AMIA Workshop WP06 Ontological Foundations of Biomedical Terminology Systems Organized by AMIA WG Formal (Bio)Medical Knowledge Representation Washington, DC, 10/22/2005

History 2002: Ronald Cornet / Stefan Schulz: Idea of foundation of a SIG on Ontologies / Knowledge Representation 2003: SIG “Formal (Bio)Medical Knowledge Representation. Approval by AMIA, Kick-Off Meeting at AMIA 2003. KR-SIG Mailing List 2004: KR-MED 2004 in Whistler (Canada) Panel at MEDINFO Upgrade SIG -> WG 2005: Intensive e-mail discussions on basic notions of terminology / ontology building, draft of a AMIA paper “Six questions on ontology building” (not accepted) AMIA Workshop submission. Purpose of workshop: To stimulate and intensify the discussion on formal and philosophical foundations of biomedical ontologies. Plan for 2006: Write a WG position paper -> JAMIA Tuesday 5:15 p.m. Business meeting of the WG: Thoroughbred room, Concourse level.

Workshop WP06 Ontological Foundations of Biomedical Terminology Systems Topic Presenter Duration (min) Introduction Stefan Schulz 5 1. Resolving ambiguities in current uses of the term "concept" Barry Smith 15 + 5 (Q&A) 2. Do divergences in philosophical thinking (Realism, Conceptualism, Nominalism) have implications the concrete tasks of ontology engineering in the biomedical domain? Stefan Schulz 15 + 5 (Q&A) 3. Should the term 'ontology' be used in a broad sense which does not exclude any of those artifacts commonly referred to as 'biomedical vocabularies' in the medical informatics community? Ronald Cornet 15 + 5 (Q&A) 4. Discussion on the basis of the three talks Led by Ira Kalet 10 Break 5 5. How can ontologies, which deal with relations between universals, be made interoperable with the electronic health data, which deal with instances of such universals? tbd. 15 + 5 (Q&A) 6. Facilitation of ontology creation by human curators using statistical and lexical approaches Olivier Bodenreider 15 + 5 (Q&A) 7. Difference between pre and post-coordinated ontologies and its implications on single and multiple inheritance. Should the design of formal ontologies be guided by concrete recommendations, e.g., single inheritance, avoidance of negative classes, pairwise disjoint siblings, jointly exhaustive siblings? Anand Kumar 15 + 5 (Q&A) Wrap-up Ronald Cornet 10

Realism, Conceptualism, Nominalism and their Impact on Biomedical Terminologies / Ontologies

Stefan Schulz Martin Boeker Freiburg University Hospital (Germany) Realism, Conceptualism, Nominalism and their Impact on Biomedical Terminologies / Ontologies as naïvely understood by non-philosophers… Stefan Schulz Martin Boeker Freiburg University Hospital (Germany)

What do the nodes in biomedical terminology systems stand for? types names sets universals sorts categories descriptors entities synsets Biomedical Terminology construction and maintenance is one of the most prominent fields in Medical Informatics and has a major impact on medical documentation and health services management. However, there is a range of seemingly disparate views represented by experts in the field. A symptomatic example for this is the difficulty to find not only commonly agreed words but even commonly agreed notions for what the nodes in biomedical terminology systems stand for. The assortment of names is impressive. Each of these names reflects different traditions and ways of thinking about closely related, albeit not equivalent notions. classes terms properties descriptors concepts

Terminological Confusion Different scientific traditions (Logics, Computer Science, Library and Information Science, Cognitive Science, Linguistics,…) Different philosophical schools of thinking: (Platonism, Aristotelian Realism, Conceptualism, Relativism, Idealism, Postmodernism, Constructivism, Nominalism, Tropism,…) Is there a common ground which suits the needs of Biomedical terminology / ontology construction ? The terminological confusion is due to different scientific traditions and different schools of philosophical thinking. Our question is whether there is a common ground which suits the needs of Biomedical terminology / ontology construction.

Mind Independent Reality I here try to sketch a framework of the different schools of thinking which have a long tradition among philosophers but are only vaguely rooted in the minds of most other people. The common ground I propose is that there exists a mind independent reality of individual objects. Without this understanding, it would be difficult perform research. Even who casts doubts on such a reality, commonly takes it as a handy working hypothesis in order to interact with it and to communicate about it. The recent controversy in Medical Informatics about the best philosophical approach to the “nodes” in terminological systems is due to different schools of thinking which have a long tradition among philosophers but are only vaguely rooted in the mind of most other people. As long as there is no or little awareness of these distinctions, the authors of biomedical terminologies and classification systems often base their systems on implicit and subconscious assumptions and end up with promiscuous systems. If they were trained in philosophical ontology (what cannot be expected on a broad scale) they would certainly streamline their thinking along one of the traded lines and, as a consequence, they rarely would reach an agreement. Since the rationale of medical terminology is to attain semantic interoperability between humans and machine agents, we have to identify the common ground. One common ground is the acceptance of a mind independent reality. Without this understanding, it would be difficult to be a researcher. Even who has doubts about such a reality, commonly takes it as a handy working hypothesis in order to interact with it and to communicate about it. Once we accept such a reality we Mind Independent Reality Individual Entities (Instances, Particulars)

Mind Independent Reality Schools of Thinking Realist Realist Conceptualist Nominalist Universals Universals Concepts Names Categories There are three main schools of philosophical thinking all of which have a certain influence on the practice of biomedical terminologies. Firstly, Realism postulates that there exist universal properties, as a kind of templates of reality. These properties exist independently of human cognition. As intelligent beings we can investigate these properties as instantiated in particular objects. For example, the universal human being is instantiated by every human, the universal “chair” is instantiated by every chair and so on. Mind Independent Reality Individual Entities (Instances, Particulars)

Mind Independent Reality Schools of Thinking Realist Realist Conceptualist Conceptualist Nominalist Universals Universals Concepts Concepts Names Categories An alternative view, called conceptualism propagates that general or universal entities are concepts, i.e. entities of human cognition. At least the more prominent proponents of this theory however, accept the existence of mind independent individual entities. However they insist that the principles of structuring these entities cannot be detached from cognition. Mind Independent Reality Individual Entities (Instances, Particulars)

Realist Conceptualist Nominalist Universals Concepts Names Schools of Thinking Realist Conceptualist Nominalist Universals Concepts Names Categories trilateral rectangle square circle triangle square circle Reference to Reality Finally, nominalists, deny that there are universals beyond linguistic predicates. Mind Independent Reality Individual Entities (Instances, Particulars)

Ordering / Organizing Reality Two approaches: Delimitation of individual entities: identifying aggregation as mereological sums of atomic individuals Classification: ordering individuals: assignment to classes What’s the implication of these different schools for the two major task for terminologists, namely first, the need to delimit individual entities, it means to determine the boundaries of entities, e.g. the boundary of brain regions or the boundary of the liver. and secondly the classification of entities. Individual Entities (Instances, Particulars)

Delimitation of Individual Entities Problem: which chunks of matter / sum of atoms are considered valid composite entities? Realist: composition / delimitation of individual entities as pattern of being Conceptualist / nominalist: composition / delimitation of individual entities as result of human cognition or decision (“fiat”) Individual Entitity

Delimitation of Individual Entities Problem: which chunks of matter / sum of atoms are considered valid composite entities? Realist: composition / delimitation of individual entities as pattern of being Conceptualist / nominalist: composition / delimitation of individual entities as result of human cognition or decision (“fiat”) Individual Entitity

Delimitation of Individual Entities Problem: which chunks of matter / sum of atoms are considered valid composite entities? Realist: composition / delimitation of individual entities as pattern of being Conceptualist / nominalist: composition / delimitation of individual entities as result of human cognition or decision (“fiat”) Individual Entitity

Delimitation of Individual Entities Problem: which chunks of matter / sum of atoms are considered valid composite entities? Realist: composition / delimitation of individual entities as pattern of being Conceptualist / nominalist: composition / delimitation of individual entities as result of human cognition or decision (“fiat”) Individual Entitity

Delimitation of Classes Problem: which individual entities belong to the same class? Realist: class membership as invariant pattern of being (instantiation of universals) Conceptualist: class membership as extension of a concept due to perceived similarities Nominalist: given name as criterion for class membership (strict N.: denial of classes)

Delimitation of Classes Problem: which individual entities belong to the same class? Realist: class membership as invariant pattern of being (instantiation of universals) Conceptualist: class membership as extension of a concept due to perceived similarities Nominalist: given name as criterion for class membership (strict N.: denial of classes)

Delimitation of Classes Problem: which individual entities belong to the same class? Realist: class membership as invariant pattern of being (instantiation of universals) Conceptualist: class membership as extension of a concept due to perceived similarities Nominalist: given name as criterion for class membership (strict N.: denial of classes)

Theoretical Upper Bound of number of individuals and classes n atoms in reality: m = 2n -1 possible entities (arbitrary aggregations), candidates for individuals / particulars entities: 2m -1 = 2 -1 different classes: possible extensions of universals, concepts, or names 2n -1 99,9999999999..% of these individuals and classes are completely irrelevant

Which classes are relevant… … and correspond to the extension of universals, concepts or names ?

Realist Conceptualist Nominalist Universals Concepts Names Schools of Thinking Realist Conceptualist Nominalist Universals Concepts Names Categories trilateral rectangle square circle triangle square circle Reference to Reality 2 objects {} a b ab 3 objects {} a b c ab bc ac abc 4 objects {} a b c d ab ac ad bc bd cd abc abd acd bcd abcd n atoms in reality: 2^n -1 possible composite entities m entities: 2^m -1 different classes Classes: Mind Independent Reality Individual Entities (Instances, Particulars)

Realism: Classes as extensions of Universals: All universals refer to non-empty (at some moment ) classes New classes can be created by common set theoretical operations, e.g. disjunction, negation, complement. Many of those classes do not correspond to a universal, e.g. “invertebrate”, “wound infection NEC”, … but such classes are nevertheless useful, e.g. in order to guarantee disjoint clinical classifications

Conceptualism: Classes as extensions of Concepts: Unlike universals, concepts do not necessarily imply the extension to classes in reality (“retinal transplant”, “yin deficiency”, “missing digit”, “prevented pregnancy”) Concepts as entities of thought may mix ontological and epistemological aspects: “Cirrhosis of liver without mention of alcohol” Concepts as mind constructs may be oriented to prototypes, their extension exhibits large inter-individual variation (deviation from prototype)

Nominalism: Classes as extensions of natural language expressions Classes are built in an ad hoc fashion from linguistic predicates. Examples: People in Room Monroe West at 8pm on October 22, 2005 “Extraction of Foreign Body from Stomach by Incision”

Universals and Continua The realist approach is most striking when applied to individuals which show crisp “bona fide” distinctions and which are easy to classify, especially atoms and molecules It runs into problems where the properties individuals exhibit lie on a continuum, which is the case with many biological objects. property “epithelial” property “neural” neural cell epithelial cell

Universals and Continua The realist approach is most striking when applied to individuals which show crisp “bona fide” distinctions and which are easy to classify, especially atoms and molecules It runs into problems where the properties individuals exhibit lie on a continuum, which is the case with many biological objects. Universal A Universal B Universal C neural cell epithelial cell

Universals and Continua The realist approach is most striking when applied to individuals which show crisp “bona fide” distinctions and which are easy to classify, especially atoms and molecules It runs into problems where the properties individuals exhibit lie on a continuum, which is the case with many biological objects. Universal V Universal W Universal X Universal Y Universal Z neural cell epithelial cell

Conclusions Most terminology builders and users have a implicitly promiscuous attitude towards philosophical categories Impossible to reach agreement on overly purist approaches There may be reasons for hybrid use of universals, concepts, and names in biomedical terminologies Talking about “classes of individuals” may be the best common denominator which allow bridging between different standpoints. Nevertheless, awareness of philosophical / logical background should be raised among terminology builders and users

Nominalism: Classes as extensions of natural language expressions Classes are built in an ad hoc fashion from linguistic predicates. Example: “Extraction of Foreign Body from Stomach by Incision” RemovalOfForeignBodyFromDigestiveSystem AND RemovalOfForeignBodyFromStomach AND IncisionOfStomach AND  has-part.( Method.RemovalAction AND  DirectMorphology.ForeignBody) AND  has-part.( Method.IncisionAction AND  ProcedureSite.stomachStructure)