The Ontology for General    Medical Science       Barry Smith       11/5/2012
The 3 Gene Ontologies (GO)          Continuant                  Occurrent Independent           Dependent  Continuant     ...
Basic Formal Ontology                            Occurrent        Continuant                            (Process)Independe...
Blinding Flash of the Obvious                                    Occurrent        Continuant                              ...
Basic Formal Ontology                                    Occurrent        Continuant                                    (P...
humanin nature, no sharp  boundaries hereembryo          fetus          neonate         infant         child          adul...
continuants                                occurrents                       human                                  course ...
temperature     in nature, no sharp       boundaries here    37°C           38°C          39°C            40°C          41...
continuants                                  occurrents                    temperature                                  co...
A Chart representing howJohn’s temperature changes                             10
A Chart representing howJohn’s temperature changes                         11
BFO: The Very Top      continuant            occurrentindependent    dependent continuant    continuant                qua...
Blinding Flash of the Obviousindependent   dependent continuant   continuant               qualityorganism              te...
Blinding Flash of the Obviousindependent   dependent continuant   continuant               qualityorganism              te...
Blinding Flash of the Obvious           inheres_inorganism             temperature    types John                 John’s   ...
independent   dependent continuant   continuant               qualityorganism              temperature   types  John      ...
independent   dependent                               occurrent continuant   continuant               quality          pro...
independent   dependent                               occurrent continuant   continuant               quality          pro...
independent   dependent                            occurrent continuant   continuant               quality      processorg...
BFO: The Very Top      continuant               occurrentindependent    dependent continuant    continuant         quality...
Disposition-   of   a glass vase, to shatter if dropped-   of   a human, to eat-   of   a banana, to ripen-   of   John, t...
Dispositionif it ceases to exist, then its bearerand/or its immediate surroundingenvironment is physically changedits real...
Function- of   liver: to store glycogen- of   birth canal: to enable transport- of   eye: to see- of   mitochondrion: to p...
independent      dependent                                   occurrent continuant      continuant                  functio...
OGMS  Ontology for General Medical             Sciencehttp://code.google.com/p/ogms                                 25
Big Picture (with thanks to Richard Scheuermann)                                              26
Physical Disorder                    27
Physical Disorder– independent   continuant    fiat object partA causally linked combinationof physical components of thee...
Clinically abnormal– (1) not part of the life plan for an organism  of the relevant type (unlike aging or  pregnancy),– (2...
Disorder1. person  – independent continuant       objects       fiat object part       object aggregate                   ...
DisorderA fiat object part of an organism whichserves as the bearer of a disposition of acertain sortThis fiat object may ...
Big Picture (with thanks to Richard Scheuermann)                                                   32
Elucidation of Primitive Terms   ‘bodily feature’ - an abbreviation for a physical    component, a bodily quality, or a b...
Definitions - Foundational Terms   Disorder =def. – A causally linked combination of    physical components that is clini...
Dispositions and Predispositions   All diseases are dispositions; not all dispositions are    diseases.   A predispositi...
coronary heart                             disease     disease                      disease          diseaseassociated wit...
independent      dependent                                      occurrent continuant      continuant                dispos...
Cirrhosis - environmental exposure   Etiological process - phenobarbitol-        Symptoms & Signs    induced hepatic cel...
Huntington’s Disease - genetic   Etiological process - inheritance of    >39 CAG repeats in the HTT gene              Sy...
HNPCC - genetic pre-disposition   Etiological process - inheritance of a mutant mismatch repair gene     produces   Dis...
Arterial AneurysmDisposition – atherosclerosis    realized inPathological process – fatty material collects within the wal...
Influenza - infectious   Etiological process - infection of          Symptoms & Signs    airway epithelial cells with in...
Upcoming SlideShare
Loading in …5
×

The OGMS Ontology for General Medical Science (November 2012)

634 views

Published on

  • Be the first to comment

  • Be the first to like this

The OGMS Ontology for General Medical Science (November 2012)

  1. 1. The Ontology for General Medical Science Barry Smith 11/5/2012
  2. 2. The 3 Gene Ontologies (GO) Continuant Occurrent Independent Dependent Continuant Continuantcell component molecular function biological process 2
  3. 3. Basic Formal Ontology Occurrent Continuant (Process)Independent Dependent Continuant Continuant(molecule, (quality,cell, organ, function,organism) disease)..... ..... .... ..... 3
  4. 4. Blinding Flash of the Obvious Occurrent Continuant (Process)Independent Continuant Dependent e.g. Continuant e.g. Side-Effect,(molecule, Functioning Stochasticcell, organ, (quality) Process, ...organism)..... ..... .... ..... 4
  5. 5. Basic Formal Ontology Occurrent Continuant (Process)Independent Continuant Dependent e.g. Continuant e.g. Side-Effect,(molecule, Functioning Stochasticcell, organ, (quality) Process, ...organism)..... ..... .... ..... 5
  6. 6. humanin nature, no sharp boundaries hereembryo fetus neonate infant child adult instantiates instantiates instantiates instantiates instantiates instantiates at t1 at t2 at t3 at t4 at t5 at t6 John (exists continuously)
  7. 7. continuants occurrents human course of developmentembryo fetus neonate infantinstantiates instantiates instantiates instantiates at t1 at t2 at t3 at t4 course of John’s John (continuant) development
  8. 8. temperature in nature, no sharp boundaries here 37°C 38°C 39°C 40°C 41°C temperature temperature temperature temperature temperature quality quality quality quality qualityinstantiates instantiates instantiates instantiates instantiates at t1 at t2 at t3 at t4 at t5 John’s temperature (exists continuously through time)
  9. 9. continuants occurrents temperature course of temperature 37ºC 37.1ºC 37.2ºC 37.3ºCinstantiates instantiates instantiates instantiates at t1 at t2 at t3 at t4 the course of John’s John’s temperature temperature has_participant
  10. 10. A Chart representing howJohn’s temperature changes 10
  11. 11. A Chart representing howJohn’s temperature changes 11
  12. 12. BFO: The Very Top continuant occurrentindependent dependent continuant continuant quality temperature 12
  13. 13. Blinding Flash of the Obviousindependent dependent continuant continuant qualityorganism temperature types John John’s instances temperature 13
  14. 14. Blinding Flash of the Obviousindependent dependent continuant continuant qualityorganism temperature types John John’s instances temperature 14
  15. 15. Blinding Flash of the Obvious inheres_inorganism temperature types John John’s instances temperature 15
  16. 16. independent dependent continuant continuant qualityorganism temperature types John John’s instances temperature 16
  17. 17. independent dependent occurrent continuant continuant quality processorganism course of temperature temperature changes John’s John’s John temperature temperature history 17
  18. 18. independent dependent occurrent continuant continuant quality processorganism temperature temperature process profile John’s John’s John temperature temperature history
  19. 19. independent dependent occurrent continuant continuant quality processorganism life of an temperature organism John’s John’s John temperature life 19
  20. 20. BFO: The Very Top continuant occurrentindependent dependent continuant continuant quality disposition 20
  21. 21. Disposition- of a glass vase, to shatter if dropped- of a human, to eat- of a banana, to ripen- of John, to lose hair 21
  22. 22. Dispositionif it ceases to exist, then its bearerand/or its immediate surroundingenvironment is physically changedits realization occurs when its bearer is insome special physical circumstancesits realization is what it is in virtue of thebearer’s physical make-up 22
  23. 23. Function- of liver: to store glycogen- of birth canal: to enable transport- of eye: to see- of mitochondrion: to produce ATPfunctions are dispositions which aredesigned or selected for 23 :.
  24. 24. independent dependent occurrent continuant continuant function process eye to see process of seeingJohn’s eye function of John’s John seeing eye: to see 24
  25. 25. OGMS Ontology for General Medical Sciencehttp://code.google.com/p/ogms 25
  26. 26. Big Picture (with thanks to Richard Scheuermann) 26
  27. 27. Physical Disorder 27
  28. 28. Physical Disorder– independent continuant fiat object partA causally linked combinationof physical components of theextended organism that isclinically abnormal. 28 :.
  29. 29. Clinically abnormal– (1) not part of the life plan for an organism of the relevant type (unlike aging or pregnancy),– (2) causally linked to an elevated risk either of pain or other feelings of illness, or of death or dysfunction, and– (3) such that the elevated risk exceeds a certain threshold level.**Compare: baldness 29
  30. 30. Disorder1. person – independent continuant objects fiat object part object aggregate 30
  31. 31. DisorderA fiat object part of an organism whichserves as the bearer of a disposition of acertain sortThis fiat object may have no determinateboundaries(compare: Downtown Santa Barbara) 31
  32. 32. Big Picture (with thanks to Richard Scheuermann) 32
  33. 33. Elucidation of Primitive Terms ‘bodily feature’ - an abbreviation for a physical component, a bodily quality, or a bodily process. disposition - an attribute describing the propensity to initiate certain specific sorts of processes when certain conditions are satisfied. clinically abnormal - some bodily feature that  (1) is not part of the life plan for an organism of the relevant type (unlike aging or pregnancy),  (2) is causally linked to an elevated risk either of pain or other feelings of illness, or of death or dysfunction, and  (3) is such that the elevated risk exceeds a certain threshold level.* *Compare: baldness 33
  34. 34. Definitions - Foundational Terms Disorder =def. – A causally linked combination of physical components that is clinically abnormal. Pathological Process =def. – A bodily process that is a manifestation of a disorder and is clinically abnormal. Disease =def. – A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. 34
  35. 35. Dispositions and Predispositions All diseases are dispositions; not all dispositions are diseases. A predisposition is a disposition. Predisposition to Disease of Type X =def. – A disposition in an organism that constitutes an increased risk of the organism’s subsequently developing the disease X. HNPCC is caused by a  disorder (mutation) in a DNA mismatch repair gene that  disposes to the acquisition of additional mutations from defective DNA repair processes, and thus is a  predisposition to the development of colon cancer. 35
  36. 36. coronary heart disease disease disease diseaseassociated with associated with associated early lesions asymptomatic with surface unstable stable and small (‘silent’) disruption of angina anginafibrous plaques infarction plaque instantiates instantiates instantiates instantiates instantiates at t1 at t2 at t3 at t4 at t5 John’s coronary heart disease 36 time
  37. 37. independent dependent occurrent continuant continuant disposition process heart coronary heart disease disease courseJohn’s heart John’s coronary of John’s coronary heart course heart disease 37
  38. 38. Cirrhosis - environmental exposure Etiological process - phenobarbitol-  Symptoms & Signs induced hepatic cell death  used_in  produces  Interpretive process Disorder - necrotic liver  produces  bears  Hypothesis - rule out cirrhosis  suggests Disposition (disease) - cirrhosis  Laboratory tests  realized_in  produces Pathological process - abnormal tissue  Test results - elevated liver enzymes in repair with cell proliferation and serum fibrosis that exceed a certain  used_in threshold; hypoxia-induced cell death  Interpretive process  produces  produces Abnormal bodily features  Result - diagnosis that patient X has a  recognized_as disorder that bears the disease Symptoms - fatigue, anorexia cirrhosis Signs - jaundice, splenomegaly 38
  39. 39. Huntington’s Disease - genetic Etiological process - inheritance of >39 CAG repeats in the HTT gene  Symptoms & Signs  produces  used_in Disorder - chromosome 4 with  Interpretive process abnormal mHTT  produces  bears  Hypothesis - rule out Huntington’s Disposition (disease) - Huntington’s  suggests disease  Laboratory tests  realized_in  produces Pathological process - accumulation of  Test results - molecular detection of mHTT protein fragments, abnormal the HTT gene with >39CAG repeats transcription regulation, neuronal cell  used_in death in striatum  produces  Interpretive process  produces Abnormal bodily features  recognized_as  Result - diagnosis that patient X has a disorder that bears the disease Symptoms - anxiety, depression Huntington’s disease Signs - difficulties in speaking and swallowing 39
  40. 40. HNPCC - genetic pre-disposition Etiological process - inheritance of a mutant mismatch repair gene  produces Disorder - chromosome 3 with abnormal hMLH1  bears Disposition (disease) - Lynch syndrome  realized_in Pathological process - abnormal repair of DNA mismatches  produces Disorder - mutations in proto-oncogenes and tumor suppressor genes with microsatellite repeats (e.g. TGF-beta R2)  bears Disposition (disease) - non-polyposis colon cancer  realized in Symptoms (including pain) 40
  41. 41. Arterial AneurysmDisposition – atherosclerosis realized inPathological process – fatty material collects within the walls of arteries producesDisorder – artery with weakened wall bearsDisposition – of artery to become distended realized_inPathological process – process of distending producesDisorder – arterial aneurysm bearsDisposition – of artery to rupture realized inPathological process – (catastrophic event) of rupturing producesDisorder – ruptured artery, arterial system with dangerously low blood pressure bearsDisposition – circulatory failure realized inPathological process – exsanguination, failure of homeostasis produces 41Death
  42. 42. Influenza - infectious Etiological process - infection of  Symptoms & Signs airway epithelial cells with influenza  used_in virus  Interpretive process  produces  produces Disorder - viable cells with influenza  Hypothesis - rule out influenza virus  suggests  bears  Laboratory tests Disposition (disease) - flu  produces  realized_in  Test results - elevated serum antibody titers  used_in Pathological process - acute inflammation  Interpretive process  produces  produces  Result - diagnosis that patient X has a Abnormal bodily features disorder that bears the disease flu  recognized_as Symptoms - weakness, dizziness But the disorder also induces normal physiological processes (immune response) Signs - fever that can results in the elimination of the 42 disorder (transient disease course).

×