SNOMED and “phenotypes”

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

2. 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.

3. 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

4. “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.

5. Terminology vs Information model:Balance, overlaps, gaps • Record the fact that “malignant mesothelial cells were found in a pleural fluid aspirate”:

6. 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

7. 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

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

9. 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

10. 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.

11. Yet another draft model for observables (3) • Differentiate between a propertyper 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

12. 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

13. DRAFT model of observables 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

14. 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

15. 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

16. Blood hemoglobin concentration OBS TARGET independent continuant 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

17. Blood hemoglobin 14.0 gm/dL OBS TARGET independent continuant 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

18. Head circumference OBS TARGET independent continuant 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

19. Head circumference 28 cm OBS TARGET independent continuant 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

20. Serum concentration of Borrelia antibody (observable) OBS TARGET independent continuant 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

21. Measurement of serum Borrelia antibody by ELISA (procedure) OBS TARGET independent continuant 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

22. The information model is used to link this finding to the Culture and specimen that came from the patient. Cultured organism serotype is O157 OBS TARGET independent continuant 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 O157 TECHNIQUE Bacterial serotyping DIRECT SITE Microbial culture

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

24. Ability to hear OBS TARGET independent continuant 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

25. Able to hear OBS TARGET independent continuant 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

26. 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

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

28. Unable to hear (2) situation ¬ INCLUDES 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

29. able to hear (2) situation INCLUDES 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

30. Left knee deep tendon reflex - briskness OBS TARGET independent continuant 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

31. Left knee jerk reflex 2+ OBS TARGET independent continuant 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

32. 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. 1998 Nov;37(4-5):426-39. • 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)

33. IHTSDO welcomes participation and collaboration • Single world-wide affiliate license, with no charge for research & evaluation • http://www.ihtsdo.org/our-standards/licensing/ • Open publication of the concept model, style guide, technical specifications: • http://www.ihtsdo.org/about-ihtsdo/snomed-ct-publications/ • Collaborative web site – open to participation without charge • https://thecap.seework.com/login • Email to: support@ihtsdo.org for free registration • Working groups and Committees: all open • Project groups, Special interest groups