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The Meaning of Part (Discussion)
Anand Kumar MBBS, PhD
IFOMIS, Department of Medicine, Univ. of Saarland, Germany.
BIOMEDICAL
ONTOLOGY
ContinuantsSNAP entities
OccurrentsSpan entities
Individuals(Particulars)
Classes(Universals)
Parts and Time
Parts and
Regions
Parts and
Classes
Parts and
Processes
Criteria for inferring part from spatial inclusion
3. Life Cycle patterns which allow to assert parthood:
Parts and
Regions
t1 t2 t3 NOW
aGlycinMolecule, aCollagenFiber
aCytoplasm, aCell
aGlioblastoma, aBrain
BIOMEDICAL
ONTOLOGY
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
BIOMEDICAL
ONTOLOGY
Processes involvedT2: Tumor invades muscularis propriaN1: Metastasis in 1 to 3 lymph nodes
M1: Distant metastasis
Pathological structuresT2N1M1 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
BIOMEDICAL
ONTOLOGY
N2 colon carcinoma structure implies1 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 impliesLung 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
BIOMEDICAL
ONTOLOGY
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-partN1 colon carcinomatous process and has-part
M1 colon carcinomatous process
BIOMEDICAL
ONTOLOGY
Instance of T2N1M1 colon carcinoma structure
inst(T2N1M1 carcinoma structure) implies mucosal carcinoma structure and
muscularis mucosal carcinoma structure and3 paracolic lymph nodal metastatic structure and
left upper lung lobe metastatic structure
T2N1M1 carcinomatous structure transformation_of T2N1M0 carcinomatous structure transformation_ofT2N0M0 carcinomatous structure transformation_ofT1N0M0 carcinomatous structure transformation_ofTisN0M0 carcinomatous structure transformation_of
Colon part
BIOMEDICAL
ONTOLOGY
Instance of T2N1M1 colon carcinoma structure
left upper lung metastatic carcinomatous process preceded-bydistant organ metastasis preceded-by
paracolic lymph nodal carcinomatous process preceded-bylymph nodal metastasis preceded-by
muscularis proprial carcinomatous process preceded-bytrans-submucosal carcinomatous invasion preceded-by
submucosal carcinomatous process preceded-bytransmucosal carcinomatous invasion preceded-by
mucosal carcinomatous process preceded-bytranscellular carcinomatous process preceded-by
epithelial cellular carcinomatous process
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 – CellChlorophyll – OrganismProstate Tumor – Prostate
Sulfur – MethioninWing – ChickenHeart – Drosophila
Cell Membrane – CellVertebra – VertebrateBody Surface – Body
Uterus – MammalSulfur – Amino AcidTooth – Human
• One-sided DependencyWhole on Part
Parts and
Classes
BIOMEDICAL
ONTOLOGY
Can not be generalized to all instances and thus are also all-some Or some-some relations
Case of historical parthoods
Mutual dependency
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
Regions
BIOMEDICAL
ONTOLOGY
Artificial femoral head part-of Femur with artificial head?Drug administration with biological prethyronine?
Drug prethyronine part-of thyroid cell?
Non-biological artefact
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)
Parts and
Regions
… but not: part-of (thisVolumeOfUrine, myBladder), because not essential for function
BIOMEDICAL
ONTOLOGY
Urine in urinary bladder has functionsPortion of Glomerular filtrate part-of Kidney?
Non-biological artefact
BIOMEDICAL
ONTOLOGY
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 properlyUterus part-of human body?
Human uterus?Human uterus within human body?
Why not female human body on the RHS?
Example
Removal of foreign body from stomach
Removal of foreign body from stomachby endoscopy
Removal of foreign body from stomachby incision
Preparation
Introduction of Endoscope
Exploration
Removal offoreign body
Extraction of Endoscope
Preparation
Incision
Exploration
Removal offoreign body
Closure
t t
Parts and
Processes
Surgical Procedure
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
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
is-a is-a is-a is-a is-a
instance-ofinstance-ofinstance-ofinstance-of
t1 t2 t3 t4
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
BIOMEDICAL
ONTOLOGY
Process p;(p, ptinit) is not the complete p;
complete p exists only when the process instance is completed
Processes
Sub-process sp1;(sp1, sp1tinit) is not the complete sp1;
sp1tinit = ptinit
complete sp exists only when the sub-process instance completed
+ sp1 … spnSub-process spn;
(spn, spntend) is the complete spn;spntend = ptend