FHIR to OMOP FHIR IG
0.1.0 - ci-build International flag

FHIR to OMOP FHIR IG, published by HL7 International / Biomedical Research and Regulation. This guide is not an authorized publication; it is the continuous build for version 0.1.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/fhir-omop-ig/ and changes regularly. See the Directory of published versions

Logical Model: Observation - Detailed Descriptions

Page standards status: Draft Maturity Level: 1

Definitions for the Observation logical model.

Guidance on how to interpret the contents of this table can be found here

0. Observation
Definition

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.

ShortObservation OMOP Table
Logical ModelInstances of this logical model are not marked to be the target of a Reference
2. Observation.observation-id
Definition

Observation Identifier

ShortObservation Identifier
Control1..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
4. Observation.person-id
Definition

The PERSON_ID of the Person for whom the Observation is recorded. This may be a system generated code.

ShortPerson
Control1..1
TypeReference(Person OMOP Table)
6. Observation.observation-concept-id
Definition

The OBSERVATION_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies.

ShortObservation
Control1..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
8. Observation.observation-date
Definition

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.

ShortObservation Date
Control1..1
Typedate
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
10. Observation.observation-datetime
Definition

Observation Datetime

ShortObservation Datetime
Control0..1
TypedateTime
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
12. Observation.observation-type-concept-id
Definition

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.

ShortObservation Type
Control1..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
14. Observation.value-as-number
Definition

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.

ShortValue as Number
Control0..1
Typeinteger
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
16. Observation.value-as-string
Definition

This is the categorical value of the Result of the Observation, if applicable and available.

ShortValue as String
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
18. Observation.value-as-concept-id
Definition

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.

ShortValue as Concept
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
20. Observation.qualifier-concept-id
Definition

This field contains all attributes specifying the clinical fact further, such as as degrees, severities, drug-drug interaction alerts etc.

ShortQualifier
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
22. Observation.unit-concept-id
Definition

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.

ShortUnit
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
24. Observation.provider-id
Definition

The provider associated with the observation record, e.g. the provider who ordered the test or the provider who recorded the result.

ShortProvider
Control0..1
TypeReference(Provider OMOP Table)
26. Observation.visit-occurrence-id
Definition

The visit during which the Observation occurred.

ShortVisit Occurence
Control0..1
TypeReference(Visit Occurrence OMOP Table)
28. Observation.visit-detail-id
Definition

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.

ShortVisit Detail
Control0..1
TypeReference(Visit Detail OMOP Table)
30. Observation.observation-source-value
Definition

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.

ShortObservation Source Value
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
32. Observation.observation-source-concept-id
Definition

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.

ShortObservation Source
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
34. Observation.unit-source-value
Definition

This field houses the verbatim value from the source data representing the unit of the Observation that occurred.

ShortUnit Source Value
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
36. Observation.qualifier-source-value
Definition

This field houses the verbatim value from the source data representing the qualifier of the Observation that occurred.

ShortQualifier Source Value
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
38. Observation.value-source-value
Definition

This field houses the verbatim result value of the Observation from the source data. Do not get confused with the Observation_source_value which captures source value of the observation mapped to observation_concept_id. This field is the observation result value from the source.

ShortValue Source Value
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
40. Observation.observation-event-id
Definition

If the Observation record is related to another record in the database, this field is the primary key of the linked record.

ShortObservation Event
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
42. Observation.obs-event-field-concept-id
Definition

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.

ShortObservation Event Field Concept
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension

Guidance on how to interpret the contents of this table can be found here

0. Observation
Definition

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.


Base definition for all types defined in FHIR type system.

ShortObservation OMOP TableBase for all types and resources
Control0..*
Is Modifierfalse
Logical ModelInstances of this logical model are not marked to be the target of a Reference
2. Observation.observation-id
Definition

Observation Identifier

ShortObservation Identifier
Control1..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
4. Observation.person-id
Definition

The PERSON_ID of the Person for whom the Observation is recorded. This may be a system generated code.

ShortPerson
Control1..1
TypeReference(Person OMOP Table)
6. Observation.observation-concept-id
Definition

The OBSERVATION_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies.

ShortObservation
Control1..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
8. Observation.observation-date
Definition

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.

ShortObservation Date
Control1..1
Typedate
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
10. Observation.observation-datetime
Definition

Observation Datetime

ShortObservation Datetime
Control0..1
TypedateTime
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
12. Observation.observation-type-concept-id
Definition

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.

ShortObservation Type
Control1..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
14. Observation.value-as-number
Definition

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.

ShortValue as Number
Control0..1
Typeinteger
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
16. Observation.value-as-string
Definition

This is the categorical value of the Result of the Observation, if applicable and available.

ShortValue as String
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
18. Observation.value-as-concept-id
Definition

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.

ShortValue as Concept
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
20. Observation.qualifier-concept-id
Definition

This field contains all attributes specifying the clinical fact further, such as as degrees, severities, drug-drug interaction alerts etc.

ShortQualifier
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
22. Observation.unit-concept-id
Definition

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.

ShortUnit
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
24. Observation.provider-id
Definition

The provider associated with the observation record, e.g. the provider who ordered the test or the provider who recorded the result.

ShortProvider
Control0..1
TypeReference(Provider OMOP Table)
26. Observation.visit-occurrence-id
Definition

The visit during which the Observation occurred.

ShortVisit Occurence
Control0..1
TypeReference(Visit Occurrence OMOP Table)
28. Observation.visit-detail-id
Definition

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.

ShortVisit Detail
Control0..1
TypeReference(Visit Detail OMOP Table)
30. Observation.observation-source-value
Definition

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.

ShortObservation Source Value
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
32. Observation.observation-source-concept-id
Definition

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.

ShortObservation Source
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
34. Observation.unit-source-value
Definition

This field houses the verbatim value from the source data representing the unit of the Observation that occurred.

ShortUnit Source Value
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
36. Observation.qualifier-source-value
Definition

This field houses the verbatim value from the source data representing the qualifier of the Observation that occurred.

ShortQualifier Source Value
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
38. Observation.value-source-value
Definition

This field houses the verbatim result value of the Observation from the source data. Do not get confused with the Observation_source_value which captures source value of the observation mapped to observation_concept_id. This field is the observation result value from the source.

ShortValue Source Value
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
40. Observation.observation-event-id
Definition

If the Observation record is related to another record in the database, this field is the primary key of the linked record.

ShortObservation Event
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
42. Observation.obs-event-field-concept-id
Definition

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.

ShortObservation Event Field Concept
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension

Guidance on how to interpret the contents of this table can be found here

0. Observation
Definition

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.

ShortObservation OMOP Table
Control0..*
Is Modifierfalse
Logical ModelInstances of this logical model are not marked to be the target of a Reference
2. Observation.observation-id
Definition

Observation Identifier

ShortObservation Identifier
Control1..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
4. Observation.person-id
Definition

The PERSON_ID of the Person for whom the Observation is recorded. This may be a system generated code.

ShortPerson
Control1..1
TypeReference(Person OMOP Table)
6. Observation.observation-concept-id
Definition

The OBSERVATION_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies.

ShortObservation
Control1..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
8. Observation.observation-date
Definition

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.

ShortObservation Date
Control1..1
Typedate
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
10. Observation.observation-datetime
Definition

Observation Datetime

ShortObservation Datetime
Control0..1
TypedateTime
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
12. Observation.observation-type-concept-id
Definition

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.

ShortObservation Type
Control1..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
14. Observation.value-as-number
Definition

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.

ShortValue as Number
Control0..1
Typeinteger
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
16. Observation.value-as-string
Definition

This is the categorical value of the Result of the Observation, if applicable and available.

ShortValue as String
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
18. Observation.value-as-concept-id
Definition

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.

ShortValue as Concept
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
20. Observation.qualifier-concept-id
Definition

This field contains all attributes specifying the clinical fact further, such as as degrees, severities, drug-drug interaction alerts etc.

ShortQualifier
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
22. Observation.unit-concept-id
Definition

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.

ShortUnit
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
24. Observation.provider-id
Definition

The provider associated with the observation record, e.g. the provider who ordered the test or the provider who recorded the result.

ShortProvider
Control0..1
TypeReference(Provider OMOP Table)
26. Observation.visit-occurrence-id
Definition

The visit during which the Observation occurred.

ShortVisit Occurence
Control0..1
TypeReference(Visit Occurrence OMOP Table)
28. Observation.visit-detail-id
Definition

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.

ShortVisit Detail
Control0..1
TypeReference(Visit Detail OMOP Table)
30. Observation.observation-source-value
Definition

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.

ShortObservation Source Value
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
32. Observation.observation-source-concept-id
Definition

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.

ShortObservation Source
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
34. Observation.unit-source-value
Definition

This field houses the verbatim value from the source data representing the unit of the Observation that occurred.

ShortUnit Source Value
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
36. Observation.qualifier-source-value
Definition

This field houses the verbatim value from the source data representing the qualifier of the Observation that occurred.

ShortQualifier Source Value
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
38. Observation.value-source-value
Definition

This field houses the verbatim result value of the Observation from the source data. Do not get confused with the Observation_source_value which captures source value of the observation mapped to observation_concept_id. This field is the observation result value from the source.

ShortValue Source Value
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
40. Observation.observation-event-id
Definition

If the Observation record is related to another record in the database, this field is the primary key of the linked record.

ShortObservation Event
Control0..1
Typestring
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
42. Observation.obs-event-field-concept-id
Definition

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.

ShortObservation Event Field Concept
Control0..1
Typecode
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension