OBSERVATION

Table Description

The OBSERVATION table captures clinical facts about a Person obtained in the context of examination, questioning or a procedure. Any data that cannot be represented by any other domains, such as social and lifestyle facts, medical history, family history, etc. are recorded here.

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