1 basic formal ontology barry smith march 2004
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The problem
Different communities of medical researchers use different and often incompatible category systems in expressing the results of their work
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The solution
“ONTOLOGY”
Remove “Ontology Impedance”
But what does “ontology” mean?
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Two alternative readings
Ontologies are oriented around terms or concepts = currently popular IT conception
Ontologies are oriented around the entities in reality = traditional philosophical conception, embraced also by IFOMIS
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Ontology as a branch of philosophy
seeks to establish
the science of the kinds and structures of objects, properties, events, processes and relations in every domain of reality
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Ontology a kind of generalized chemistry or zoology
(Aristotle’s ontology grew out of biological classification)
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Aristotle
world’s first ontologist
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World‘s first ontology
(from Porphyry’s Commentary on Aristotle’s Categories)
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Linnaean Ontology
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Ontology is distinguished from the special sciences
it seeks to study all of the various types of entities existing at all levels of granularity
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and to establish how they hang together to form a single whole (‘reality’ or ‘being’)
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different concept/terminology systems
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need not interconnect at all
for example they may relate to entities of different granularity
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we cannot make incompatible terminology-systems interconnect
just by looking at concepts, or knowledge or language
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we cannot make incompatible terminology-systems interconnect
by staring at the terminology systems themselves
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to decide which of a plurality of competing definitions to accept
we need some tertium quid
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we need, in other words,
to take the world itself into account
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BFO
= basic formal ontology
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BFO
ontology is defined not as the ‘standardization’ or ‘specification’ of conceptualizations
(not as a branch of knowledge or concept engineering)
but as an inventory of the entities existing in reality
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The BFO framework
will solve the problem of ontological impedance and provide tools for quality-control on the output of computer applications
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BFO not a computer application
but a Reference Ontology
(something like old-fashioned metaphysics)
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Reference Ontology
a theory of a domain of entities in the world
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BFOnot just a system of categoriesbut a formal theory with definitions, axioms, theoremsdesigned to provide the resources for
reference ontologies for specific domainsof sufficient richness that terminological incompatibilities can be resolved intelligently rather than by brute force
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Proposed solutiondistinguish two separate tasks:- the task of developing computer applications
capable of running in real time- the task of developing an expressively rich
framework of a sort which will allow us to resolve incompatibilities between definitions and formulate intuitive and reliable principles for database curation
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Reference Ontology
a theory of the tertium quid
– called reality –
needed to hand-callibrate database/terminology systems
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Methodology
Get ontology right first
(realism; descriptive adequacy; rather powerful logic);
solve tractability problems later
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Realist Perspectivalism
There is a multiplicity of ontological perspectives on reality, all equally veridical i.e. transparent to reality
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Anatomy vs. Pathology
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The Problem
The tumor developed in John’s lung over 25 years
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The Problem
____ developed in _____ over 25 years
process
state
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The Problem
The tumor developed in the lung over 25 years
substances
things
objects
continuants
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The Problem
The tumor developed in John’s lung over 25 years
PARTHOOD NOT DETERMINATE
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The Problem
The tumor developed in the lung over 25 years
substances
GLUING THESE TOGETHER YIELDS ONTOLOGICAL MONSTERS
processes
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Substances and processes exist in time in different ways
substance
t i m
e
process
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SNAP vs SPAN
Endurants vs perdurants
Continuants vs occurrents
In preparing an inventory of reality
we keep track of these two different kinds of entities in two different ways
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No way in which sums of substances and processes can exist in time
… hence
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Fourdimensionalism– only processes exist
– time is just another dimension, analogous to the three spatial dimensions
– substances are analyzed away as worms/fibers within the four-dimensional plenum
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There are no substances
Bill Clinton does not exist
Rather: there exists within the four-dimensional plenum a continuous succession of processes which are similar in a Billclintonizing way
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Fourdimensionalism (the SPAN perspective) is right in
everything it says
But incomplete
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Realist Perspectivalism
There is a multiplicity of ontological perspectives on reality, all equally veridical = transparent to reality
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Need for different perspectives
Not one ontology, but a multiplicity of complementary ontologies
Cf. particle vs. wave ontologies in quantum mechanics
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Two Orthogonal, Complementary Perspectives
SNAP and SPAN
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Snapshot Video ontology ontology
substance
t i m
e
process
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SNAP and SPANstocks and flows
commodities and services
product and process
anatomy and physiology
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SNAP and SPANSNAP entities
- have continuous existence in time
- preserve their identity through change
- exist in toto if they exist at all
SPAN entities
- have temporal parts
- unfold themselves phase by phase
- exist only in their phases/stages
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You are a substance
Your life is a process
You are 3-dimensional
Your life is 4-dimensional
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Many SNAP Ontologies
t1
t3t2
here time exists outside the ontology, as an index or time-stamp
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each SNAPi section through reality
includes everything which exists (present tense)
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mereology works without restriction (parthood is everywhere determinate) in
every SNAPi ontology
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Three kinds of SNAP entities
1. Substances (Independent)
2. SNAP Dependent Entities
3. Spatial regions, contexts, niches, environments
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SNAP dependent entities
States, powers, qualities, roles …
functions, dispositions, plans, shapes, status, habitus, liabilities …
= dependent SNAP entities
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SNAP dependent entities:
one-place:
your temperature, color, heightmy knowledge of French
the whiteness of this cheese the warmth of this stone
the fragility of this glass
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relational SNAP dependent entities
John Mary
love
stand in relations of one-sided dependence to a plurality of substances simultaneously
specific dependence
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Three kinds of SNAP entities
1. Substances
2. Dependents
3. Spatial regions, contexts, niches, environments
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Spatial regions + sites (contexts, niches, environments)
Organism species evolve into environments
Domesticated spatial regions: rooms, nostrils, your alimentary tract
Fiat spatial regions: JFK designated airspace
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SNAP: Entities existing in toto at a time
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The SPAN Ontology
t i m e
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here time exists as part of the domain of the ontology
The SPAN ontology
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mereology works without restriction everywhere here
t i m e
clinical trial
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Processes, too, are dependent on substances
One-place vs. relational processes
One-place processes:
your getting warmer
your getting hungrier
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Examples of relational processes
kissings, thumpings, conversations,
dancings,
join their carriers together into collectives of greater or lesser duration
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SPAN: Entities extended in time
SPANEntity extended in time
Portion of Spacetime
Fiat part of process *First phase of a clinical trial
Spacetime worm of 3 + Tdimensions
occupied by life of organism
Temporal interval *projection of organism’s life
onto temporal dimension
Aggregate of processes *Clinical trial
Process[±Relational]
Circulation of blood,secretion of hormones,course of disease, life
Processual Entity[Exists in space and time, unfolds
in time phase by phase]
Temporal boundary ofprocess *
onset of disease, death
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Relations to DOLCE
SNAP vs. SPAN
One ontology or many?
Qualities are SNAP entities
Treatment of space as quality
Quality regions (temperature, color, height)
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Two kinds of SPAN entities
1. Processes (including events: process-boundaries, settings)
2. Spatio-temporal regions
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Settings = 4-dimensional environments
Lobsters have evolved into environments marked by cyclical patterns of temperature change
Tudor EnglandThe Afghan winterThe window of opportunity for an invasion of Iraq
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How do you know whether an entity is SNAP or SPAN?
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problem cases
forest fire
anthrax epidemic
hurricane Maria
traffic jam
ocean wave
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forest fire:
a process
a pack of monkeys jumping from tree to tree and eating up the trees as they go
the Olympic flame:
a process or a thing?
(anthrax spores are little monkeys)
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The Epidemic (SNAP)
The Spread of an Epidemic (SPAN)
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Material examples:
performance of a symphonyprojection of a filmexpression of an emotionutterance of a sentenceapplication of a therapycourse of a diseaseincrease of temperature
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The Gene Ontology
is so confused about ‘functions’ and ‘processes’ because it does not have the distinction between SNAP and SPAN (between function and functioning)
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How link SNAP and SPAN together?
via formal relations
= entities which do not add anything to being
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Successive Causality
SNAP-SPAN: Agent causationA substance produces causally a process
SPAN-SPAN: Process causationOne process causes another process
SPAN-SNAP: Causal repercussionA process results in the modification of a substance (always mediated by process causation)
SNAP-SNAP: Causal originOne substance is the causal origin of another (mediated by other types of causal relations)
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Successive Causality
SNAP-SPAN: Agent causation
SPAN-SPAN: Process causation
SPAN-SNAP: Causal repercussion
SNAP-SNAP: Causal origin
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Simultaneous causality
SPAN-SPAN
The rise in temperature causes the (simultaneous) increase in pressure
(Boyle’s law)
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Substance Process
PARTICIPATION(a species of dependence)
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Participation (SNAP-SPAN)
A substance (SNAP) participates in a process (SPAN)
A runner participates in a race
A voter participates in an election
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Axes of variation
activity/passivity (agentive)
direct/mediated
benefactor/malefactor (conducive to existence) [MEDICINE]
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SNAP-SPAN
Participation
Perpetration (+agentive)
Initiation
Perpetuation
Termination
Influence
Facilitation
Hindrance
Mediation
Patiency(-agentive)
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Perpetration
A substance perpetrates an action (direct and agentive participation in a process):
The referee fires the starting-pistol
The captain gives the order
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Initiation
A substance initiates a process:
The referee starts the race
The attorney initiates the process of appeal
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Perpetuation
A substance sustains a process:
The singer sings the song
The charged filament perpetuates the emission of light
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Termination
A substance terminates a process:
The operator terminates the projection of the film
The judge terminates the imprisonment of the pardoned convict
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Influence
A substance (or its quality) has an effect on a process
The steepness of the slope affects the movement of the troopsThe politicians influence the course of the war
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Hindrance, prevention
A substance has a negative effect on the unfolding of a process (by participating in other processes)
The drug hinders the progression of the disease
The strikers prevent the airplane from departing
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Mediation
A substance plays an indirect role in the unfolding of a process relating other participants:
The Norwegians mediate the discussions between the warring parties
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Patiency
Dual of agentive participation
John kisses [Mary] (John agent)
Mary is kissed [by John] (Mary patient)
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Signatures of meta-relations
SNAP Component SPAN Component
Substances
SPQR…
Space Regions
Processuals
Processes
Events
Space-Time Regions
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Signatures of meta-relations
SNAP Component SPAN Component
Substances
SPQR…
Space Regions
Processuals
Processes
Events
Space-Time Regions
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Signatures of meta-relations
SNAP Component SPAN Component
Substances
SPQR…
Space Regions
Processuals
Processes
Events
Space-Time Regions
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Signatures of meta-relations
SNAP Component SPAN Component
Substances
SPQR…
Space Regions
Processuals
Processes
Events
Space-Time Regions
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REALIZATION
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Signatures of meta-relations
SNAP Component SPAN Component
Substances
SPQR…
Spatial Regions
Processuals
Processes
Events
Space-Time Regions
participation
realization
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Realization (SPQR process)
The most general relation between a dependent (SPQR…) entity and a process
The power to legislate is realized through the passing of a law
The role of antibiotics in treating infections is via the killing of bacteria
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Realization (SNAP-SPAN)
the execution of a plan, algorithm
the expression of a function
the exercise of a role
the realization of a disposition
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SPQR… entities and their SPAN realizations
plan
function
role
disposition
algorithm
SNAP
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SPQR… entities and their SPAN realizations
execution
expression
exercise
realization
application
course
SPAN
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SNAP SPAN
Participation
Substance Process
Realization
SPQR Process
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Creation
A process brings into being a substance:
The declaration of independence creates the new state
The work of the potter creates the vase
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Sustaining in being
A process sustains in being a substance:
The circulation of the blood sustains the body
Levying taxes sustains the army
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Degradation
A process has negative effects upon a substance
Eating sugar contributes to the deterioration of your teeth.
The flow of water erodes the rock
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Destruction
A process puts a substance out of existence
The explosion destroys the car
The falling of the vase on the floor breaks it
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Demarcation
A process creates (fiat or bona fide) boundaries of substances.
The signing of the treaty establishes fixed borders between the two nations
The tracing of the area of operation by the surgeon defines a boundary, the incision performed by the surgeon yet another one
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Blurring
A process destroys boundaries of substances:
The military stand-off creates the no man's land
The successful transplant obliterates the boundary between original and grafted tissue
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Creation
A process brings into being a dependent SNAP entity (quality, shape)
The accident reshapes the car.
The baking of the clay gives the vase its rigidity and color.
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Continuation
A process sustains the existence of a dependent SNAP entity
The firing of the fireworks maintains the coloration of the sky
The intake of alcohol sustains the rosiness of his cheeks
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Destruction
A process destroys/changes a dependent SNAP entity
The accident destroys the car's shape
The burning of the vase destroys its color
The demotion relieved him of his rank as an officer
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SNAP-SPAN
Participation
Perpetration (+agentive)
Initiation
Perpetuation
Termination
Influence
Facilitation
Hindrance
Mediation
Patiency(-agentive)
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SPAN-SNAP
Involvement
Creation
Sustenance
Destruction
Continuation
DegradationDestruction
Creation
DemarcationBlurring
Qualitative projection
Degradation
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Realist Perspectivalism
There is a multiplicity of ontological perspectives on reality, all equally veridical i.e. transparent to reality
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Cardinal Perspectives
SNAP vs. SPAN
Granularity (Micro vs. Meso vs. Macro)
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Cardinal Perspectives
SNAP vs. SPAN
Granularity (Micro vs. Meso vs. Macro)
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Ontological Zooming
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Ontological Zooming
human anatomy
cellular anatomy
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Part-Whole
Basic relation exclusively intra-ontological: either SNAP-SNAP or SPAN-SPAN.
SNAP-SNAP: only if SNAPis have the same temporal index
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Relations crossing the SNAP/SPAN border are never part-relations
John’s lifesubstance John
physiological processes
sustaining in existence
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Granularity
spatial region substance
parts of substances are always substances
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Granularity
spatial region substance
parts of spatial regions are always spatial regions
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Granularity
process
parts of processes are always processes
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Intra-granular and cross-granular parthood
across SNAPs:Kevin’s arm is part of KevinKevin’s molecule is part of Kevin
across SPANs:Kevin’s leg-movement is part of Kevin’s runningKevin’s cytometabolism is part of Kevin’s running
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THE END