Concept Model for observables, investigations, and observation results For the IHTSDO Observables...

Concept Model forobservables, investigations, and

observation results

For the IHTSDO Observables Project Groupand LOINC Coordination ProjectRevision Date: March 14, 2014

Part-2

observation result model (5)– Continue from Part-1 slide deck

– 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.

The observation part of the model

• Main attributes are:– scale– units– technique– direct site

observablescale scale types

model for observables

units units

technique techniques

direct site body structures, specimens

is about Dep. Qualities/Dispositions, Indep. continuants

quality

property type property types

model for dependent qualities

independent continuantsinheres in

towards functions, substances

precondition body states

observable


scale scale types

model for ‘quality’ observables



units units


is about

precondition body states (challenges, fasting etc.)


quality

observable


scale scale types

model for ‘quality’ observables



units unitstechnique techniques

is about



IFCC-IUPAC NPU elementsLOINC elements

Kind-of-property property

System/specimen system

component component

scale

units

method method

System/specimen

component

quality

observable

property type Substance concentration

scale quantitative

LOINC Example:Sodium:SCnc:PT:Ser/Plas:Qn

plasmainheres in

towards Sodium ion


is about


direct site Serum/plasma specimen

quality

Kind-of-property

component

scale

System/specimen

Qualities are continuantsthat exist in their entiretyat a single point in time

observableentity

property type Substance concentration

scale quantitative

IFCC-IUPAC NPU Example:P—Sodium ion; subst.c. = ? mmol/l

plasmainheres in

towards Sodium ion

units mmol/l


is about



quality

property

system

component

units

observation result

scale scale types

DRAFT model for observation results

units units



is about qualities, dispositions, independent continuants

has value Numeric, ordinal, nominal

observation result


scale scale types

DRAFT model for results of observations of qualities



units units


is about



quality

has value Numeric, ordinal, nominal

observation procedure


scale scale types

DRAFT model for procedures that observe qualities



units units


is about



quality

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

• Detail• Dimension• Feature• Fluid property• Force property• Location• Quantity

• Ratio• Result• Stage• Temperature• Time• Velocity• Wave property

Top levels of value hierarchy – determined by empiricalanalysis of values in the observables hierarchy

• 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 propertiesInfluenced 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”.

*Draft* suggestion for general site object property

• A possible attribute hierarchy could be:site

inheres indirect site (used for procedures, observation results, and

observables)indirect site (still used only for procedures)

• 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

• Proposal:– 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

observableentity

property type Threshold

scale quantitative

Auditory threshold at 3kHz, in dB

Auditory systeminheres in

towards Hearing (function)

units dB

technique 3 kHz audiometry

is about


direct site ear

quality


quality

property type Mass concentration

Blood hemoglobin concentration (quality)

Intravascular bloodinheres in

towards hemoglobin

precondition

observableentity


scale quantitative

Blood hemoglobin concentration,quantitative (observable)


towards hemoglobin


is about

body states


quality

precondition

observation result


scale quantitative

Blood hemoglobin 14 gm/dL (observation result)


towards hemoglobin

units gm/dL


is about

body states


quality

has value 14


quality

property type circumference

Head circumference (quality)

Head (necessarily also: surface along fronto-parietal coronal

plane of head)

inheres in

towards hemoglobin

precondition

observation result


scale quantitative

Head circumference in cm (observable)

headinheres in

towards hemoglobin

units cm


is about

body states


quality

precondition

observation result


scale quantitative

Head circumference 42 cm (observation result)

headinheres in

towards hemoglobin

units cm


is about

body states


quality

has value 42

precondition

observableentity

property type concentration

scale quantitative

Serum concentration of Borrelia antibody

plasmainheres in

towards Borrelia antibody


is about

body states

direct site Serum specimen

quality

precondition

observation procedure

property type concentration

scale quantitative

Measurement of serum concentration of Borrelia antibody by ELISA technique (procedure)

plasmainheres in

towards Borrelia antibody

units unitstechnique ELISA

is about

body states

direct site Serum specimen

quality

method Measurement action

precondition

observation result

property type serogroup

scale scales

Cultured E.coli serotype is O157

E. Coli (organism)inheres in

towards hemoglobin

units units

technique Bacterial serotyping

is about

body states

direct site Microbial culture

quality

has value O157

The information model is used to link this result to the Culture and specimen that came from the patient.

What about abilities?

• Continued in Part-3 slide deck

• 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)

Concept Model for observables, investigations, and observation results For the IHTSDO Observables...

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