Specimen Domain

Specimen D-MIM Walk Through

Overview

The Specimen Domain Information Model (D-MIM) captures information regarding a specimen and its container. Both the specimen and the source of the specimen are scoped by a specimenEntity which may be located in a container. The specimen itself may be the result of a process and can be acted on by any number of processes in order to handle both the specimen and the container.

Description: A substance, extracted from a person, non-person living thing, or environmental site which is tested in order to make an observation. It is often a small sample or part taken to show the nature of the whole. The Specimen role is structured as follows:

• Specimen: The specimen as a role. Examples include specimen, aliquot, isolate, etc.

  • Participations: Specimen includes the following participations:

    • productOf: The specimen role is a product of a specimen collection process. This captures information regarding any procedure to produce the specimen. For example, this would document a biopsy performed to obtain tissue needed for laboratory testing.

      Attributes of Process

      • precondition: The process to collect the specimen may have any number of Criterion Observations as a precondition, such as fasting before a glucose tolerance test.

        Attributes of Criterion

      • performer:An R_AssignedEntity [universal] CMET captures information regarding the performer of the specimen collection.
    • subjectOf1: A specimen can be the subject of any number of observations to record information about the state of the specimen in a human readible format such as temperature and dilution. A constraint has been placed on the datatype of the value attribute that is dependent on the type of observation that is being performed. For instance, if the dilution of the specimen is being recorded the value attribute must be a ratio or a coded value.

      Attributes of SpecimenObservationEvent

    • subjectOf2: The specimen or its container may be the subject of any number of ProcessStep Acts. This is defined as any process that can act on a specimen or its container such as specimen accession, specimen treatment or container registration. The inclusion of this observation is intended to illustrate that an observation has taken place but not the value or the outcome of that observation. For instance, when Cold Agglutinins are discovered in the specimen during the processing of a CBC test the specimen is placed in a 37 degree wash for two hours. This observation would record that this was had been performed.

      Attributes of ProcessStep

      • authorOrPerformer: Zero to many R_AssignedEntity [universal] CMETs to capture information regarding the author or performer of the process step. In the above example this would identify the medical technician that performed the wash of the specimen.
      • subject: IdentifiedEntity2 defines the identifiers for a holder that is the subject of the ProcessStep, such as during container registration.
      • subject1: IdentifiedEntity defines the identifiers for a container that is the subject of ProcessStep.

  • sourceEntity(scoping entity): The Specimen role is scoped by specimenEntities which is a choice of entities. These entities represent the possible sources of the specimen:

    • Natural: A generic entity which can be anything, for example a parent specimen can be the source of a specimen.

      Attributes of Natural Entity

    • Manufactured: The source of a specimen can be a manufactured material

      Attributes of Manufactured Material

      • ManufacturedProduct: a role scoped by the E_organization [universal] CMET capturing information regarding the source of the manufactured material.

    • NonPersonLivingSubject:The specimen may be from a living subject of some sort that is not human. For example an isolate or animal subject.

      Attributes of Non-Person Living Subject

    • Person: The specimen may be from a human subject. In the case of specimens from a patient, this is the identifier for the patient that the specimen was taken from.

      Attributes of Person Subject

  • specimenEntity(playing entity): The specimen role is played by specimenEntities which is a choice of entities. It's the same four entities defined above but the meanings are slightly different.
    • Natural: The specimen is defined as some natural substance, such as blood, urine, water or soil.
    • Manufactured: The specimen is defined as a manufactured product which may be used to perform QC or QA.
    • NonPersonLivingSubject: The specimen may be an entire non-human subject such as an animal or an isolate.
    • Person: A whole human being such as in the case of an autopsy.
  • specimenEntities: This is a choice of entities that can either be the source of specimens or the specimens themselves. This choice of entities can scope an additive role, as well as play the role of content for a container.
    • SpecimenStub: if the specimen source itself is a parent specimen, the specimen stub identifies the source specimen of the parent specimen.
      • SpecimenAlternateIdentifier: This role provides storage for non-specimen identifiers, such as patient MRNs. This role is scoped by the E_Organization [universal] CMET.
    • additive: Additive mixed into the specimen, e.g., in an aliquot of citrate blood.

      Attributes of Additive

    • containedEntity(played): The specimenEntities play the role of content for a container.
      • Content1: The container for the specimen. Scoped by a Container entity.
        • Container: The container entity contains the specimen and may also itself be the content of a holder, such as a vial containing a specimen that is placed in a carrier.

          Attributes of Container

          • Additive2: Additive in container, e.g., a blood specimen tube with EDTA or citrate in it. Content2 role is played by an AdditiveMaterial (MAT) entity to identify the material being added to the specimen, which in turn plays the role of Additive
          • Content3: Container in holder, e.g., a specimen container in a carrier. Content3 is scoped by Holder (an entity).
          • R_LocationLocatedEntity [universal] CMET: The location of a container.
          • IdentifiedEntity: The identifier for the container.
        • Holder: Entity which contains either a container or another holder. Scopes and plays the role of Content4 (holder in a holder, e.g, a carrier on a tray).
          • R_LocationLocatedEntity [universal] CMET: This identifies the location of the holder or the container. Also plays the role of identifiedEntity. The identifiedEntity may be the subject of a ContainerRegistration.

Natural Entity Attributes

Attribute	Vocabulary	Description
classCode	ENT	Signifies that a specimen can be virtually anything
determinerCode	INSTANCE	One specific occurrence of anything
code	EntityCode	Serum, soil, water, or any natural substance
riskCode	EntityRisk	Identifies any risk associated with the specimen or handling the specimen such as an infectious agent.
handlingCode	EntityHandling	Ways to handle a specimen. For example, protect from air or keep frozen.

Manufactured Material Entity Attributes

Attribute	Vocabulary	Description
classCode	MMAT	A manufactured material
determinerCode	INSTANCE	Single occurrence of a manufactured material
code	EntityCode	Quality Control serum or unknown medication
quantity		The amount of the material
desc		Free text attribute to describe the manufactured material
riskCode	EntityRisk	Identifies any risk associated with the specimen or handling the specimen such as a radioactive material.
handlingCode	EntityHandling	Ways to handle a specimen. For example, protect from air or keep frozen.
lotNumberText		Free text attribute identifying the material's lot number
expirationTime		Interval Time Stamp describing the expiration date and time of the material

Non-Person Living Subject Entity Attributes

Attribute	Vocabulary	Description
classCode	NLIV	Non-person living subject
determinerCode	INSTANCE	Single occurrence of a non-person living subject
code	EntityCode	Any entity such as a dog, a tick, or mold
quantity		The amount of the material
name		Free text attribute naming the non-person living subject
desc		Free text attribute describing the non-person living subject
statusCode	EntityStatus	Codes describing the states of a non-person living subject. Codes include normal, active, terminated or nullified.
existenceTime		The interval of time specifying period in which the non-person living subject existed
telecom		Telecommunication address
riskCode	EntityRisk	Identifies any risk associated with the specimen or handling the specimen such as a dangerous animal.
handlingCode	EntityHandling	Ways to handle a specimen. For example, keep contained or protect from light
administrativeGenderCode	AdministrativeGender	The gender of the non-person living subject
birthTime		Birth date
deceasedInd		Whether or not the non-person living subject is deceased
deceasedTime		Date and time the non-person living subject became deceased
multipleBirthInd		Whether or not the non-person living subject is part of a multiple birth
multipleBirthOrderNumber		The order in which the non-person living subject was born
organDonorInd		Indication that the non-person living subject is available to be an organ donor
strainText		A text string indicating the genotype or phenotype of the non-person living subject
genderStatusCode	GenderStatus	Indication of the presence of reproductive organs

Person Subject Entity Attributes

Attribute	Vocabulary	Description
classCode	PSN	A human beings
determinerCode	INSTANCE	An occurrence of a person
code	EntityCode	homo sapiens
quantity		one
name		Name of the person
desc		Description of the person
statusCode	EntityStatus	Codes describing the states of a non-person living subject. Codes include normal, active, terminated or nullified.
existenceTime		The interval of time specifying period in which the person existed
telecom		Telecommunication address
riskCode	EntityRisk	Risk associated with handling the person such as disposition or infection
handlingCode	EntityHandling	Ways to handle a human body. For example, handicapped provisions.
administrativeGenderCode	AdministrativeGender	The gender of a person used for administrative purposes (as opposed to clinical gender)
birthTime		Birth date
deceasedInd		Whether or the person is deceased
deceasedTime		Date and time the person became deceased
multipleBirthInd		Whether or not the person is part of a multiple birth
multipleBirthOrderNumber		The order in which the person was born as part of a multiple birth.
organDonorInd		Indication that the person is able to be an organ donor
addr		Person's address
disabilityCode	PersonDisabilityType	Indicates any current disabilities for the person
raceCode	Race	The race of the person
ethnicGroupCode	Ethnicity	The ethnic group of the person

Additive Entity Attributes

Attribute	Vocabulary	Description
classCode	MAT	An additive
determinerCode	INSTANCE	An occurrence of the additive
id		The id of the additive
code	MaterialEntityAdditive	The code of the additive, such EDTA or Citrate
desc		A free text description of the additive

Container Entity Attributes

Attribute	Vocabulary	Description
classCode	CONT	The container
determinerCode	INSTANCE	An occurrence of a container
code	EntityCode	The type of container
desc		A free text description of the container
riskCode	EntityRisk	Risk associated with the container or material contained in the container
handlingCode	EntityHandling	Ways to handle the container, such as frozen or room temperature
capacityQuantity		The capacity of the container
heightQuantity		The height of the container
diameterQuantity		The diameter of the container
capTypeCode	ContainerCap	The code indicating the type of cap used on the container
separatorTypeCode	ContainerSeparator	The code indicating the type of separator used in the container
barrierDeltaQuantity		The difference between the top of the tube and the top of the tube container
bottomDeltaQuantity		The difference between the bottom of the tube and the bottom of the tube container

Process Act Attributes

Attribute	Vocabulary	Description
classCode	PROC	A process that acts on a specimen
moodCode	x_ActMoodIntentEvent	The intention or plan to perform a service
id		The id of the observation
code		The type of process used to retrieve a specimen
text		The free text describing the process
statusCode	ActStatus	The status of the process such as aborted, cancelled or completed
effectiveTime		The time specimen was collected

ObservationEvent (Criterion) Attributes

Attribute	Vocabulary	Description
classCode	OBS	An observation
moodCode	EVN.CRT	An event criterion for the specimen collection process
id		The id of the observation
code	ActCode	A particular type of an Act that is a precondition observation for the process that creates the specimen, such as fasting
text		A free text description of the the observation
value		The resulting value of the observation such as length of time
interpretationCode	ObservationInterpretation	The interpretation of the observation value

SpecimenObservationEvent Attributes

Attribute	Vocabulary	Description
classCode	SPCOBS	A specimen observation
moodCode	EVN	An event
id		The id of the specimen observation
code	ActSpecObsCode	Identifies the type of observation that is made about a specimen that may affect its processing, analysis or further result interpretation, such as a hemolyzed serum sample for potassium analysis
text		A free text description of the the observation, such as serum hemolyzed
statusCode	ActStatus	The status of the specimen observation such as aborted, cancelled or completed
effectiveTime		The time the specimen observation took place
value		The value of the specimen observation such as dilution, volume or temperature

ProcessStep Attributes

Attribute	Vocabulary	Description
classCode	x_LabProcessClassCodes	The type of process that is currently acting on the specimen or container, such as container registration or specimen accession.
moodCode	EVN	The act is an event
id		The id of the process
code	x_LabProcessCodes	The Code for the current process that is acting on the specimen or container, such as container registration procedure.
text		The free text describing the process
statusCode	ActStatus	The status of the procedure such as aborted, cancelled or completed
effectiveTime		The time the process is effective