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fixes #676

This commit is contained in:
Clair Blacketer 2025-03-06 11:22:38 -05:00
parent 4a08b6276e
commit 014b50fcda
4 changed files with 5 additions and 6 deletions
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5
docs/cdm54.html
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@ -5063,9 +5063,8 @@ You can use the TYPE_CONCEPT_ID to denote the provenance of the record,
as in whether the record is from administrative claims or EHR.
</td>
<td style="text-align:left;">
Choose the drug_type_concept_id that best represents the provenance of
the record, for example whether it came from a record of a prescription
written or physician administered drug. <a
Choose the device_type_concept_id that best represents the provenance of
the record. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>. A more detailed explanation of each Type Concept can be
found on the <a

2
docs/cdm60.html
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@ -4941,7 +4941,7 @@ href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&amp;standa
Concepts</a>.
</td>
<td style="text-align:left;">
Choose the drug_type_concept_id that best represents the provenance of
Choose the device_type_concept_id that best represents the provenance of
the record, for example whether it came from a record of a prescription
written or physician administered drug.
</td>

2
inst/csv/OMOP_CDMv5.4_Field_Level.csv
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@ -134,7 +134,7 @@ device_exposure,device_exposure_start_date,Yes,date,Use this date to determine t
device_exposure,device_exposure_start_datetime,No,datetime,NA,"This is not required, though it is in v6. 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
device_exposure,device_exposure_end_date,No,date,"The DEVICE_EXPOSURE_END_DATE denotes the day the device exposure ended for the patient, if given.",Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable.,No,No,NA,NA,NA,NA,NA
device_exposure,device_exposure_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
device_exposure,device_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR.","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&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
device_exposure,device_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR.","Choose the device_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=). 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
device_exposure,unique_device_id,No,varchar(255),"This is the Unique Device Identification (UDI-DI) number for devices regulated by the FDA, if given.","For medical devices that are regulated by the FDA, a Unique Device Identification (UDI) is provided if available in the data source and is recorded in the UNIQUE_DEVICE_ID field.",No,No,NA,NA,NA,NA,NA
device_exposure,production_id,No,varchar(255),This is the Production Identifier (UDI-PI) portion of the Unique Device Identification.,NA,No,No,NA,NA,NA,NA,NA
device_exposure,quantity,No,integer,NA,"If there is a record of device exposure in the source but no quantity value, then set to 1.",No,No,NA,NA,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
134 device_exposure 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 Unit 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
135 measurement measurement_id Yes integer The unique key given to a Measurement record for a Person. Refer to the ETL for how duplicate Measurements during the same Visit were handled. Each instance of a measurement present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same measurement within the same visit. It is valid to keep these duplicates and assign them individual, unique, MEASUREMENT_IDs, though it is up to the ETL how they should be handled. Yes No NA NA NA NA NA
136 measurement person_id Yes integer The PERSON_ID of the Person for whom the Measurement is recorded. This may be a system generated code. NA No Yes PERSON PERSON_ID NA NA NA
137 measurement measurement_concept_id Yes integer The MEASUREMENT_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 measurement. The CONCEPT_ID that the MEASUREMENT_SOURCE_VALUE maps to. Only records whose source values map to concepts with a domain of �Measurement� should go in this table. No Yes CONCEPT CONCEPT_ID Measurement NA NA
138 measurement measurement_date Yes date Use this date to determine the date of the measurement. If there are multiple dates in the source data associated with a record such as order_date, draw_date, and result_date, choose the one that is closest to the date the sample was drawn from the patient. No No NA NA NA NA NA
139 measurement measurement_datetime No datetime NA This is not required, though it is in v6. 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
140 measurement measurement_time No varchar(10) NA This is present for backwards compatibility and will be deprecated in an upcoming version. No No NA NA NA NA NA

2
inst/csv/OMOP_CDMv6.0_Field_Level.csv
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@ -133,7 +133,7 @@ device_exposure,device_exposure_start_date,Yes,date,Use this date to determine t
device_exposure,device_exposure_start_datetime,No,datetime,NA,"This is not required, though it is in v6. 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
device_exposure,device_exposure_end_date,No,date,"The DEVICE_EXPOSURE_END_DATE denotes the day the device exposure ended for the patient, if given.",Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable.,No,No,NA,NA,NA,NA,NA
device_exposure,device_exposure_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
device_exposure,device_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug.",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA
device_exposure,device_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).","Choose the device_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug.",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA
device_exposure,unique_device_id,No,varchar(50),"This is the Unique Device Identification number for devices regulated by the FDA, if given.","For medical devices that are regulated by the FDA, a Unique Device Identification (UDI) is provided if available in the data source and is recorded in the UNIQUE_DEVICE_ID field.",No,No,NA,NA,NA,NA,NA
device_exposure,quantity,No,integer,NA,NA,No,No,NA,NA,NA,NA,NA
device_exposure,provider_id,No,bigint,"The Provider associated with device record, e.g. the provider who wrote the prescription or the provider who implanted the device.",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.,No,Yes,PROVIDER,PROVIDER_ID,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
133 measurement measurement_date Yes date Use this date to determine the date of the measurement. If there are multiple dates in the source data associated with a record such as order_date, draw_date, and result_date, choose the one that is closest to the date the sample was drawn from the patient. No No NA NA NA NA NA
134 measurement measurement_datetime No datetime NA This is not required, though it is in v6. 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
135 measurement measurement_time No varchar(10) NA This is present for backwards compatibility and will be deprecated in an upcoming version. No No NA NA NA NA NA
136 measurement measurement_type_concept_id Yes integer This field can be used to determine the provenance of the Measurement record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources. Choose the MEASUREMENT_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](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
137 measurement operator_concept_id No integer The meaning of Concept [4172703](https://athena.ohdsi.org/search-terms/terms/4172703) for '=' is identical to omission of a OPERATOR_CONCEPT_ID value. Since the use of this field is rare, it's important when devising analyses to not to forget testing for the content of this field for values different from =. Operators are <, <=, =, >=, > and these concepts belong to the 'Meas Value Operator' domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Meas+Value+Operator&standardConcept=Standard&page=1&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID NA NA NA
138 measurement value_as_number No float This is the numerical value of the Result of the Measurement, if available. Note that measurements such as blood pressures will be split into their component parts i.e. one record for systolic, one record for diastolic. If there is a negative value coming from the source, set the VALUE_AS_NUMBER to NULL, with the exception of the following Measurements (listed as LOINC codes):<br>- [1925-7](https://athena.ohdsi.org/search-terms/terms/3003396) Base excess in Arterial blood by calculation - [1927-3](https://athena.ohdsi.org/search-terms/terms/3002032) Base excess in Venous blood by calculation - [8632-2](https://athena.ohdsi.org/search-terms/terms/3006277) QRS-Axis - [11555-0](https://athena.ohdsi.org/search-terms/terms/3012501) Base excess in Blood by calculation - [1926-5](https://athena.ohdsi.org/search-terms/terms/3003129) Base excess in Capillary blood by calculation - [28638-5](https://athena.ohdsi.org/search-terms/terms/3004959) Base excess in Arterial cord blood by calculation [28639-3](https://athena.ohdsi.org/search-terms/terms/3007435) Base excess in Venous cord blood by calculation No No NA NA NA NA NA
139 measurement value_as_concept_id No integer If the raw data gives a categorial result for measurements those values are captured and mapped to standard concepts in the 'Meas Value' domain. If the raw data provides categorial results as well as continuous results for measurements, it is a valid ETL choice to preserve both values. The continuous value should go in the VALUE_AS_NUMBER field and the categorical value should be mapped to a standard concept in the 'Meas Value' domain and put in the VALUE_AS_CONCEPT_ID field. This is also the destination for the 'Maps to value' relationship. No Yes CONCEPT CONCEPT_ID NA NA NA