Formal Ontology for the improvement and integration of biomedical terminologies J. Simon*

1. Formal Ontology for the improvement and integration of biomedical terminologies J. Simon* Ontology-based algorithms for error checking and semantic relationships expansion M. Casella dos Santos** AMIA 2003 *Institute for Formal Ontology and Medical Information Science (IFOMIS), Leipzig, Germany ** Language & Computing nv, Zonnegem, Belgium

2. PRESENTATION OVERVIEW • Introducing LinKBase • Introducing BFO; The Philosophical Ground • Ontology integration problems and solutions • Applying correct subsumption • Axiomatizing LinKBase with BFO • Conclusion

3. An Integrated Approach L L L & & & C C C NLU enabling tools for knowledge supported data-entry and -retrieval Linguistic application components Medical and linguistic knowledge required for language understanding LinKBase Data structure and function library for language understanding LinKFactory

4. LinKBase A Medical Domain Ontology designed to support NLP applications and to integrate different medical terminologies and ontologies. • Enables cross-mappings between external medical terminologies • (i.e. ICD-9-CM, ICD-10, SNOMED, Mesh, MedDRA, etc.). • The world’s largest medical ontology totalling more than 2,000,000 • concepts and 5,300,000 links. • The ontological elements (concepts, linktypes, criteria) are language • independent and are linked to about 3,500,000 terms in various • languages (English, Spanish, French, etc.).

5. Language A Proprietary Terminologies L & C LanguageB Lexicon Lexicon Others ... Grammar ICPC Grammar SNOMED ICD Medico-linguistic Ontology Formal Domain Ontology Cassandra Linguistic Ontology MEDDRA LinKBase

7. Language A Proprietary Terminologies L & C LanguageB Lexicon Lexicon Others ... Grammar ICPC Grammar SNOMED ICD Medico-linguistic Ontology Formal Domain Ontology Cassandra Linguistic Ontology MEDDRA LinKBase

9. BFO/MedO and LinkBase BFO/MedO “validates”

10. Theory of Granular Partitions (B. Smith) Think of it as Alberti’s grid

11. Partitions • An ontology is a partition of reality • A partition cuts the world in a certain way • There can be many different partitions of the same reality

12. Maryland Congressional Representative Voting Zones

13. Maryland Appellate Judicial Districts

17. A Partition View on Meningitis meninges anatomical partition disorder of meninges disorder partition inflammation of CNS inflammation partition meningitis

18. Partitions and LinkBase® • domain-entity: represents cells of different partitions of reality • MENINGITIS (captured e.g. by the inflammation partition) • MENINGES (captured by an anatomical map) • meta-entity: represents cells of a partition prepared by third parties • ICD-10 : G03.9 : MENINGITIS, UNSPECIFIED • domain-entity-link: aspect of domain-entities determining a partition/perspective • HAS-SYSTEMIC-MEDIUM • HAS-CONSEQUENCE • criterion: perspective on a domain-entity yielded by a given partition • HAS-SYSTEMIC-MEDIUM MENINGES • HAS-CONSEQUENCE HEADACHE

19. Substances, States, Powers and Functions • Strict Dependence: ODP(A,B) • A strictly depends on B whenever A cannot exist unless B does • John’s headache depends on John • Mary’s smile depends on Mary • Peter’s power of performing weddings depends on Peter • The beating function of Sarah’s heart depends on Sarah’s heart

20. Generic Dependence • Generic Dependence: • A generically depends on Bs whenever A cannot exist without there being some B • A person cannot exist without having some temperature

21. Weak Foundation • Weak Foundation: WF(A,B) • A is weakly founded on B whenever A strictly depends on B and all parts of B

22. Substances • A Substance is an entity which is not strictly dependent on anything • SB(x) • SB(x) iff • y (x strictly depends on y)

23. States, Powers and Functions • States (the state of being happy, having a headache, having a temperature of 98.6°) • Powers (The power to wed people) • Functions (the function of pumping blood) • These are not substances; they have bearers on whom they strictly depend

24. Inherence • States, Powers and Functions inhere on the substances that bear them • IH(x,y) • Thus, • Inhere(x,y)  StrictlyDepends(x,y)

25. Endurants and Perdurants • Some things persist differently through time than others • There are on the one hand objects: tables, chairs, countries, and people. These entities are said to endure through time, which means that they do not have temporal parts, but rather are wholly present at every moment in which they exist.

26. Endurants and Perdurants • On the other hand are processes like brain surgeries, heart attacks, lives. These are said to perdure through time, which means that they do have temporal parts, such as the first half of the surgery, the last phase of the heart attack, one’s childhood

27. Endurants and Perdurants • We call enduring, objectual entities “Endurants”: End(x) • We call perduring, processual entities “perdurants”: Perd(x) • No endurant is a perdurant, and no perdurant is an endurant

28. Endurants and Perdurants • Endurants and perdurants relate in the relationships of participation and realization • Perdurants strictly depend on endurants

29. Participation • The surgeon operates, the heart beats, lungs inhale • PP(x,y) • PP(surgeon, surgery) • PP(heart,beating processes) • PP(lungs, respiratory processes)

30. Realization • Powers and Functions may go unrealized • A stopped heart is not realizing its function of pumping blood • The heart of a tachycardic is not fulfilling the function of beating at a proper rate • Peter may not currently be realizing his power of wedding couples

31. Participation and Realization • Participation is generally a relation between a substance and a process which depends on it (it would not have been the same particular surgery if Dr. Jones had not been there) • Realization is a relation between a power or function and a process

32. Functions and Processes • No function is the same as a process realizing it • No process is the same as any endurant participating in it

33. Parts and Wholes • Proper Parthood:  • x  x • x  y   y  x • x  y & y  z  x  z • Parthood:  • x  y iff x  y or x = y

34. Parthood A A < B B

35. SNAP BFO

36. SPAN BFO

37. Terminology Integration in LinKBase The Endurant/Perdurant Distinction at Work

38. Homonymy!

40. Terminology Integration in LinKBase Mereological Scrutiny at Work

42. Terminology Integration in LinKBase The Function/Realization Distinction at Work

43. Functions and Processes IS-ACTOR-OF (HAS-FUNCTION) LIVER LIVER ACTIVITY IS-A IS-ACTOR-OF ABERRANT LIVER

44. Functions and Processes LIVER FUNCTION IS-REALIZATION-OF HAS-FUNCTION HAS-ACTOR LIVER LIVER ACTIVITY IS-A ABERRANT LIVER

45. LIVER HAS-FUNCTION LIVER FUNCTION

46. The Need for a Systematic Top-Level • While LinkBase currently features certain reasoning capabilities, it lacks the sort of coherent underlying structure necessary for advanced reasoning applications • A more systematic top-level is needed

47. What Does LinKBase Say About the World ? • if a real-world entity is an instance of a domain-entity, all that is said about the domain-entity applies to the instance; • the statement “A-Link-B” says something about all instances of A, but nothing about instances of B unless the Link is declared to have an inverse;

48. The BFO Top-Level Standard • To each concept and link there is already a space for definitions and characterization, but this is specified informally, – it is not relevant to current applications, and there are no standards governing definitions of links or concepts • This means there is no systematic uniformity to how we understand them, and consequently their information content is much lower than it could be

49. The BFO Top-Level Standard • Define a standard protocol for definitions of concepts and links (ideally in some formal language with as concise a set of predicates as possible). • This is a repair-the-ship-at-sea kind of project: It may be necessary to revise the links, as well as to try and be creative enough to find a logical form common to all of them

50. The BFO Top-Level Standard • An extra level of structure and coherent information will allow for the automation of processes currently run by hand • Preliminary work already enables L&C to infer flaws in their taxonomy: links that unite categories and are missing, existing links that are misclassified