1. 102.10.2006Gergely Héja - SMCS2006 Copyright Notice Usage of semanticHEALTH public presentations Each slide is copied 1 exactly as it is presented by the speaker. This means with the same colors and backgrounds, and including all headers and footers. It is not allowed to add any items including your styles and logos without written permission of the author(s). Your presentation should acknowledge the author(s) of the semanticHEALTH public presentation You are encouraged to use slides from this collection for your presentations on the condition that:

2. 02.10.2006 Gergely Héja - SMCS2006 2 Ontological analysis of SNOMED CT Gergely Héja MSc., György Surján MD., Péter Varga MSc. National Institute for Strategic Health Research, Budapest, Hungary

3. 302.10.2006Gergely Héja - SMCS2006 Aims ESKI needs a reference terminology To represent of classification systems (ICD, ICPM) and public health indicators To represent of classification systems (ICD, ICPM) and public health indicators To provide pre co-ordinated code lists for enabling semantic interoperability in Hungary (and potentially in the EU) To provide pre co-ordinated code lists for enabling semantic interoperability in Hungary (and potentially in the EU) SNOMED CT seems to be a first choice candidate

4. 402.10.2006Gergely Héja - SMCS2006 Needs for classification systems Combinatory representation of categories based on a reference ontology to enable supporting statistical analysis supporting statistical analysis formal consistency checking formal consistency checking (semi)automatic interconnection of different classification systems (e.g. ICD and ICPM) (semi)automatic interconnection of different classification systems (e.g. ICD and ICPM) A high-quality formal ontology is needed, but it needs not to be very detailed

5. 502.10.2006Gergely Héja - SMCS2006 Needs for interoperability Detailed common terminology covering the whole domain of medicine Mapping the concepts of the HIS to the concepts of the common terminology and vice versa A common, consistent, comprehensive and decidable ontology is needed

6. 602.10.2006Gergely Héja - SMCS2006 Computational issues Computability vs. comprehensiveness Clean hierarchies Less emphasis on coverage (the multitude of non-defined leaf categories) and greater emphasis on rich and well-organized high- level categories is needed SNOMED CT contains too much concepts

7. 702.10.2006Gergely Héja - SMCS2006 Methods Based on DOLCE formal top-level ontology Review of high and low-level concepts needed for the representation of classification systems and public health indicators Is the subsumption relation valid? Is the subsumption relation valid? Meaning derived from the FSN vs. meaning derived from synonyms vs. meaning derived from formal definition Meaning derived from the FSN vs. meaning derived from synonyms vs. meaning derived from formal definition

8. 802.10.2006Gergely Héja - SMCS2006 Error types - 1  Misplacing concepts in the hierarchy  smoker (an agent) is subsumed by tobacco smoking behaviour – finding (a role)  severe asthma is not a kind of asthma, but a kind of asthma finding.  Mixing the subsumption relation with other roles (typically part of)  haemoglobin subsumes haemin (instead of constitutional part)  exacerbation of asthma attack is subsumed by asthma (instead of temporal part)

9. 902.10.2006Gergely Héja - SMCS2006 Error types - 2  Hierarchy violating medical thinking and biomedical knowledge  Disease, observation and finding are subsumed by clinical finding  acute on chronic, which is both subsumed by acute and chronic  polycarbonate is a polymer (instead of synthetic polymer)

10. 1002.10.2006Gergely Héja - SMCS2006 Error types - 3  Contracting disjoint entities into one concept  Smoker (an agent) and smoker (finding) (a description of a situation)  additional pathologic finding in tumor specimen (observable entity) and additional pathologic finding  Function is classified as an observable entity Ontological definition: ability of an object to play a certain role in a certain kind of activity functions (e.g. gene function, adaptation) measures (quality) that evaluate the realisation of a function (e.g. respiratory rhythm, excretory rate)  Inflammation (morphological abnormality) (a physical object) and inflammatory reaction (perdurant)

11. 1102.10.2006Gergely Héja - SMCS2006 Additional problems - 1 Categories taken form classification systems pneumonia in other diseases classified elsewhere (marked as “ConceptStatus Limited”) pneumonia in other diseases classified elsewhere (marked as “ConceptStatus Limited”) The danger of taking over concepts from other conceptual systems: the context of the concept is lost. What is meant by “other diseases classified elsewhere”? The danger of taking over concepts from other conceptual systems: the context of the concept is lost. What is meant by “other diseases classified elsewhere”? relations (such as part of) are represented also as concepts It prohibits the direct conversion to any formalism based on first order logic, thus to any DL formalism It prohibits the direct conversion to any formalism based on first order logic, thus to any DL formalism

12. 1202.10.2006Gergely Héja - SMCS2006 Additional problems - 2 Underspecification: roles are not quantified (existential / universal) roles are not quantified (existential / universal) criteria are not specified (necessary / sufficient) criteria are not specified (necessary / sufficient) conversion to DL: do we have to decide in each particular case, or can it be done universally? conversion to DL: do we have to decide in each particular case, or can it be done universally? Multiple hierarchy alcoholic beverage (through its parent ingestible alcohol) is subsumed by central depressant, ethyl alcohol and psychoactive substance of abuse – non-pharmaceutical. Alcoholic drinks contain ethyl alcohol, which plays a role of depressant and substance of abuse (with respect to human beings) alcoholic beverage (through its parent ingestible alcohol) is subsumed by central depressant, ethyl alcohol and psychoactive substance of abuse – non-pharmaceutical. Alcoholic drinks contain ethyl alcohol, which plays a role of depressant and substance of abuse (with respect to human beings) Is this a general phenomenon in SNOMED? Is this a general phenomenon in SNOMED? Which relations are asserted and which are inferred? Which relations are asserted and which are inferred?

13. 1302.10.2006Gergely Héja - SMCS2006 Discussion - 1 The intended meaning of the categories is not always clear: possible translation errors Is it reasonable to import categories from medical classifications? Size Size Artificial concepts Artificial concepts Consistency errors Consistency errors

14. 1402.10.2006Gergely Héja - SMCS2006 Discussion - 2 Real world entities listed heterogeneously Mars bar and Kit Kat (chocolate candy would suffice) Mars bar and Kit Kat (chocolate candy would suffice) UFO is subsumed by transport vehicle UFO is subsumed by transport vehicle tendon pulley reconstruction is represented, but tendon pulley not tendon pulley reconstruction is represented, but tendon pulley not

15. 1502.10.2006Gergely Héja - SMCS2006Solutions  Use SNOMED as a plain or loosely structured list of terms (with extending the coverage). Not appropriate for intelligent services.  Restructure SNOMED into a high-quality ontology.  Build a new medical ontology from scratch (partial reuse of the existing ones), and to restrict the use of SNOMED for interoperability by mapping concepts to it.

16. 1602.10.2006Gergely Héja - SMCS2006 Restructuring SNOMED A formal top level ontology (e.g. DOLCE). A high level core reference ontology of general medical knowledge (e.g. anatomy, physiology, pathology, medical procedures). Logic-based formalism Logic-based formalism Single hierarchies with formal definitions Single hierarchies with formal definitions (sub)domain ontologies of specialities Compound entities (e.g. tonsillitis) Compound entities (e.g. tonsillitis) Manual assertion (e.g. autism) Manual assertion (e.g. autism)

17. 02.10.2006 Gergely Héja - SMCS2006 17 Questions?