1. The Meaning of Part (Discussion) Anand Kumar MBBS, PhD IFOMIS, Department of Medicine, Univ. of Saarland, Germany. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY

2. Continuants SNAP entities Occurrents Span entities Individuals (Particulars) Classes (Universals) Parts and Time Parts and Region s Parts and Classes Parts and Processes

3. Example II t1t1 t2t2 Parts and Time d d’ t

4. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY Colon with complete destruction of mucosa

5. Criteria for inferring part from spatial inclusion 3.Life Cycle patterns which allow to assert parthood: Parts and Region s t 1 t 2 t 3 NOW aGlycinMolecule, aCollagenFiber aCytoplasm, aCell aGlioblastoma, aBrain

6. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY Normal colon parts

7. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY Normal colon

8. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY Colon tumor

9. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY Rectal carcinoma with metastasis

10. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY Metastasized structures

11. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY 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 Problem with Cancerous structures

12. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY 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 carcinoma structure T2N1M1 colon carcinoma structure

13. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY N2 colon carcinoma structure implies 1 lymph node with colon carcinoma metastatic structure or 2 lymph node with colon carcinoma metastatic structure or 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 T2N1M1 colon carcinoma structure is a Collection of pathological structures

14. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY T2N1M1 colon carcinoma structure has-member T2 colon carcinoma structure and has-member N1 colon carcinoma structure and has-member M1 colon carcinoma structure T2N1M1 colon carcinoma process: is constituted by abnormal processes associated with the carcinoma development T2N1M1 colon carcinoma structure 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. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY 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. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY 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. Class-level Part-Of : Different Interpretations One-sided Dependency Part on Whole Mutual Mereological Dependency Mereological Independency Class A (part) Class B (whole) Examples Cell Nucleus – Cell Chlorophyll – Organism Prostate 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 Dependency Whole on Part Parts and Classes

18. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY Can not be generalized to all instances and thus are also all-some Or some-some relations Case of historical parthoods Mutual dependency

19. 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) Parts and Region s

20. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY Artificial femoral head part-of Femur with artificial head? Drug administration with biological prethyronine? Drug prethyronine part-of thyroid cell? Non-biological artefact

21. Criteria for inferring part from spatial inclusion 4.specific and essential for function Transplants functionally_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) Parts and Region s … but not: part-of (thisVolumeOfUrine, myBladder), because not essential for function

22. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY Urine in urinary bladder has functions Portion of Glomerular filtrate part-of Kidney? Non-biological artefact

23. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY Part-of Part-Of 12 (A, B) = def* Part-Of 1 (A, B)  Part-Of 2 (A, B) Part-Of 1 (A, B) = def*  x: inst-of (x, A)   y: inst-of (y, B)  part-of (x, y) Part-Of 2 (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. Example Removal of foreign body from stomach Removal of foreign body from stomach by endoscopy Removal of foreign body from stomach by incision Preparation Introduction of Endoscope Exploration Removal of foreign body Extraction of Endoscope Preparation Incision Exploration Removal of foreign body Closure t t Parts and Processes Surgical Procedure

25. 1.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) 2.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 What are the instances of processes? Concurrent views Parts and Processes

26. Theory 1: Process is instantiated by its subprocesses Parts and Processes P1P1 P2P2 P3P3 P4P4 P t P1P1 P2P2 P3P3 P4P4 P p P1P1 P2P2 P3P3 P4P4 P p P1P1 P2P2 P3P3 P4P4 P p P1P1 P2P2 P3P3 P4P4 P p is-a instance-of t1t1 t2t2 t3t3 t4t4

27. Parts and Processes P1P1 P2P2 P‘‘‘P1P1 P‘‘P2P2 P1P1 P‘P3P3 P2P2 P1P1 PP3P3 P4P4 t t1t1 t2t2 t3t3 t4t4 pppp is-a instance-of  has-part Theory 2: Subprocesses are parts of their parent processes

28. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY Process p; (p, pt init ) is not the complete p; complete p exists only when the process instance is completed Processes Sub-process sp1; (sp1, sp1t init ) is not the complete sp1; sp1t init = pt init complete sp exists only when the sub-process instance completed + sp1 … spn Sub-process spn; (spn, spnt end ) is the complete spn; spnt end = pt end

29. The Meaning of Part (Discussion) Anand Kumar MBBS, PhD IFOMIS, Department of Medicine, Univ. of Saarland, Germany. BIOMEDICALONTOLOGYBIOMEDICALONTOLOGY