Post on 18-Jan-2016
description
SNOMED and “phenotypes”Signs, symptoms, findings, etc
Signs, Symptoms and Findings: Steps Toward an Ontology of Clinical Phenotypes
Sept 3-4, 2008Dallas 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 question Terminology value
Pleural fluid finding Malignant mesothelial cells
Site of malignant mesothelial cells
Pleural fluid
Lab test result Malignant 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 ASPECTSCALE
Time aspects
Scale types
DRAFT model of observables
independent continuantINHERES IN
TOWARDS Functions, substances
UNITS units
TECHNIQUE techniques
GPRECONDITION Body states
DIRECT SITE Body structures, specimens
observable
PROPERTY Properties
TIME ASPECTSCALE
Time aspects
Scale types
DRAFT model of observables
independent continuantINHERES IN
TOWARDS Functions, substances
UNITS units
TECHNIQUE techniques
GPRECONDITION Body states
DIRECT SITE Body structures, specimens
IFCC-IUPAC NPU elementsLOINC elements
Kind-of-property property
System/specimen system
component component
Time aspect
scale
units
method method
System/specimen
component
observable
PROPERTY Substance concentration
TIME ASPECTSCALE
Single point in time
quantitative
LOINC Example:Sodium:SCnc:PT:Ser/Plas:Qn
PlasmaINHERES IN
TOWARDS Sodium ion
UNITS units
TECHNIQUE techniques
GPRECONDITION Body states
DIRECT SITE Serum/Plasma
Kind-of-property
component
Time aspect
scale
System/specimen
observable
PROPERTY Substance concentration
TIME ASPECTSCALE
Single point in time
quantitative
IFCC-IUPAC NPU Example:P—Sodium ion; subst.c. = ? mmol/l
PlasmaINHERES IN
TOWARDS Sodium ion
UNITS mmol/l
TECHNIQUE techniques
GPRECONDITION Body states
DIRECT SITE Body structures, specimens
property
system
component
units
observable
PROPERTY concentration
TIME ASPECTSCALE
Time aspects
Scale types
Blood hemoglobin concentration
Intravascular bloodINHERES IN
TOWARDS hemoglobin
UNITS units
TECHNIQUE techniques
GPRECONDITION Body states
DIRECT SITE Body structures, specimens
OBS TARGET independent continuant
finding
PROPERTY Mass concentration
TIME ASPECTSCALE
Single point in time
quantitative
VALUE 14
HAS INTERPRETATION Incr, decr, normal, abnormal
Blood hemoglobin 14.0 gm/dL
Intravascular bloodINHERES IN
TOWARDS hemoglobin
UNITS gm/dL
TECHNIQUE techniques
GPRECONDITION Body states
DIRECT SITE Body structures, specimens
OBS TARGET independent continuant
observable
PROPERTY circumference
TIME ASPECTSCALE
Time aspects
Scale types
Surface of headINHERES IN
TOWARDS Functions, substances
UNITS units
TECHNIQUE techniques
GPRECONDITION Body states
DIRECT SITE Body structures, specimens
Head circumference
OBS TARGET independent continuant
finding
PROPERTY circumference
TIME ASPECTSCALE
Time aspects
Scale types
VALUE 28
HAS INTERPRETATION Incr, decr, normal, abnormal
Surface of headINHERES IN
TOWARDS Functions, substances
UNITS cm
TECHNIQUE techniques
GPRECONDITION Body states
DIRECT SITE Body structures, specimens
Head circumference 28 cm
OBS TARGET independent continuant
observable
PROPERTY concentration
TIME ASPECTSCALE
Time aspects
Scale types
Serum concentration of Borrelia antibody (observable)
plasmaINHERES IN
TOWARDS Borrelia antibody (substance)
UNITS units
TECHNIQUE Light microscopy
GPRECONDITION Body states
DIRECT SITE Serum specimen
OBS TARGET independent continuant
procedure
PROPERTY concentration
TIME ASPECTSCALE
Time aspects
Scale types
VALUE Numeric, ordinal, nominal
HAS INTERPRETATION Incr, decr, normal, abnormal
Measurement of serum Borrelia antibody by ELISA(procedure)
plasmaINHERES IN
TOWARDS Borrelia antibody (substance)
UNITS units
TECHNIQUE ELISA
GPRECONDITION Body states
DIRECT SITE serum specimen
METHOD Observation action
OBS TARGET independent continuant
finding
PROPERTY serotype
TIME ASPECTSCALE
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
GPRECONDITION 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 ASPECTSCALE
Time aspects
Scale types
Auditory systemINHERES IN
TOWARDS To hear (function)
UNITS units
TECHNIQUE techniques
GPRECONDITION Body states
DIRECT SITE Body structures, specimens
Ability to hear
OBS TARGET independent continuant
finding
PROPERTY Ability
TIME ASPECTSCALE
Time aspects
Scale types
VALUE Numeric, ordinal, nominal
HAS INTERPRETATION able
Auditory systemINHERES IN
TOWARDS To hear (function)
UNITS units
TECHNIQUE techniques
GPRECONDITION 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 ASPECTSCALE
Time aspects
Scale types
VALUE Numeric, ordinal, nominal
HAS INTERPRETATION unable
Auditory systemINHERES IN
TOWARDS To hear (function)
UNITS units
TECHNIQUE techniques
GPRECONDITION Body states
DIRECT SITE Body structures, specimens
Unable to hear (1)
OBS TARGET independent continuant
finding
PROPERTY Ability
TIME ASPECTSCALE
Time aspects
Scale types
VALUE Numeric, ordinal, nominal
HAS INTERPRETATION able
Auditory systemINHERES IN
TOWARDS To hear (function)
UNITS units
TECHNIQUE techniques
GPRECONDITION Body states
DIRECT SITE Body structures, specimens
Unable to hear (2)
situation INCLUDES¬
finding
PROPERTY Ability
TIME ASPECTSCALE
Time aspects
Scale types
VALUE Numeric, ordinal, nominal
HAS INTERPRETATION able
Auditory systemINHERES IN
TOWARDS To hear (function)
UNITS units
TECHNIQUE techniques
GPRECONDITION Body states
DIRECT SITE Body structures, specimens
able to hear (2)
situation INCLUDES
observable
PROPERTY Briskness of response
TIME ASPECTSCALE
Time aspects
Scale types
Neuromuscular structures of the left knee deep tendon reflexINHERES IN
TOWARDS Deep tendon reflex
UNITS units
TECHNIQUE techniques
GPRECONDITION Body states
DIRECT SITE Body structures, specimens
Left knee deep tendon reflex - briskness
OBS TARGET independent continuant
finding
PROPERTY Briskness of response
TIME ASPECTSCALE
Time aspects
Scale types
VALUE 2+ out of 4+
HAS INTERPRETATION Incr, decr, normal, abnormal
Neuromusc. Struc. L knee DTRINHERES IN
TOWARDS Deep tendon reflex
UNITS units
TECHNIQUE techniques
GPRECONDITION 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. 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)
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