SNOMED and “phenotypes” Signs, symptoms, findings, etc Signs, Symptoms and Findings: Steps Toward an Ontology of Clinical Phenotypes Sept 3-4, 2008 Dallas TX

Symptoms & signs Conclusions of the SNOMED RT group (1996): – There is no point attempting to put all observations or findings or manifestations into the mutually-exclusive categories “symptom” and “sign” – But: it is ok to classify and observation by the source of information (subject, observer, carer, etc) when that is explicit, clear, and necessarily so. Pain is not necessarily reported by the patient. Tenderness is not necessarily reported by the clinician.

Findings & disorders Conclusion after (literally) years of attempting to find a clean reproducible boundary: – It is pointless to attempt to pursue a boundary between “findings” and “disorder” – It probably is both possible and useful to differentiate “disease” (as a potentiality), from qualities, the results of observations “Diagnosis” is not the same as disease, and is used as a (variable-across-sites) administrative category

“lab” tests & results A clinical laboratory is an environment in which tests are performed on patient specimens, and which is specifically designed and configured for that purpose Many “lab” observations are moving out of the laboratory and into point-of- care testing environments, e.g. operating room (and an OR is not a lab). – Trend is likely to continue It is not important to (ontologically) categorize observations as being necessarily “lab tests” – And they MUST NOT be categorized as lab tests if they are not necessarily performed in a laboratory setting (otherwise what is a lab test?) A prothrombin time (PT) is NOT a laboratory test (sorry). It may be useful to produce a subset of observations that are “ordinarily thought of in our institution as lab tests”, but being a lab test is not a necessary definitional aspect of the observations.

Terminology vs Information model: Balance, overlaps, gaps Record the fact that “malignant mesothelial cells were found in a pleural fluid aspirate”: Field or questionTerminology value Pleural fluid findingMalignant mesothelial cells Site of malignant mesothelial cells Pleural fluid Lab test resultMalignant mesothelial cells in pleural fluid Type of mesothelial cells in pleural fluid Malignant Type of malignant cells in pleural fluid Mesothelial

Terminology vs Information model: Balance, overlaps, gaps There is no single best way to split assertions between the information model and the terminology model (or between the observables and the other values in the terminology!) The best we can do is recognize equivalence The best tools for recognizing equivalence (by machine) are logic-based Therefore, a logic-based model of semantics is the foundation not just for the terminology but also for the combination

Observations / observables An observation is an act (a procedure) The result of the observation may be a statement about a phenotype or finding An observable: what is it? – Incomplete finding

Observables: examples Head circumference Blood hemoglobin concentration MRSA POC test result Contents of urine on microscopy

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.

Yet another draft model for observables (3) – Differentiate between a property per se and a property type. – Concentration is a property type. – The concentration of sodium in serum is a property. – In the current model, the values of the PROPERTY attribute are property types. – Consider what happens by avoiding the use of “presence” as a property type. (This also presumes avoiding the use of “absence” as a property type.) – Asserting absence requires negation (possibly using the situation model). – Consider a separate pre-coordinated “property” hierarchy as a work-around for the lack of nested expressions in definitions

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

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

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

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

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

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

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

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

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

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

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

What about abilities? Able, unable, etc. with respect to normal functions and activities

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

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

What about negation? Option 1: use different values of HAS INTERPRETATION and deal with opposites outside the model of meaning (not recommended) Option 2: use the situation model

finding PROPERTY Ability TIME ASPECT SCALE Time aspects Scale types VALUE Numeric, ordinal, nominal HAS INTERPRETATION unable Auditory system INHERES IN TOWARDS To hear (function) UNITS units TECHNIQUE techniques G PRECONDITION Body states DIRECT SITE Body structures, specimens Unable to hear (1) OBS TARGET independent continuant

finding PROPERTY Ability TIME ASPECT SCALE Time aspects Scale types VALUE Numeric, ordinal, nominal HAS INTERPRETATION able Auditory system INHERES IN TOWARDS To hear (function) UNITS units TECHNIQUE techniques G PRECONDITION Body states DIRECT SITE Body structures, specimens Unable to hear (2) situation INCLUDES ¬

finding PROPERTY Ability TIME ASPECT SCALE Time aspects Scale types VALUE Numeric, ordinal, nominal HAS INTERPRETATION able Auditory system INHERES IN TOWARDS To hear (function) UNITS units TECHNIQUE techniques G PRECONDITION Body states DIRECT SITE Body structures, specimens able to hear (2) situation INCLUDES

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

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

Technological and scientific foundation Collaborative development (“social computing”) – SNOMED RT and CT were built using collaborative tools and techniques Campbell KE, Cohn SP, Chute CG, Shortliffe EH, Rennels G. Scalable methodologies for distributed development of logic-based convergent medical terminology. Methods Inf Med Nov;37(4-5): – IHTSDO is serious about re-energizing collaborative development Open standards-based technology platform (Open Health Tools) Multilingual workbench RFP Description logic – Semantics is understood and being used and studies by the DL scientific community (DL is called EL +) a number of papers at DL2008 use SNOMED CT as test bed Stated form to be officially part of the release as of July 2008 – A variety of different classifiers (CEL, FaCT++) have been used to verify and validate (e.g. no post-processing, etc)

IHTSDO welcomes participation and collaboration Single world-wide affiliate license, with no charge for research & evaluation – Open publication of the concept model, style guide, technical specifications: – Collaborative web site – open to participation without charge – – to: for free registration Working groups and Committees: all open – Project groups, Special interest groups