1. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U MEDINFO 2010 A Unified Framework for Biomedical Terminologies and Ontologies September 13, 2010; 15.30 PM - 17.15 PM Cape Town, South Africa Werner CEUSTERS 1 and Barry SMITH 2 1,2 Ontology Research Group, Center of Excellence in Bioinformatics and Life Sciences 1 Department of Psychiatry, University at Buffalo, NY, USA 2 Department of Philosophy, University at Buffalo, NY, USA

2. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U UMLS approach to countering silo formation –By ‘linking between different clinical or biomedical vocabularies’ –However: ‘… the Metathesaurus does not represent a comprehensive NLM-authored ontology of biomedicine or a single consistent view of the world. The Metathesaurus preserves the many views of the world present in its source vocabularies because these different views may be useful for different tasks.’ http://www.nlm.nih.gov/pubs/factsheets/umlsmeta.html

3. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U

4. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Linking of concept-based resources Declaring equivalence (synonymy) between concepts from distinct resources comes down to: –stating that these concepts mean the same thing, –however not what they mean. There is no common underlying ontology: –Trying to decipher what is meant by concept structures from separate resources is hampered by inconsistencies between these resources. Use of an ontology language such as OWL might reveal the inconsistencies, but not resolve them.

5. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U OBO Foundry approach to countering silo formation –a single, expanding family of ontologies designed to be interoperable and logically well-formed and to incorporate accurate representations of biological reality.

6. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U

7. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U OBO Foundry principles Ontologies are admitted into the Foundry only if their developers commit to an evolving set of common principles, including: –terms and s should be built up compositionally out of more basic terms from a small set of robust feeder ontologies; –for each domain there should be convergence upon exactly one Foundry ontology; –all working with same upper-level categories and relations drawn from Basic Formal Ontology (BFO) and OBO Relation Ontology (RO).

8. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Linking concept-based terminologies to OBO Motivations: huge quantities of data have already been annotated or compiled in their terms where Foundry ontologies seek to represent the entities on the side of reality, traditional terminology systems are designed to reflect the ways language is used e.g. by clinicians. this closeness to the needs of clinicians suggests that concept-based systems may still be in common use in the future.

9. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Objective of our work Underlying idea: –both terminology artifacts and ontologies are representations Goal: –subject these artifacts to careful inspection of a sort which can allow representations organized around ‘concepts’ to be mapped to appropriate ontological counterparts.

10. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U OBO Foundry ?

11. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U http://terminology.vetmed.vt.edu/SCT/menu.cfm An example: SNOMED-CT

12. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Synonyms Terms in legacy terminologies are declared as ‘synonyms’ even where they refer – on face value – to entities of different types. Requirement How create adequate mappings of terms and their synonyms to Foundry ontologies?

13. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Key distinctions in our framework 1.between concepts, language and entities in reality 2.between generic and specific portions of reality (PORs) 3.between the various purposes that can be served by s.

14. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 1.There is an external reality which is ‘objectively’ the way it is; 2.That reality is accessible to us; 3.We build in our brains cognitive representations of reality; 4.We use language to communicate with others about what is there, and what we believe is there. Ontological realism Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, Biomedical Ontology in Action, November 8, 2006, Baltimore MD, USA

15. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Realism versus other philosophies Basic questions: –What does a general term such as ‘disorder’ refer to? –Do generic entities exist? yes: in particulars perhaps: in minds no UniversalConcept Group of particulars RealismConceptualismNominalism

16. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Representations First Order Reality (1) Entities with objective existence which are not about anything (2)Clinicians’ beliefs about (1) (3)Linguistic representations about (1), (2) or (3) Three levels of reality in ontological realism

17. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Basic Formal Ontology in a nutshell The world consists of –entities that are Either particulars or universals; Either occurrents or continuants; Either dependent or independent; and, –relationships between these entities of the form e.g. is-instance-of, e.g. is-member-of e.g. isa (is-subtype-of) Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

18. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U BFO / RO / OGMS framework Continuant Occurrent e.g. pathological process Independent Continuant e.g. organism Dependent Continuant e.g. patient role................ universals particulars has_participant inheres_in instance_of is_a

19. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Generic versus specific portions of reality Universal –denoted by ‘human being’ ‘lung’ Generic configuration –denoted by ‘lobe of lung part_of cell’ Particular –denoted by ‘Werner Ceusters’, ‘Werner’s left lung’ Specific configuration –denoted by ‘Obama’s nose part_of Obama’,

20. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Basic mapping principle Problem: terms from concept-based terminologies often denote multiple distinct sorts of portions of reality. Each representational element of each concept- based terminology should be inspected in order to identify, in terms of corresponding representations in Foundry ontologies, what sorts of portions of reality it is able to denote.

21. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U http://terminology.vetmed.vt.edu/SCT/menu.cfm An example from SNOMED-CT

22. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U http://terminology.vetmed.vt.edu/SCT/menu.cfm Fractured nasal bones is_a group of bones Fractured nose is_a nose Fracture of nose is_a fracture An example from SNOMED-CT

23. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Group versus single independent continuant Group –limbs of Mary –Nobel Prize winners single independent continuant –Werner –Earth

24. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Different sorts of groups Bona fide group: –Mary’s limbs, Mary’s cells, Mary’s molecules Fiat group: –left lungs of people currently in Cape Town, –left lungs of all participants in clinical trial #77639. Extension of universal U: –group of instances of U at a given time.

25. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Distinct purposes for definitions P1: to specify the conditions that must be satisfied for a term to be an acceptable designator for a given entity in some given community: –chronic pain =def. a pain that has been present for more than 3 months P2: to specify what is characteristic of particulars that instantiate a certain universal, for instance: –disorder =def. a part of an organism which serves as the bearer of a disposition to pathological processes; P3:to demarcate groups by specifying characteristics that their members must exhibit.

26. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Another example ‘Finger structure’ in SNOMED CT subsumes: –‘entire finger’ (designates a universal under a realist framework) and –‘all fingers’ (a group) (in different contexts can mean: ‘all fingers in the world’, ‘all fingers of a given patient’, ‘all fingers on a given hand’)

27. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U ‘Fractured nasal bones’ Denote different sorts of entities under our framework

28. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The solution (Part I) Treat such ambiguous representations in concept- based terminologies as abbreviations for disjunctions of representations in realism-based ontologies. SCT:fractured nasal bones =def. group of fractured nasal bones OR fractured nose OR fracture of nose.

29. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Parents Fracture of midfacial bones (disorder) Fracture of skull and facial bones (disorder) Injury of nasal bones (disorder) Grandparents Bone injury (disorder) Disorder of nasal bone (disorder) Fracture of face bones (disorder) Fracture of skull (disorder) Injury of nose (disorder) 3rd Generation Disorder of bone (disorder) Disorder of external nose (disorder) Disorder of facial bone (disorder) Disorder of skull (disorder) Disorder of the nose (disorder) Fracture of bone of head (disorder) Injury of connective tissue (disorder) Injury of face (disorder) Injury of musculoskeletal system (disorder) 4th Generation Bone finding (finding) Disorder of bone (disorder) Disorder of connective tissue (disorder) Disorder of face (disorder) Disorder of head (disorder) Disorder of musculoskeletal system (disorder) Disorder of nose AND/OR nasopharynx (disorder) Disorder of skeletal system (disorder) Disorder of the nose (disorder) Fracture of bone (disorder) Injury of anatomical site (disorder) Injury of head (disorder) Musculoskeletal and connective tissue disorder (disorder) Nose finding (finding) Skull finding (finding) Traumatic injury (disorder) 5th Generation Bone finding (finding) Bone injury (disorder) Disorder by body site (disorder) Disorder of body system (disorder) Disorder of connective tissue (disorder) Disorder of face (disorder) Disorder of head (disorder) Disorder of musculoskeletal system (disorder) Disorder of nose AND/OR nasopharynx (disorder) Disorder of skeletal system (disorder) Finding of face (finding) Head and neck injury (disorder) Head finding (finding) Musculoskeletal and connective tissue disorder (disorder) Musculoskeletal finding (finding) Nose finding (finding) Traumatic AND/OR non-traumatic injury (disorder)

30. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Some is_a ancestors of ‘fractured nasal bones’ Fracture of skull and facial bones (disorder) Fracture of skull (disorder) Nose finding (finding) Traumatic AND/OR non-traumatic injury (disorder) Injury of connective tissue (disorder)

31. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Un-‘realistic’ SNOMED hierarchy ‘Fractured nasal bones (disorder)’ –is_a ‘bone finding’ synonym: ‘bone observation’ Confusion between –fractured nose: a type of nose – fractured nose  [in someone’s mind]: content of an act of observation –‘fractured nose’ [appearing in some record]: the expression of an observation

32. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Representations First Order Reality L1. Entities (particular or generic) with objective existence which are not about anything L2. Clinicians’ beliefs about (1) L3. Linguistic representations about (1), (2) or (3) Three levels of reality in Ontological Realism

33. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Un-‘realistic’ SNOMED hierarchy ‘Fractured nasal bones (disorder)’ –is_a ‘bone finding’ synonym: ‘bone observation’ Confusion between L3. L3. ‘fractured nose’ [appearing in some record]: the expression of an observation) L2. fractured nose  [in someone’s mind]: content of an act of observation L1. fractured nose: a type of nose, a particular nose

34. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Future proofing SNOMED data No biomedically useful inferences can be drawn from any assertion about Xs, if ‘X’ can refer either to some linguistic string, or to some mental act, or to some mental state, or to some type of nose.

35. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The solution (Part II) Distinguish between contexts where ‘Fractured nasal bones (disorder)’ means: Those fractured bones, whether or not observed (L1) Observational processes relating thereto (L1) Hypotheses and beliefs resulting from such observations (L2) Corresponding statements (L3). and repeat as necessary for all other SNOMED CT expressions.