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Merge pull request #622 from AlaikseiKatyshou/value_source_concept_id 

This is a PR from the private branch. After merging this, we will open a PR to the dev branch.
Add value_source_concept_id field in measurement and observation tables
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Alexander 2024-05-14 17:39:08 +02:00 committed by GitHub
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inst/csv/OMOP_CDMv5.4_Field_Level.csv
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@ -167,6 +167,7 @@ measurement,measurement_source_concept_id,No,integer,"This is the concept repres
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,NA,NA,NA,NA,NA
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,NA,NA,NA
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,NA,NA,NA,NA,NA
measurement,value_source_concept_id,No,integer,"This is the Concept representing the VALUE_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 VALUE_AS_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.","If the VALUE_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,NA,NA,NA
measurement,measurement_event_id,No,integer,"If the Measurement 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.",No,No,NA,NA,NA,NA,NA
measurement,meas_event_field_concept_id,No,integer,"If the Measurement 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 MEASUREMENT_EVENT_ID came from.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
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,NA,NA,NA,NA,NA
@ -188,6 +189,7 @@ observation,observation_source_concept_id,No,integer,"This is the concept repres
observation,unit_source_value,No,varchar(50),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.,No,No,NA,NA,NA,NA,NA
observation,qualifier_source_value,No,varchar(50),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.,No,No,NA,NA,NA,NA,NA
observation,value_source_value,No,varchar(50),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.",No,No,NA,NA,NA,NA,NA
observation,value_source_concept_id,No,integer,"This is the Concept representing the VALUE_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 VALUE_AS_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.","If the VALUE_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,NA,NA,NA
observation,observation_event_id,No,integer,"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](https://ohdsi.github.io/CommonDataModel/cdm60.html#observation) table for more details.",No,No,NA,NA,NA,NA,NA
observation,obs_event_field_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
death,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
167 observation qualifier_concept_id value_as_concept_id No integer Integer This field contains all attributes specifying the clinical fact further, such as as degrees, severities, drug-drug interaction alerts etc. 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. 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. 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](https://athena.ohdsi.org/search-terms/terms/45581076) 'Family history of ischaemic heart disease and other diseases of the circulatory system' has a 'Maps to' relationship to [4167217](https://athena.ohdsi.org/search-terms/terms/4167217) 'Family history of clinical finding' as well as a 'Maps to value' record to [134057](https://athena.ohdsi.org/search-terms/terms/134057) 'Disorder of cardiovascular system'. No Yes CONCEPT CONCEPT_ID NA NA NA
168 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 NA NA NA
169 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 NA Unit NA NA
170 observation provider_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. 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 PROVIDER PROVIDER_ID NA NA NA
171 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 NA NA NA
172 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 NA NA NA
173 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 NA NA NA NA NA
189 note note_date person_id Yes date integer The date the note was recorded. NA NA No No Yes NA PERSON NA PERSON_ID NA NA NA
190 note note_datetime note_date No Yes datetime date NA The date the note was recorded. If time is not given set the time to midnight. NA No No NA NA NA NA NA
191 note note_type_concept_id note_datetime Yes No integer datetime The provenance of the note. Most likely this will be EHR. NA Put the source system of the note, as in EHR record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). If time is not given set the time to midnight. No Yes No CONCEPT NA CONCEPT_ID NA Type Concept NA NA NA
192 note note_type_concept_id Yes integer The provenance of the note. Most likely this will be EHR. Put the source system of the note, as in EHR record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). No Yes CONCEPT CONCEPT_ID Type Concept NA NA
193 note note_class_concept_id Yes integer A Standard Concept Id representing the HL7 LOINC Document Type Vocabulary classification of the note. Map the note classification to a Standard Concept. For more information see the ETL Conventions in the description of the NOTE table. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&conceptClass=Doc+Kind&conceptClass=Doc+Role&conceptClass=Doc+Setting&conceptClass=Doc+Subject+Matter&conceptClass=Doc+Type+of+Service&domain=Meas+Value&page=1&pageSize=15&query=). This Concept can alternatively be represented by concepts with the relationship 'Kind of (LOINC)' to [706391](https://athena.ohdsi.org/search-terms/terms/706391) (Note). No Yes CONCEPT CONCEPT_ID NA NA NA
194 note note_title No varchar(250) The title of the note. NA No No NA NA NA NA NA
195 note note_text Yes varchar(MAX) The content of the note. NA No No NA NA NA NA NA