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closes #504

This commit is contained in:
Clair Blacketer 2025-03-06 11:48:31 -05:00
parent 4c707cdd64
commit 4b96b13b55
3 changed files with 5 additions and 4 deletions
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5
docs/cdm54.html
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@ -3583,7 +3583,7 @@ Concept and are recorded in the following order of precedence: Marketed
Product, Branded Pack, Clinical Pack, Branded Drug, Clinical Drug,
Branded Drug Component, Clinical Drug Component, Branded Drug Form,
Clinical Drug Form, and only if no other information is available
<EFBFBD>Ingredient<EFBFBD>. Note: If only the drug class is known, the DRUG_CONCEPT_ID
Ingredient. Note: If only the drug class is known, the DRUG_CONCEPT_ID
field should contain 0. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Drug&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
@ -5750,7 +5750,8 @@ from =.
Operators are =, &gt; and these concepts belong to the ‘Meas Value
Operator’ domain. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Meas+Value+Operator&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>. Leave it NULL if there’s an exact numeric value given
Concepts</a>. The operator_concept_id explictly refers to the value of
the measurement. Leave it NULL if there’s an exact numeric value given
(instead of putting ‘=’) or there’s no numeric value at all.
</td>
<td style="text-align:left;">

2
inst/csv/OMOP_CDMv5.4_Field_Level.csv
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@ -153,7 +153,7 @@ measurement,measurement_date,Yes,date,Use this date to determine the date of the
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
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
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=). 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
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=). Leave it NULL if there's an exact numeric value given (instead of putting '=') or there's no numeric value at all.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
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=). The operator_concept_id explictly refers to the value of the measurement. Leave it NULL if there's an exact numeric value given (instead of putting '=') or there's no numeric value at all.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
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.",[Convention for negative values](https://ohdsi.github.io/Themis/negative_value_as_number.html),No,No,NA,NA,NA,NA,NA
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 there is no categorial result in the source data, set VALUE_AS_CONCEPT_ID to NULL, if there is a categorial result in a source data but without mapping, set VALUE_AS_CONCEPT_ID to 0, else map to a CONCEPT_ID.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
measurement,unit_concept_id,No,integer,"At present, there isn't a prescribed unit for individual measurements, such as Hemoglobin A1C, meaning it's not obligatory to express these measurements as a percentage. UNIT_SOURCE_VALUES should be linked to a Standard Concept within the Unit domain that most accurately reflects the unit provided in the source data.","If the source data does not include units, set UNIT_CONCEPT_ID to NULL. If units are provided but not mapped, set UNIT_CONCEPT_ID to 0. Otherwise, map the units to a CONCEPT_ID. Remember that units are case-sensitive in vocabulary.",No,Yes,CONCEPT,CONCEPT_ID,Unit,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
153 measurement unit_source_value No varchar(50) This field contains the exact value from the source data that represents the unit of measurement used. This value corresponds to a standardized CONCEPT_ID found in UNIT_CONCEPT_ID and in the 'Unit' domain within the Standardized Vocabularies. The original code is retained here for reference purposes. No No NA NA NA NA NA
154 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
155 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
156 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
157 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
158 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
159 observation person_id Yes integer The PERSON_ID of the Person for whom the Observation is recorded. This may be a system generated code. NA No Yes PERSON PERSON_ID NA NA NA

2
inst/csv/OMOP_CDMv6.0_Field_Level.csv
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@ -148,7 +148,7 @@ measurement,measurement_date,Yes,date,Use this date to determine the date of the
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
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
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
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
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 =.","The operator_concept_id explictly refers to the value of the measurement. 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
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
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
measurement,unit_concept_id,No,integer,"There is currently no recommended unit for individual measurements, i.e. it is not mandatory to represent Hemoglobin a1C measurements as a percentage. 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 MEASUREMENT_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit.",No,Yes,CONCEPT,CONCEPT_ID,Unit,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
148 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
149 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
150 observation observation_id Yes bigint 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
151 observation person_id Yes bigint The PERSON_ID of the Person for whom the Observation is recorded. This may be a system generated code. NA No Yes PERSON PERSON_ID NA NA NA
152 observation observation_concept_id Yes integer 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. No Yes CONCEPT CONCEPT_ID NA NA NA
153 observation observation_date No 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. No No NA NA NA NA NA
154 observation observation_datetime Yes datetime NA If no time is given set to midnight (00:00:00). No No NA NA NA NA NA