procedures added

inst/csv/OMOP_CDMv5.4_Field_Level.csv

@@ -106,7 +106,7 @@ CONDITION_ERA,cdm,condition_occurrence_count,No,,,integer,0,,"The number of indi
 Occurrences used to construct the
 condition era.",,No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,1,1,,,,,,,,,,No,,,Yes,,,,,,,,,
 CONDITION_ERA,cdm,person_id,Yes,0,,integer,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,Yes,,,,,,,,,
-CONDITION_OCCURRENCE,cdm,condition_concept_id,Yes,0,,integer,0,,"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,0,,CONCEPT,CONCEPT_ID,Condition,0,,,,,Yes,0,,Yes,0,,Yes,5,,No,,,No,,,,,,,,,,,,,,,No,,,Yes,,,,4090861,1,Male genitalia finding,4095793,,Female genitalia finding
+CONDITION_OCCURRENCE,cdm,condition_concept_id,Yes,0,,integer,0,,"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,0,,CONCEPT,CONCEPT_ID,Condition,0,,,,,Yes,0,,Yes,0,,Yes,5,,No,,,No,,,,,,,,,,,,,,,No,,,Yes,,,,4090861,1,Male genitalia finding,4095793,1,Female genitalia finding
 CONDITION_OCCURRENCE,cdm,condition_end_date,No,,,date,0,,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,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,CONDITION_OCCURRENCE,CONDITION_START_DATE,1,,Yes,1,,Yes,,,,,,,,,
 CONDITION_OCCURRENCE,cdm,condition_end_datetime,No,,,datetime,0,,,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,CONDITION_OCCURRENCE,CONDITION_START_DATETIME,1,,Yes,1,,Yes,,,,,,,,,
 CONDITION_OCCURRENCE,cdm,condition_occurrence_id,Yes,0,,integer,0,,The unique key given to a condition record for a person. Refer to the ETL for how duplicate conditions during the same visit were handled.,"Each instance of a condition present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same condition within the same visit. It is valid to keep these duplicates and assign them individual, unique, CONDITION_OCCURRENCE_IDs, though it is up to the ETL how they should be handled.",Yes,0,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,,,,,,,,,,,,,
@@ -405,7 +405,7 @@ PERSON,cdm,year_of_birth,Yes,0,,integer,0,,Compute age using year_of_birth.,"For
 PROCEDURE_OCCURRENCE,cdm,modifier_concept_id,No,,,integer,0,,The modifiers are intended to give additional information about the procedure but as of now the vocabulary is under review.,"It is up to the ETL to choose how to map modifiers if they exist in source data. These concepts are typically distinguished by 'Modifier' concept classes (e.g., 'CPT4 Modifier' as part of the 'CPT4' vocabulary). If there is more than one modifier on a record, one should be chosen that pertains to the procedure rather than provider. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?conceptClass=CPT4+Modifier&conceptClass=HCPCS+Modifier&vocabulary=CPT4&vocabulary=HCPCS&standardConcept=Standard&page=1&pageSize=15&query=).",No,,,Yes,0,,CONCEPT,CONCEPT_ID,,,,,,,Yes,0,,Yes,100,,Yes,100,,No,,,No,,,,,,,,,,,,,,,No,,,Yes,,,,,,,,,
 PROCEDURE_OCCURRENCE,cdm,modifier_source_value,No,,,varchar(50),0,,,The original modifier code from the source is stored here for reference.,No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,Yes,100,,MODIFIER_CONCEPT_ID,,,,,,,,,,,,No,,,Yes,,,,,,,,,
 PROCEDURE_OCCURRENCE,cdm,person_id,Yes,0,,integer,0,,The PERSON_ID of the PERSON for whom the procedure is recorded. This may be a system generated code.,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,Yes,,,,,,,,,
-PROCEDURE_OCCURRENCE,cdm,procedure_concept_id,Yes,0,,integer,0,,"The PROCEDURE_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 procedure","The CONCEPT_ID that the PROCEDURE_SOURCE_VALUE maps to. Only records whose source values map to standard concepts with a domain of ""Procedure"" should go in this table. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Procedure&standardConcept=Standard&page=1&pageSize=15&query=).",No,,,Yes,0,,CONCEPT,CONCEPT_ID,Procedure,0,,,,,Yes,0,,Yes,0,,Yes,5,,No,,,No,,,,,,,,,,,,,,,No,,,Yes,,,,1,,,1,,
+PROCEDURE_OCCURRENCE,cdm,procedure_concept_id,Yes,0,,integer,0,,"The PROCEDURE_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 procedure","The CONCEPT_ID that the PROCEDURE_SOURCE_VALUE maps to. Only records whose source values map to standard concepts with a domain of ""Procedure"" should go in this table. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Procedure&standardConcept=Standard&page=1&pageSize=15&query=).",No,,,Yes,0,,CONCEPT,CONCEPT_ID,Procedure,0,,,,,Yes,0,,Yes,0,,Yes,5,,No,,,No,,,,,,,,,,,,,,,No,,,Yes,,,,,,"4134149 - Procedure on male genital organ - can't be used as a lot of CPT4 codes have wrong hierarchy, for example https://athena.ohdsi.org/search-terms/terms/2313992",4041261,1,Procedure on female genital system
 PROCEDURE_OCCURRENCE,cdm,procedure_date,Yes,0,,date,0,,Use this date to determine the date the procedure started.,This is meant to be the **start date** of the procedure. It will be renamed in a future version to **PROCEDURE_START_DATE**.,No,,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,Yes,5,,,,,,,
 PROCEDURE_OCCURRENCE,cdm,procedure_datetime,No,,,datetime,0,,,"If the procedure has a start time in the native date, use this field to house that information. This will be renamed in a future version to **PROCEDURE_START_DATETIME**.",No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,,,,,,,,,
 PROCEDURE_OCCURRENCE,cdm,procedure_end_date,No,,,date,0,,Use this field to house the date that the procedure ended.,This is meant to be the end date of the procedure. It is not required and for most cases will be the same as the PROCEDURE_START_DATE.,No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PROCEDURE_OCCURRENCE,PROCEDURE_DATE,1,,Yes,1,,Yes,,,,,,,,,