘Kind of (LOINC)’ to 706391 (Note). | integer | Yes | No | Yes | CONCEPT | |
| note_title | The title of the note. | varchar(250) | No | No | No | |||
| note_text | The content of the note. | varchar(MAX) | Yes | No | No | |||
| encoding_concept_id | This is the Concept representing the character encoding type. | Put the Concept Id that represents the encoding character type here. Currently the only option is UTF-8 (32678). It the note is encoded in any other type, like ASCII then put 0. | integer | Yes | No | Yes | CONCEPT | |
| language_concept_id | The language of the note. | Use Concepts that are descendants of the concept 4182347 (World Languages). | integer | Yes | No | Yes | CONCEPT | |
| provider_id | The Provider who wrote the note. | The ETL may need to make a determination on which provider to put here. | bigint | No | No | Yes | PROVIDER | |
| visit_occurrence_id | The Visit during which the note was written. | bigint | No | No | Yes | VISIT_OCCURRENCE | ||
| visit_detail_id | The Visit Detail during which the note was written. | bigint | No | No | Yes | VISIT_DETAIL | ||
| note_source_value | The source value mapped to the NOTE_CLASS_CONCEPT_ID. | varchar(50) | No | No | No |
Table Description
The NOTE_NLP table encodes all output of NLP on clinical notes. Each row represents a single extracted term from a note.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| note_nlp_id | A unique identifier for the NLP record. | bigint | Yes | Yes | No | |||
| note_id | This is the NOTE_ID for the NOTE record the NLP record is associated to. | integer | Yes | No | No | |||
| section_concept_id | The SECTION_CONCEPT_ID should be used to represent the note section contained in the NOTE_NLP record. These concepts can be found as parts of document panels and are based on the type of note written, i.e. a discharge summary. These panels can be found as concepts with the relationship ‘Subsumes’ to CONCEPT_ID 45875957. | integer | No | No | Yes | CONCEPT | ||
| snippet | A small window of text surrounding the term | varchar(250) | No | No | No | |||
| "offset" | Character offset of the extracted term in the input note | varchar(50) | No | No | No | |||
| lexical_variant | Raw text extracted from the NLP tool. | varchar(250) | Yes | No | No | |||
| note_nlp_concept_id | integer | No | No | Yes | CONCEPT | |||
| note_nlp_source_concept_id | integer | No | No | Yes | CONCEPT | |||
| nlp_system | Name and version of the NLP system that extracted the term. Useful for data provenance. | varchar(250) | No | No | No | |||
| nlp_date | The date of the note processing. | date | Yes | No | No | |||
| nlp_datetime | The date and time of the note processing. | datetime | No | No | No | |||
| term_exists | Term_exists is defined as a flag that indicates if the patient actually has or had the condition. Any of the following modifiers would make Term_exists false: Negation = true Subject = [anything other than the patient] Conditional = true/li> Rule_out = true Uncertain = very low certainty or any lower certainties A complete lack of modifiers would make Term_exists true. | varchar(1) | No | No | No | |||
| term_temporal | Term_temporal is to indicate if a condition is present or just in the past. The following would be past:<br><br> - History = true - Concept_date = anything before the time of the report | varchar(50) | No | No | No | |||
| term_modifiers | For the modifiers that are there, they would have to have these values:<br><br> - Negation = false - Subject = patient - Conditional = false - Rule_out = false - Uncertain = true or high or moderate or even low (could argue about low). Term_modifiers will concatenate all modifiers for different types of entities (conditions, drugs, labs etc) into one string. Lab values will be saved as one of the modifiers. | varchar(2000) | No | No | No |
Table Description
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.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| specimen_id | Unique identifier for each specimen. | bigint | Yes | Yes | No | |||
| person_id | The person from whom the specimen is collected. | bigint | Yes | No | Yes | PERSON | ||
| specimen_concept_id | The standard CONCEPT_ID that the SPECIMEN_SOURCE_VALUE maps to in the specimen domain. Accepted Concepts | integer | Yes | No | Yes | CONCEPT | ||
| specimen_type_concept_id | Put the source of the specimen record, as in an EHR system. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Type Concept | |
| specimen_date | The date the specimen was collected. | date | Yes | No | No | |||
| specimen_datetime | datetime | No | No | No | ||||
| quantity | The amount of specimen collected from the person. | float | No | No | No | |||
| unit_concept_id | The unit for the quantity of the specimen. | Map the UNIT_SOURCE_VALUE to a Standard Concept in the Unit domain. Accepted Concepts | integer | No | No | Yes | CONCEPT | |
| anatomic_site_concept_id | This is the site on the body where the specimen is from. | Map the ANATOMIC_SITE_SOURCE_VALUE to a Standard Concept in the Spec Anatomic Site domain. This should be coded at the lowest level of granularity Accepted Concepts | integer | No | No | Yes | CONCEPT | |
| disease_status_concept_id | integer | No | No | Yes | CONCEPT | |||
| specimen_source_id | This is the identifier for the specimen from the source system. | varchar(50) | No | No | No | |||
| specimen_source_value | varchar(50) | No | No | No | ||||
| unit_source_value | This unit for the quantity of the specimen, as represented in the source. | varchar(50) | No | No | No | |||
| anatomic_site_source_value | This is the site on the body where the specimen was taken from, as represented in the source. | varchar(50) | No | No | No | |||
| disease_status_source_value | varchar(50) | No | No | No |
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).
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
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| domain_concept_id_1 | integer | Yes | No | Yes | CONCEPT | |||
| fact_id_1 | bigint | Yes | No | No | ||||
| domain_concept_id_2 | integer | Yes | No | Yes | CONCEPT | |||
| fact_id_2 | bigint | Yes | No | No | ||||
| relationship_concept_id | integer | Yes | No | Yes | CONCEPT |
Table Description
The SURVEY_CONDUCT table is used to store an instance of a completed survey or questionnaire.
User Guide
This table captures details of the individual questionnaire such as who completed it, when it was completed and to which patient treatment or visit it relates to (if any).
ETL Conventions
Each SURVEY has a SURVEY_CONCEPT_ID, a concept in the CONCEPT table identifying the questionnaire e.g. EQ5D, VR12, SF12. Each questionnaire should exist in the CONCEPT table. Each SURVEY can be optionally related to a specific Visit in order to link it both to the Visit during which it was completed and any subsequent Visit where treatment was assigned based on the patient’s responses.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| survey_conduct_id | Unique identifier for each completed survey. | For each instance of a survey completion create a unique identifier. | bigint | Yes | Yes | No | ||
| person_id | bigint | Yes | No | Yes | PERSON | |||
| survey_concept_id | This is the Concept that represents the survey that was completed. | Put the CONCEPT_ID that identifies the survey that the Person completed. There is no specified domain for this table but the concept class ‘staging/scales’ contains many common surveys. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | |
| survey_start_date | Date on which the survey was started. | date | No | No | No | |||
| survey_start_datetime | If no time given, set to midnight. | datetime | No | No | No | |||
| survey_end_date | Date on which the survey was completed. | date | No | No | No | |||
| survey_end_datetime | If no time given, set to midnight. | datetime | Yes | No | No | |||
| provider_id | This is the Provider associated with the survey completion. | The ETL may need to make a choice as to which Provider to put here. This could either be the provider that ordered the survey or the provider who observed the completion of the survey. | bigint | No | No | Yes | PROVIDER | |
| assisted_concept_id | This is a Concept that represents whether the survey was completed with assistance or independently. | There is no specific domain or class for this field, just choose the one that best represents the value given in the source. | integer | Yes | No | Yes | CONCEPT | |
| respondent_type_concept_id | This is a Concept that represents who actually recorded the answers to the survey. For example, this could be the patient or a research associate. | There is no specific domain or class for this field, just choose the one that best represents the value given in the source. | integer | Yes | No | Yes | CONCEPT | |
| timing_concept_id | This is a Concept that represents the timing of the survey. For example this could be the 3-month follow-up appointment. | There is no specific domain or class for this field, just choose the one that best represents the value given in the source. | integer | Yes | No | Yes | CONCEPT | |
| collection_method_concept_id | This Concept represents how the responses were collected. | Use the concepts that have the relationship ‘Has Answer’ with the CONCEPT_ID 42529316. | integer | Yes | No | Yes | CONCEPT | |
| assisted_source_value | Source value representing whether patient required assistance to complete the survey. Example: ‘Completed without assistance’, ‘Completed with assistance’. | varchar(50) | No | No | No | |||
| respondent_type_source_value | Source code representing role of person who completed the survey. | varchar(100) | No | No | No | |||
| timing_source_value | Text string representing the timing of the survey. Example: Baseline, 6-month follow-up. | varchar(100) | No | No | No | |||
| collection_method_source_value | The collection method as it appears in the source data. | varchar(100) | No | No | No | |||
| survey_source_value | The survey name as it appears in the source data. | varchar(100) | No | No | No | |||
| survey_source_concept_id | If unavailable, set to 0. | integer | Yes | No | Yes | CONCEPT | ||
| survey_source_identifier | Unique identifier for each completed survey in source system. | varchar(100) | No | No | No | |||
| validated_survey_concept_id | If unavailable, set to 0. | integer | Yes | No | Yes | CONCEPT | ||
| validated_survey_source_value | Source value representing the validation status of the survey. | integer | No | No | No | |||
| survey_version_number | Version number of the questionnaire or survey used. | varchar(20) | No | No | No | |||
| visit_occurrence_id | The Visit during which the Survey occurred. | bigint | No | No | Yes | VISIT_OCCURRENCE | ||
| response_visit_occurrence_id | The Visit during which any treatment related to the Survey was carried out. | bigint | No | No | Yes | VISIT_OCCURRENCE |
Table Description
The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Sites. New to CDM v6.0 The LOCATION table now includes latitude and longitude.
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. For standardized geospatial visualization and analysis, addresses need to be, at the minimum be geocoded into latitude and longitude.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| location_id | The unique key given to a unique Location. | Each instance of a Location in the source data should be assigned this unique key. | bigint | Yes | Yes | No | ||
| address_1 | This is the first line of the address. | varchar(50) | No | No | No | |||
| address_2 | This is the second line of the address | varchar(50) | No | No | No | |||
| city | varchar(50) | No | No | No | ||||
| state | varchar(2) | No | No | No | ||||
| zip | Zip codes are handled as strings of up to 9 characters length. For US addresses, these represent either a 3-digit abbreviated Zip code as provided by many sources for patient protection reasons, the full 5-digit Zip or the 9-digit (ZIP + 4) codes. Unless for specific reasons analytical methods should expect and utilize only the first 3 digits. For international addresses, different rules apply. | varchar(9) | No | No | No | |||
| county | varchar(20) | No | No | No | ||||
| location_source_value | Put the verbatim value for the location here, as it shows up in the source. | varchar(50) | No | No | No | |||
| latitude | The geocoded latitude. | float | No | No | No | |||
| longitude | The geocoded longitude. | float | No | No | No |
Table Description
The LOCATION HISTORY table stores relationships between Persons or Care Sites and geographic locations over time. This table is new to CDM v6.0
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| location_id | This is the LOCATION_ID for the LOCATION_HISTORY record. | bigint | Yes | No | Yes | LOCATION | ||
| relationship_type_concept_id | This is the relationship between the location and the entity (PERSON, PROVIDER, or CARE_SITE) | Concepts in this field must be in the Location class. Accepted Concepts. If the DOMAIN_ID is CARE_SITE this should be 0 and when the domain is PROVIDER the value is Office. | integer | Yes | No | Yes | CONCEPT | |
| domain_id | The domain of the entity that is related to the location. Either PERSON, PROVIDER, or CARE_SITE. | varchar(50) | Yes | No | No | |||
| entity_id | The unique identifier for the entity. References either person_id, provider_id, or care_site_id, depending on domain_id. | bigint | Yes | No | No | |||
| start_date | The date the relationship started | date | Yes | No | No | |||
| end_date | The date the relationship ended | date | No | No | No |
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.).
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.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| care_site_id | Assign an id to each unique combination of location_id and place_of_service_source_value. | bigint | Yes | Yes | No | |||
| care_site_name | The name of the care_site as it appears in the source data | varchar(255) | No | No | No | |||
| place_of_service_concept_id | This is a high-level way of characterizing a Care Site. Typically, however, Care Sites can provide care in multiple settings (inpatient, outpatient, etc.) and this granularity should be reflected in the visit. | Choose the concept in the visit domain that best represents the setting in which healthcare is provided in the Care Site. If most visits in a Care Site are Inpatient, then the place_of_service_concept_id should represent Inpatient. If information is present about a unique Care Site (e.g. Pharmacy) then a Care Site record should be created. If this information is not available then set to 0. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | |
| location_id | The location_id from the LOCATION table representing the physical location of the care_site. | bigint | No | No | Yes | LOCATION | ||
| care_site_source_value | The identifier of the care_site as it appears in the source data. This could be an identifier separate from the name of the care_site. | varchar(50) | No | No | No | |||
| place_of_service_source_value | Put the place of service of the care_site as it appears in the source data. | varchar(50) | No | No | No |
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.
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.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| provider_id | It is assumed that every provider with a different unique identifier is in fact a different person and should be treated independently. | This identifier can be the original id from the source data provided it is an integer, otherwise it can be an autogenerated number. | bigint | Yes | Yes | No | ||
| provider_name | This field is not necessary as it is not necessary to have the actual identity of the Provider. Rather, the idea is to uniquely and anonymously identify providers of care across the database. | varchar(255) | No | No | No | |||
| npi | This is the National Provider Number issued to health care providers in the US by the Centers for Medicare and Medicaid Services (CMS). | varchar(20) | No | No | No | |||
| dea | This is the identifier issued by the DEA, a US federal agency, that allows a provider to write prescriptions for controlled substances. | varchar(20) | No | No | No | |||
| specialty_concept_id | This field either represents the most common specialty that occurs in the data or the most specific concept that represents all specialties listed, should the provider have more than one. This includes physician specialties such as internal medicine, emergency medicine, etc. and allied health professionals such as nurses, midwives, and pharmacists. | If a Provider has more than one Specialty, there are two options: 1. Choose a concept_id which is a common ancestor to the multiple specialties, or, 2. Choose the specialty that occurs most often for the provider. Concepts in this field should be Standard with a domain of Provider. If not available, set to 0. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | |
| care_site_id | This is the CARE_SITE_ID for the location that the provider primarily practices in. | If a Provider has more than one Care Site, the main or most often exerted CARE_SITE_ID should be recorded. | bigint | No | No | Yes | CARE_SITE | |
| year_of_birth | integer | No | No | No | ||||
| gender_concept_id | This field represents the recorded gender of the provider in the source data. | If given, put a concept from the gender domain representing the recorded gender of the provider. If not available, set to 0. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | Gender |
| provider_source_value | Use this field to link back to providers in the source data. This is typically used for error checking of ETL logic. | Some use cases require the ability to link back to providers in the source data. This field allows for the storing of the provider identifier as it appears in the source. | varchar(50) | No | No | No | ||
| specialty_source_value | This is the kind of provider or specialty as it appears in the source data. This includes physician specialties such as internal medicine, emergency medicine, etc. and allied health professionals such as nurses, midwives, and pharmacists. | Put the kind of provider as it appears in the source data. This field is up to the discretion of the ETL-er as to whether this should be the coded value from the source or the text description of the lookup value. | varchar(50) | No | No | No | ||
| specialty_source_concept_id | This is often zero as many sites use proprietary codes to store physician speciality. | If the source data codes provider specialty in an OMOP supported vocabulary store the concept_id here. If not available, set to 0. | integer | Yes | No | Yes | CONCEPT | |
| gender_source_value | This is provider’s gender as it appears in the source data. | Put the provider’s gender as it appears in the source data. This field is up to the discretion of the ETL-er as to whether this should be the coded value from the source or the text description of the lookup value. | varchar(50) | No | No | No | ||
| gender_source_concept_id | This is often zero as many sites use proprietary codes to store provider gender. | If the source data codes provider gender in an OMOP supported vocabulary store the concept_id here. If not available, set to 0. | integer | Yes | No | Yes | CONCEPT |
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.
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.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| payer_plan_period_id | A unique identifier for each unique combination of a Person, Payer, Plan, and Period of time. | bigint | Yes | Yes | ||||
| person_id | The Person covered by the Plan. | A single Person can have multiple, overlapping, PAYER_PLAN_PERIOD records | bigint | Yes | No | Yes | PERSON | |
| contract_person_id | The Person who is the primary subscriber/contract owner for Plan. | This may or may not be the same as the PERSON_ID. For example, if a mother has her son on her plan and the PAYER_PLAN_PERIOD record is the for son, the sons’s PERSON_ID would go in PAYER_PLAN_PERIOD.PERSON_ID and the mother’s PERSON_ID would go in PAYER_PLAN_PERIOD.CONTRACT_PERSON_ID. | bigint | No | No | Yes | PERSON | |
| payer_plan_period_start_date | Start date of Plan coverage. | date | Yes | No | No | |||
| payer_plan_period_end_date | End date of Plan coverage. | date | Yes | No | No | |||
| payer_concept_id | This field represents the organization who reimburses the provider which administers care to the Person. | Map the Payer directly to a standard CONCEPT_ID. If one does not exists please contact the vocabulary team. There is no global controlled vocabulary available for this information. The point is to stratify on this information and identify if Persons have the same payer, though the name of the Payer is not necessary. If not available, set to 0. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | |
| payer_source_value | This is the Payer as it appears in the source data. | varchar(50) | No | No | No | |||
| payer_source_concept_id | If the source data codes the Payer in an OMOP supported vocabulary store the concept_id here. If not available, set to 0. | integer | Yes | No | Yes | CONCEPT | ||
| plan_concept_id | This field represents the specific health benefit Plan the Person is enrolled in. | Map the Plan directly to a standard CONCEPT_ID. If one does not exists please contact the vocabulary team. There is no global controlled vocabulary available for this information. The point is to stratify on this information and identify if Persons have the same health benefit Plan though the name of the Plan is not necessary. If not available, set to 0. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | |
| plan_source_value | This is the health benefit Plan of the Person as it appears in the source data. | varchar(50) | No | No | No | |||
| plan_source_concept_id | If the source data codes the Plan in an OMOP supported vocabulary store the concept_id here. If not available, set to 0. | integer | Yes | No | Yes | CONCEPT | ||
| contract_concept_id | This field represents the relationship between the PERSON_ID and CONTRACT_PERSON_ID. It should be read as PERSON_ID is the CONTRACT_CONCEPT_ID of the CONTRACT_PERSON_ID. So if CONTRACT_CONCEPT_ID represents the relationship ‘Stepdaughter’ then the Person for whom PAYER_PLAN_PERIOD record was recorded is the stepdaughter of the CONTRACT_PERSON_ID. | If available, use this field to represent the relationship between the PERSON_ID and the CONTRACT_PERSON_ID. If the Person for whom the PAYER_PLAN_PERIOD record was recorded is the stepdaughter of the CONTRACT_PERSON_ID then CONTRACT_CONCEPT_ID would be 4330864. If not available, set to 0. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | |
| contract_source_value | This is the relationship of the PERSON_ID to CONTRACT_PERSON_ID as it appears in the source data. | varchar(50) | Yes | No | No | |||
| contract_source_concept_id | If the source data codes the relationship between the PERSON_ID and CONTRACT_PERSON_ID in an OMOP supported vocabulary store the concept_id here. If not available, set to 0. | integer | Yes | No | Yes | CONCEPT | ||
| sponsor_concept_id | This field represents the sponsor of the Plan who finances the Plan. This includes self-insured, small group health plan and large group health plan. | Map the sponsor directly to a standard CONCEPT_ID. If one does not exists please contact the vocabulary team. There is no global controlled vocabulary available for this information. The point is to stratify on this information and identify if Persons have the same sponsor though the name of the sponsor is not necessary. If not available, set to 0. Accepted Concepts. | integer | Yes | No | Yes | CONCEPT | |
| sponsor_source_value | The Plan sponsor as it appears in the source data. | varchar(50) | No | No | No | |||
| sponsor_source_concept_id | If the source data codes the sponsor in an OMOP supported vocabulary store the concept_id here. | integer | No | No | Yes | CONCEPT | ||
| family_source_value | The common identifier for all people (often a family) that covered by the same policy. | Often these are the common digits of the enrollment id of the policy members. | varchar(50) | No | No | No | ||
| stop_reason_concept_id | This field represents the reason the Person left the Plan, if known. | Map the stop reason directly to a standard CONCEPT_ID. If one does not exists please contact the vocabulary team. There is no global controlled vocabulary available for this information. Accepted Concepts. | integer | No | No | Yes | CONCEPT | |
| stop_reason_source_value | The Plan stop reason as it appears in the source data. | varchar(50) | No | No | No | |||
| stop_reason_source_concept_id | If the source data codes the stop reason in an OMOP supported vocabulary store the concept_id here. | integer | No | No | Yes | CONCEPT |
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.
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.
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).
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| cost_id | A unique identifier for each COST record. | bigint | Yes | Yes | No | |||
| person_id | bigint | Yes | No | No | ||||
| cost_event_id | If the Cost record is related to another record in the database, this field is the primary key of the linked record. | Put the primary key of the linked record, if applicable, here. | bigint | Yes | No | No | ||
| cost_event_field_concept_id | If the Cost record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. | Put the CONCEPT_ID that identifies which table and field the COST_EVENT_ID came from. | integer | Yes | No | Yes | CONCEPT | |
| cost_concept_id | A foreign key that refers to a Standard Cost Concept identifier in the Standardized Vocabularies belonging to the ‘Cost’ vocabulary. | integer | No | No | Yes | CONCEPT | ||
| cost_type_concept_id | A foreign key identifier to a concept in the CONCEPT table for the provenance or the source of the COST data and belonging to the ‘Type Concept’ vocabulary | integer | No | No | Yes | CONCEPT | Type Concept | |
| cost_source_concept_id | A foreign key to a Cost Concept that refers to the code used in the source. | integer | No | No | Yes | CONCEPT | ||
| cost_source_value | The source value for the cost as it appears in the source data | varchar(50) | No | No | No | |||
| currency_concept_id | A foreign key identifier to the concept representing the 3-letter code used to delineate international currencies, such as USD for US Dollar. These belong to the ‘Currency’ vocabulary | integer | No | No | No | CONCEPT | ||
| cost | The actual financial cost amount | float | No | No | No | |||
| incurred_date | The first date of service of the clinical event corresponding to the cost as in table capturing the information (e.g. date of visit, date of procedure, date of condition, date of drug etc). | date | No | No | No | |||
| billed_date | The date a bill was generated for a service or encounter | date | No | No | No | |||
| paid_date | The date payment was received for a service or encounter | date | No | No | No | |||
| revenue_code_concept_id | A foreign key referring to a Standard Concept ID in the Standardized Vocabularies for Revenue codes belonging to the ‘Revenue Code’ vocabulary. | integer | No | No | Yes | CONCEPT | ||
| drg_concept_id | A foreign key referring to a Standard Concept ID in the Standardized Vocabularies for DRG codes belonging to the ‘DRG’ vocabulary. | integer | No | No | Yes | CONCEPT | ||
| revenue_code_source_value | The source value for the Revenue code as it appears in the source data, stored here for reference. | varchar(50) | No | No | No | |||
| drg_source_value | The source value for the 3-digit DRG source code as it appears in the source data, stored here for reference. | varchar(50) | No | No | No | |||
| payer_plan_period_id | A foreign key to the PAYER_PLAN_PERIOD table, where the details of the Payer, Plan and Family are stored. Record the payer_plan_id that relates to the payer who contributed to the paid_by_payer field. | bigint | No | No | No |
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.
ETL Conventions
The SQL script for generating DRUG_ERA records can be found here.
| CDM Field | User Guide | ETL Conventions | Datatype | Required | Primary Key | Foreign Key | FK Table | FK Domain |
|---|---|---|---|---|---|---|---|---|
| drug_era_id | bigint | Yes | Yes | No | ||||
| person_id | bigint | Yes | No | Yes | PERSON | |||
| drug_concept_id | The Concept Id representing the specific drug ingredient. | integer | Yes | No | Yes | CONCEPT | Drug | |