documentation:vocabulary:data_etl
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documentation:vocabulary:data_etl [2015/01/24 13:05] cgreich |
documentation:vocabulary:data_etl [2015/01/24 14:23] cgreich |
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| ^domain_id^CDM table^Field^Comment^ | ^domain_id^CDM table^Field^Comment^ | ||
| - | |Generic|Any|Any|Generic Concepts can be in any field that ends in concept_id.| | + | |[[documentation:vocabulary:generic|Generic]]|Any|Any|Generic Concepts can be in any field that ends in concept_id.| |
| - | |Gender|[[documentation:cdm:person|PERSON]]|gender_concept_id| | | + | |[[documentation:vocabulary:gender|Gender]]|[[documentation:cdm:person|PERSON]]|gender_concept_id| | |
| - | |Race|[[documentation:cdm:person|PERSON]]|race_concept_id| | | + | |[[documentation:vocabulary:race|Race]]|[[documentation:cdm:person|PERSON]]|race_concept_id| | |
| - | |Ethnicity|[[documentation:cdm:person|PERSON]]|ethnicity_concept_id| | | + | |[[documentation:vocabulary:ethnicity|Ethnicity]]|[[documentation:cdm:person|PERSON]]|ethnicity_concept_id| | |
| - | |Visit|[[documentation:cdm:visit_occurrence|VISIT_OCCURRENCE]]|visit_concept_id| | | + | |[[documentation:vocabulary:visit|Visit]]|[[documentation:cdm:visit_occurrence|VISIT_OCCURRENCE]]|visit_concept_id| | |
| - | |Procedure|[[documentation:cdm:procedure_occurrence|PROCEDURE_OCCURRENCE]]|procedure_concept_id| | | + | |[[documentation:vocabulary:procedure|Procedure]]|[[documentation:cdm:procedure_occurrence|PROCEDURE_OCCURRENCE]]|procedure_concept_id| | |
| - | |Modifier|[[documentation:cdm:procedure_occurrence|PROCEDURE_OCCURRENCE]]|modifier_concept_id| | | + | |[[documentation:vocabulary:modifier|Modifier]]|[[documentation:cdm:procedure_occurrence|PROCEDURE_OCCURRENCE]]|modifier_concept_id| | |
| - | |Drug|[[documentation:cdm:drug_exposure|DRUG_EXPOSURE]]|drug_concept_id| | | + | |[[documentation:vocabulary:drug|Drug]]|[[documentation:cdm:drug_exposure|DRUG_EXPOSURE]]|drug_concept_id| | |
| - | |Route|[[documentation:cdm:drug_exposure|DRUG_EXPOSURE]]|route_concept_id| | | + | |[[documentation:vocabulary:route|Route]]|[[documentation:cdm:drug_exposure|DRUG_EXPOSURE]]|route_concept_id| | |
| - | |Unit|[[documentation:cdm:measurement|MEASUREMENT]] or [[documentation:cdm:observation|OBSERVATION]] or [[documentation:cdm:specimen|SPECIMEN]]|unit_concept_id|Units are used in different contexts. *| | + | |[[documentation:vocabulary:unit|Unit]]|[[documentation:cdm:measurement|MEASUREMENT]] or [[documentation:cdm:observation|OBSERVATION]] or [[documentation:cdm:specimen|SPECIMEN]]|unit_concept_id|Units are used in different contexts. *| |
| - | |Device|[[documentation:cdm:device_exposure|DEVICE_EXPOSURE]]|device_concept_id| | | + | |[[documentation:vocabulary:device|Device]]|[[documentation:cdm:device_exposure|DEVICE_EXPOSURE]]|device_concept_id| | |
| - | |Condition|[[documentation:cdm:condition_occurrence|CONDITION_OCCURRENCE]]|condition_concept_id| | | + | |[[documentation:vocabulary:condition|Condition]]|[[documentation:cdm:condition_occurrence|CONDITION_OCCURRENCE]]|condition_concept_id| | |
| - | |Measurement|[[documentation:cdm:measurement|MEASUREMENT]]|measurement_concept_id| | | + | |[[documentation:vocabulary:measurement|Measurement]]|[[documentation:cdm:measurement|MEASUREMENT]]|measurement_concept_id| | |
| - | |Meas Value Operator|[[documentation:cdm:measurement|MEASUREMENT]]|operator_concept_id| | | + | |[[documentation:vocabulary:meas_value_operator|Meas Value Operator]]|[[documentation:cdm:measurement|MEASUREMENT]]|operator_concept_id| | |
| - | |Meas Value|[[documentation:cdm:measurement|MEASUREMENT]]|value_as_concept_id| | | + | |[[documentation:vocabulary:meas_value|Meas Value]]|[[documentation:cdm:measurement|MEASUREMENT]]|value_as_concept_id| | |
| - | |Observation|[[documentation:cdm:observation|OBSERVATION]]|observation_concept_id| | | + | |[[documentation:vocabulary:observation|Observation]]|[[documentation:cdm:observation|OBSERVATION]]|observation_concept_id| | |
| - | |Relationship|[[documentation:cdm:fact_relationship|FACT_RELATIONSHIP]]|relationship_concept_id| | | + | |[[documentation:vocabulary:relationship|Relationship]]|[[documentation:cdm:fact_relationship|FACT_RELATIONSHIP]]|relationship_concept_id| | |
| - | |Place of Service|[[documentation:cdm:care_site|CARE_SITE]]|place_of_service_concept_id| | | + | |[[documentation:vocabulary:place_of_service|Place of Service]]|[[documentation:cdm:care_site|CARE_SITE]]|place_of_service_concept_id| | |
| - | |Provider Specialty|[[documentation:cdm:provider|PROVIDER]]|specialty_concept_id| | | + | |[[documentation:vocabulary:provider_specialty|Provider Specialty]]|[[documentation:cdm:provider|PROVIDER]]|specialty_concept_id| | |
| - | |Currency|[[documentation:cdm:visit_cost|VISIT_COST]] or [[documentation:cdm:procedure_cost|PROCEDURE_COST]] or [[documentation:cdm:drug_cost|DRUG_COST]] or [[documentation:cdm:device_cost|DEVICE_COST]]|currency_concept_id|Currency values appear in any of the *_COST tables. *| | + | |[[documentation:vocabulary:currency|Currency]]|[[documentation:cdm:measurement|MEASUREMENT]] or [[documentation:cdm:observation|OBSERVATION]] or [[documentation:cdm:specimen|SPECIMEN]]|currency_concept_id|Currency values appear in any of the *_COST tables. *| |
| - | |Revenue Code|[[documentation:cdm:procedure_cost|PROCEDURE_COST]]|revenue_code_concept_id| | | + | |[[documentation:vocabulary:revenue_code|Revenue Code]]|[[documentation:cdm:procedure_cost|PROCEDURE_COST]]|revenue_code_concept_id| | |
| - | |Specimen|[[documentation:cdm:specimen|SPECIMEN]]|specimen_concept_id| | | + | |[[documentation:vocabulary:specimen|Specimen]]|[[documentation:cdm:specimen|SPECIMEN]]|specimen_concept_id| | |
| - | |Spec Anatomic Site|[[documentation:cdm:specimen|SPECIMEN]] or [[documentation:cdm:measurement|MEASUREMENT]] or [[documentation:cdm:observation|OBSERVATION]]|anatomic_site_concept_id or value_as_concept_id or value_as_concept_id|Anatomical Site Concepts are used to characterize the origin of a Specimen, but also the result of a Measurement or Observation. *| | + | |[[documentation:vocabulary:spec_anatomic_site|Spec Anatomic Site]]|[[documentation:cdm:specimen|SPECIMEN]] or [[documentation:cdm:measurement|MEASUREMENT]] or [[documentation:cdm:observation|OBSERVATION]]|anatomic_site_concept_id or value_as_concept_id or value_as_concept_id|Anatomical Site Concepts are used to characterize the origin of a Specimen, but also the result of a Measurement or Observation. *| |
| - | |Spec Disease Status|[[documentation:cdm:specimen|SPECIMEN]]|disease_status_concept_id| | | + | |[[documentation:vocabulary:spec_disease_status|Spec Disease Status]]|[[documentation:cdm:specimen|SPECIMEN]]|disease_status_concept_id| | |
| * If there is more than one potential destination table the ETL needs to identify the context in which a Standard Concept is used, and select the right table from this table. | * If there is more than one potential destination table the ETL needs to identify the context in which a Standard Concept is used, and select the right table from this table. | ||
| - | * For some Source Concepts there is **no mapping to a Standard Concept** (there is no record in the CONCEPT_RELATIONSHIP or SOURCE_TO_CONCEPT_MAP tables), usually because the Source Concept is too generic or otherwise ill-defined. In these cases, the domain_id field of the Source Concept itself should be used to place the record in the right table. Some Source Concepts have combination Domains, such as "Device/Procedure". In these cases, write a record into each of the combination Domain table (in this case to the DEVICE_OCCURRENCE and PROCEDURE_OCCURRENCE tables). As the Standard Concept write Concept 0 (concept_id=0) into the respective *_concept_id field. | + | * For some Source Concepts there is **no mapping to a Standard Concept** (there is no record in the CONCEPT_RELATIONSHIP or SOURCE_TO_CONCEPT_MAP tables), usually because the Source Concept is too generic or otherwise ill-defined. In these cases, the domain_id field of the Source Concept itself should be used to place the record in the right table. Some Source Concepts have combination Domains, such as "Device/Procedure". In these cases, write a record into each of the combination Domain table (in this case to the DEVICE_OCCURRENCE and PROCEDURE_OCCURRENCE tables). As the Standard Concept write Concept 0 (concept_id=0) into the respective <domain>_concept_id field. |
| If in the mapping process a Concept of the "Domain" or "Metadata" Domains are retrieved, an error has snuck into the mapping table. Please report those cases in the [[http://forums.ohdsi.org/c/cdm-builders/l/latest|CDM-Builder]]. | If in the mapping process a Concept of the "Domain" or "Metadata" Domains are retrieved, an error has snuck into the mapping table. Please report those cases in the [[http://forums.ohdsi.org/c/cdm-builders/l/latest|CDM-Builder]]. | ||
| - | The same is true if a Type Concept Domain, like "Obs Period Type", "Death Type", "Visit Type", "Procedure Type", etc. is produced. Though these Type Concepts are valid concepts and have to be placed into the <domain>_type_concept_id field of the respective CDM tables, they cannot be the result of the mapping process. They denote the origin of the record and the selection of Type Concepts have to be hard-wired in the ETL process. | + | The same is true if a Type Concept Domain, like "Obs Period Type", "Death Type", "Visit Type", "Procedure Type", etc. is produced. Though these Type Concepts are valid concepts and have to be placed into the <domain>_type_concept_id field of the respective CDM tables, they cannot be the result of the mapping process. They denote the origin of the record and the selection of Type Concepts should be hard-wired into the ETL process. |
documentation/vocabulary/data_etl.txt · Last modified: 2024/09/02 09:43 by jcruz
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