https://w3id.org/omop/ontology/Concept
The Standardized Vocabularies contains records, or Concepts, that uniquely identify each fundamental unit of meaning used to express clinical information in all domain tables of the CDM. Concepts are derived from vocabularies, which represent clinical information across a domain (e.g. conditions, drugs, procedures) through the use of codes and associated descriptions. Some Concepts are designated Standard Concepts, meaning these Concepts can be used as normative expressions of a clinical entity within the OMOP Common Data Model and within standardized analytics. Each Standard Concept belongs to one domain, which defines the location where the Concept would be expected to occur within data tables of the CDM.
Concepts can represent broad categories (like 'Cardiovascular disease'), detailed clinical elements ('Myocardial infarction of the anterolateral wall') or modifying characteristics and attributes that define Concepts at various levels of detail (severity of a disease, associated morphology, etc.).
Records in the Standardized Vocabularies tables are derived from national or international vocabularies such as SNOMED-CT, RxNorm, and LOINC, or custom Concepts defined to cover various aspects of observational data analysis.
Instances of Concept can have the following properties:
| PROPERTY | TYPE | DESCRIPTION | RANGE |
|---|---|---|---|
| From class Concept | |||
| Code | owl:DatatypeProperty | For Concept: The concept code represents the identifier of the Concept in the source vocabulary, such as SNOMED-CT concept IDs, RxNorm RXCUIs etc. Note that concept codes are not unique across vocabularies. | string |
| Standard | owl:DatatypeProperty | For Concept: This flag determines where a Concept is a Standard Concept, i.e. is used in the data, a Classification Concept, or a non-standard Source Concept. The allowable values are 'S' (Standard Concept) and 'C' (Classification Concept), otherwise the content is NULL. | string |
| Has vocabulary | owl:FunctionalProperty | For Concept: A foreign key to the [VOCABULARY](https://ohdsi.github.io/CommonDataModel/cdm531.html#vocabulary) table indicating from which source the Concept has been adapted. | Vocabulary |
| From class OMOP CDM thing | |||
| Id | owl:DatatypeProperty | For Note: A unique identifier for each note. - For Vocabulary: A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit. - For Observation: 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. - For Note Nlp: A unique identifier for the NLP record. - For Location: The unique key given to a unique Location. Each instance of a Location in the source data should be assigned this unique key. - For Drug Exposure: 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. - For Specimen: Unique identifier for each specimen. - For Observation Period: A Person can have multiple discrete Observation Periods which are identified by the Observation_Period_Id. Assign a unique observation_period_id to each discrete Observation Period for a Person. - For Cohort Definition: This is the identifier given to the cohort, usually by the ATLAS application - For Concept Class: A unique key for each class. - For Device Exposure: The unique key given to records a person's exposure to a foreign physical object or instrument. Each instance of an exposure to a foreign object or device present in the source data should be assigned this unique key. - For Procedure Occurrence: The unique key given to a procedure record for a person. Refer to the ETL for how duplicate procedures during the same visit were handled. Each instance of a procedure occurrence in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same procedure within the same visit. It is valid to keep these duplicates and assign them individual, unique, PROCEDURE_OCCURRENCE_IDs, though it is up to the ETL how they should be handled. - For Cost: A unique identifier for each COST record. - For Domain: A unique key for each domain. - For Survey Conduct: Unique identifier for each completed survey. For each instance of a survey completion create a unique identifier. - For Visit Detail: Use this to identify unique interactions between a person and the health care system. This identifier links across the other CDM event tables to associate events with a visit detail. This should be populated by creating a unique identifier for each unique interaction between a person and the healthcare system where the person receives a medical good or service over a span of time. - For Care Site: Assign an id to each unique combination of location_id and place_of_service_source_value. - For Concept: A unique identifier for each Concept across all domains. - For Measurement: 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. - For Condition Occurrence: 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. - For Provider: It is assumed that every provider with a different unique identifier is in fact a different person and should be treated independently. This identifier can be the original id from the source data provided it is an integer, otherwise it can be an autogenerated number. - For Person: It is assumed that every person with a different unique identifier is in fact a different person and should be treated independently. Any person linkage that needs to occur to uniquely identify Persons ought to be done prior to writing this table. This identifier can be the original id from the source data provided if it is an integer, otherwise it can be an autogenerated number. - For Visit Occurrence: Use this to identify unique interactions between a person and the health care system. This identifier links across the other CDM event tables to associate events with a visit. This should be populated by creating a unique identifier for each unique interaction between a person and the healthcare system where the person receives a medical good or service over a span of time. - For Payer Plan Period: A unique identifier for each unique combination of a Person, Payer, Plan, and Period of time. | owl:Thing |
| From class Thing | |||
| OMOP CDM name | owl:AnnotationProperty | owl:Thing | |
@prefix omop: <https://w3id.org/omop/ontology/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
omop:Concept a owl:Class ;
rdfs:label "Concept"^^xsd:string ;
rdfs:comment """The Standardized Vocabularies contains records, or Concepts, that uniquely identify each fundamental unit of meaning used to express clinical information in all domain tables of the CDM. Concepts are derived from vocabularies, which represent clinical information across a domain (e.g. conditions, drugs, procedures) through the use of codes and associated descriptions. Some Concepts are designated Standard Concepts, meaning these Concepts can be used as normative expressions of a clinical entity within the OMOP Common Data Model and within standardized analytics. Each Standard Concept belongs to one domain, which defines the location where the Concept would be expected to occur within data tables of the CDM.
Concepts can represent broad categories (like 'Cardiovascular disease'), detailed clinical elements ('Myocardial infarction of the anterolateral wall') or modifying characteristics and attributes that define Concepts at various levels of detail (severity of a disease, associated morphology, etc.).
Records in the Standardized Vocabularies tables are derived from national or international vocabularies such as SNOMED-CT, RxNorm, and LOINC, or custom Concepts defined to cover various aspects of observational data analysis."""@en ;
rdfs:subClassOf [ a owl:Restriction ;
owl:allValuesFrom omop:ConceptClass ;
owl:onProperty omop:has_class ],
[ a owl:Restriction ;
owl:onProperty omop:has_class ;
owl:someValuesFrom omop:ConceptClass ],
[ a owl:Restriction ;
owl:allValuesFrom omop:Domain ;
owl:onProperty omop:has_domain ],
[ a owl:Restriction ;
owl:onProperty omop:has_domain ;
owl:someValuesFrom omop:Domain ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty omop:name ],
[ a owl:Restriction ;
owl:onProperty omop:name ;
owl:someValuesFrom xsd:string ],
[ a owl:Restriction ;
owl:allValuesFrom omop:Vocabulary ;
owl:onProperty omop:has_vocabulary ],
[ a owl:Restriction ;
owl:onProperty omop:has_vocabulary ;
owl:someValuesFrom omop:Vocabulary ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty omop:standard ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty omop:code ],
[ a owl:Restriction ;
owl:onProperty omop:code ;
owl:someValuesFrom xsd:string ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:date ;
owl:onProperty omop:valid_start_date ],
[ a owl:Restriction ;
owl:onProperty omop:valid_start_date ;
owl:someValuesFrom xsd:date ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:date ;
owl:onProperty omop:valid_end_date ],
[ a owl:Restriction ;
owl:onProperty omop:valid_end_date ;
owl:someValuesFrom xsd:date ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty omop:invalid_reason ],
omop:OmopCDMThing ;
omop:omop_cdm_name "concept"^^xsd:string .