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Scalable representations of diseases in biomedical ontologies

Scalable representations of diseases in biomedical ontologies. Stefan Schulz, Djamila Raufie, Martin Boeker Institute of Medical Biometry und Medical Informatics University Medical Center Freiburg. Ontological Nature of Disease. Hucklenbroich 2007: diseases are processes, events, or states

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Scalable representations of diseases in biomedical ontologies

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  1. Scalable representations of diseases in biomedical ontologies Stefan Schulz, Djamila Raufie, Martin Boeker Institute of Medical Biometry und Medical Informatics University Medical Center Freiburg

  2. Ontological Nature of Disease • Hucklenbroich 2007: diseases are processes, events, or states • Williams 2007: diseases are dispositional entities • Scheuermann, Smith 2009: (i) diseases are dispositions, (ii) disorders are abnormal bodily components, and the (iii) manifestation of diseases are pathological processes • SNOMED CT: Diseases under “Disorder”, “Finding”, “Event”, (rearrangement currently being discussed in the IHTSDO Event, condition, episode PG)

  3. Diseases, disorders, pathological processes in disjoint BFO categories acknowledgements: Ed Cheetham

  4. Two Major Problems • Being pathological is rather a result of interpretation than a categorial property • Example: bleeding, pain, depression • Ontologically motivated distinctions between disease, disorder, pathological process no not match the current meaning of words like “disease”, “disorder”, “abnormality” etc.

  5. Disease matrix Discrete and disjoint ontological categories structure disposition process pathological Fracture Fracture Geneticdisease Allergicreaction Bleeding Allergy Gradingof canonicity Alopecia Geneticdispo-sition normal

  6. Disease matrix Discrete and disjoint ontological categories structure disposition process pathological Fracture Fracture Geneticdisease Allergicreaction Bleeding Allergy Gradingof canonicity Alopecia Geneticdispo-sition normal

  7. Redefinition: avoiding ambiguous terms like disease, disorder • Disorder Pathological Structure: a combination of bodily components of or in an organism • that is not part of the life plan for an organism of the relevant type (thus aging or pregnancy are not clinically abnormal), • that is causally linked to an elevated risk of pain or other feelings of illness or of death or dysfunction on the part of the organism, and • that it is such that this elevated risk exceeds a certain threshold level. • Disease Pathological Disposition: disposition • to undergo pathological processes that • exists in an organism because of one or more pathological structures in that organism. • Pathological Process: bodily process that is a manifestation of a pathological disposition. according to Scheuermann & Smith, 2009

  8. Formalization of Scheuermann & Smiths definitions PathologicalDisposition ⊑ ∃ inheresIn.PathologicalStructure PathologicalProcess ⊑ ∃ hasParticipant.PathologicalStructure PathologicalProcess ⊑ ∃ realizationOf. PathologicalDisposition PathologicalDisposition ⊑ ∀hasRealization. PathologicalProcess ?

  9. Example 1 • Allergy is a disposition of specific components of the immune system of an organism. • All instances of the process type Allergic Reaction, are realizations of a disposition of this type, and have an allergen as their causative agent. Image credit: http://www.topnews.in/health/files/Allergy.jpg

  10. Example 2 • A specific binding of thalidomide to DNA forms a pathological structure on a molecular level • This structure is the bearer of the pathological disposition realized by the misdevelopment of limbs (process) and results in a body without forearms (pathologicalstructure) Thalidomide Image credit: http://www.mensch-home.com/Bilder/contergan-co-b/missbild-bild5g.jpg

  11. Example 3 • The fracture (process) is caused by an external force, and has a fractured bone (pathological structure) as its characteristic outcome. This event is, however, not the realization of a disposition. • A fractured bone (structure) has many pathological dispositions which can result in a variety of pathological processes (e.g. the development of a pseudarthrosis). Imagecredit:http://www.bcyr.ca/Survivor/Fracture[1].jpg

  12. Ontological soundness vs. engineering requirements • Ontology engineering: labor-intensive, use case-driven • Not realistic to implement this model • in every well-founded ontology from the very beginning • for all pathological entities to be represented • Challenge: let a coarse-grained, pragmatic representation (which ignores the structure / disposition / process distinction) gracefully evolve towards a more fully-fledged ontology? • Can this be done in a intuitive, user-friendly, ontologically sound, computable, and scalable way?

  13. Disjunctive top level category • PathologicalEntity≡PathologicalStructure⊔ PathologicalDisposition⊔PathologicalProcess • Top node of disease / disorder hierarchy (regardles of whether a distinction is made between processes, structures, dispositions)

  14. Relation to organism parts / locations … crucial for defining pathological entities Different relations (e.g. OBO RO, BioTop) • Pathological Structures: part-of / located-in • Pathological Dispositions: inheres- in • Pathological Processes: has-participantlocated-in

  15. Redesign of relation hierarchy … allows connection to organism parts or locations, without commitment to structure, disposition, or process part-of ⊑ has-locus has-location ⊑ has-locus inheres-in ⊑ has-locus has-participant ⊑ locus-of locus-of ≡ has-locus-1 : reflexive and transitive …

  16. Corollaries of relation abstraction • a disposition of a part is also borne by the whole • a pathological structure located in a part is also located in the whole • a process located in a part is also located in the whole • all participants of a process are located where the process is located

  17. Construction of basic disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of PE PS PD PP OS OS1 PE1 OS2 PE2 OS3 PE2 OS4 OS5

  18. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 OS2 PE2 OS3 PS PD PE2 PP OS4 OS5

  19. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 •  inheres-in OS2 PE2 OS3 PS PD PE2 PP OS4 OS5

  20. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 OS2 PE2 OS3 PE OS PE2 OS OS4 OS5

  21. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 OS2 PE2 OS3 PE OS PE2 OS OS4  has-participant OS5

  22. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 OS2 PE2 OS3 PE OS PE2 OS OS4 OS5

  23. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 OS2 •  has-location PE2 OS3 PE OS PE2 OS OS4 OS5

  24. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 OS2 PE2 OS3 PE OS PE2 OS OS4 OS5

  25. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 OS2 PE2 OS3 PE OS PE2 OS OS4  has-participant OS5

  26. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 OS2 PE2 OS3 PE  inheres-in OS PE2 OS OS4  has-participant OS5

  27. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 OS2 PE2 OS3 PE  inheres-in OS PE2 INCONSISTENT ! OS OS4  has-participant OS5

  28. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 OS2 PE2 OS3 PE  inheres-in OS PE2 INCONSISTENT ! OS OS4 • inheres-in.⊤⊑ PD • has-participant.⊤⊑ PP • PD ⊓ PP ⊑ ⊥  has-participant OS5

  29. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 OS2 PE2 PE2 OS3 PE  inheres-in OS PE2a OS OS4  has-participant OS5

  30. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 OS2 PE2 PE2 OS3 PE OS PE2a OS OS4  has-participant OS5

  31. Construction of advanced disease ontology PE OS • Basic components: • Top nodesPathological EntityOrganism Structure • Disease classes (broad sense) • Organism structure classes • transitive relations •  has-locus •  locus-of • Advanced components • PathologicalStructure • PathologicalDisposition • Pathological Process • Relations •  inheres-in •  has-location •  has-participant PE PS PD PP OS OS1 PE1 OS2 PE2 PE2 OS3 PE  inheres-in PE2b OS PE2a OS OS4  has-participant OS5

  32. Conclusions • “Disease”: ontologically polymorphic category • Refinement of disease classes into pathological structures, pathological dispositions, and pathological processes often not necessary • Introduction of umbrella category Pathological entity, together with the high-level relation has-locus: • construction of simple model which already supports important inferences • permits graceful evolution towards more sophisticated models in which the above distinctions are introduced where necessary • Implemented in BioTop (http://purl.org/biotop) and under discussion at IHTSDO for SNOMED CT

  33. Scalable representations of diseases in biomedical ontologies Acknowledgements DFG, grant agreement JA 1904/2-1, SCHU 2515/1-1 GoodOD (Good Ontology Design). German HL-7 users group IHTSDO Event, condition, episode PG

  34. Acknowledgements • DFG, grant agreement JA 1904/2-1, SCHU 2515/1-1 GoodOD (Good Ontology Design). • EU 7th FP, grant agreement ICT-2007.5.2-217139, DebugIT (Detecting and eliminating bacteria using information technologies)

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