1 vt. 2 ifomis institute for formal ontology and medical information science faculty of medicine...
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VT
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IFOMIS
Institute for Formal Ontology and Medical Information Science
Faculty of Medicine
University of Leipzig
http://ifomis.de
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Reference Ontology
An ontology is a theory of a domain of entities in the world
Ontology is outside the computer
seeks maximal expressiveness and adequacy to reality
and sacrifices computational tractability for the sake of representational adequacy
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Reference Ontology
rejects Gruber’s doctrine of minimal ontological commitment
-- this doctrine has been a disaster e.g. in medical informatics ontology
(it will cause further disasters in Semantic Web ontologies)
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Reference Ontology
a theory of reality
designed as quality control for
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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The Reference Ontology Community
IFOMIS (Leipzig) Laboratories for Applied Ontology (Trento/Rome,
Turin)Foundational Ontology Project (Leeds)Ontology Works (Baltimore)Ontek Corporation (Buffalo/Leeds)Language and Computing (L&C)
(Belgium/Philadelphia)
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Two basic BFO oppositions
Granularity
(of molecules, genes, cells, organs, organisms ...)
SNAP vs. SPAN
getting time right of crucial importance for medical informatics
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Research projects
UMLS – Unified Medical Language System
“Leipzig is an idea or concept”“An Amino Acid Sequence is an idea
or concept”“A human being is a physical entity”“A finger is an idea or concept”“A physician is a group”
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Research projects
ISO Standardization
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User Ontologies for Adaptive Interactive Software Systems
The problem: to extract information about users in a form that can be exploited by adaptive software.
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1. types of users2. characteristics of users
a. permanent (independent of experience with the software system)b. variable
i. change independently of use of system(for example: age, disease state)ii. change with experience of use of system
3. types of user behaviora. behavior independent of the systemb. behavior involving the system
i. types of system use (keyboard actions, etc.)ii. other behavior involving the system (rejection, etc.)
4. contexts/environments of usersa. contexts independent of the systemb. contexts of system use
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The Theory of Granular Partitions
Grids
Theory of Grain-Size
Mappings
Knowledge-increase
vs. Closed World Assumption
Complete and incomplete partitions
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Mereotopological Theories for Medical Ontology
Parts of anatomy of the human body
Parts of physiology of the human body Formal Theories for Layered Structures
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The Ontology of the Gene Ontology Medical Ontology and Medical Anthropology
Foundations of Spatiotemporal Ontology
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Testing the BFO/MedO approach
collaboration with
Language and Computing nv (www.landcglobal.be)
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L&C Technology
‘Semantic Indexing for Smart Information Retrieval and Extraction’
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L&C Technology
FreePharma®, L&C’s natural language analyzer for converting free text (spoken or typed) prescription and pharmacology information into XML.
FastCode®, L&C’s automated clinical coding product for translation of free text strings into ICD, SNOMED, MedDRA, etc.
LinKBase®, the largest formal medical knowledge base in the world, representing medicine in such a way that it is understandable for a computer.
LinKFactory®, L&C’s product suite for developing and managing large formal multilingual ontologies.
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L&C’s long-term goal
Transform the mass of unstructured free text patient records into a gigantic medical experiment
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The Project
collaborate with L&C to show how a realist ontology constructed on the basis of philosophical principles can help in overhauling and validating the large terminology-based medical ontology LinkBase® used by L&C for NLP
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IFOMIS’s long-term goal
Build a robust high-level BFO-MedO framework
THE WORLD’S FIRST INDUSTRIAL-STRENGTH PHILOSOPHY
which can serve as the basis for an ontologically coherent unification of medical knowledge and terminology
and for quality control in medical informatics software
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A language-independent ontology
an ontology of reality as it is independently of thought and language
realism about instances
realism about universals
mismatch between our concepts (expressed in any given language) and the universals existing in reality
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IFOMIS
will provide the open source upper level framework for L&C’s large terminology based ontology
QUESTION: what language to use for this purpose?
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Ontology:A Generalization of Davidsonian
Semantics
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NOT ALL FORMALISMS ARE CREATED
EQUAL
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Armstrong’s
spreadsheet ontology
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F G H I J K L M N O P Q R S T U V
a
b
c
d
e
f
g
h
i
j
k
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F G H I J K L M N O P Q R S T U V
a x x x x x
b
c
d
e
f
g
h
i
j
k
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F G H I J K L M N O P Q R S T U V
a x x x x x
b x x x x x
c
d
e
f
g
h
i
j
k
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F G H I J K L M N O P Q R S T U V
a x x x x x
b x x x x x
c x x x x x
d
e
f
g
h
i
j
k
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F G H I J K L M N O P Q R S T U V
a x x x x x
b x x x x x
c x x x x x
d x x
e
f
g
h
i
j
k
and so on …
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Fantology
The doctrine, usually tacit, according to which ‘Fa’ (or ‘Rab’) is the key to ontological structure
The syntax of first-order predicate logic is a mirror of reality
(Fantology a special case of linguistic Kantianism: the structure of language is they key to the structure of [knowable] reality)
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Formal Ontology and Symbolic Logic
Great advances of Frege, Russell, Wittgenstein, Peano
(in logic, and in philosophy of mathematics)
Leibnizian idea of a universal characteristic
…symbols are a good thing
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First-order logic
F(a), G(a)
R(a,b)
F(a) v G(a)
F(a) & G(a)
F(a) v xR(a,x)
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Booleanism
if F stands for a property and G stands for a property
then
F&G stands for a property
FvG stands for a property
not-F stands for a property
FG stands for a property
and so on
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Strong Booleanism
There is a complete lattice of properties:
self-identity
FvG
F G
F&G
non-self-identity
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Strong Booleanism
There is a complete lattice of properties:
self-identity
FvG
not-F F G not-G
F&G
non-self-identity
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Booleanism
responsible, among other things, for Russell’s paradox
Armstrong, D. Lewis free from Booleanism
With their sparse theory of properties
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20th-Century Analytic Metaphysics
embraced Booleanism as the default position
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that Lewis and Armstrong
arrived at their sparse view of properties against the solid wall of fantological Booleanist orthodoxy
is a miracle of modern intellectual historyanalogous to a 5 stone weakling climbing
up to breathe the free air at the top of Mount Everest with 1000 ton weights attached to his feet
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leading them back, on this point,
to where Aristotelians were from the very beginning
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Standard semantics
F stands for a propertya stands for an individual
properties belong to Platonic realm of forms
orproperties are sets of individuals for which
F(a) is true (circularity)
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Fantology infects computer science, too
here I will concentrate on the role of fantology within analytical metaphysics
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Fantology
Works very well in mathematics
Platonist theories of properties here are very attractive
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Fantology
Fa
All generality belongs to the predicate
‘a’ is a mere name
Contrast this with the way scientists use names:
The electron has a negative charge
DNA-Binding Requirements of the Yeast Protein Rap1p as selected In Silico from Ribosomal Protein Gene Promoter Sequences
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For extreme fantologists ‘a’ leaves no room for ontological complexity
Hence: reality is made of atoms
Hence: all probability is combinatoric
Fantology reduces all complexity to Boolean combination
All true ontology is the ontology of ultimate universal furniture – the ontology of some future, perfected physics
Thus fantology is conducive to reductionism in philosophy
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Fantology
Tends to make you believe in some future state of ‚total science‘
when the values of ‚F‘ and ‚a‘, all of them,will be revealed to the elect
(A science is a totality of propositions closed under logical consequence)
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Fantological Mysterianism
Fa
noumenal view of particularsCf. Wittgenstein’s Tractatus (doctrine of
simples)
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Fantology leads you to talk nonsense about family
resemblances
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Fantology
emphasizes the linguistic over the perceptual/physiognomic
(the digitalized over the analogue)
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Fantology implies a poor treatment of relations
R(a,b)
in terms of adicity
What is the adicity of your headache (A relation between your consciousness and various processes taking place in an around your brain) ?
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For the fantologist
“(F(a)”, “R(a,b)” … is the language for ontology
This language reflects the structure of reality
The fantologist sees reality as being made up of atoms plus abstract (1- and n-place) ‘properties’ or ‘attributes’
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Fantology
Fa
To understand properties is to understand predication
(effectively in terms of functional application à la Frege)
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The limitations of fantology
lead one into the temptations of possible world metaphysics,
and other similar fantasies
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Fantology leads one to talk nonsense about possible worlds
Definition: A possible world W is a pair (L,D) consisting of a set of first-order propositions L and a set of ground-level assertions D. …
Informally, the set L is called the laws of W, and the set D is called the database of W. Other informal terms might be used: L may be called the set of axioms or database constraints for W.
(John Sowa)
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Fantology and time
Fa
No clear way to deal with time and tense
(Set theory neglects the dimension of time)
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Fantology
(given its roots in mathematics)
has no satisfactory way of dealing with time
hence leads to banishment of time from the ontology
(as in Quine’s and Armstrong’s four-dimensionalism)
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The alternative to fantology
‘a’ in ‘F(a)’ refers to something that is complexThus we must take the spatiality and materiality and modular complexity and temporality of substances seriously
Mereology plus granularity plus theory of spatial extension plus dimension of TIME
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Strange goings on!
Jones did it slowly, deliberately, in the bathroom, with a knife, at midnight. What he did was butter a piece of toast.
There is an action x such that Jones did x slowly and Jones did x deliberately and Jones did x in the bathroom:
x Did(Jones, x)
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Solution
not FOPL
but FOLWUT
first-order logic with universal terms
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A better syntax
variables x, y, z … range over
universals and particulars
predicates stand only for FORMAL relations such as instantiates, part-of, connected-to, is-a-boundary-of, is-a-niche-for, etc.
FORMAL relations are not extra ingredients of being
(compare jigsaw puzzle pieces and the relations between them)
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Linguistic Ontologiesdesign issues
Network basedhierarchy (taxonomy)
WordNet
heterarchySIMPLE
Frame basedMikrokosmos
Generative Lexicon
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<parte>part
Isa
Isa
Isa
<volare>fly
Used_for
Used_for
<aeroplano>airplane
Is_a_part_of
<uccello>bird
Is_a_part_of
<edificio>building
Is_a_part_of
Ala (wing)
SemU: 3232Type: [Part]Part of an airplane
SemU: 3268Type: [Part]Part of a building
SemU: D358Type: [Body_part]Organ of birds for flying
SemU: 3467Type: [Role]Role in football
<giocatore>player
Isa
Agentive
Linguistic OntologiesSIMPLE
<fabbricare>make
Agentive
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FOLWUT
All predicates are formal predicates (analogous to ’=’)
(cf. Filmore-style case grammars)
Material content is captured entirely by terms, both constant and variable
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A new syntax:
=(x,y)Part(x,y)Inst(x,y)Dep(x,y)Isa(x,y)
John is wise: Inst(John, wisdom)John is a man: Isa(John, man)
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Jones buttered the toast
x Did(Jones, x) & Inst(x, buttering)
A man buttered the toast
xy Did(y, x) & Inst(x, buttering)
& Inst(y, man)
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Sparse repertoire of predicates
insurance against Booleanism, and against paradoxes
Combined with quantification over universals, gives us some of the power of 2nd-order logic
(2nd-order logic is problematic only when Boolean combination is allowed in the space of predicates)
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Compare the syntax of set theory
(x,y)
one (formal) predicate
+
constant and variable terms for material entities called sets
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First-order logic with identity
= interpretation of identity is fixed
(does not vary with semantics)
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Syntax of FOLWUT
A few dozen formal predicates
+
constant and variable terms for particulars and universals
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Which formal relations we need is not an a priori matter
Logic gives us no clue as to what the few dozen formal relations are
(they must include: location in space, location at a time …)
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Which universals exist is not an a priori matter
Logic gives us no clue as to what universals exist in reality
(they must include: universals corresponding to each of the elements in the periodic table)
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New syntax:
=(x,y)
Part(x,y)
Inst(x,y)
Dep(x,y)
Does(x,y)’
What else?
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what ARE the formal relations?
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Different ontological perspectives
Universals vs. Particulars
Different levels of granularity:
molecular, cellular, organism ...
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Nouns and verbs
Substances and processes
Continuants and occurrents
Endurants and perdurants
In preparing an inventory of reality
we keep track of these two different categories of entities in two different ways
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Substances and processes
t i m
e
process
demand different sorts of inventories
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Endurants/continuants
Objects, things, substances +
states, powers, qualities, roles,
functions, dispositions, plans, shapes …
Perdurants/Occurrents
Processes = the expressions, realizations of functions, roles, powers in time
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Endurants/continuants
SNAP ontology
Perdurants/Occurrents
SPAN ontology
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Substances and processes form two distinct orders of being
Substances exist as a whole at every point in time at which they exist at all
Processes unfold through time, and are never present in full at any given instant during which they exist.
When do both exist to be inventoried together?
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SNAP: Entities existing in toto at a time
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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 between SNAP and SPAN
SNAP-entities participate in processes
they have lives, histories
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SPQR… entities and their SPAN realizations
the expression of a function
the exercise of a role
the execution of a plan
the realization of a disposition
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SPQR… entities and their SPAN realizations
function
role
plan
disposition
therapy
disease
SNAP
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SPQR… entities and their SPAN realizations
expression
exercise
execution
realization
application
course
SPAN
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How are entities in the SNAP and SPAN ontologies related together?
via FORMAL RELATIONS
such as expression (between a function and a process) …
Other formal relations:
instantiation, part-whole, identity
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A hypothesis (first rough version)
Formal relations are those relations which are not captured by either SNAP or SPAN because they traverse the SNAP-SPAN dividethey glue SNAP and SPAN entities together
above all participation: Does(John,x)
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The idea (modified version)
Formal relations are the relations that hold SNAP and SPAN entities/ontologies together+ analogous relations that come for free, they do not add anything to being
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Generating a typology
Two main types of formal relations:
inter-ontological („transcendental“): obtain between entities of different ontologies
intra-ontological: obtain between entities of the same ontology (intra-SNAP, intra-SPAN)
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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
An organ participates in a sickness
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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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Participation
the tumor and its growth
the surgeon and the operation
the virus and its spread
the temperature and its rise
the disease and its course
the therapy and its application
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Three parameters:
- the arity of the relation
- the types of the relata, expressed as an ordered list, called the signature of the relation
- the formal nature of the relation (benevolent, malevolent, etc.)
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Participation (genus)
A substance (SNAP) participates in a process (SPAN)
A runner participates in a race
An organ participates in a sickness
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Perpetration (species)
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 (species)
A substance initiates a process:
The referee starts the race
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Perpetuation (species)
A substance sustains a process:
The charged filament perpetuates the emission of light
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Termination (species)
A substance terminates a process:
The operator terminates the projection of the film
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Influence (species)
A substance (or its quality) has an effect on a process
The politicians influence the course of the war
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Facilitation (species)
A substance plays a secondary role in a process (for example by participating in a part or layer of the process)
The traffic-police facilitate our rapid progress to the airport
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Hindrance, prevention (species)
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 (species)
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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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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2nd Family
REALIZATION
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Realization
the performance of a symphonythe projection of a filmthe expression of an emotionthe utterance of a sentencethe application of a therapythe course of a diseasethe increase of temperature
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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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SNAP->SPAN
Participation (genus)
Substance -> Process
Realization (genus)
SPQR -> Process
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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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SNAP-SPAN
Participation
Perpetration (+agentive)
Initiation
Perpetuation
Termination
Influence
Facilitation
Hindrance
Mediation
Patiency(-agentive)
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Types of Formal Relation
IntracategorialMereological (part)Topological (connected, temporally precedes)Dependency (e.g. functional ?)
IntercategorialInherence (quality of)Location Participation (agent)Dependency (of process on substance)
TranscendentalsIdentity