When microbiology laboratory results are encoded, it is important to be aware of the context provided by the observation, i.e. the test performed and, therefore, the implied meaning of the result value, i.e. the organism.

For example, the combination of Logical Observation Identifiers Names and Codes (LOINC) for the lab test and SNOMED CT for the organism, provides a unique and specific meaning:

• LOINC provides microbiology reporting codes with attributes including the property through the use of PRID(presence or identity) and the scale through the use of NOM (nominal or categorical response that does not have a natural ordering) as the result value (typically the name of organism).

  • Use of organism concepts in combination with such LOINC codes implies that a specific organism is seen, detected, identified, isolated, or present.

Use organism X or organism Y when a laboratory report indicates a single isolate is assumed, but the lab is unable (for any reason) to differentiate the result instance.

For example,

• 703015006 | Human coxsackievirus or human echovirus (finding)|

Use organism X, not organism Y when a laboratory report indicates a class of organisms described by the exclusion of specific Linnaean or non-Linnaean classes. These concepts are found in the organism hierarchy (based on reasonable use cases to avoid a combinatorial explosion). They are a primitive super class, in between the species or species subtype.

For example,

• 115407004 | Haemophilus influenzae, not b (organism)|

Exception

The common term yeast can refer to two separate classes: 1) a morphologic form of a dimorphic fungus; or 2) an organism in kingdom Fungi that is truly a yeast. Therefore, while the super class yeast is represented as an organism, “X, not organism Y” type concept is represented in the clinical finding hierarchy (as descendant of 769070007 |Yeast detected (finding)|) since one potential meaning of use is a diagnostic morphologic form of an organism rather than an organism itself.

For example,

• 769071006 | Yeast not Candida albicans detected (finding)|

Use Genus X, not species Y and not species Z when a laboratory report indicates a species of Genus X and confirms that it is not species Y, nor species Z. E.g. Bacillus species, not Bacillus anthracis and not Bacillus cereus (organism).

Use this naming convention only with Genus, species, and subspecies levels of the hierarchy.

Laboratory reports and journal articles may include an organism that could not be serotyped, e.g. E. coli, untypable. The requests for such concepts are declined due to ambiguity. Instead, use the closest taxonomic level in the hierarchy.

Laboratory findings may be reported with a status of preliminary, presumptive, provisional, etc. These typically cover reportable or notifiable lab values. The status of a report is different from the result; it is part of the electronic health application model/message. The requests for such concepts are declined as they are ambiguous and subject to limitless combinations.

Some laboratories report findings indicating a mixed population of bacteria from several classes, e.g. mixed anaerobic Gram negative bacilli. The request for such a concept is added as a clinical finding. The actual organism is unknown, however there is a result, although more general.

Laboratories perform and report on specific tests to identify the absence, as well as the presence, of a particular pathogenic organism. Laboratories typically report negative result values, such as X not seen , X not detected , X not isolated , and no X seen (or identified or isolated) and positive results as X seen , X detected , and X isolated. The following tables includes the acceptable modeling for negative and positive results.

Microbiology Tests: Reporting of Negative and Positive Values with Examples

Test Observable Entity Naming Conventions

Naming conventions for the fully specified name (FSN) for observable entities and for naming evaluation procedures or observable entities that are submitted with names from the IFCC-IUPAC NPU systems are as follows:

General naming pattern: Property, Component, Direct Site

• First: Property

  • Property (the property type of the observable) is named first, when possible.

  • Modifier: Scale Method.

    • Scale Method refines the Property, and, therefore, precedes the action in the naming order. (Scale Method, Property)

    • Naming pattern: (Scale Method, Property), Component, Direct Site

• Second: Component

  • Property is named first, followed by the entity that is the value of Component, when possible.

• Third: Direct Site

  • Modifier: Time aspect. Time aspect provides information about the direct site and precedes it in the naming order. (Time aspect, Direct Site)

• For example,

  • 416125006 | Concentration of hemoglobin in erythrocyte (observable entity) |

Serology and serologic test are ambiguous terms and should not be included in FSNs. These terms can be included in the descriptions for antibody observable or evaluation concepts but cannot be included in the preferred term. Existing content will be fixed in a future release.

Logical Observation Identifiers Names and Codes (LOINC) terms are defined using the Observable Entity model in SNOMED CT as produced in the LOINC - SNOMED CT Cooperation Project releases.

The project release documentation contains information about how LOINC terms and parts are aligned with SNOMED CT concepts using the model.

Observable Entity Modeling

When observable entity concepts have been given a value, they behave like clinical findings, with respect to the concept model for context.

When observable entity concepts have not been given a value, they behave like procedures, with respect to the concept model for context.

Modeling

The observable entity model has been implemented in limited content areas in SNOMED CT thus far. Most of the content in the hierarchy is primitive.

• Over 165 observable entity concepts have been modeled describing physiological measurements (body temperature, respiratory rate, heart rate, blood pressure). Most of these are sufficiently defined using the attributes. |Vital sign (observable entity)| has been inactivated since it could not be universally defined.

• Additional concepts using observable entity attributes have been defined since the January 2020 release. The majority of the changes are related to nutritional intake (e.g., food intake, vitamin intake, fasting pattern) observable entity concepts.

Susceptibility observables should be modeled in accordance with the specified templates.

Core body temperature is the temperature in the deep tissues and internal organs, including the brain. The gold standard site for measuring core body temperature is the pulmonary artery. Other sites for measuring core body temperature include the nasopharynx, esophagus, bladder, gastrointestinal tract, and vagina. Some peripheral sites are commonly used to estimate core body temperature but are not a true representation of core body temperature on their own, e.g., axillary region, inguinal region, sublingual space. Body surface temperature is measured at several sites, e.g., skin, foot, spine.

For example,

• 698831002 |Core body temperature measured in nasopharynx (observable entity)|

  • 415882003 |Estimated core body temperature measured in axillary region (observable entity)|

  • 364518005 |Temperature of foot (observable entity)|

Naming conventions for estimated and measured intake or nutrient administration, in aggregate or as a portion of intake via a specified route (ie, oral, gastroenteral [enteral nutrition], parenteral nutrition, and via intravenous fluids), is as follows:

FSN: [technique] quantity of intake of [substance] via [route] in [timeframe] (observable entity)

SYN: [technique] quantity of intake of [substance] via [route] in [timeframe]

See the specific template: A nutritional intake (observable entity) - v1.0.

• For example,

  • 789106008 | Estimated quantity of intake of phosphorous in 24 hours (observable entity)|

    • FSN: Estimated quantity of intake of phosphorous in 24 hours (observable entity)

      • PT: Estimated quantity of intake of phosphorous in 24 hours

Templates are available for modeling quality observables and for process observables:

• Simple template for Quality Observable (observable entity) - v2.0

• Simple template for Process Observable (observable entity) - v3.0

  • A nutritional intake (observable entity) - v3.0

• • The Susceptibility template is a disposition observable; there is no simple template at this time.

Nomenclature, Properties, and Units (NPU) is a coding system and terminology for identification and communication of examination results from clinical laboratories. Please see their website for more information: .

Logically there is a relationship between NPU and SNOMED CT observable entities. A pilot project examined overlaps and possible alignment; further work may be done. However, there is no formally maintained SNOMED CT documentation on this alignment.

Characterizes

This attribute specifies the process which the property describes, and on which the property (of this observable) depends. The process can be very general (e.g. excretion).

• For example,

  • Mass concentration ratio of silver to creatinine in 24-hour urine (observable entity) has 704321009 | Characterizes (attribute)| of excretion process

    • 789098002 |Estimated quantity of intake of potassium in 24 hours (observable entity)| has a 704321009 |Characterizes (attribute)| of administration of substance

This attribute is used to specify the numerator of a relational property types, e.g. ratio, concentration.

• For example,

  • Arbitrary concentration of Varicella-Zoster virus (observable entity) has the 246093002 | Component (attribute) | of Human herpesvirus 3

This attribute is used to specify the entity on which the observation is directly made. It may also be used when the observation is indirect, i.e. when a direct observation cannot be done.

• For example,

  • 415974002 | Core body temperature measured at tympanic membrane (observable entity) | has the 704327008 | Direct site (attribute)| of 42859004 | Tympanic membrane structure (body structure) |

This attribute is used to specify the process or activity that is the consequence of realization of the function.

• For example,

  • 282097004 | Ability to walk (observable entity)| 719722006 | Has realization (attribute) | of 870595007 |Walking (qualifier value)|

This attribute is used to specify a body site or other location of the independent continuant in which the property exists.

• For example,

  • 5310001000004108 |Histologic type of neoplasm of skin (observable entity) | has 718497002 | Inherent location (attribute) | of 39937001 |Skin structure (body structure) |

This attribute specifies the independent continuant in which the quality exists and on which the dependent quality (of this observable) depends.

• For example,

  • 307047009 |Core body temperature measured in rectum (observable entity)| has 704319004 | Inheres in (attribute) | of 278826002 | Body internal region (body structure) |

This attribute is used to specify body state, timing, challenges, or other situations that must be true of the entity to be observed.

• For example,

  • Plasma creatinine concentration 7 days post challenge (observable entity) has a Precondition of 7 days post challenge

  • 163033001 | Lying blood pressure (observable entity) | has a 704326004 | Precondition (attribute) | of 102538003 | Recumbent body position (finding) |

This attribute is used to model devices associated with a procedure. This attribute is used to define high-level, general concepts that aggregate procedures according to the device involved.

This attribute is used to describe that a process specifically acts on some entity, e.g. by transporting that entity in or out of the body, i.e. Rate of intake of protein.

• For example,

  • 789350001 |Estimated quantity of intake of iron in 24 hours (observable entity)| has a 1003735000 | Process acts on (attribute) | of iron

This attribute is used to specify the continuant (e.g. body structure or organism) that is causally active in the process on which the property depends. It is used to refine the meaning of the process named as the value of 704321009 | Characterizes (attribute)| , or it may simply repeat the meaning that is already there.

• For example,

  • Substance rate of secretion of somatotropin by pituitary following clonidine per os (observable entity) has the 704322002 | Process agent (attribute) | of 56329008 | Pituitary structure (body structure) |.

This attribute specifies the duration of the process characterized by the observable property type.

• For example,

  • Mass rate of excretion of cortisone in 24 hour urine (observable entity) has the 704323007 | Process duration (attribute) | of 123027009 | 24 hours (qualifier value) |

This attribute specifies that the process which the property characterizes has led to the inclusion of a previously not included structure.

• For example,

  • The concept |Presence of direct invasion by primary malignant neoplasm of prostate to seminal vesicle (observable entity)| has a 1003703000 |Process extends to (attribute)| of | Seminal vesicle structure (body structure) |

This attribute is used to specify the substance or process produced by the process characterized by the observable property type.

• For example,

  • Substance rate of excretion of pregnanediol in micromoles per day (observable entity) has a 704324001 | Process output (attribute) | of 28268006 | Pregnanediol (substance) |

This attribute is used to specify the type of feature (i.e. quality, disposition, function, or process characteristic) to be observed. Its values are abstract types of quality (length, odor, concentration) or abstract types of process features (rate, speed).

• For example,

  • Blood glucose mass concentration (observable entity) has the 370130000 | Property (attribute) | of 118539007 | Mass concentration (property) (qualifier value) |

The Property (qualifier value) hierarchy contains the following:

• 118538004 | Mass, a measure of quantity of matter (property) (qualifier value) |

• 726527001 | Weight (property) (qualifier value) |

Very rarely is the physics definition of weight used. When the term weight is used, it is most often referring to mass , as further demonstrated by the units of measure i.e., grams, kilograms, etc. Unless units specific to the physics definition of weight are specified using Newtons, assume that mass is implied.

To summarize, always use the mass qualifier value unless a concept is requested with Newton units that specifically refer to weight.

This attribute is used to specify the denominator of a relational property type, e.g. a ratio or proportion.

• For example,

  • Urine alpha aminobutyrate to creatinine ratio (observable entity) has 704325000 | Relative to (attribute) | 15373003 | Creatinine (substance) |

  • Neutrophils per 100 leukocytes in blood (observable entity) has 704325000 | Relative to (attribute) | 702962009 | Population of all leukocytes in portion of fluid (body structure) |

This attribute is used to specify the denominator of a relative relational property, such as a ratio of ratios.

• For example,

  • Relative substance concentration of cerebrospinal fluid IgM to plasma IgM (observable entity) has 719715003 | Relative to part of (attribute) | of 50863008 | Plasma (substance) |

This attribute is used to specify the scale of the result of an observation or a diagnostic test (i.e., quantitative, qualitative, semi-quantitative).

This attribute is used to specify the systematic method of an observation.

• For example,

  • Presence of Brucella abortus antibody in serum by latex agglutination (observable entity) has the 246501002 | Technique (attribute) | of 703448004 | Latex agglutination test technique (qualifier value) |

  • 146611000146107 |Breast Imaging Reporting and Data System assessment category (observable entity)| has the 246501002 | Technique (attribute) | of 1348266008 |Breast Imaging and Reporting and Data System (assessment scale)|

This attribute is used to specify the timing of an observation.

• For example,

  • Substance concentration of acetone in urine (observable entity) has the 370134009 | Time aspect (attribute) | of 123029007 | Single point in time (qualifier value) |

This attribute is used to specify a disposition, what the disposition is towards, i.e. a specific triggering agent, or more generally, participant in the realization of the disposition.

• For example,

  • Quantitative susceptibility of Pseudomonas aeruginosa to amikacin in microbial isolate by disk diffusion (observable entity) has 704320005 | Towards (attribute) | of 387266001 | Amikacin (substance) |

This attribute is used to specify the units used in assigning a value to an observation.

• For example,

  • Basophils per 100 leukocytes (observable entity) has the 246514001 | Units (attribute)| of 415067009 | Percentage unit (qualifier value) |

This attribute is used to specify the instrument or equipment utilized to execute an action. Using device is appropriate when the device is actually used to carry out the action that is the focus of the procedure.

For example,

• 415921007 | Temperature of forehead using skin strip thermometer (observable entity) | has 424226004 | Using device (attribute) | of 448916003 | Skin strip thermometer (physical object) |

Observable entity concepts representing histopathology examination observables of neoplasms are being modeled according to a series of templates.

Please see the templates listed here: Observable entity templates See the Cancer Synoptic Reporting area for more information about the project.

Concepts containing a primary malignant neoplasm from the observable entity subhierarchy employ the 704321009 |Characterizes (attribute)| with the target qualifier value of 1234914003 |Malignant proliferation of primary neoplasm (qualifier value)| in order to define primary (which matches the target value of the Pathological process (attribute) used by concepts in the Disorder hierarchy).

For example,

1136681000004107 |Anatomic location of excised primary malignant neoplasm (observable entity)| applies the Characterizes (attribute) with a target of Malignant proliferation of primary neoplasm (qualifier value).

Stated view of 1136681000004107 |Anatomic location of excised primary malignant neoplasm (observable entity)|:

Stated view of 372087000 |Primary malignant neoplasm (disorder)|:

Concepts containing a metastatic malignant neoplasm from the observable entity subhierarchy do not use 704321009 |Characterizes (attribute)|, but instead are defined by the specific metastatic morphologic abnormality. For example, 444384007 |Number of regional lymph nodes containing metastatic neoplasm in excised specimen (observable entity)| has the attribute 246093002 |Component (attribute)| with a target value of 14799000 |Neoplasm, metastatic (morphologic abnormality)|.

Concepts containing a metastatic malignant neoplasm from the observable entity subhierarchy do not use 704321009 |Characterizes (attribute)|, but instead are defined by the specific metastatic morphologic abnormality. For example, 444384007 |Number of regional lymph nodes containing metastatic neoplasm in excised specimen (observable entity)| has the attribute 246093002 |Component (attribute)| with a target value of 14799000 |Neoplasm, metastatic (morphologic abnormality)|.

Concepts containing a metastatic malignant neoplasm from the observable entity subhierarchy do not use 704321009 |Characterizes (attribute)|, but instead are defined by the specific metastatic morphologic abnormality. For example, 444384007 |Number of regional lymph nodes containing metastatic neoplasm in excised specimen (observable entity)| has the attribute 246093002 |Component (attribute)| with a target value of 14799000 |Neoplasm, metastatic (morphologic abnormality)|.

When authoring in this domain, these are the approved attributes and allowable ranges.

See also the respective Templates.

Domain Information for Observable Entity

Use of Observable Entities

Observables entities may be used to code headers on a template, elements on a checklist, or to assign values to elements.

• For example,

  • |Color of nail| is an observable entity. |Gray nails| is a finding.

There are four general types of observable entities for use in health care. Each has different representation requirements and patterns, i.e. the set of attributes will vary.

• Quality. A characteristic, feature, or property that is inherent in someone or something.

  • For example, mass of a person, temperature of internal organs, concentration of sodium in plasma, angle of a joint

• Disposition. A characteristic or feature that is not always realized in full.

The observable entity and evaluation procedure hierarchies have some of the same attributes. While there should not be a one-to-one correspondence between concepts in these hierarchies, legacy implementations, as described below, may result in the occasional duplication of content.

SNOMED CT contains some concepts in the evaluation procedure hierarchy that logically belong in the observable entity hierarchy. This is a legacy issue that has been discussed extensively with the community of practice without resolution. At this time, the existing evaluation procedure hierarchy will be retained to support existing use cases. No new laboratory content under 122869004 |Measurement procedure (procedure)| will be added in the international release, as this domain is comprehensively covered by the LOINC extension to SNOMED CT. New laboratory content needed to satisfy existing use cases should be sourced from that extension. For non-laboratory content in the evaluation procedure hierarchy — such as clinical measurements performed directly on a patient rather than on a patient sample — new concepts may continue to be added where needed, although it is preferred that they be represented as observable entities.

While some users have indicated they require the use of a measurement procedure concept for ordering and an observable entity concept for reporting the result, this is not the preferred approach for the international release of SNOMED CT nor is it in line with other terminology standards such as LOINC and NPU. When a laboratory or clinical measurement procedure is ordered, there is an expectation that a value will be provided in association with that order. In these cases, measurement procedures are, for all intents and purposes, observables with a different semantic tag. The nature of their top-level parent (122869004 |Measurement procedure (procedure)|) implies that they require a value in order to be assessed and are therefore equivalent to observables.

As for the progression of the completion of an assessment, that is related to the state diagram (i.e., status) of the progression of a procedure and should not be precoordinated, but handled by the information system in which orders are processed (it is dynamic, not static). The information system should be able to capture the status of a procedure (e.g., ordered, in process, completed). We would not expect the terminology to pre-coordinate this.

For example, LOINC recognizes three different aspects to an observable:

1. those that can serve as both an order and an observation (e.g. blood glucose level);

2. those that can be ordered but not directly resulted (e.g. urinalysis, which is a convenience order for multiple individual observations on urine); and

3. those that can only be resulted and not directly ordered (usually part of an automated system, such as computation of MCHC in hematology).

LOINC assigns this aspect with an attribute value. It is not one of the six main LOINC parts typically visible to users; however, it is included in the LOINC database.

The Property (qualifier value) hierarchy contains the following:

• 118538004 |Mass, a measure of quantity of matter (property) (qualifier value)|

• 726527001 |Weight (property) (qualifier value)|

Very rarely is the physics definition of weight used. When the term weight is used, it is most often referring to mass , as further demonstrated by the units of measure i.e., grams, kilograms, etc. Unless units specific to the physics definition of weight are specified using Newtons, assume that mass is implied.

To summarize, always use the mass qualifier value unless a concept is requested with Newton units that specifically refer to weight.