update cdm_source documentation

inst/csv/OMOP_CDMv5.4_Field_Level.csv

@@ -88,7 +88,7 @@ condition_occurrence,condition_source_concept_id,No,integer,"This is the concept
 condition_occurrence,condition_status_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the condition status.,This information may be called something different in the source data but the field is meant to contain a value indicating when and how a diagnosis was given to a patient. This source value is mapped to a standard concept which is stored in the CONDITION_STATUS_CONCEPT_ID field.,No,No,NA,NA,NA,NA,NA
 drug_exposure,drug_exposure_id,Yes,integer,The unique key given to records of drug dispensings or administrations for a person. Refer to the ETL for how duplicate drugs during the same visit were handled.,"Each instance of a drug dispensing or administration present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same drug within the same visit. It is valid to keep these duplicates and assign them individual, unique, DRUG_EXPOSURE_IDs, though it is up to the ETL how they should be handled.",Yes,No,NA,NA,NA,NA,NA
 drug_exposure,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the drug dispensing or administration is recorded. This may be a system generated code.,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA
-drug_exposure,drug_concept_id,Yes,integer,"The DRUG_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 concept id which represents a drug product or molecule otherwise introduced to the body. The drug concepts can have a varying degree of information about drug strength and dose. This information is relevant in the context of quantity and administration information in the subsequent fields plus strength information from the DRUG_STRENGTH table, provided as part of the standard vocabulary download.","The CONCEPT_ID that the DRUG_SOURCE_VALUE maps to. The concept id should be derived either from mapping from the source concept id or by picking the drug concept representing the most amount of detail you have. Records whose source values map to standard concepts with a domain of Drug should go in this table. When the Drug Source Value of the code cannot be translated into Standard Drug Concept IDs, a Drug exposure entry is stored with only the corresponding SOURCE_CONCEPT_ID and DRUG_SOURCE_VALUE and a DRUG_CONCEPT_ID of 0. The Drug Concept with the most detailed content of information is preferred during the mapping process. These are indicated in the CONCEPT_CLASS_ID field of the 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 �Ingredient�. Note: If only the drug class is known, the DRUG_CONCEPT_ID field should contain 0. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Drug&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Drug,NA,NA
+drug_exposure,drug_concept_id,Yes,integer,"The DRUG_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 concept id which represents a drug product or molecule otherwise introduced to the body. The drug concepts can have a varying degree of information about drug strength and dose. This information is relevant in the context of quantity and administration information in the subsequent fields plus strength information from the DRUG_STRENGTH table, provided as part of the standard vocabulary download.","The CONCEPT_ID that the DRUG_SOURCE_VALUE maps to. The concept id should be derived either from mapping from the source concept id or by picking the drug concept representing the most amount of detail you have. Records whose source values map to standard concepts with a domain of Drug should go in this table. When the Drug Source Value of the code cannot be translated into Standard Drug Concept IDs, a Drug exposure entry is stored with only the corresponding SOURCE_CONCEPT_ID and DRUG_SOURCE_VALUE and a DRUG_CONCEPT_ID of 0. The Drug Concept with the most detailed content of information is preferred during the mapping process. These are indicated in the CONCEPT_CLASS_ID field of the 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 �Ingredient�. Note: If only the drug class is known, the DRUG_CONCEPT_ID field should contain 0. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Drug&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Drug,NA,NA
 drug_exposure,drug_exposure_start_date,Yes,date,Use this date to determine the start date of the drug record.,"Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration was recorded. It is a valid ETL choice to use the date the drug was ordered as the DRUG_EXPOSURE_START_DATE.",No,No,NA,NA,NA,NA,NA
 drug_exposure,drug_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
 drug_exposure,drug_exposure_end_date,Yes,date,The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended for the patient.,"If this information is not explicitly available in the data, infer the end date using the following methods:<br><br> 1. Start first with duration or days supply using the calculation drug start date + days supply -1 day. 2. Use quantity divided by daily dose that you may obtain from the sig or a source field (or assumed daily dose of 1) for solid, indivisibile, drug products. If quantity represents ingredient amount, quantity divided by daily dose * concentration (from drug_strength) drug concept id tells you the dose form. 3. If it is an administration record, set drug end date equal to drug start date. If the record is a written prescription then set end date to start date + 29. If the record is a mail-order prescription set end date to start date + 89. The end date must be equal to or greater than the start date. Ibuprofen 20mg/mL oral solution concept tells us this is oral solution. Calculate duration as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL) 200*5/20 = 50 days. [Examples by dose form](https://ohdsi.github.io/CommonDataModel/drug_dose.html)<br><br>For detailed conventions for how to populate this field, please see the [THEMIS repository](https://ohdsi.github.io/Themis/tag_drug_exposure.html).",No,No,NA,NA,NA,NA,NA
@@ -148,7 +148,7 @@ device_exposure,unit_source_value,No,varchar(50),"This field houses the verbatim
 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
 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
 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
-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
+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
 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
 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
@@ -396,8 +396,8 @@ cdm_source,cdm_source_name,Yes,varchar(255),The name of the CDM instance.,NA,No,
 cdm_source,cdm_source_abbreviation,Yes,varchar(25),The abbreviation of the CDM instance.,NA,No,No,NA,NA,NA,NA,NA
 cdm_source,cdm_holder,Yes,varchar(255),The holder of the CDM instance.,NA,No,No,NA,NA,NA,NA,NA
 cdm_source,source_description,No,varchar(MAX),The description of the CDM instance.,NA,No,No,NA,NA,NA,NA,NA
-cdm_source,source_documentation_reference,No,varchar(255),NA,NA,No,No,NA,NA,NA,NA,NA
-cdm_source,cdm_etl_reference,No,varchar(255),NA,Version of the ETL script used. e.g. link to the Git release,No,No,NA,NA,NA,NA,NA
+cdm_source,source_documentation_reference,No,varchar(255),Refers to a publication or web resource describing the source data, e.g. a data dictionary.,NA,No,No,NA,NA,NA,NA,NA
+cdm_source,cdm_etl_reference,No,varchar(255),Version of the ETL script used. e.g. link to the Git release,NA,No,No,NA,NA,NA,NA,NA
 cdm_source,source_release_date,Yes,date,The date the data was extracted from the source system. In some systems that is the same as the date the ETL was run. Typically the latest even date in the source is on the source_release_date.,NA,No,No,NA,NA,NA,NA,NA
 cdm_source,cdm_release_date,Yes,date,The date the ETL script was completed. Typically this is after the source_release_date.,NA,No,No,NA,NA,NA,NA,NA
 cdm_source,cdm_version,No,varchar(10),Version of the OMOP CDM used as string. e.g. v5.4,NA,No,No,NA,NA,NA,NA,NA