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The Meaning of Part (Discussion)

B I O M E D I C A L O N T O L O G Y. The Meaning of Part (Discussion). Anand Kumar MBBS, PhD I FOMIS, Department of Medicine, Univ. of Saarland, Germany. Continuants SNAP entities. Occurrents Span entities. Parts and Time. Parts and Regions. Individuals (Particulars).

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The Meaning of Part (Discussion)

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  1. B I O M E D I C A L O N T O L O G Y The Meaning of Part (Discussion) Anand KumarMBBS, PhD IFOMIS, Department of Medicine, Univ. of Saarland, Germany.

  2. ContinuantsSNAP entities OccurrentsSpan entities Parts and Time Parts and Regions Individuals(Particulars) Parts and Processes Parts and Classes Classes(Universals)

  3. Parts and Time Example II d’ d t t1 t2

  4. B I O M E D I C A L O N T O L O G Y Colon with complete destruction of mucosa

  5. Parts and Regions Criteria for inferring part from spatial inclusion 3. Life Cycle patterns which allow to assert parthood: aGlycinMolecule, aCollagenFiber aCytoplasm, aCell aGlioblastoma, aBrain t1 t2 t3 NOW

  6. B I O M E D I C A L O N T O L O G Y Normal colon parts

  7. B I O M E D I C A L O N T O L O G Y Normal colon

  8. B I O M E D I C A L O N T O L O G Y Colon tumor

  9. B I O M E D I C A L O N T O L O G Y Rectal carcinoma with metastasis

  10. B I O M E D I C A L O N T O L O G Y Metastasized structures

  11. B I O M E D I C A L O N T O L O G Y Problem with Cancerous structures • Cancerous structures with metastasis • Lung tumor • Lung tumor continuous with pleural extension • Local lymph node tumor • Brain tumor (metastasis) • These entities are Collections • Entities not physically continuous, connected, overlapping • Clear transformation present with temporality

  12. B I O M E D I C A L O N T O L O G Y T2N1M1 colon carcinoma structure Processes involved T2: Tumor invades muscularis propria N1: Metastasis in 1 to 3 lymph nodes M1: Distant metastasis Pathological structures T2N1M1 colon carcinoma pathological structure: T2 colon carcinoma pathological structure implies Portion of colon mucosa carcinoma pathological structure and Portion of colon submucosa carcinoma pathological structure and Portion of colon muscularis propria carcinomastructure

  13. B I O M E D I C A L O N T O L O G Y T2N1M1 colon carcinoma structure N2 colon carcinoma structureimplies 1 lymph node with colon carcinoma metastatic structureor 2 lymph node with colon carcinoma metastatic structureor 3 lymph node with colon carcinoma metastatic structure M1 colon carcinoma structure implies Lung with colon carcinoma metastatic structure or Liver with colon carcinoma metastatic structure or …. T2N1M1 colon carcinoma structure is a Collectionof pathological structures

  14. B I O M E D I C A L O N T O L O G Y T2N1M1 colon carcinoma structure T2N1M1 colon carcinoma structure has-member T2 colon carcinoma structureand has-memberN1 colon carcinoma structureand has-memberM1 colon carcinoma structure T2N1M1 colon carcinoma process: is constituted by abnormal processes associated with the carcinoma development T2N1M1 colon carcinomatous process has-part T2 colon carcinomatous process and has-part N1 colon carcinomatous process and has-part M1 colon carcinomatous process

  15. B I O M E D I C A L O N T O L O G Y Instance of T2N1M1 colon carcinoma structure inst(T2N1M1 carcinoma structure)implies mucosal carcinoma structure and muscularis mucosal carcinoma structure and 3 paracolic lymph nodal metastatic structure and left upper lung lobe metastatic structure T2N1M1 carcinomatous structure transformation_of T2N1M0 carcinomatous structure transformation_of T2N0M0 carcinomatous structure transformation_of T1N0M0 carcinomatous structure transformation_of TisN0M0 carcinomatous structure transformation_of Colon part

  16. B I O M E D I C A L O N T O L O G Y Instance of T2N1M1 colon carcinoma structure left upper lung metastatic carcinomatous process preceded-by distant organ metastasis preceded-by paracolic lymph nodal carcinomatous process preceded-by lymph nodal metastasis preceded-by muscularis proprial carcinomatous process preceded-by trans-submucosal carcinomatous invasion preceded-by submucosal carcinomatous process preceded-by transmucosal carcinomatous invasion preceded-by mucosal carcinomatous process preceded-by transcellular carcinomatous process preceded-by epithelial cellular carcinomatous process

  17. Parts and Classes Class-level Part-Of :Different Interpretations Class A (part) Class B (whole) Examples • One-sided DependencyPart on Whole Cell Nucleus – CellChlorophyll – OrganismProstate Tumor – Prostate Sulfur – Methionin Wing – Chicken Heart – Drosophila Cell Membrane – Cell Vertebra – Vertebrate Body Surface – Body Uterus – Mammal Sulfur – Amino Acid Tooth – Human • One-sided DependencyWhole on Part • Mutual Mereological Dependency • Mereological Independency

  18. B I O M E D I C A L O N T O L O G Y Mutual dependency Can not be generalized to all instances and thus are also all-some Or some-some relations Case of historical parthoods

  19. Parts and Regions Criteria for inferring part from spatial inclusion 1. Sortality: Rules out objects of certain sort as parts: • x is material, y is immaterial:Solid (x)  Hole  (y)  spatially-included (x, y)   part-of (x, y)spatially-included (myBrain, myCranialCavity)   part-of (myBrain, myCranialCavity) • x is an non-biological artifact: spatially-included (myPacemaker, myBody)  part-of (myPacemaker, myBody) spatially-included (myInlay, myTooth)  part-of (myInlay, myTooth)

  20. B I O M E D I C A L O N T O L O G Y Non-biological artefact Artificial femoral head part-of Femur with artificial head? Drug administration with biological prethyronine? Drug prethyronine part-of thyroid cell?

  21. Parts and Regions Criteria for inferring part from spatial inclusion 4. specific and essential for function • Transplantsfunctionally_related (aTransplant, anOrganism)  spatially-included (aTransplant, anOrganism)  part-of (aTransplant, anOrganism) • Body Substances: functionally_related (myCSF, myBrain)  spatially-included (myCSF, myBrain)  part-of (myCSF, myBrain) … but not: part-of (thisVolumeOfUrine, myBladder), becausenot essential for function

  22. B I O M E D I C A L O N T O L O G Y Non-biological artefact Urine in urinary bladder has functions Portion of Glomerular filtrate part-of Kidney?

  23. B I O M E D I C A L O N T O L O G Y Part-of Part-Of12 (A, B) = def* Part-Of1 (A, B)  Part-Of2 (A, B) Part-Of1 (A, B) = def* x: inst-of (x, A)  y: inst-of (y, B)  part-of (x, y) Part-Of2 (A, B) = def*y: inst-of (y, B)  x: inst-of (x, A)  part-of (x, y) Classes have not been chosen properly Uterus part-of human body? Human uterus? Human uterus within human body? Why not female human body on the RHS?

  24. Parts and Processes Example Surgical Procedure Removal of foreign body from stomach Removal of foreign body from stomachby endoscopy Removal of foreign body from stomachby incision Preparation Closure Preparation Extraction of Endoscope Incision Introduction of Endoscope Removal offoreign body Removal offoreign body Exploration Exploration t t

  25. What are the instances of processes? Concurrent views Parts and Processes • A process is (sequentially) instantiated by its subprocesses: • Subprocesses do not exist simultaneously • You are doing something even if you have not done it (completely) • A process is instantiated by its temporal parts • Before having performed the complete procedure it is open whether the process will really be completed • An aborted (token) process does not fulfill the necessary conditions which define the (type) process

  26. P1 P2 P3 P4 P Parts and Processes Theory 1: Process is instantiated by its subprocesses P1 P2 P3 P4 P1 P2 P3 P4 P1 P2 P3 P4 P1 P2 P3 P4 is-a is-a is-a is-a is-a P P P P instance-of instance-of instance-of instance-of p p p p t t1 t2 t3 t4

  27. P1 P1 P1 P1 P4 P2 P3 P2 P2 P3 P‘‘‘ P‘‘ P‘ P Parts and Processes Theory 2: Subprocesses are parts of their parent processes  has-part is-a  has-part is-a  has-part is-a  has-part instance-of instance-of instance-of instance-of p p p p t t1 t2 t3 t4

  28. B I O M E D I C A L O N T O L O G Y Processes Processp; (p, ptinit) is not the complete p; complete p exists only when the process instance is completed Sub-processsp1; (sp1, sp1tinit) is not the complete sp1; sp1tinit = ptinit complete sp exists only when the sub-process instance completed + sp1 … spn Sub-processspn; (spn, spntend) is the complete spn; spntend = ptend

  29. B I O M E D I C A L O N T O L O G Y The Meaning of Part (Discussion) Anand KumarMBBS, PhD IFOMIS, Department of Medicine, Univ. of Saarland, Germany.

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