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

Example II

t1 t2

Parts and Time

d

d’

t

BIOMEDICAL

ONTOLOGY

Colon with complete destruction of mucosa

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

Normal colon parts

BIOMEDICAL

ONTOLOGY

Normal colon

BIOMEDICAL

ONTOLOGY

Colon tumor

BIOMEDICAL

ONTOLOGY

Rectal carcinoma with metastasis

BIOMEDICAL

ONTOLOGY

Metastasized structures

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

The Meaning of Part (Discussion)

Anand Kumar MBBS, PhD

IFOMIS, Department of Medicine, Univ. of Saarland, Germany.

BIOMEDICAL

ONTOLOGY