https://w3id.org/omop/ontology/Specimen
The specimen domain contains the records identifying biological samples from a person.
Instances of Specimen can have the following properties:
| PROPERTY | TYPE | DESCRIPTION | RANGE |
|---|---|---|---|
| From class Specimen | |||
| Anatomic site source value | owl:DatatypeProperty | For Specimen: This is the site on the body where the specimen was taken from, as represented in the source. | string |
| Disease status source value | owl:DatatypeProperty | string | |
| Has anatomic site | owl:FunctionalProperty | For Specimen: This is the site on the body where the specimen is from. Map the ANATOMIC_SITE_SOURCE_VALUE to a Standard Concept in the Spec Anatomic Site domain. This should be coded at the lowest level of granularity [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Spec+Anatomic+Site&conceptClass=Body+Structure&page=4&pageSize=15&query=) | Concept |
| Has disease status | owl:FunctionalProperty | Concept | |
| From class Event | |||
| Date | owl:DatatypeProperty | For Procedure Occurrence: Use this date to determine the date the procedure occurred. If a procedure lasts more than a day, then it should be recorded as a separate record for each day the procedure occurred, this logic is in lieu of the procedure_end_date, which will be added in a future version of the CDM. - For Note Nlp: The date of the note processing. - For Observation: The date of the Observation. Depending on what the Observation represents this could be the date of a lab test, the date of a survey, or the date a patient's family history was taken. For some observations the ETL may need to make a choice as to which date to choose. - For Note: The date the note was recorded. - For Specimen: The date the specimen was collected. - For Measurement: 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. | date |
| Datetime | owl:DatatypeProperty | For Note Nlp: The date and time of the note processing. - For Measurement: 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) - For Procedure Occurrence: 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) - For Observation: If no time is given set to midnight (00:00:00). - For Note: If time is not given set the time to midnight. | dateTime |
| 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:Specimen a owl:Class ;
rdfs:label "Specimen"^^xsd:string ;
rdfs:comment "The specimen domain contains the records identifying biological samples from a person."@en ;
rdfs:subClassOf [ a owl:Restriction ;
owl:allValuesFrom omop:Concept ;
owl:onProperty omop:has_concept ],
[ a owl:Restriction ;
owl:onProperty omop:has_concept ;
owl:someValuesFrom omop:Concept ],
[ a owl:Restriction ;
owl:allValuesFrom omop:Concept ;
owl:onProperty omop:has_type ],
[ a owl:Restriction ;
owl:onProperty omop:has_type ;
owl:someValuesFrom omop:Concept ],
[ a owl:Restriction ;
owl:allValuesFrom owl:Thing ;
owl:onProperty omop:has_source ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:decimal ;
owl:onProperty omop:quantity ],
[ a owl:Restriction ;
owl:allValuesFrom omop:Concept ;
owl:onProperty omop:has_unit ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty omop:unit_source_value ],
[ a owl:Restriction ;
owl:onProperty [ owl:inverseOf omop:has_specimen ] ;
owl:someValuesFrom omop:Person ],
[ a owl:Restriction ;
owl:allValuesFrom omop:Concept ;
owl:onProperty omop:has_anatomic_site ],
[ a owl:Restriction ;
owl:allValuesFrom omop:Concept ;
owl:onProperty omop:has_disease_status ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty omop:anatomic_site_source_value ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty omop:disease_status_source_value ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty omop:source_value ],
omop:Event ;
omop:omop_cdm_name "specimen"^^xsd:string .