The Meaning of Part
description
Transcript of The Meaning of Part
![Page 1: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/1.jpg)
The Meaning of Part
Stefan SchulzDepartment of Medical Informatics
University Hospital Freiburg (Germany)
Ontology and Biomedical InformaticsAn International Conference organized by the Network of Excellence Semantic Interoperability and Data Mining in Biomedicine under the auspices of Working Group 6 of the International Medical Informatics AssociationRome 29 April – 2 May 2005
![Page 2: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/2.jpg)
Relations in Biomedical Terminologies / Ontologies
Purpose-Specific
Relations in Clinical
Terminologies
Foundational Relations in
Formal OntologiesPart-Of
![Page 3: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/3.jpg)
Individuals
Part-Of
• Algebraic Properties:Part-of: Transitive, Reflexive, AntisymmetricProper-Part-Of:Transitive, Irreflexive, Asymmetric
• Mereological Principles:Sum, Product, Supplementation, Extensionality, Proper Part Principle… P.Simons, Casati & Varzi
• Subrelations:direct-part-of, functional-part-of, component-of, subdivision-of, boundary-of, … GALEN, FMA
![Page 4: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/4.jpg)
Individuals
Part-Of
• Algebraic Properties:Part-of: Transitive, Reflexive, AntisymmetricProper-Part-Of:Transitive, Irreflexive, Asymmetric
• Mereological Principles:Sum, Product, Supplementation, Extensionality, Proper Part Principle… P.Simons, Casati & Varzi
• Subrelations:direct-part-of, functional-part-of, component-of, subdivision-of, boundary-of, … GALEN, FMA
Continuants Occurrents
![Page 5: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/5.jpg)
• Algebraic Properties:Part-of: Transitive, Reflexive, AntisymmetricProper-Part-Of:Transitive, Irreflexive, Asymmetric
• Mereological Principles:Sum, Product, Supplementation, Extensionality, Proper Part Principle… P.Simons, Casati & Varzi
• Subrelations:direct-part-of, functional-part-of, component-of, subdivision-of, boundary-of, … GALEN, FMA
Continuants Occurrents
Individuals
Classes,
Part-Of
![Page 6: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/6.jpg)
Continuants Occurrents
Individuals
Classes
Parts and Time
Parts and
Regions
Parts and
Classes
Parts and
Processes
Part-Of
![Page 7: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/7.jpg)
Continuants Occurrents
Individuals
Classes
Parts and Time
Parts and
Regions
Parts and
Classes
Parts and
Processes
Part-Of
![Page 8: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/8.jpg)
Example I
t1 t2 t3 t4 t5
Parts and Time
![Page 9: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/9.jpg)
Example II
t1 t2
Parts and Time
d
d’
t
![Page 10: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/10.jpg)
Two views1. The tooth is no longer considered part of the
dental arcade after extraction: d = d’Problem: it has still some kind of relation with the dental arcade. Which one ?
2. The tooth continues being considered a (now disconnected) part of the dental arcade even after extraction: d = d’+ t d d’Problem: what is then the spatial extension of the dentition? Is the dental arcade no longer the same ?
Parts and Time
![Page 11: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/11.jpg)
Historic Parthood Don’t take historic parthood for parthood
“bone (in an archeologic site) forming part of a skeleton…”“transplanting part of a liver…”“sample of gastric mucosa of patient X was examined”
Time-indexed parthood:part-of (a, b, t)
Historic parthood:hist-part-of (a, b) =def t,u: part-of (a, b, t)
part-of (a, b, u) earlier(t, u)
Parts and Time
![Page 12: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/12.jpg)
Continuants Occurrents
Individuals
Classes
Parts and Time
Parts and
Regions
Parts and
Classes
Parts and
Processes
Part-Of
![Page 13: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/13.jpg)
Regions At every moment in time a spatial
object is located in a single region of space
At different moments spatial objects may be located in different regions
Parts and
Regions
t1 t5t2 t3 t4
r1 r5r2c r4r3
![Page 14: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/14.jpg)
Regions At every moment in time a spatial
object is located in a single region of space
At different moments spatial objects may be located in different regions
Parts and
Regions
t1 t5t2 t3 t4
r1 r5r2c r4r3
![Page 15: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/15.jpg)
Regions At every moment in time a spatial
object is located in a single region of space
At different moments spatial objects may be located in different regions
Parts and
Regions
t1 t5t2 t3 t4
r1 r5r2 c r4
![Page 16: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/16.jpg)
Regions At every moment in time a spatial
object is located in a single region of space
At different moments spatial objects may be located in different regions
Parts and
Regions
t1 t5t2 t3 t4
r1 r5r2 cr3
![Page 17: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/17.jpg)
Regions At every moment in time a spatial
object is located in a single region of space
At different moments spatial objects may be located in different regions
Parts and
Regions
t1 t5t2 t3 t4
r1 r5r2 cr4r3
![Page 18: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/18.jpg)
Parthood and Spatial Inclusion
Parts and
Regions
R(z) z is a region in spacez = r (x, t) z is the region where x is located at t
part-of (x, y, t) part-of (r (x ,t), r (y, t)) (Donnelly, IJCAI 03)
Spatial inclusion (coverage, (partly) location,…)
spatially-included (x, y, t) =def part-of (r (x, t), r (y ,t)) x is spatially included by y at t
![Page 19: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/19.jpg)
Phagocytosis / Digestion
v
c
t1 t2 t3 t4 t5
Parts and
Regions
virus
cell
Objects: Cell, Virus
![Page 20: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/20.jpg)
Phagocytosis / Digestion
t1 t2 t3 t4 t5
Parts and
Regions
r (c, t1) r (c, t2) r (c, t3) r (c, t4) r (c, t5)
r (v, t1)r (v, t2)
r (v, t3)
part-of (r (v, t3), r (c, t3))
Regions: Space occupied by Cell, space occupied by Virus
![Page 21: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/21.jpg)
General Problem Parthood always implies spatial inclusion,
but spatial inclusion does not always imply parthood:part-of (x, y, t) spatially-included (x, y, t)
Under which circumstances can we infer parthood from spatial inclusion ? When does inclusion without parthood obtain ?spatially-included (x, y, t) part-of (x, y, t)spatially-included (x, y, t) ‘ part-of (x, y, t)
Parts and
Regions
![Page 22: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/22.jpg)
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
Regions
![Page 23: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/23.jpg)
Inferring part from spatial inclusion: 2. Genetic Identity
Rules out objects of different genetic origin: Symbionts:
spatially-included (anEcoliBacterium , myIntestine) part-of (anEcoliBacterium , myIntestine)
Parasites: spatially-included (anEchinococcus, myLiver) part-of (anEchinococcus, myLiver)
Preys: spatially-included (anElephant, aSnake) part-of (anElephant, aSnake)
Embryos, Fetuses: spatially-included (Leonardo, Caterina) p (Leonardo, Caterina)
Parts and
Regions
![Page 24: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/24.jpg)
Inferring part from spatial inclusion: 3. Life Cycle
3. Life Cycle patterns which allow to assert parthood:
Parts and
Regions
t1 t2 t3 NOW
aGlycinMolecule, aCollagenFiber
aCytoplasm, aCell
aGlioblastoma, aBrain
![Page 25: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/25.jpg)
3. Life Cycle patterns which allow to rule out parthood:
Parts and
Regions
t1 t2 t3 NOW
aWaterMolecule, aCell
aBrainMetastasis, aBrain
but : part-of what ?
Inferring part from spatial inclusion: 3. Life Cycle
![Page 26: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/26.jpg)
4. Essential for function Transplants
functionally_related (aTransplant, anOrganism) spatially-included (aTransplant, anOrganism)
part-of (aTransplant, anOrganism)
Body Substances:functionally_related (myCSF, myCNS)
spatially-included (myCSF, myCNS) part-of (myCSF, myCNS)
Parts and
Regions
… but not: part-of (thisVolumeOfUrine, myBladder), because not essential for function
Inferring part from spatial inclusion: 4. Function
![Page 27: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/27.jpg)
Parts and
Regions
Inferring part from spatial inclusion: Decision algorithm
![Page 28: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/28.jpg)
Continuants Occurrents
Individuals
Classes
Parts and Time
Parts and
Regions
Parts and
Classes
Parts and
Processes
Part-Of
![Page 29: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/29.jpg)
Part-of between individuals and universals (classes)
Thumb part-of HandItaly part-of Europe
myThumb part-of myHand
Parts and
Classes
Individuals Classes
![Page 30: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/30.jpg)
Do Classes or Concepts Have Parts ?
Parts and
Classes
C0043520|A2655138|AUI|CHD|C1181977|A2658064|AUI|part_of|R17790075||UWDA|UWDA|||N||C0043520|A2655138|AUI|RN|C0225343|A2657439|AUI|part_of|R04504403||UWDA|UWDA|||N||C0043520|A2655138|AUI|RN|C1181590|A2656840|AUI|part_of|R04504402||UWDA|UWDA|||N||C0043520|A2655138|AUI|RN|C1181669|A2661552|AUI|part_of|R04504406||UWDA|UWDA|||N||C0043520|A2655138|AUI|RN|C1181740|A2670613|AUI|part_of|R04504407||UWDA|UWDA|||N||C0043520|A2655138|AUI|RN|C1181967|A2658311|AUI|part_of|R04504405||UWDA|UWDA|||N||C0043520|A2655138|AUI|RN|C1181977|A2658064|AUI|part_of|R04504404||UWDA|UWDA|||N||C0061622|A3026278|SCUI|RN|C0230663|A2928036|SCUI|part_of|R13611316|729422023|SNOMEDCT|SNOMEDCT|0|Y|N||C0061622|A3026278|SCUI|RN|C0230664|A2937887|SCUI|part_of|R13611317|748262021|SNOMEDCT|SNOMEDCT|0|Y|N||C0085268|A4320745|AUI|CHD|C0005974|A1180016|AUI|part_of|R24694280||GO|GO||N|N||C0085268|A4320745|AUI|CHD|C0029433|A2386282|AUI|part_of|R24694281||GO|GO||N|N||C0085268|A4320745|AUI|CHD|C1327401|A4329865|AUI|part_of|R24694282||GO|GO||N|N||C0085515|A1831585|AUI|CHD|C0559982|A1836877|AUI|part_of|R17785296||UWDA|UWDA|||N||C0085515|A1831585|AUI|CHD|C0559987|A1839331|AUI|part_of|R17785298||UWDA|UWDA|||N||C0085515|A1831585|AUI|CHD|C0828658|A1838548|AUI|part_of|R17785297||UWDA|UWDA|||N||C0085515|A1831585|AUI|CHD|C1305781|A1839335|AUI|part_of|R17785299||UWDA|UWDA|||N||C0085515|A1831585|AUI|RN|C0559982|A1836877|AUI|part_of|R04499637||UWDA|UWDA|||N||C0085515|A1831585|AUI|RN|C0559987|A1839331|AUI|part_of|R04499639||UWDA|UWDA|||N||C0085515|A1831585|AUI|RN|C0828658|A1838548|AUI|part_of|R04499638||UWDA|UWDA|||N||C0085515|A1831585|AUI|RN|C1305781|A1839335|AUI|part_of|R04499640||UWDA|UWDA|||N||C0085816|A0390532|AUI|CHD|C0226498|A0407514|AUI|part_of|R17773983||UWDA|UWDA|||N||C0085816|A0390532|AUI|CHD|C0935429|A1986901|AUI|part_of|R17773984||UWDA|UWDA|||N||
CUI1 CUI2 RELA
UMLS Metathesurus: MRREL table
![Page 31: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/31.jpg)
Do Classes Have Parts ?
“Axon part-of Neuron” (FMA) Does every neuron
has an axon?
“Axon part-of Cell ” (Gene Ontology) Do cells without
axons exist ? Do axons without
cells exist ?
Parts and
Classes
![Page 32: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/32.jpg)
“Axon part-of Neuron” (FMA) Does every neuron
has an axon?
“Axon part-of cell” (Gene Ontology) Do cells without
axons exist ? Do axons without
cells exist ?
“Keep in mind that part_of means can be a part of, not is always a part of “GO Editorial Style Guide, Oct 2003
“The part_of relationship (…) is usually “necessarily is_part”” GO Editorial Style Guide, May 2005
“A part_of B if and only if: for any instance x of A there is some instance y of B which is such that x stands to y in the instance-level part relation, and vice versa”.
Rosse & Smith MEDINFO 2004
Do Classes Have Parts ?Parts and
Classes
![Page 33: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/33.jpg)
Class-level Part-Of :Different Interpretations
One-sided DependencyPart on Whole
Mutual Mereological Dependency
Mereological Independency
Class A (part) Class B (whole) Examples
Cell Nucleus – CellUterus – Human Body Prostate Tumor – Prostate
Sulfur – MethioninCell – Human BodyConnective Tissue – Liver
Cell Membrane – CellVertebra – VertebrateBrain - Head
Uterus – MammalSulfur – Amino AcidTooth – Human
One-sided DependencyWhole on Part
Parts and
Classes
![Page 34: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/34.jpg)
One-sided DependencyPart on Whole
Mutual Mereological Dependency
Mereological Independency
Class A (part) Class B (whole) Examples
Cell Nucleus – CellUterus – Human Body Prostate Tumor – Prostate
Sulfur – MethioninCell – Human BodyConnective Tissue – Liver
Cell Membrane – CellVertebra – VertebrateBrain - Head
Uterus – MammalSulfur – Amino AcidTooth – Human
One-sided DependencyWhole on Part
GALEN, Gene Ontology 05 / 2005
FMA
Gene Ontology 11 / 2003
Class-level Part-Of :Different Interpretations
Parts and
Classes
![Page 35: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/35.jpg)
One-sided DependencyPart on Whole
Mutual Mereological Dependency
Mereological Independency
One-sided DependencyWhole on Part
Possible-Part (A, B) = def x,y: inst-of (x, A) inst-of (y, B) part-of (x, y)
* Notation according to Donnelly & Bittner(forthcoming)
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)
Part-Of12 (A, B) = def* Part-Of1 (A, B) Part-Of2 (A, B)
Class-level Part-Of :Different Interpretations
Parts and
Classes
![Page 36: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/36.jpg)
Continuants Occurrents
Individuals
Classes
Parts and Time
Parts and
Regions
Parts and
Classes
Parts and
Processes
Part-Of
![Page 37: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/37.jpg)
Example
Removal of foreign body from stomach
Removal of foreign body from stomachby endoscopy
Removal of foreign body from stomachby incision
Preparationfor Endoscopy
Introduction of Endoscope
Exploration
Removal offoreign body
Extraction of Endoscope
Preparationfor Surgery
Incision
Exploration
Removal offoreign body
Closure
t t
Parts and
Processes
Surgical Procedure
![Page 38: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/38.jpg)
Example
Removal of foreign body from stomach
Removal of foreign body from stomachby endoscopy
Removal of foreign body from stomachby incision
Preparationfor Endoscopy
Introduction of Endoscope
Exploration
Removal offoreign body
Extraction of Endoscope
Preparationfor Surgery
Incision
Exploration
Removal offoreign body
Closure
t t
Parts and
Processes
Surgical ProcedureTaxonomy of Processes
![Page 39: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/39.jpg)
Example
Removal of foreign body from stomach
Removal of foreign body from stomachby endoscopy
Removal of foreign body from stomachby incision
Preparationfor Endoscopy
Introduction of Endoscope
Exploration
Removal offoreign body
Extraction of Endoscope
Preparationfor Surgery
Incision
Exploration
Removal offoreign body
Closure
t t
Parts and
Processes
Surgical Procedure
Mereology of Processes
![Page 40: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/40.jpg)
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 process 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
![Page 41: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/41.jpg)
Theory 1: Process is instantiated by its subprocesses
Parts and
Processes
P1 P2 P3 P4
P
t
P1 P2 P3 P4
P
p
P1 P2 P3 P4
P
p
P1 P2 P3 P4
P
p
P1 P2 P3 P4
P
p
instance-ofinstance-ofinstance-ofinstance-of
t1 t2 t3 t4
Boris Hennig, unpublished
![Page 42: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/42.jpg)
Parts and
Processes
P1
P2
P‘‘‘
P1
P‘‘
P2
P1
P‘
P3
P2
P1
P
P3
P4
tt1 t2 t3 t4
pp p p
is-a
is-a
is-a
instance-of instance-of instance-ofinstance-of
has-part
has-part
has-part
has-part
Theory 2: Subprocesses are parts of their parent processes
![Page 43: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/43.jpg)
Conflicting views in Medical Terminologies
Parts and
Processes
Removal of foreign body from stomach by incision
Removal of foreign body from stomach by incision
Removal of foreign body from stomach
Incisionof Stomach
Removal of foreign body from stomach
Incisionof Stomach
is-a is-a
Most procedure classifications(roughly Theory 1)
SNOMED CT(Theory 2)
rg rg
Subprocesses are parts of their parent processesProcess is subsumed by its subprocesses
![Page 44: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/44.jpg)
SNOMED CT Rg (relation group) can be re-
interpreted as has-part
Parts and
Processes
![Page 45: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/45.jpg)
Conclusions Parthood has multiple meanings Interoperability between ontologies and
ontology based systems requires normative measures to avoid conflict between different meanings
Spatial inclusion may be a “better” foundational relation for describing biological continuants
Parthood between occurrents still requires thorough ontological enquiry
![Page 46: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/46.jpg)
Thanks
![Page 47: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/47.jpg)
![Page 48: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/48.jpg)
Meaning of Part in Biomedical OntologiesMereological relations are fundamental for any formal ontological description of entities of the biomedical domain. A formal account of what part is and isn’t is an indispensable requirement for interoperability between human and software agents
![Page 49: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/49.jpg)
Basics Mereology(-ies): Formal theory(-ies) of parts
and wholes (P. Simons 1987, Casati & Varzi 1999)
part-of: transitive, reflexive, antisymmetric relation between individuals: part-of (myThumb, myHand) & part-of (myHand,
myBody) -> part-of (myThumb, myHand)
part-of (myThumb, myHand) -> NOT part-of (myHand, myThumb)
part-of (myThumb, myThumb)
![Page 50: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/50.jpg)
Part-Of: derived relations proper-part-of:
proper-part-of (myThumb, myHand) NOT proper-part-of (myThumb, myThumb)more suitable for the biomedical domain, e.g.:“partial resection of stomach” “total resection of stomach”
proper overlap sharing of proper parts
overlap (myThorax, myVagusNerve)(“exclusive part-of”, cf. R. Schubert 1999)
unorthodox understanding of parthood-not to be taken for parthood
![Page 51: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/51.jpg)
Part-Of Subrelations (1) Partitions / Subdivisions:
disjoint parts which jointly sum up to a whole (Bittner 2004)decomposition of the entire body or any anatomical structure in a given context (Mejino 2004)
p1 = {my Body}p2 = {my head, my neck, my torso, my limbs}p3 = {my head, my neck, my torso, my left leg, my right leg, my left arm,
my right arm}p4 = {my head, my neck, my thorax, my abdomen, my left leg, my right leg,
my left upper arm, my left lower arm, my right upper arm, my right lower arm}
![Page 52: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/52.jpg)
Part-Of Subrelations (2) (Functional) Components
of integral compounds: The part contributes to the whole
not just as a structural unit but as essential to the purposeful activity of the whole(Pat Lambrix)
How to define function ?
![Page 53: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/53.jpg)
Part-Of Variations (3) Collections, Partonomic Inclusion
Uniform elements, e.g. blood, water, urine(Gerstl 1995, Bittner 2004) homomerous = parts are of the same
sort
![Page 54: The Meaning of Part](https://reader035.fdocuments.us/reader035/viewer/2022062315/56815c1c550346895dc9f1a2/html5/thumbnails/54.jpg)
Part-of: Dimensionality part-of (a, b) requires dim(a) dim(a):
-> e.g. 2D boundaries can be part of 3D objects
in Medicine: different conceptualizations, e.g. in the FMA boundaries cannot be part of 3D objects