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Issue #259 [measurement table] added unit_source_concept_id

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unknown 2021-08-18 11:55:08 -04:00
parent 0f1d9333dd
commit 0941a0783c
1 changed files with 2 additions and 1 deletions
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inst/csv/OMOP_CDMv5.4_Field_Level.csv
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@ -165,6 +165,7 @@ MEASUREMENT,visit_detail_id,No,integer,"The VISIT_DETAIL record during which the
MEASUREMENT,measurement_source_value,No,varchar(50),"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.,No,No,,,,,
MEASUREMENT,measurement_source_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,,,
MEASUREMENT,unit_source_value,No,varchar(50),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.,No,No,,,,,
MEASUREMENT,unit_source_concept_id,No,integer,"This is the concept representing the UNIT_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Measurement necessary for a given analytic use case. Consider using UNIT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the UNIT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,,,
MEASUREMENT,value_source_value,No,varchar(50),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.",No,No,,,,,
OBSERVATION,observation_id,Yes,integer,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. ,Yes,No,,,,,
OBSERVATION,person_id,Yes,integer,The PERSON_ID of the Person for whom the Observation is recorded. This may be a system generated code.,,No,Yes,PERSON,PERSON_ID,,,
@ -523,4 +524,4 @@ ATTRIBUTE_DEFINITION,attribute_definition_id,Yes,integer,,,No,No,,,,,
ATTRIBUTE_DEFINITION,attribute_name,Yes,varchar(255),,,No,No,,,,,
ATTRIBUTE_DEFINITION,attribute_description,No,varchar(MAX),,,No,No,,,,,
ATTRIBUTE_DEFINITION,attribute_type_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,,
ATTRIBUTE_DEFINITION,attribute_syntax,No,varchar(MAX),,,No,No,,,,,
ATTRIBUTE_DEFINITION,attribute_syntax,No,varchar(MAX),,,No,No,,,,,

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
165 OBSERVATION unit_concept_id qualifier_concept_id No integer 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. This field contains all attributes specifying the clinical fact further, such as as degrees, severities, drug-drug interaction alerts etc. 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. 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. No Yes CONCEPT CONCEPT_ID Unit
166 OBSERVATION provider_id unit_concept_id No integer The provider associated with the observation record, e.g. the provider who ordered the test or the provider who recorded the result. 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. 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. 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. No Yes PROVIDER CONCEPT PROVIDER_ID CONCEPT_ID Unit
167 OBSERVATION visit_occurrence_id provider_id No integer The visit during which the Observation occurred. The provider associated with the observation record, e.g. the provider who ordered the test or the provider who recorded the result. 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. 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. No Yes VISIT_OCCURRENCE PROVIDER VISIT_OCCURRENCE_ID PROVIDER_ID
168 OBSERVATION visit_occurrence_id No integer 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. No Yes VISIT_OCCURRENCE VISIT_OCCURRENCE_ID
169 OBSERVATION visit_detail_id No integer 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. No Yes VISIT_DETAIL VISIT_DETAIL_ID
170 OBSERVATION observation_source_value No varchar(50) 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. No No
171 OBSERVATION observation_source_concept_id No integer 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. No Yes CONCEPT CONCEPT_ID
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