Introduction                                 Functions and dispositions                         Conclusions               ...
Introduction                        Functions and dispositions     ConclusionsFunctions in biomedical ontologies          ...
Introduction                          Functions and dispositions                ConclusionsFunctions in biomedical ontolog...
Introduction                      Functions and dispositions   ConclusionsFunctions in biomedical ontologiesBFO: The funct...
Introduction                        Functions and dispositions        ConclusionsFunctions in biomedical ontologiesBFO: Th...
Introduction                         Functions and dispositions               ConclusionsFunctions in biomedical ontologie...
Introduction                      Functions and dispositions             ConclusionsFunctions in biomedical ontologiesBFO:...
Introduction                        Functions and dispositions              ConclusionsFunctions in biomedical ontologiesB...
Introduction                        Functions and dispositions              ConclusionsFunctions in biomedical ontologiesB...
Introduction                        Functions and dispositions              ConclusionsFunctions in biomedical ontologiesB...
Introduction                            Functions and dispositions       ConclusionsFunctions in biomedical ontologiesFunc...
Introduction                         Functions and dispositions             ConclusionsFunctions in biomedical ontologiesR...
Introduction         Functions and dispositions                    ConclusionsOntology of Functions (OF)                  ...
Introduction                         Functions and dispositions         ConclusionsOntology of Functions (OF)Open question...
Introduction                        Functions and dispositions       ConclusionsLarry WrightReducing function to causality...
Introduction                        Functions and dispositions                 ConclusionsJohn SearleFunctions as social c...
Introduction                        Functions and dispositions   ConclusionsNicolai HartmannFunction ascription and causal...
Introduction                        Functions and dispositions             ConclusionsMalfunctioningsOverview             ...
Introduction                       Functions and dispositions             ConclusionsMalfunctioningsFormal characterizatio...
Introduction                       Functions and dispositions             ConclusionsMalfunctioningsFormal characterizatio...
Introduction                         Functions and dispositions              ConclusionsMalfunctioningsNon-monotonicity   ...
Introduction                        Functions and dispositions              ConclusionsApplicationFunctions and malfunctio...
Introduction                          Functions and dispositions           ConclusionsSummary               BFO’s definitio...
Introduction                     Functions and dispositions   ConclusionsAcknowledgements               Heinrich Herre    ...
Introduction    Functions and dispositions   Conclusions               Thank you!
Introduction                         Functions and dispositions               ConclusionsDispositions       An individual ...
Upcoming SlideShare
Loading in …5
×

Relating functions and dispositions using nonmonotonic reasoning

424
-1

Published on

Published in: Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
424
On Slideshare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
4
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Relating functions and dispositions using nonmonotonic reasoning

  1. 1. Introduction Functions and dispositions Conclusions Relating functions and dispositions using nonmonotonic reasoning Robert Hoehndorf1,2 , Janet Kelso2 , Heinrich Herre1 1 Institute for Informatics and Research Group Ontologies in Medicine, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig 2 Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology
  2. 2. Introduction Functions and dispositions ConclusionsFunctions in biomedical ontologies Gene Ontology (molecule function) Celltype Ontology (cell function) FMA, Anatomie (organ function) Disease Ontology, (Human/Mammalian) Phenotype Ontology (malfunctioning) OBI (device function) Protein Ontology
  3. 3. Introduction Functions and dispositions ConclusionsFunctions in biomedical ontologiesA solved problem? A function f is 1 a realizable dependent continuant, which 2 has a bearer which is an independent continuant, and 3 is of a type instances of which typically have realizations; each realization is 1 a process in which the bearer is a participant, 2 that occurs in virtue of the bearer’s physical makeup, 3 this physical make-up is something which that bearer possesses because of how it came into being. Arp and Smith, 2008
  4. 4. Introduction Functions and dispositions ConclusionsFunctions in biomedical ontologiesBFO: The function of the heart is to make thumping noises A function f is a realizable dependent continuant, which “To make thumping noises” is realizable.
  5. 5. Introduction Functions and dispositions ConclusionsFunctions in biomedical ontologiesBFO: The function of the heart is to make thumping noises A function f is a realizable dependent continuant, which “To make thumping noises” is realizable. has a bearer which is an independent continuant, and The heart is an independent continuant.
  6. 6. Introduction Functions and dispositions ConclusionsFunctions in biomedical ontologiesBFO: The function of the heart is to make thumping noises A function f is a realizable dependent continuant, which “To make thumping noises” is realizable. has a bearer which is an independent continuant, and The heart is an independent continuant. is of a type instances of which typically have realizations; “To make thumping noises” is typically realized.
  7. 7. Introduction Functions and dispositions ConclusionsFunctions in biomedical ontologiesBFO: The function of the heart is to make thumping noises Each realization is a process in which the bearer is a participant, Hearts participate in thumping-noise-making processes.
  8. 8. Introduction Functions and dispositions ConclusionsFunctions in biomedical ontologiesBFO: The function of the heart is to make thumping noises Each realization is a process in which the bearer is a participant, Hearts participate in thumping-noise-making processes. that occurs in virtue of the bearer’s physical makeup, Thumping-noise-making occurs due to the physical makeup of the heart.
  9. 9. Introduction Functions and dispositions ConclusionsFunctions in biomedical ontologiesBFO: The function of the heart is to make thumping noises Each realization is a process in which the bearer is a participant, Hearts participate in thumping-noise-making processes. that occurs in virtue of the bearer’s physical makeup, Thumping-noise-making occurs due to the physical makeup of the heart. this physical make-up is something which that bearer possesses because of how it came into being. Heart possess their makeup due to how they came into being.
  10. 10. Introduction Functions and dispositions ConclusionsFunctions in biomedical ontologiesBFO: The function of the heart is to make thumping noises Each realization is a process in which the bearer is a participant, Hearts participate in thumping-noise-making processes. that occurs in virtue of the bearer’s physical makeup, Thumping-noise-making occurs due to the physical makeup of the heart. this physical make-up is something which that bearer possesses because of how it came into being. Heart possess their makeup due to how they came into being. Therefore: The function of the heart is to make thumping noises. (BFO)
  11. 11. Introduction Functions and dispositions ConclusionsFunctions in biomedical ontologiesFunction in BFO functions may “typically” not be realized: sperm cells functions may be acquired after through transformation (not at time of creation): angiotensin I to angiotensin II what is a realization?
  12. 12. Introduction Functions and dispositions ConclusionsFunctions in biomedical ontologiesRealizations What makes a process a realization of a function? Participation of the function bearer is not sufficient. A protein’s function “to transport” is realized by transport processes, in which the protein participates as a transporter. Mode of participation in a process necessary to understand realizations. Use of processual or relational roles/qua entities
  13. 13. Introduction Functions and dispositions ConclusionsOntology of Functions (OF) Conceptual framework to model functions Implemented in OWL
  14. 14. Introduction Functions and dispositions ConclusionsOntology of Functions (OF)Open questions What is the relation between function and disposition? What is the relation between function and causality? How do functions come into being? What is a function?
  15. 15. Introduction Functions and dispositions ConclusionsLarry WrightReducing function to causality The function of X is Z means 1 X is there because it does Z , 2 Z is a consequence (or result) of X ’s being there.
  16. 16. Introduction Functions and dispositions ConclusionsJohn SearleFunctions as social concepts All functions are socially ascribed by an agent to an object. Functions are always observer-relative. Function ascription is based on brute facts.
  17. 17. Introduction Functions and dispositions ConclusionsNicolai HartmannFunction ascription and causality 1 Setting a goal (in the future) 2 Planning the goal’s realization 3 Realizing the goal (causally) (1) and (2) create functionality Must realization be possible?
  18. 18. Introduction Functions and dispositions ConclusionsMalfunctioningsOverview Setting a goal Planning No realization possible: missing disposition Malfunctioning is function without disposition. Functionality does not imply causality. But: normally, function-bearers have the disposition to realize their function. Normally, entities do not malfunction.
  19. 19. Introduction Functions and dispositions ConclusionsMalfunctioningsFormal characterization If e has the function f (with goal Tgoal ), and e is not malfunctioning, then e has a disposition with goal Tgoal . A(mf ) = hasFunction(e, f ) ∧ f :: F ∧ ¬mf (e) → ∃d(d :: D ∧ isa(D, Disposition) ∧ inheresIn(d, e)∧ Treq (F ) = Treq (D) ∧ Tgoal (F ) = Tgoal (D))
  20. 20. Introduction Functions and dispositions ConclusionsMalfunctioningsFormal characterization If e has the function f (with goal Tgoal ), and e is not malfunctioning, then e has a disposition with goal Tgoal . A(mf ) = hasFunction(e, f ) ∧ f :: F ∧ ¬mf (e) → ∃d(d :: D ∧ isa(D, Disposition) ∧ inheresIn(d, e)∧ Treq (F ) = Treq (D) ∧ Tgoal (F ) = Tgoal (D)) Normally, e is not malfunctioning. A(mf )∧∀P((A(P) ∧ ∀x(P(x) → mf (x))) → (∀x(P(x) ↔ mf (x))))
  21. 21. Introduction Functions and dispositions ConclusionsMalfunctioningsNon-monotonicity Classical (monotonic) inference: S ⊆ T → S |= ⊆ T |= non-monotonic inference permits default reasoning e is not malfunctioning as long as not proven otherwise use of default logics, circumscription or auto-epistemic logics implementation using answer-set programming
  22. 22. Introduction Functions and dispositions ConclusionsApplicationFunctions and malfunctionings Human (functional) anatomy: Ear CC-hasFunction Hearing ∀x(x :: Ear → ∃y (y :: Hearing ∧ II-hasFunction(x, y ))) Disposition D to participate in hearing processes (realization) as receiver (role) If an instance e of Ear is not malfunctioning, it has a disposition d (which is an instance of D). Normally, instances of Ear are not malfunctioning (with respect to Hearing ). Deafness (HP:0000404) implies malfunctioning of its bearer w.r.t. Hearing
  23. 23. Introduction Functions and dispositions ConclusionsSummary BFO’s definition of function needs refinement. Philosophical explanations of biological functions can be divided in: reductions to causality social ascription each relates functionality to causality most use normality or typicality non-monotonic reasoning is necessary to formalize normality focus on necessary conditions and inferences instead of definitions for function
  24. 24. Introduction Functions and dispositions ConclusionsAcknowledgements Heinrich Herre Janet Kelso Patryk Burek Frank Loebe Hannes Michalek
  25. 25. Introduction Functions and dispositions Conclusions Thank you!
  26. 26. Introduction Functions and dispositions ConclusionsDispositions An individual e has the disposition d to cause an instance of Tgoal iff e causes a situation s :: Tgoal whenever e is placed in the right circumstances. Describe “in the right circumstances” using a situational/relational role. Dispositions are possibilities to cause certain states of affairs to become factual. What is the relation between function and disposition?
  1. A particular slide catching your eye?

    Clipping is a handy way to collect important slides you want to go back to later.

×