For the IHTSDO Content Team and Project Groups Concept Models for observables, investigations, and observation results For the IHTSDO Content Team and Project Groups Revision Date: Dec 26, 2014

clinical entity (definition): Integrating / splitting “(finding)”, “(disorder)”, observables and observation results We have adopted a formal meaning that covers most of the concepts in the current “(finding)” hierarchy : Formal definition: A phase of life of the subject during which he/she is the bearer of a clinical entity that is reportable in the context of health records clinical entity (definition): A subject-related body process, disposition, or (patho-) anatomical structure, which is reportable in the context of health records.

Integrating / splitting “(finding)”, “(disorder)”, observables and observation results Some of the content of the current |Clinical finding| hierarchy does not fit the definition of “clinical phase” information artifacts observation results: the output of observation procedures explicit context: probability (suspected; likely; unlikely) or future (at risk, etc) family history (someone other than the subject) These meanings need to be separated out (moved, or else retired and re-created) into a different hierarchy (or hierarchies)

observation result It is proposed that the results of observations should be placed under a top-level category that is distinct from |clinical finding|. Proposed: new “information artifact” top level: Information artifact observation result situation with explicit context

Integrating the models of |clinical finding| and |observation result| Keep the current |Clinical finding| hierarchy. Place |observation result| in its own hierarchy Terms that record that something has been observed to be (or interpreted to be) increased, decreased, normal or abnormal are considered observation results Remove “interprets” and “has interpretation” attributes from current |clinical finding| model

Observable, observation procedure, observation result It is proposed that these all have closely-coordinated models observation procedure Uses most of the same attributes as observable, and adds method = evaluation action observation result Uses most of the same attributes as observable, and adds has value Assumes that the meaning of “evaluation action” includes all types of observation procedures, including physical examination, imaging, etc.

Concept model attributes: OBSERVABLE ENTITY Current Proposed (none) property type inheres in (location,ingredient) towards characterizes (agent, duration, output) relative to (part of) precondition scale units technique direct site informer

observation procedure observation result observation procedure output of specified by observes observable entity property or quality An observable entity is specified by an observation procedure, which observes some property. [An observation procedure specifies an observable entity.] An observation result is the output of an observation procedure, which observes some property An observation procedure produces as output an observation result. is about

observation procedure observation result observation procedure output of specified by observes observable entity property or quality An observable entity is specified by an observation procedure, which observes some property. [An observation procedure specifies an observable entity.] An observation result is the output of an observation procedure, which observes some property An observation procedure produces as output an observation result. The “is about” relation (x is about z) can be inferred from: the combination x specified-by y observes z or the combination x output-of y observes z is about

observation procedure observation result observation procedure output of specified by observes observable entity property or quality An observable entity is about some property. An observation result is about some property. Here the observation procedure is anonymous. is about

observation procedure observation result observation procedure output of specified by observes observable entity property or quality An observable entity is specified by an observation procedure, which observes some property. [An observation procedure specifies an observable entity.] An observation result is the output of an observation procedure, which observes some property An observation procedure produces as output an observation result. is about

observable model for qualities/properties [ infer the “observes” relation ] observable entity has value <values> specified by observation procedure scale scale types units units technique techniques direct site material entities informer subjects observes is about quality or property property type property types inheres in independent continuants (inherent) location material entities (inherent) ingredient substances towards independent continuants relative to substances (rel-to) part of independent continuants precondition precondition values characterizes processes process agent material entities process duration time frames process output substances

observable for qualities observable entity has value <values> property type property types inheres in independent continuants (inherent) location material entities is about (inherent) ingredient substances quality towards independent continuants relative to substances (rel-to) part of independent continuants precondition precondition values characterizes processes process agent material entities specified-by ○ observes ⊑ is-about process duration time frames process output substances scale scale types specified by units units observation procedure technique techniques direct site material entities observes informer subjects

completely “flattened” model for ‘quality’ observables (deprecated) entity is about quality with property type property types is about quality that inheres in independent continuants is about quality with inherent location material entities is about quality with inherent ingredient substances is about quality that is towards functions, substances is about quality with precondition body states (challenges, fasting) The “flattened” attributes are not the same as other attributes with almost identical meanings, that would have similar ranges (value sets) but different domains. An attribute that means “specified by procedure with scale” is not the same as an attribute that means “with scale”. The former defines an observable, the latter defines a procedure. specified-by-procedure-with-scale scale types specified-by-procedure-with-units units specified-by-procedure-with-technique techniques specified-by-procedure-with-direct site body structures, specimens specified-by-procedure-with-informer subjects

process observables observable entity has value <values> property type property types inheres in independent continuants (inherent) location material entities is about (inherent) ingredient substances property of process towards independent continuants relative to substances (rel-to) part of independent continuants precondition precondition values characterizes processes process agent material entities process duration time frames process output substances scale scale types specified by units units observation procedure technique techniques direct site material entities observes informer subjects

Concept model attributes: CLINICAL FINDING Current Proposed associated with associated morphology finding site pathological process occurrence clinical course episodicity severity has definitional manifestation finding method finding informer associated with associated morphology site pathological process occurrence clinical course episodicity severity

Clinical finding / disorder (current) associated morphology <morphologically abnormal structures> G finding site <anatomical or acquired body structures> laterality <sides> associated with &/subs <association values> pathological process <pathological processes> has definitional manifestation <findings> occurrence <periods of life> severity <severities> clinical course <courses> episodicity <episodicities> interprets <observables, evaluation procedures> G has interpretation <findings values> finding method <techniques> finding informer <performer of method; or subject of record>

Clinical finding / disorder -> finding includes (structure, process, disposition) associated morphology <morphologically abnormal structures> includes condition site <anatomical or acquired body structures> laterality <sides> associated with &/subs <association values> pathological process <pathological processes> has definitional manifestation <findings> occurrence <periods of life> severity <severities> clinical course <courses> The role group can be interepreted as “includes some condition and …”, meaning that the other attributes are attributes of the included condition. Note: the papers of Schulz et al that refer to “situation” are using the word “situation” to refer to what is here called “clinical finding”. episodicity <episodicities> interprets <observables, evaluation procedures> G has interpretation <findings values> finding method <techniques> finding informer <performer of method; or subject of record>

Concept model attributes: CLINICAL FINDING (2) Current Proposed finding informer finding method interprets has interpretation -> observation result

Concept model attributes: OBSERVATION RESULT Current Proposed finding informer finding method interprets has interpretation informer technique observes has value units scale

Concept model attributes: MEASUREMENT procedure Current Proposed – observation procedure method = measurement action property has specimen scale type time aspect measurement method component method = evaluation action property type direct site scale process duration technique towards + inheres in + precondition units informer

independent continuants quality or property (inherent) location observation result property type property types inheres in independent continuants quality or property (inherent) location material entities (inherent) ingredient substances is about characterizes processes process agent material entities process duration time frames observation result process output substances towards independent continuants has value relative to substances <values> (rel-to) part of independent continuants output of precondition precondition values observation procedure scale scale types units units technique techniques observes direct site material entities informer subjects

observation result for a quality property type property types inheres in independent continuants quality (inherent) location material entities (inherent) ingredient substances is about observation result towards independent continuants has value relative to substances <values> (rel-to) part of independent continuants output of precondition precondition values observation procedure scale scale types units units technique techniques observes direct site material entities informer subjects

observation procedure performer of observation / subject observation result for property of a process property type property types property of process is about characterizes processes process agent material entities process duration time frames observation result process output substances has value <values> output of precondition precondition values observation procedure scale scale types units units technique techniques observes direct site material entities informer performer of observation / subject

left knee jerk reflex 2+ out of 4+ (observation result) property type briskness of response property of process is about characterizes knee jerk reflex (process) process agent material entities process duration time frames observation result process output substances has value ++ out of ++++ output of precondition precondition values observation procedure scale ordinal units units technique techniques observes direct site left knee/patellar tendon informer performer of observation / subject

left knee jerk reflex 2+ out of 4+ (observation result) property of process property type briskness of response is about characterizes knee jerk reflex (process) observation procedure scale ordinal output of direct site left knee/patellar tendon has value ++ out of ++++

Presence, absence of condition Proper description logic representation of the presence or absence of a condition in a patient could be represented using the object property INCLUDES: “life phase and INCLUDES some condition” and “life phase and not INCLUDES some condition” The OWL 2 EL profile does not provide negation. ‘Clinical finding which does not include condition’ concepts will have to be primitive in a module that is based on EL or else these absence concepts will need to be separated into a module that is classified using a reasoner that can handle a profile that includes negation

observation result An information artifact Is-about some observable Has-value some {value}

observation result model (1) This model makes a distinction between the target of an observation – the thing the observation is about - such as an inherent quality or independent continuant that is being observed – and any aspects of the act of observation that defines the observation Two parts of the observables model: A) the quality/property part of the model: This models the thing being observed, which is the intended object of the observation This part of the model deals with real entities that exist independent of being observed B) the observation procedure part of the model: This models the defining characteristics of the observation act This part of the model deals with the various characteristics that define the type of observation that is done, such as technique, units, time scale, etc. These characteristics may also help us infer how we know, and how accurately we know, that the object of observation has the characteristics that are observed. The defining characteristics of the observation act are ontological with respect to acts of observation. Some people have called these “epistemological” and declared them out of bounds for an ontology, but this is a misunderstanding of what observables are about. These features are only out of bounds for an ontology of the targets of observation, but not out of bounds for “observables” as intended to be covered with this proposed model. Note: It is important to differentiate the object of an observation (the thing it “is about”) from the purpose of an observation. Some people interpret the word “object” to mean “objective”, meaning “purpose.” This is NOT what is meant by the object of the observation. This potential for confusion is a good reason to avoid proposing attribute names containing the word “object”.

observation result model (2) uses a nested expression or pre-coordinated named dependent quality (or other type of entity) to represent what is being observed Note: there is a difference between “what is being observed” and “what the thing observed is a quality of” E.g. “color of skin”: What is being observed is color. The color happens to be a quality of skin, which might happen to have a particular location. we assume only one set of observation characteristics per act of observation If the results of an observation are multiple, then the model requires that there be multiple individual observations. observation result is a replacement for the name “finding” for those entities (including things already represented in SNOMED CT that have the tag “finding”) that fit this model.

observation result model (3) What does this model do to existing measurement procedure attributes? Replaces HAS SPECIMEN with direct site The direct site is the immediate direct locus of the observation action (as opposed to the exact locus of the quality that is intended to be measured or assessed) and is available to be used when the entity that is being directly observed is not at the same locus as the intended object of the observation. (The intended object of the observation is the entity in which the observed property inheres; or the independent continuant which is ideally intended to be observed). Replaces measurement method with technique Not all observations of interest are measurements, and “measurement method” is too close a name to “method” which takes values from the action hierarchy to define procedures in SNOMED CT. There is a new techniques hierarchy from which the values will be drawn Revises and changes the configuration of COMPONENT, PROPERTY, SYSTEM COMPONENT and SYSTEM Replaced by inheres in and towards. These are expected to achieve better reproducibility via clearer ontological definitions. property type Retains current properties and adds values related to PATO (ontology of qualities) scale TYPE Retains scale TYPE in the observation part of model, and adds units to coordinate with IFCC-IUPAC. TIME ASPECT Eliminates TIME ASPECT from quality type observations because they are necessarily present at a single point in time; adds process duration for processes Moves to their own hierarchies, separate from observables: functions processes activities Allows functions, processes, activities also to be values of towards (in addition to substances, etc) Does not allow observables to be values of inheres in or towards. Direct object versus intended object: Core temperature estimated from rectal temperature: If we measure rectal temperature as a surrogate for core body temperature, then the direct object is the rectum but the “core” of the body is the locus of the quality intended to be assessed. If the slightly lower temperature in the rectum is clinically meaningful in some context, it is possible to use a standard correction factor. (which has been estimated to be 0.04 degrees C). For most purposes, this is insignificant, so most people ignore the difference between rectal and core body temp, and use rectal temp measured without correction as the core body temp. Plasma sodium concentration, measured in serum: If I measure sodium concentration in serum, the direct object is serum but the intended object is the intravascular blood plasma (there is no serum in the body – serum is plasma with the coagulation proteins removed, and only exists as an out-of-the-body preparation).

observation result model (4) Differentiates between a dependent quality per se and a property type. Concentration is a property type. The concentration of sodium in serum is a dependent quality. Renames PROPERTY to property type

observation result model (5) Deprecates the use of “absence” as a property type Asserting absence of findings/functions/abilities/etc. requires negation (using a modification of the situation model). Observables would also not use “associated morphology” But note: Conditions can be modeled using “associated morphology” with a value that implies physical absence of a structure that is normally present E.g. 56457002 congenital atresia, 55425006 traumatic acquired absence Deprecates the use of “presence” as a property type. Presence is necessarily implied by conditions modeled with associated-morphology, but presence is not a property type for observables E.g. 91431006 supernumerary structure (morphologic abnormality) implies presence of an extra structure not normally present.

Model for observable entities First attribute is: is about (observation target) Its domain includes observables, observation procedures, and observation results. Its range includes: dependent qualities of independent continuants properties of processes (may be called “process profiles” in BFO2) Range MAY include: Dependent continuants (qualities, dispositions, roles) Independent continuants – but interpretation rules are needed. Occurrents, and in particular, situations

The observation part of the model Main attributes are: scale units technique direct site

model for observables is about observable scale scale types units Dep. Qualities/Dispositions, Indep. continuants is about observable scale scale types units units technique techniques direct site body structures, specimens

independent continuants model for dependent qualities property type property types inheres in independent continuants quality towards functions, substances precondition body states What about subject? Donor, mother, fetus etc who are not the subject of record -> Invokes context, and would be situation concepts.

model for ‘quality’ observables property type property types inheres in independent continuants is about quality towards functions, substances precondition body states (challenges, fasting etc.) observable scale scale types units units technique techniques direct site body structures, specimens

model for ‘quality’ observables LOINC elements IFCC-IUPAC NPU elements property type property types Kind-of-property property inheres in independent continuants System/specimen system is about quality towards functions, substances component component precondition body states component observable scale scale types scale units units units technique techniques method method direct site body structures, specimens System/specimen

Sodium:SCnc:PT:Ser/Plas:Qn LOINC Example: Sodium:SCnc:PT:Ser/Plas:Qn Qualities are continuants that exist in their entirety at a single point in time property type Substance concentration Kind-of-property inheres in plasma is about quality towards Sodium ion component precondition body states observable scale quantitative scale units units technique techniques direct site Serum/plasma specimen System/specimen

IFCC-IUPAC NPU Example: P—Sodium ion; subst.c. = ? mmol/l property type Substance concentration property inheres in plasma system is about quality towards Sodium ion component precondition body states observable entity scale quantitative units mmol/l units technique techniques direct site body structures, specimens

DRAFT model for observation results qualities, dispositions, independent continuants is about observation result scale scale types units units technique techniques direct site body structures, specimens has value Numeric, ordinal, nominal

DRAFT model for results of observations of qualities property type property types inheres in independent continuants is about quality towards functions, substances precondition body states observation result scale scale types units units has value Numeric, ordinal, nominal technique techniques direct site body structures, specimens

DRAFT model for procedures that observe qualities property type property types inheres in independent continuants is about quality towards functions, substances precondition body states observation procedure Note the removal of VALUE, relative to observation results, and the addition of method = observation action, relative to the observable. scale scale types units units technique techniques direct site body structures, specimens method observation action

Attributes that define the quality that the observation is intended to elucidate Property type Coordinated with BFO Qualities. Quality: a dependent continuant that is exhibited if it inheres in an entity or entities at all. (See BFO Manual, definition of “Quality”) Inheres-in Relationship between a quality (property) and the independent continuant on which it depends for its existence, in which it is manifest Towards (meaning the object or target of the property) Third element of a relational quality, (other than the quality, and the continuant in which it inheres) e.g. sodium, in the quality of concentration of sodium in serum Precondition States of the individual that contextualize the property (e.g. standing, fasting, post-challenge, etc)

Values for property type Top levels of value hierarchy – determined by empirical analysis of values in the observables hierarchy Detail Dimension Feature Fluid property Force property Location Quantity Ratio Result Stage Temperature Time Velocity Wave property

dimension [2] (possible: size) observable entity property types dimension [2] (possible: size) area [20] distance (synonym: linear dimension) breadth [20] circumference [27] depth [7] diameter [31] height [29] length [42] width [11]

Approach to properties Influenced by OBO Quality ontology

precondition body states that define the context in which the property is defined. For example, “standing blood pressure” is defined in the context of the body state “standing position”. Various challenge tests would be defined in terms of body states specifying the challenge that occurred, e.g. “2 hour post-prandial glucose” would have body state = “2 hours after meal”.

Attributes that define the characteristics of the observation scale type Same as LOINC scale type and current measurement procedure attribute units Same as IFCC-IUPAC NPU units direct site the direct object of the observation action; the site or specimen where the observation takes place. May be different from the value of inheres in, since the property being observed may be inferred from a specimen or from a remote site. Examples: rectum as the site of temperature measurement, where the property being observed is the core body temperature (rectal temperature being a surrogate); or serum specimen being used to determine body plasma sodium concentration. The concentration inheres in the plasma, but is being measured in a serum specimen. Needs to be modeled only when this site is different from the value of inheres in technique Any specialization of “observation” that tells us how we did the observing; for example, “enzyme-linked immunosorbent assay” or “immunofluorescence”.

Revision of “site” object property A possible attribute hierarchy could be: site inheres in direct site indirect site inheres in can be a sub-role of site. This works for observation findings and observation procedures, and direct site would be used in addition where necessary The attribute procedure site direct, in the current procedure model, is the same meaning as direct site in the observable model.

Replace measurement method with more general technique observables model revision: For observation and evaluation procedures, the method (with values from the action hierarchy) represents the goal or objective of what is done: evaluation, testing, imaging, measurement, examination observation techniques define the observable, via technique (with values from a value set that includes lab techniques and other specific measurement and evaluation actions, such as inspection, palpation, percussion, auscultation) Techniques are the means by which the action is carried out, not the intended outcome. Techniques include specific measurement techniques such as Enzyme-linked immunosorbent assay (ELISA). Need to examine whether this works for procedures other than evaluations, i.e. can we make the distinction between method (means) and technique for all procedures

Auditory threshold at 3kHz, in dB property type Threshold inheres in Auditory system is about quality towards Hearing (function) precondition body states observable entity Need to define what relational properties are, and how to recognize them. Concentration is a relational property. IS threshold also? scale quantitative units dB technique 3 kHz audiometry direct site ear

Blood hemoglobin concentration (quality) property type Mass concentration inheres in Intravascular blood quality towards hemoglobin precondition body states

body structures, specimens Blood hemoglobin concentration, quantitative (observable) property type Mass concentration inheres in Intravascular blood is about quality towards hemoglobin precondition body states observable entity scale quantitative units units technique techniques direct site body structures, specimens

body structures, specimens Blood hemoglobin 14 gm/dL (observation result) property type Mass concentration inheres in Intravascular blood is about quality towards hemoglobin precondition body states observation result scale quantitative units gm/dL has value 14 technique techniques direct site body structures, specimens

Head circumference (quality) property type circumference inheres in Head (necessarily also: surface along fronto-parietal coronal plane of head) quality towards hemoglobin precondition body states

body structures, specimens Head circumference in cm (observable) property type circumference inheres in head is about quality towards hemoglobin precondition body states observation result scale quantitative units cm technique techniques direct site body structures, specimens

body structures, specimens Head circumference 42 cm (observation result) property type circumference inheres in head is about quality towards hemoglobin precondition body states observation result scale quantitative units cm has value 42 technique techniques direct site body structures, specimens

Serum concentration of Borrelia antibody property type concentration inheres in plasma is about quality towards Borrelia antibody precondition body states observable entity scale quantitative units units technique techniques direct site Serum specimen

observation procedure Measurement of serum concentration of Borrelia antibody by ELISA technique (procedure) property type concentration inheres in plasma is about quality towards Borrelia antibody precondition body states observation procedure There could be an attempt to specify a difference between observation action and measurement action: Some draft definitions: observation is the determination of the type of a dependent quality, or the presence or identity of an independent continuant. observation can involve the determination of a nominal quality (one that has no magnitude). measurement is the determination of the magnitude of a quality (one that has a magnitude). Nominal, ordinal, differential, and rational: nominal: no magnitude ordinal: magnitude ordered, but not on a scale that can be subtracted differential: magnitude that can be subtracted, but not divided rational: magnitude that can be divided scale quantitative units units technique ELISA direct site Serum specimen method Measurement action

Cultured E.coli serotype is O157 The information model is used to link this result to the Culture and specimen that came from the patient. Cultured E.coli serotype is O157 property type serogroup inheres in E. Coli (organism) is about quality towards hemoglobin precondition body states observation result “E. Coli serotype” is a nominal quality ( one without magnitude ). scale scales units units has value O157 technique Bacterial serotyping direct site Microbial culture

What about abilities? Able with respect to normal functioning and activities Ontologically these are “realizables”. Two types: Sure-fire (“dispositions”): if you have the ability to feel pain, then when a painful stimulus is applied, you feel it (assuming you are conscious – and actually even if you are unconscious – with some exceptions based on threshold of intensity) Those abilities that depend on the bearer’s decision (ability to walk, talk, throw a ball, eat an apple, etc)

Disposition type Possible replacement for “property type” where the value of “is about” is neither a quality nor a process, but instead is a disposition or function * could consider expanding the domain/range for property type instead

ability to hear (meaning the “sure-fire” disposition for a hearing process to be instantiated on exposure to sound) disposition type ability inheres in auditory system disposition towards hearing (process) precondition body states Note: a disposition is defined as something that necessarily occurs given a certain condition; it is not the same as tendency, which is defined as something that is likely to occur but in different circumstances it may or may not occur. The relationship between force applied and the shattering of a pane of glass is a disposition. A pane of glass has a disposition to shatter when exposed to enough force; it will always shatter once the force reaches the threshold required. The relationship between smoking and lung cancer is a tendency. People who smoke have a tendency to develop lung cancer, but regardless of the amount they smoke, some people don’t develop lung cancer.

body structures, specimens Able to hear (as an observation result) (there exists some observation result which has a target of some disposition which is ability to hear) disposition type ability inheres in auditory system is about disposition towards hearing (process) precondition body states observation result Maybe ability should be regarded as a quality. “whether is able” is rendered unnecessary. Consider “ablity to do x = able, unable, does, does not, assisted, etc.” ?? There should be a difference between volitional skill-based abilities and functional/dispositional abilities. For example, “ability to feel pain” (functional / dispositional) is not the same type of thing as “ability to sign name” (volitional / skill-based) scale scale types units units has value able technique techniques direct site body structures, specimens

Able to hear (clinical phase) Interpreted as disposition present in life of patient, or “ability to hear = present” (the clinical phase includes the existence of some disposition which is ability to hear) disposition type ability inheres in auditory system includes disposition towards hearing (process) precondition body states clinical phase

body structures, specimens Able to hear (observation result) Interpreted as an observation result, using the VALUE attribute disposition type ability inheres in auditory system is about disposition towards hearing (process) precondition body states observation result There exists some observation result, in which the target of the observation is some disposition, and which has value = able. scale scale types units units has value able technique techniques direct site body structures, specimens

Impaired ability to hear (as a disposition) disposition type Impaired ability inheres in auditory system disposition towards hearing (process) precondition body states Ontologically, the impairment of ability to hear exists independently of being observed.

body structures, specimens Impaired ability to hear (as an observation result) disposition type ability inheres in auditory system is about disposition towards hearing (process) precondition body states observation result Now what about “hearing not impaired” ? How do we determine that “hearing not impaired” implies “able to hear”? One option: “not impaired” is a value subtype of “able” AND do not use the negation for this model. There are some things that we should regard as “positives” even though expressed in the negative. Hearing NOT impaired is one of those, IF we model “able to hear” as a positive. OTHERWISE, we could turn it around and model the deficits as the positives. This might be more consistent with “NORMAL” as the absence of abnormality. This would mean that “ability = able” would be disallowed, and we would have the double negative of “ability = unable” with situation NOT includes “ability = unable”. That seems awkward. scale scale types units units has value impaired technique techniques direct site body structures, specimens

Impaired ability to hear (as disposition included in situation, or “impaired hearing = present”) disposition type Impaired ability inheres in auditory system includes disposition towards hearing (process) precondition body states clinical phase In this model, impaired ability is a disposition, and “whether is able” is not necessary. what do we do with “ablity to do x = able, unable, does, does not, assisted, etc.” ?? There should be a difference between volitional actions and functional properties. For example, “ability to feel pain” is not the same as “ability to sign name”.

Other dispositions Antimicrobial sensitivity

Antimicrobial susceptibility test (procedure) disposition type Resistance/sensitivity inheres in Microbial isolate is about disposition towards Antimicrobial precondition body states observation procedure TIME ASPECT Time aspects scale scale types units units technique techniques direct site body structures, specimens method observation action

Process observables/observations characterizes process duration other process attributes

Left knee deep tendon reflex – briskness (observable) property type Briskness of response property of process inheres in Neuromuscular structures of the left knee deep tendon reflex is about characterizes Deep tendon reflex (process) precondition body states observable entity scale scale types units units technique techniques direct site body structures, specimens

Left knee jerk reflex 2+ (observation result) property type Briskness of response property of process inheres in Neuromuscular structures of the left knee deep tendon reflex is about characterizes Deep tendon reflex (process) precondition body states observation result scale scale types units units has value 2+ out of 4+ technique techniques direct site body structures, specimens

Other question/answer pairs as quality / quality region pairs

Histologic type (of lesion) property type Histologic type inheres in lesion quality towards functions, substances precondition body states

(located-in would be a relational spatial quality) Tumor site (located-in would be a relational spatial quality) property type Located in inheres in tumor quality towards functions, substances precondition body states

Dealing with “presence” Disallow “presence” and “absence” as a value of property type But allow “detected”, “present”, “absent” as an observation result, if the value of “is about” is a situation, or independent continuant (not a dependent continuant). and possibly also a process with process properties.

observation result observation result has value <values> property type property types inheres in independent continuants (inherent) location material entities is about (inherent) ingredient substances quality or property towards independent continuants relative to substances (rel-to) part of independent continuants precondition precondition values characterizes processes process agent material entities process duration time frames process output substances scale scale types output of units units observation procedure technique techniques direct site material entities observes informer subjects

independent continuant observation procedure Observation result for presence / absence observation result is about output of observes independent continuant observation procedure has location <location> has value scale scale types units units technique techniques present/absent direct site material entities informer subjects

Methicillin-resistant staphylococcus aureus (MRSA) present in abdominal wound, swab specimen, by PCR rapid detection method observation result is about output of observes MRSA observation procedure has location abdominal wound has value scale qualitative units units technique PCR rapid detection method detected direct site abdominal wound swab (specimen) informer subjects

is about MRSA (organism) observation result has value detected Methicillin-resistant staphylococcus aureus (MRSA) present This is a “close to user” form. It is a sufficient definition, supplemented with a second sufficient definition that says: observation_result and (output-of = (observation_procedure and observes = MRSA)) and (has_value = detected) is about MRSA (organism) observation result has value detected

Mycoplasma pneumoniae Mycoplasma pneumoniae detected is about Mycoplasma pneumoniae observation result scale qualitative units units has value detected technique techniques direct site specimens

PCR rapid detection method Methicillin-resistant staphylococcus aureus (MRSA) in abdominal wound, swab specimen, by PCR rapid detection method (observable) is about MRSA (organism) has location Abd. wound observable entity scale qualitative units units technique PCR rapid detection method direct site Wound swab (specimen)

MRSA (methicillin resistant staph aureus) POC (point-of-care) test (procedure) is about MRSA (organism) observationprocedure scale scale types units units has value Numeric, ordinal, nominal technique MRSA POC detection technique direct site specimen method observation action

Radial pulse palpability is about arterial pulsation has location radial artery at the wrist observable entity scale scale types units units technique palpation direct site Ventral aspect of wrist over radial artery

radial pulse present by palpation is about arterial pulsation has location radial artery at the wrist observation result scale scale types units units has value present technique palpation direct site ventral aspect of wrist over radial artery

abdominal wall stoma present (observation result) is about stoma has location Abdominal wall observation result scale scale types units units has value present technique techniques direct site place

colostomy present (observation result) is about colostomy has location Abdominal wall observation result scale scale types units units has value present technique techniques direct site place

adenocarcinoma of the colon present (observation result) is about adenocarcinoma has location colon observation result Probably we don’t need this meaning because one can’t directly observe that there is an adenocarcinoma present. But – “malignant tumor present” is something that can be directly a result of observation based on the characteristics observed (and can be mistaken, etc). scale scale types units units has value present technique techniques direct site place

associated morphology adenocarcinoma of the colon (disorder) disorder includes associated morphology adenocarcinoma site colon adenocarcinoma lesion observed in colon (observation result) adenocarcinoma of the colon present (finding) - deprecated FSN observation result is about A disorder and an observation result are not the same thing. Disorders are interpreted as phases of a subject’s life during which they are the bearer of the condition. adenocarcinoma has location colon has value present

Determining “contents” observations that seek to answer: What things are present as physical parts of a specimen (such as a fluid) or structure? What things are present and contained within a structure (but not part of it)?

body structures, specimens Contents of urine by light microscopy (observable) Assumes “having physical part” is a valid relation between discrete solid entities in a fluid and the fluid substance. property type Having physical part inheres in urine is about quality towards functions, substances precondition body states observable scale scale types units units technique Light microscopy direct site body structures, specimens

observationprocedure Determining contents of urine by light microscopy on urine sample (procedure) Synonym: microscopic urinalysis property type Having physical part inheres in urine is about quality towards functions, substances precondition body states observationprocedure scale scale types units units technique Light microscopy direct site Urine sample method observation action

Urine microscopy: hyaline casts present property type Having physical part inheres in urine is about quality towards Hyaline casts precondition body states observation result scale scale types units units has value Observed technique Light microscopy direct site Urine specimen

What about counts? Count >=1 seems to mean the same as “retinal hemorrhage present” But does it? There is a difference between an observation result in which a count was made, and a phase of a subject’s life during which the countable entity was present (or not present) And this difference matters because counts can be incorrect a count of zero can be made when the situation is that there is a hemorrhage present and a count of 1 can be mistakenly made when the situation is that there is no hemorrhage and we may need to be able to record and do quality assurance based on the difference between the count and the actual situation

body structures, specimens 4 retinal hemorrhages present (observation result) property type entitic number inheres in retina is about quality towards hemorrhages precondition body states observation result The property type is 118536000 entitic number if the result means “4 hemorrhages in a single entire retina”. The property type is 410681005 count of entities, if the result means “4 hemorrhages were counted altogether, regardless of how many retinas or what proportions of the retinas were examined”. scale quantitative units units has value 4 technique techniques direct site body structures, specimens

body structures, specimens retinal hemorrhage count >= 1 (observation result) property type entitic number inheres in retina is about quality towards hemorrhage precondition body states observation result scale quantitative units units has value >= 1 technique techniques direct site body structures, specimens

observation procedure retinal hemorrhage present (observation result) observation result has value detected is about hemorrhage has location retina scale qualitative output of units units observation procedure technique techniques direct site material entities observes informer subjects

associated morphology Retinal hemorrhage present (clinical phase) clinical phase includes associated morphology hemorrhage site retina These probably should be regarded as having the same meaning. How can we correlate this with the observation that count >= 1 ?

Which models are preferred and why? Several different options have been presented Criteria for choosing among options: 1) semantic consistency 2) simplicity 3) interoperability 4) reproducibility of modeling individual concepts 5) lower degree of disruption of existing implementations and content 6) lower comparative cost of the change 7) computability