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fix admitted_from_concept_id / source_value mix up

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Florian Katsch 2024-06-12 11:40:17 +02:00
parent 3b84ef6114
commit 6ec05635ce
1 changed files with 115 additions and 115 deletions
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inst/csv/OMOP_CDMv6.0_Field_Level.csv
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@ -64,8 +64,8 @@ visit_detail,provider_id,No,bigint,"There will only be one provider per **visit
visit_detail,care_site_id,No,bigint,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.,No,Yes,CARE_SITE,CARE_SITE_ID,NA,NA,NA visit_detail,care_site_id,No,bigint,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.,No,Yes,CARE_SITE,CARE_SITE_ID,NA,NA,NA
visit_detail,visit_detail_source_value,No,varchar(50),"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.",No,No,NA,NA,NA,NA,NA visit_detail,visit_detail_source_value,No,varchar(50),"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.",No,No,NA,NA,NA,NA,NA
visit_detail,visit_detail_source_concept_id,Yes,integer,NA,"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.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA visit_detail,visit_detail_source_concept_id,Yes,integer,NA,"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.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
visit_detail,admitted_from_concept_id,No,varchar(50),NA,"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.",No,No,NA,NA,NA,NA,NA visit_detail,admitted_from_source_value,No,varchar(50),NA,"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.",No,No,NA,NA,NA,NA,NA
visit_detail,admitted_from_source_value,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,NA,NA visit_detail,admitted_from_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,NA,NA
visit_detail,discharge_to_source_value,No,varchar(50),NA,"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.",No,No,NA,NA,NA,NA,NA visit_detail,discharge_to_source_value,No,varchar(50),NA,"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.",No,No,NA,NA,NA,NA,NA
visit_detail,discharge_to_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,NA,NA visit_detail,discharge_to_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,NA,NA
visit_detail,preceding_visit_detail_id,No,bigint,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"".",No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,NA,NA,NA visit_detail,preceding_visit_detail_id,No,bigint,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"".",No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
64 condition_occurrence condition_concept_id Yes integer 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](https://athena.ohdsi.org/search-terms/terms?domain=Condition&standardConcept=Standard&page=1&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID Condition NA NA
65 condition_occurrence condition_start_date Yes 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. No No NA NA NA NA NA
66 condition_occurrence condition_start_datetime No datetime NA If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) No No NA NA NA NA NA
67 condition_occurrence condition_end_date No 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. No No NA NA NA NA NA
68 condition_occurrence condition_end_datetime No datetime NA If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) No No NA NA NA NA NA
69 condition_occurrence condition_type_concept_id Yes integer 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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID Type Concept NA NA
70 condition_occurrence condition_status_concept_id Yes integer 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](https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status&standardConcept=Standard&page=1&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID NA NA NA
71 condition_occurrence stop_reason No varchar(20) 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. No No NA NA NA NA NA