IHTSDO Observables Project Group July 23, 2008

IHTSDO Observables Project Group July 23, 2008
Exploration of Possible Concept Models for Observable Entities Revision 3 IHTSDO Observables Project Group July 23, 2008

Yet another draft model for observables (1)
Define a model for observables that makes a distinction between the inherent quality that is being observed and any aspects of the actual observation Two parts of the model: the property part, and the observation part. The property part deals with real properties that exist independent of observation; the observation part deals with how we know about the quality/property (it is ontological with respect to acts of observation) For the inherent property, use a role group instead of nesting; this would allow more than one property per observation Need to validate whether it is necessary to have more than one property; if not, we can eliminate the role group For the observation part, no role group is needed because we assume a different code for each observation If a concept (finding) involves the results of multiple observations, then assume it is a situation. E.g. “hyponatremia with hypokalemia” Expand observable model to make a model for observation FINDINGS and a model for observation PROCEDURES: observation PROCEDURES add the attribute: METHOD = observation action. observation FINDINGS add attributes HAS INTERPRETATION and HAS VALUE

Yet another draft model for observables (2)
What happens to existing measurement procedure attributes? HAS SPECIMEN Replaced by a DIRECT SITE attribute, which is the direct object of the observation action and is to be used when the entity that is being observed is different from the entity in which the property inheres. Replace MEASUREMENT METHOD with TECHNIQUE Create a new value set for techniques Revise and change the configuration of COMPONENT, PROPERTY, SYSTEM COMPONENT and SYSTEM Replace by INHERES-IN and TOWARDS, to get better reproducibility PROPERTY Retain current properties and add values from PATO (ontology of qualities) TIME ASPECT, and SCALE TYPE Retain in observation part of model, and add UNITS to coordinate with IFCC-IUPAC Move to their own hierarchies, separate from observables: functions processes activities Allow functions, processes, activities also to be values of TOWARDS (in addition to substances, etc) Do not allow observables to be values of INHERES-IN or TOWARDS.

Draft model: property part
Main attributes are: PROPERTY INHERES-IN TOWARDS (see Mungall etal “Representing Phenotypes in OWL”) PRECONDITION

Draft model: observation part
Main attributes are: TIME ASPECT SCALE TYPE UNITS TECHNIQUE DIRECT SITE

DRAFT model of observables
PROPERTY Properties INHERES IN independent continuant G TOWARDS Functions, substances PRECONDITION Body states observable TIME ASPECT Time aspects SCALE Scale types UNITS units TECHNIQUE techniques DIRECT SITE Body structures, specimens

LOINC elements IFCC-IUPAC NPU elements PROPERTY Properties Kind-of-property property INHERES IN independent continuant System/specimen system G TOWARDS Functions, substances component component PRECONDITION Body states component observable TIME ASPECT Time aspects Time aspect SCALE Scale types scale UNITS units units TECHNIQUE techniques method method DIRECT SITE Body structures, specimens System/specimen

Substance concentration
LOINC Example: Sodium:SCnc:PT:Ser/Plas:Qn PROPERTY Substance concentration Kind-of-property INHERES IN Plasma G TOWARDS Sodium ion component PRECONDITION Body states observable TIME ASPECT Single point in time Time aspect SCALE quantitative scale UNITS units TECHNIQUE techniques DIRECT SITE Serum/Plasma System/specimen

IFCC-IUPAC NPU Example: P—Sodium ion; subst.c. = ? mmol/l
PROPERTY Substance concentration property INHERES IN Plasma system G TOWARDS Sodium ion component PRECONDITION Body states observable TIME ASPECT Single point in time SCALE quantitative UNITS mmol/l units TECHNIQUE techniques DIRECT SITE Body structures, specimens

DRAFT model of observation findings
(possible to reconfigure as subtypes of observables, where there is either an interpretation or value) PROPERTY Properties INHERES IN independent continuant G TOWARDS Functions, substances PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE Numeric, ordinal, nominal TECHNIQUE techniques DIRECT SITE Body structures, specimens

DRAFT model of observation procedures
(observation action not allowed to be specialized; use TECHNIQUE instead) PROPERTY Properties INHERES IN independent continuant G TOWARDS Functions, substances PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal procedure TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE Numeric, ordinal, nominal TECHNIQUE techniques DIRECT SITE Body structures, specimens METHOD Observation action

Attributes that define the property that the observation is intended to elucidate
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 (? Object)(? Target)(? Of) 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)

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
Time aspect Same as LOINC time aspect and current measurement procedure attribute 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”.

SITE The attribute PROCEDURE SITE DIRECT could have its name changed to DIRECT SITE and could allow additional domains of observation finding and observable Could also revise PROCEDURE SITE to be SITE, and FINDING SITE to be 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 Role hierarchy would look like this: SITE INHERES-IN DIRECT SITE (used for procedures, observation findings and observables) INDIRECT SITE (still used only for procedures)

DRAFT model of observation findings (as subtypes of observables,
where there is either an interpretation or value) PROPERTY Properties INHERES IN independent continuant G TOWARDS Functions, substances PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE Numeric, ordinal, nominal TECHNIQUE techniques DIRECT SITE Body structures, specimens

Methicillin-resistant staphylococcus aureus
(MRSA) present in abdominal wound, swab specimen, by PCR rapid detection method PROPERTY presence INHERES IN wound INHERES IN abdomen G TOWARDS MRSA (organism) PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Single point in time SCALE qualitative UNITS units VALUE positive TECHNIQUE PCR rapid detection method DIRECT SITE Wound swab (specimen)

DRAFT model of observation procedures
PROPERTY Properties INHERES IN independent continuant G TOWARDS Functions, substances PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal procedure TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE Numeric, ordinal, nominal TECHNIQUE techniques DIRECT SITE Body structures, specimens METHOD Observation action

Body structures, specimens
Blood hemoglobin concentration PROPERTY concentration INHERES IN Intravascular blood G TOWARDS hemoglobin PRECONDITION Body states observable TIME ASPECT Time aspects SCALE Scale types UNITS units TECHNIQUE techniques DIRECT SITE Body structures, specimens

Blood hemoglobin 14.0 gm/dL
PROPERTY Mass concentration INHERES IN Intravascular blood G TOWARDS hemoglobin PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Single point in time SCALE quantitative UNITS gm/dL VALUE 14 TECHNIQUE techniques DIRECT SITE Body structures, specimens

Ability to hear PROPERTY ability INHERES IN Auditory system G TOWARDS To hear (function) PRECONDITION Body states observable TIME ASPECT Time aspects SCALE Scale types UNITS units TECHNIQUE techniques DIRECT SITE Body structures, specimens

Able to hear PROPERTY Ability INHERES IN Auditory system G TOWARDS
To hear (function) PRECONDITION Body states HAS INTERPRETATION able finding TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE Numeric, ordinal, nominal TECHNIQUE techniques DIRECT SITE Body structures, specimens

Left knee deep tendon reflex - briskness
PROPERTY Briskness of response INHERES IN Neuromuscular structures of the left knee deep tendon reflex G TOWARDS Deep tendon reflex PRECONDITION Body states observable TIME ASPECT Time aspects SCALE Scale types UNITS units TECHNIQUE techniques DIRECT SITE Body structures, specimens

Left knee jerk reflex 2+ PROPERTY Briskness of response INHERES IN
Neuromusc. Struc. L knee DTR G TOWARDS Deep tendon reflex PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE 2+ out of 4+ TECHNIQUE techniques DIRECT SITE Body structures, specimens

Head circumference PROPERTY circumference INHERES IN Surface of head G TOWARDS Functions, substances PRECONDITION Body states observable TIME ASPECT Time aspects SCALE Scale types UNITS units TECHNIQUE techniques DIRECT SITE Body structures, specimens

Head circumference 28 cm PROPERTY circumference INHERES IN
Surface of head G TOWARDS Functions, substances PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Time aspects SCALE Scale types UNITS cm VALUE 28 TECHNIQUE techniques DIRECT SITE Body structures, specimens

4 retinal hemorrhages present
PROPERTY count INHERES IN retina G TOWARDS hemorrhages PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE 4 TECHNIQUE techniques DIRECT SITE Body structures, specimens

Radial pulse palpability
PROPERTY Presence INHERES IN Radial artery at the wrist G TOWARDS Arterial pulsation PRECONDITION Body states observable TIME ASPECT Time aspects SCALE Scale types UNITS units TECHNIQUE palpation DIRECT SITE Ventral aspect of wrist over radial artery

Radial pulse present by palpation
PROPERTY Presence INHERES IN Radial artery at the wrist G TOWARDS Arterial pulsation PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE present TECHNIQUE palpation DIRECT SITE Ventral aspect of wrist over radial artery

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 Having physical part INHERES IN urine G TOWARDS Functions, substances PRECONDITION Body states observable TIME ASPECT Time aspects SCALE Scale types UNITS units TECHNIQUE Light microscopy DIRECT SITE Body structures, specimens

Determining contents of urine by light microscopy
on urine sample (procedure) Synonym: microscopic urinalysis PROPERTY Having physical part INHERES IN urine G TOWARDS Functions, substances PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal procedure TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE Numeric, ordinal, nominal TECHNIQUE Light microscopy DIRECT SITE Urine sample METHOD Observation action

Incr, decr, normal, abnormal
Urine microscopy: hyaline casts (finding) PROPERTY Having physical part INHERES IN urine G TOWARDS Hyaline casts PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE observed TECHNIQUE Light microscopy DIRECT SITE Urine specimen

Borrelia antibody (substance)
Serum concentration of Borrelia antibody (observable) PROPERTY concentration INHERES IN plasma G TOWARDS Borrelia antibody (substance) PRECONDITION Body states observable TIME ASPECT Time aspects SCALE Scale types UNITS units TECHNIQUE Light microscopy DIRECT SITE Serum specimen

Measurement of serum Borrelia antibody by ELISA (procedure)
PROPERTY concentration INHERES IN plasma G TOWARDS Borrelia antibody (substance) PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal procedure TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE Numeric, ordinal, nominal TECHNIQUE ELISA DIRECT SITE serum specimen METHOD Observation action

MRSA (methicillin resistant staph aureus)
POC (point-of-care) test (procedure) PROPERTY presence INHERES IN body G TOWARDS MRSA (organism) PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal procedure TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE Numeric, ordinal, nominal TECHNIQUE MRSA POC detection technique DIRECT SITE specimen METHOD Observation action

Incr, decr, normal, abnormal
Cultured organism serotype is O157 The information model is used to link this finding to the Culture and specimen that came from the patient. PROPERTY serotype INHERES IN E coli (organism) G TOWARDS Functions, substances PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE E coli O157 (organism) TECHNIQUE Bacterial serotyping DIRECT SITE Microbial culture

Abdominal wall stoma present
PROPERTY presence INHERES IN Abdominal wall G TOWARDS stoma PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE present TECHNIQUE techniques DIRECT SITE Body structures, specimens

Colostomy present PROPERTY presence INHERES IN Abdominal wall
Colon G TOWARDS colostomy PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE present TECHNIQUE techniques DIRECT SITE Body structures, specimens

Adenocarcinoma of the colon present
PROPERTY presence INHERES IN colon G TOWARDS Adenocarcinoma (morph) PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE present TECHNIQUE techniques DIRECT SITE Body structures, specimens

Histologic type (of lesion) PROPERTY Histologic type INHERES IN lesion G TOWARDS Functions, substances PRECONDITION Body states observable TIME ASPECT Time aspects SCALE Scale types UNITS units TECHNIQUE techniques DIRECT SITE Body structures, specimens

Tumor site (located-in would be a relational spatial quality) PROPERTY
INHERES IN tumor G TOWARDS Functions, substances PRECONDITION Body states observable TIME ASPECT Time aspects SCALE Scale types UNITS units TECHNIQUE techniques DIRECT SITE Body structures, specimens

Values for PROPERTY 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 kind 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

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

Antimicrobial susceptibility test
PROPERTY Resistance/sensitivity INHERES IN Microbial isolate G TOWARDS antimicrobial PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal procedure TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE Numeric, ordinal, nominal TECHNIQUE techniques DIRECT SITE Body structures, specimens METHOD Observation action

Lateralization of observations
Use values attached to SITE or its sub-roles

Potential values that could take a laterality attribute

PROPERTY Properties INHERES IN independent continuant G TOWARDS Functions, substances PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal finding TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE Numeric, ordinal, nominal TECHNIQUE techniques DIRECT SITE Body structures, specimens

PROPERTY Properties INHERES IN independent continuant G TOWARDS Functions, substances PRECONDITION Body states HAS INTERPRETATION Incr, decr, normal, abnormal procedure TIME ASPECT Time aspects SCALE Scale types UNITS units VALUE Numeric, ordinal, nominal TECHNIQUE techniques DIRECT SITE Body structures, specimens METHOD Observation action

IHTSDO Observables Project Group July 23, 2008

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IHTSDO Observables Project Group July 23, 2008

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