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closes OHDSI/Themis #121

This commit is contained in:
Clair Blacketer 2024-04-24 17:07:03 -04:00
parent 13fc5982ef
commit 4869f7c4ca
2 changed files with 2 additions and 2 deletions
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2
inst/csv/OMOP_CDMv5.3_Field_Level.csv
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@ -180,7 +180,7 @@ observation,unit_source_value,No,varchar(50),This field houses the verbatim valu
observation,qualifier_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the qualifier of the Observation 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 observation,qualifier_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the qualifier of the Observation 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
death,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA death,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA
death,death_date,Yes,date,The date the person was deceased.,"If the precise date include day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day. For additional conventions related to this field, please refer to the [THEMIS repository](https://ohdsi.github.io/Themis/tag_death_date.html). ",No,No,NA,NA,NA,NA,NA death,death_date,Yes,date,The date the person was deceased.,"If the precise date include day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day. For additional conventions related to this field, please refer to the [THEMIS repository](https://ohdsi.github.io/Themis/tag_death_date.html). ",No,No,NA,NA,NA,NA,NA
death,death_datetime,No,datetime,NA,If not available set time to midnight (00:00:00),No,No,NA,NA,NA,NA,NA death,death_datetime,No,datetime,NA,"If you have date and time of death, populate death_datetime, otherwise leave NULL",No,No,NA,NA,NA,NA,NA
death,death_type_concept_id,No,integer,"This is the provenance of the death record, i.e., where it came from. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc.",Use the type concept that be reflects the source of the death 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 death,death_type_concept_id,No,integer,"This is the provenance of the death record, i.e., where it came from. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc.",Use the type concept that be reflects the source of the death 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
death,cause_concept_id,No,integer,"This is the Standard Concept representing the Person's cause of death, if available.","There is no specified domain for this concept, just choose the Standard Concept Id that best represents the person's cause of death.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA death,cause_concept_id,No,integer,"This is the Standard Concept representing the Person's cause of death, if available.","There is no specified domain for this concept, just choose the Standard Concept Id that best represents the person's cause of death.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
death,cause_source_value,No,varchar(50),NA,"If available, put the source code representing the cause of death here.",No,No,NA,NA,NA,NA,NA death,cause_source_value,No,varchar(50),NA,"If available, put the source code representing the cause of death here.",No,No,NA,NA,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
180 note note_title No varchar(250) The title of the note. NA No No NA NA NA NA NA
181 note note_text Yes varchar(MAX) The content of the note. NA No No NA NA NA NA NA
182 note encoding_concept_id Yes integer This is the Concept representing the character encoding type. Put the Concept Id that represents the encoding character type here. Currently the only option is UTF-8 ([32678](https://athena.ohdsi.org/search-terms/terms/32678)). It the note is encoded in any other type, like ASCII then put 0. No Yes CONCEPT CONCEPT_ID NA NA NA
183 note language_concept_id Yes integer The language of the note. Use Concepts that are descendants of the concept [4182347](https://athena.ohdsi.org/search-terms/terms/4182347) (World Languages). No Yes CONCEPT CONCEPT_ID NA NA NA
184 note provider_id No integer The Provider who wrote the note. The ETL may need to make a determination on which provider to put here. No Yes PROVIDER PROVIDER_ID NA NA NA
185 note visit_occurrence_id No integer The Visit during which the note was written. NA No Yes VISIT_OCCURRENCE VISIT_OCCURRENCE_ID NA NA NA
186 note visit_detail_id No integer The Visit Detail during which the note was written. NA No Yes VISIT_DETAIL VISIT_DETAIL_ID NA NA NA

2
inst/csv/OMOP_CDMv5.4_Field_Level.csv
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@ -192,7 +192,7 @@ observation,observation_event_id,No,integer,"If the Observation record is relate
observation,obs_event_field_concept_id,No,integer,"If the Observation 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 OBSERVATION_EVENT_ID came from.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA observation,obs_event_field_concept_id,No,integer,"If the Observation 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 OBSERVATION_EVENT_ID came from.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
death,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA death,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA
death,death_date,Yes,date,The date the person was deceased.,"If the precise date include day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day. For additional conventions related to this field, please refer to the [THEMIS repository](https://ohdsi.github.io/Themis/tag_death_date.html). ",No,No,NA,NA,NA,NA,NA death,death_date,Yes,date,The date the person was deceased.,"If the precise date include day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day. For additional conventions related to this field, please refer to the [THEMIS repository](https://ohdsi.github.io/Themis/tag_death_date.html). ",No,No,NA,NA,NA,NA,NA
death,death_datetime,No,datetime,NA,If not available set time to midnight (00:00:00),No,No,NA,NA,NA,NA,NA death,death_datetime,No,datetime,NA,"If you have date and time of death, populate death_datetime, otherwise leave NULL",No,No,NA,NA,NA,NA,NA
death,death_type_concept_id,No,integer,"This is the provenance of the death record, i.e., where it came from. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc.",Use the type concept that be reflects the source of the death 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 death,death_type_concept_id,No,integer,"This is the provenance of the death record, i.e., where it came from. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc.",Use the type concept that be reflects the source of the death 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
death,cause_concept_id,No,integer,"This is the Standard Concept representing the Person's cause of death, if available.","There is no specified domain for this concept, just choose the Standard Concept Id that best represents the person's cause of death.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA death,cause_concept_id,No,integer,"This is the Standard Concept representing the Person's cause of death, if available.","There is no specified domain for this concept, just choose the Standard Concept Id that best represents the person's cause of death.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
death,cause_source_value,No,varchar(50),NA,"If available, put the source code representing the cause of death here.",No,No,NA,NA,NA,NA,NA death,cause_source_value,No,varchar(50),NA,"If available, put the source code representing the cause of death here.",No,No,NA,NA,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
192 note note_title No varchar(250) The title of the note. NA No No NA NA NA NA NA
193 note note_text Yes varchar(MAX) The content of the note. NA No No NA NA NA NA NA
194 note encoding_concept_id Yes integer This is the Concept representing the character encoding type. Put the Concept Id that represents the encoding character type here. Currently the only option is UTF-8 ([32678](https://athena.ohdsi.org/search-terms/terms/32678)). It the note is encoded in any other type, like ASCII then put 0. No Yes CONCEPT CONCEPT_ID NA NA NA
195 note language_concept_id Yes integer The language of the note. Use Concepts that are descendants of the concept [4182347](https://athena.ohdsi.org/search-terms/terms/4182347) (World Languages). No Yes CONCEPT CONCEPT_ID NA NA NA
196 note provider_id No integer The Provider who wrote the note. The ETL may need to make a determination on which provider to put here. No Yes PROVIDER PROVIDER_ID NA NA NA
197 note visit_occurrence_id No integer The Visit during which the note was written. NA No Yes VISIT_OCCURRENCE VISIT_OCCURRENCE_ID NA NA NA
198 note visit_detail_id No integer The Visit Detail during which the note was written. NA No Yes VISIT_DETAIL VISIT_DETAIL_ID NA NA NA