Ontology in Buffalo August 27, 2012
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Ontology in Buffalo
August 27, 2012
Barry Smith
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Problems
How to find data
How to reason with data when you find it
How to integrate with other data
How to label the data you are collecting
Answer annotate your data with a common ontology
How to build a common ontology = an ontology that will integrate well with ontologies built for neighboring domains?
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Science requires a common suite of ontologies covering all scientific domains
Science is global and seamlessScientific data is public
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Ontologists in UB
• Barry Smith (Philosophy, Bioinformatics)• Werner Ceusters (Psychiatry, Bioinformatics)• Alan Ruttenberg (Director of UB Clinical and
Translational Data Exchange)• Alex Diehl (Neurology, Director of Ontology
Services for School of Medicine)
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• Pain Ontology grant with NIDCR• Protein Ontology grant with NIGMS• Infectious Disease Ontology grant with NIAID• National Center for Biomedical Ontology grant with
NIHGR• Cell Ontology grant with NIHGR• SNOMED grant with NLM• ARGOS on EU/US cooperation in Health IT• VIVO / eagle-I collaboration
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CollaborationsCenter for Brain and Behavior Informatics (http://cbbi.buffalo.edu)
Stroke Patient RegistryAlzheimers Patient RegistryDegenerative Disease Ontology Immunology Ontology
Roswell Park Cancer Institute (Malignancy Ontology)School of Dental Medicine (Pain Ontology, Picasso EHR)
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Institute for Healthcare Informatics•http://ahc.buffalo.edu/ihi/Center of Excellence in Bioinformatics and Life Sciences•http://www.bioinformatics.buffalo.edu/
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Ontologists in Buffalo
• Jason Corso (Computer Science – video analysis)
• Albert Goldfain (Blue Highway, Inc. – Infectious Disease Ontology, data exchange between devices)
• Dagobert Soergel (Information Studies – online advanced certificate program in ontology)
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National Center for Biomedical Ontology (NCBO)
Stanford University Biomedical Research
Mayo Clinic
University at Buffalo
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Uses of ‘ontology’ in PubMed abstracts
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By far the most successful: GO (Gene Ontology)
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GO provides a controlled system of terms for use in annotating (describing, tagging) data
• multi-species, multi-disciplinary, open source
• contributing to the cumulativity of scientific results obtained by distinct research communities
• compare use of kilograms, meters, seconds in formulating experimental results
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US $200 mill. invested in literature and data curation using GO
over 11 million annotations relating gene products described in the UniProt, Ensembl and other databases to terms in the GOexperimental results reported in 52,000 scientific journal articles manually annoted by expert biologists using GO
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GO is amazingly successful in overcoming the data balkanization problem
but it covers only generic biological entities of three sorts:
– cellular components– molecular functions– biological processes
and it does not provide representations of diseases, symptoms, …
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RELATION TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Biological Process
(GO)CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
Original OBO Foundry ontologies (Gene Ontology in yellow) 15
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RELATION TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Biological Process
(GO)CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
Environment Ontology
envi
ron
men
ts
are
her
e
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RELATION TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
COMPLEX OFORGANISMS
Family, Community, Deme, Population
OrganFunction
(FMP, CPRO)
Population Phenotype
PopulationProcess
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO) Phenotypic
Quality(PaTO)
Biological Process
(GO)CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Componen
t(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
http://obofoundry.org
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Developers commit to working to ensure that, for each domain, there is community convergence on a single ontology
and agree in advance to collaborate with developers of ontologies in adjacent domains.
http://obofoundry.org
The OBO Foundry: a step-by-step, evidence-based approach to expand
the GO
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OBO Foundry Principles
Common governance (coordinating editors)
Common training
Common architecture
• simple shared top level ontology
• shared Relation Ontology: www.obofoundry.org/ro
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Open Biomedical Ontologies Foundry
Seeks to create high quality, validated terminology modules across all of the life sciences which will be
• non-redundant
• close to language use of experts
• evidence-based
• incorporate a strategy for motivating potential developers and users
• revisable as science advances20
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The OBO Foundryis a collective experiment involving many biological and clinical communities attempting to create terminology resources which will support the goal of modularity
one ontology for each domain
No need for ‘mappings’
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OBO Foundry (example ontologies)GO Gene Ontology
CL Cell Ontology
SO Sequence Ontology
ChEBI Chemical Ontology
PATO Phenotype (Quality) Ontology
FMA Foundational Model of Anatomy Ontology
ChEBI Chemical Entities of Biological Interest
PRO Protein Ontology
Plant Ontology
Environment Ontology
Ontology for Biomedical Investigations
RNA Ontology
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Introduction to Basic Formal Ontology
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The central distinction
universal vs. instance
human being vs. Arnold Schwarzenegger
science text vs. diary
catalog vs. inventory
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Ontologies arerepresentations of universals in reality
aka kinds, types, categories, species, genera, ...
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A 515287 DC3300 Dust Collector Fan
B 521683 Gilmer Belt
C 521682 Motor Drive Belt
inventory
catalog26
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A 515287 DC3300 Dust Collector Fan
B 521683 Gilmer Belt
C 521682 Motor Drive Belt
instances
universals27
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siamese
mammal
cat
organism
object
animal
instances
frog
universals
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Pleural Cavity
Pleural Cavity
Interlobar recess
Interlobar recess
Mesothelium of Pleura
Mesothelium of Pleura
Pleura(Wall of Sac)
Pleura(Wall of Sac)
VisceralPleura
VisceralPleura
Pleural SacPleural Sac
Parietal Pleura
Parietal Pleura
Anatomical SpaceAnatomical Space
OrganCavityOrganCavity
Serous SacCavity
Serous SacCavity
AnatomicalStructure
AnatomicalStructure
OrganOrgan
Serous SacSerous Sac
MediastinalPleura
MediastinalPleura
TissueTissue
Organ PartOrgan Part
Organ Subdivision
Organ Subdivision
Organ Component
Organ Component
Organ CavitySubdivision
Organ CavitySubdivision
Serous SacCavity
Subdivision
Serous SacCavity
Subdivision
part
_of
is_a
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An example of a simple rule:Each term in an ontology represents
exactly one universal
For this reason ontology terms should be singular nouns
organism
headache
drug administration
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The Pre-History of BFO
• Aristotle (4th Century BC)
• Edmund Husserl’s Logical Investigations (1900-01)
• “Truthmaker” (1984)
• Patrick Hayes, “Naïve Physics Manifesto” (1985)
• Qualitative spatial reasoning (1990 – )
• DOLCE (1991 – )
• GO, FMA (2004 – )
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Aristotle’s Ontological Square
Substantial Accidental
Second substance
man
cat
ox
Second accident
headache
sun-tan
dread
First substance
this man
this cat
this ox
First accident
this headache
this sun-tan
this dread
Uni
vers
alP
artic
ular
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Edmund Husserl• Coined ‘formal ontology’• Introduced formal mereology• First formal account of dependence relations
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Substantial Accidental
Independent continuant Second accident
this man
this ox
this man’s headache that man’s knowledge of Greek
Par
ticul
arU
nive
rsal
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Truthmaker (1984)
Q: What is it in reality in virtue of which a true assertion such as
“John has a headache”
is true?
A: John’s current headache
34Kevin Mulligan, Peter M. Simons and Barry Smith, “Truth-Makers”, Philosophy and Phenomenological Research, 44 (1984), 287–321.
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John Searle
mind-to-world direction of fit – have truthmakers
Belief
Statement
Photograph
Scientific theory
world-to mind direction of fitPlan
Instruction
Request
Command
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Hayes’ Naïve Physics Manifesto
BFO 1.n: How can we construct a formal ontology (= an ontology formalized using first-order predicate logic) that will represent the entities we experience in our everyday perception and action?
BFL 2.n: How can we do this in a way that will also be compatible with what we know from physics?
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Qualitative spatial reasoning / mereotopology
• COSIT Conferences on Spatial Information Theory– http://www.cosit.info/
• Leeds Qualitative Spatial Reasoning Group – http://www.comp.leeds.ac.uk/qsr/
• Anthony Galton– http://empslocal.ex.ac.uk/people/staff/apgalton/
• Thomas Bittner– http://www.buffalo.edu/~bittner3
• Roberto Casati and Achille Varzi, Parts and Places (MIT Press, 1999)
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The History of BFO
2004 BFO 1.0
2005 OBO Relation Ontology (RO)
2006 BFO 1.1
adds generically dependent continuants
2012 BFO 2.0
incorporates top-level relations from RO
addresses problem of process measurement data (e.g. heart rates)
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BFO: A First Look
Continuant Occurrent(Process, Event)
IndependentContinuant
DependentContinuant
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..... ..... .....universals
instances
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Basic Formal Ontology
• a true upper level ontology
• no interference with domain ontologies
• no interference with issues of cognition
• no putative fictions
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Main reason to use BFO
BFO has the largest body of users
(compare: This telephone network has the largest number of subscribers)
Snowballing network effects:
data annotated using BFO-conformant ontologies becomes more valuable
numbers of people with expertise in building BFO-conformant ontologies increases
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How BFO is constructed and maintained
Simplicity
BFO has objects
BFO has qualities of objects
BFO has no qualities of qualities
Simplicity
BFO has particulars
BFO has universals
Only particulars instantiate universals
(no ‘meta-universals’)
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How BFO is constructed and maintained
Perspectivalism:
Ontologies are windows on reality
There is a multiplicity of windows (perspectives), all equally veridical, i.e. transparent to reality
For example we can view an organism as a single object or as a collection of molecules (granular perspectives)
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reality exists behind a transparent grid
= a veridical partition
Barry Smith, “Beyond Concepts, or: Ontology as Reality Representation”, (FOIS 2004), http://ontology.buffalo.edu/bfo/Beyond_Concepts.pdf
Ontological realism
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Alberti‘s Grid
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Common sense involves many verdical partitions
otherwise we would all be dead
The common sense partitions of folk physics, folk psychology, folk biology, are to a large degree transparent to realityIt is such common sense partitions that are involved, for instance, when someone takes your temperature in the hospital
Many veridical partitions
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The fundamental thesis of ontological realism
that many of our natural-language and scientific partitions are transparent to reality
is in fact quite trivial
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BFO 1.0
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Three Fundamental Dichotomies
• Universal/Type vs. instance
• Continuant vs. occurrent
• Dependent vs. independent
http://ontology.buffalo.edu/bfo/ 50
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Basic Formal Ontology
Continuant Occurrent(Process, Event)
IndependentContinuant
DependentContinuant
http://ifomis.uni-saarland.de/bfo/51
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Blinding Flash of the Obvious
Continuant Occurrent(Process, Event)
IndependentContinuant
DependentContinuant
http://ifomis.uni-saarland.de/bfo/52
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Continuant entities
- have continuous existence in time
- preserve their identity through change
- exist in toto if they exist at all
Occurrent 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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BFO: the very top
ContinuantOccurrent
(always dependent on one or more
independent continuants)
IndependentContinuant
Specifically DependentContinuant
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instance_of
Continuant Occurrent
process, eventIndependentContinuant
thing
Specifically DependentContinuant
quality
.... ..... .......
types
instances 56
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Specifically dependent continuants
• ‘
Qualities • of whiteness of this cheese, of mass of
this banana, of rigidity of this stone
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Continuant
IndependentContinuant
Specifically DependentContinuant
..... .....
Non-realizableDependentContinuant(quality)
Realizable DependentContinuant(function, role, disposition)
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Realizable dependent continuants
Role: nurse role, pathogen role, food role
Disposition: fragility, virulence, susceptibility, genetic disposition to disease X
Function: to pump (of the heart), to unlock (of the key)
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realization specifically_depends_on realizable
Continuant Occurrent
IndependentContinuant
bearer
SpecificallyDependentContinuant
disposition
.... ..... .......60
Process of realization
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BFO
ContinuantOccurrent(Process)
IndependentContinuant
(molecule, cell, organ,organism)
DependentContinuant
(quality, function,disease)
e.g. Functioning
e.g. Side-Effect, Stochastic Process, ...
..... ..... .... .....61
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BFO partitions reality
all terms included in the ontology are intended to designate universals in reality, in conformity with the basic principle of science-based ontology
but this means that science-based ontologies are on the one hand windows on the universals in reality, but on the other hand windows on the instances in reality
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Realizable dependent entities
role
disposition
functioncontinuants
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Their realizations
execution
expression
exercise
application
course
occurrents
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Continuant Occurrent
IndependentContinuant
Specifically DependentContinuant
Quality Disposition
e.g. FunctioningFunctione.g. Disease
Role
Realizable DependentContinuant
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BFO 1.1
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Specifically Dependent Continuants
SpecificallyDependentContinuant
Quality, PatternRealizable Dependent Continuant
if any bearer ceases to exist, then the quality or function ceases to exist
the color of my skin
the function of my heart
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Generically Dependent Continuants
GenericallyDependentContinuant
Information Object
Sequence
if one bearer ceases to exist, then the entity can survive, because there are other bearers
(copyability)
the pdf file on my laptop
the DNA (sequence) in this chromosome
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Information objects
pdf file
poem
symphony
algorithm
symbol
sequence
molecular structure
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Generically dependent continuants such as plans, laws …
are concretized in specifically dependent continuants
(the plan in your head, the protocol being realized by your research team, the law being implemented by this government agency)
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Generically dependent continuants
are concretized in specifically dependent continuants
Beethoven’s 9th Symphony is concretized in the pattern of ink marks which make up this score in my hand
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Universal or instance
ContinuantOccurrent(Process)
IndependentContinuant
human being,protocol document
DependentContinuant
pattern of ink marks
Applying the protocol
Side-Effect …
... .. ..... .... .....73
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Generically Dependent Continuants
GenericallyDependentContinuant
Information Entity
Sequence
.pdf file .doc file
instances 74
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BFO 2.0
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not a sum of objects, but something like a set:
a certain part of material reality, picked out by a certain granular partition
BFO:object_aggregate
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The Beatles
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The Beatles
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We use the
partition to pick out a certain object aggregate in this particular portion of material reality, then
we mask all other portions of reality, from external (the water) and internal (the cells and
molecules)
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John Paul George Ringo
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is a veridical partition. The
Beatles truly do (did) exist
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John Paul George Ringo
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king rook queen pawn knight bishop
chess pieces table topsurrounding
space
molecules
all these partitions are verdical
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which can however change its members over time
(e.g. the aggregate of members of the International Association for Ontology and Its Applications)
examples: populations, families, tribes, species, planetary systems – anything associated with a count, a registry, an inventory, a census
BFO:object_aggregate
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inventory
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member_part_of
a member_part_of b at t =Def. a is an object at t
& there is at t a mutually exhaustive and pairwise disjoint partition of b into objects x1, …, xn with a = xi for some natural number i.
Use this as basis for a theory of groups, organizations and other social objects
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human
John85
embryo fetus adultneonate infant child
instantiates at t1
instantiates at t2
instantiates at t3
instantiates at t4
instantiates at t5
instantiates at t6
in nature, no sharp boundaries here
Non-rigid universals = universals which (may) hold of a continuant
only for a certain time in the life of the continuant
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portion of water
this portion of H20
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portion of ice
portion of liquid water
portion of gas
instantiates at t1
instantiates at t2
instantiates at t3
Phase transitions
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temperature
John’s temperature endures through time87
37ºC 37.1ºC 37.5ºC37.2ºC 37.3ºC 37.4ºC
instantiates at t1
instantiates at t2
instantiates at t3
instantiates at t4
instantiates at t5
instantiates at t6
When we measure temperatures we impose a quantitative partition on a portion of reality
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temperature
John’s temperature (a quality instance) 88
37ºC 37.1ºC 37.5ºC37.2ºC 37.3ºC 37.4ºC
instantiates at t1
instantiates at t2
instantiates at t3
instantiates at t4
instantiates at t5
instantiates at t6
rigid
Determinable and determinate qualities
non-rigid
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temperature
John’s temperature 89
37ºC 37.1ºC 37.5ºC37.2ºC 37.3ºC 37.4ºC
instantiates at t1
instantiates at t2
instantiates at t3
instantiates at t4
instantiates at t5
instantiates at t6
in nature, no sharp boundaries here
in nature, no sharp boundaries here
Determinable and determinate qualities
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Recall how we deal with phase sortals
John instance_of nurse at t =Def.
John instance_of human being at t
& for some x, x instance_of nurse role
& x inheres_in John at t
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Role universals are rigid universals
Nurse role is_a role
(Role universals are rigid universals)
If x instance_of role at t, then x instance_of role at all times at which x exists.
Quality, disposition, region, material entity – these too are rigid universals
Is object a rigid universal?
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Full processes
p is a full process =Def. for some spatiotemporal region s,
p occupies s
& every process q which occupies some part of s is part of p
All full processes occupying any given spatiotemporal region are identical
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History
history of a material entity m = the full process which is the sum of processes taking place in the spatiotemporal region occupied by m
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HistoryThe relation between a material entity and its
history is one-to-one:
for any material entity a, there is exactly one process which is the history of a,
for every history h, there is exactly one material entity which h is the history of.
Histories are additive. Thus for any two material entities a and b, the history of the sum of a and b is the sum of their histories.
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Lives (for OGMS)
The life of an organism is the history of the corresponding OGMS:extended organism
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Partial processes
p is a partial process = p is a process & p is not a full process
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A spinning top is simultaneously getting warmer
Two distinguishable (indeed separately measurable process profiles) in a single region of spacetime
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Typically, processes are very complicated
a single running process p might be an instance of multiple universals such as
– 3.12 m/s motion process, – 9.2 calories per minute energy burning process,– 30.12 liters per kilometer oxygen utilizing process, – cardiovascular exercise process of type #16and so on.
Each of these corresponds to a partial process within p.
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Solution
• focus not on ‘thick’ processes, such as runnings or hearts’ beating
• but on ‘thin’ structural parts of processes
–called ‘process profiles’• (event patterns, …)
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• a process of the sort that can be represented by a chart plotting quality measurement results on a single dimension against a time axis
• a quality process profile is a truthmaker for a time series graph of this sort
Single quality process profile
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Examples of single quality process profiles
Examples of 1.the course of Jim’s temperature2.the course of Jim’s weight3.the course of Jim’s height4.the course of Jim’s fortuneEach is depictable by means of a time series graph
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Process profile that which the output of a correct device would
represent
= that which a correct time-series graph would represent
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Temperature
Call the process represented by this graph a (temperature) quality process profile
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The graph picks out just one dimension of qualitative change within a much larger
conglomerate of processes
Hence ‘quality process profile’
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What did your temperature do over the last month, Jim?
a target of a certain sort of cognitive selection, or cognitive profiling
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Some processes can incorporate multiple quality process profiles
Cardiac Cycle, Left Ventricle
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…corresponding to the multiple different sorts of partition of the same reality involved during measurement
Cardiac Cycle, Left Ventricle
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multi-quality process profile
Cardiac Cycle, Left Ventricle
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Compare perception of polyphonic music
• Cognitive selection of the cello part when you listen to a string quartet
• Picking out a certain process profile within a larger body of vibrations
• Ignoring sneezes, coughs, …• (sometimes focusing on sneezes and coughs
for diagnostic purposes)
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simultaneous causality
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specifically_depends_on
Continuant Occurrent
process
IndependentContinuant
thing
DependentContinuant
quality
.... ..... .......temperature dependson bearer
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The Beatles
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... red orange yellow green ...
... crimson reddeep red
blood red
...
Quality partitions
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Example: a chess game
W: Pawn to King4
B: Pawn to Queen’s Bishop 3
W. Pawn to Queen 3
...
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Two directions of fit
world-to-mind and mind-to-world
what begins as a plan, ends as a record (with truthmaker – if it is a true record – the journey you took)
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Example: An airline ticket
7:00am LH 465 Vienna
arrive London Heathrow 8:15am
9:45am LH 05 London Heathrow
arrive New York (JFK) 3:45pm
5:50pm UA 1492 New York (JFK)
arrive Columbus, OH 7:05pm
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Example: An airline ticket
7:00am LH 465 Vienna
arrive London Heathrow 8:15am
9:45am LH 05 London Heathrow
arrive New York (JFK) 3:45pm
5:50pm UA 1492 New York (JFK)
arrive Columbus, OH 7:05pm
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Example: An airline ticket
7:00am LH 465 Vienna
arrive London Heathrow 8:15am
9:45am LH 05 London Heathrow
arrive New York (JFK) 3:45pm
5:50pm UA 1492 New York (JFK)
arrive Columbus, OH 7:05pm
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Example: An airline ticket
7:00am LH 465 Vienna
arrive London Heathrow 8:15am
9:45am LH 05 London Heathrow
arrive New York (JFK) 3:45pm
5:50pm UA 1492 New York (JFK)
arrive Columbus, OH 7:05pm
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Example: An airline ticket
7:00am LH 465 Vienna
arrive London Heathrow 8:15am
9:45am LH 05 London Heathrow
arrive New York (JFK) 3:45pm
5:50pm UA 1492 New York (JFK)
arrive Columbus, OH 7:05pm
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Example: An airline ticket
7:00am LH 465 Vienna
arrive London Heathrow 8:15am
9:45am LH 05 London Heathrow
arrive New York (JFK) 3:45pm
5:50pm UA 1492 New York (JFK)
arrive Columbus, OH 7:05pm
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When you understood the airline ticket,
when you understood the reality of the corresponding portion of spacetime at the level of granularity dictated by the airline ticket,
you were directed towards a process profile called a journey
the journey is the truthmaker for the ticket
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Two directions of fit
world-to-mind and mind-to-world
what begins as a plan, ends as a record (with truthmaker – if it is a true record – the journey you took)
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Process profiles and the role of standardized notations
music
chess
choreography
ship stow planning
military manoeuvres
language
traffic law
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Process profiles and linguistics
Phonetics deals with the production of speech sounds by humans, often without prior knowledge of the language being spoken.
Phonology is about patterns of sounds in all spoken languages
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Protocol#1 protocol (GDC) instance_of OBI: type plan
specification.
#1 concretized_in #2 (= plan in mind of leader of research team, a realizable SDC to carry out some experiment.
realization of #2 starts with the creation of a series of sub-protocols, which are plan specifications for each team member.
The experiment itself is the sum of the realizations of these plans, having outputs further GDCs such as publications, databases …
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MusicBeethoven’s 9th Symphony, a certain abstract pattern
(generically dependent continuant), which we shall call #9
#9 instance_of symphony
symphony is_a musical work.
#9 instance_of musical work
#9 concretized_in specifically dependent continuant pattern of ink marks borne by this printed copy of the score #10
#9 concretized_in specifically dependent continuant pattern of grooves in this vinyl disk.
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Music
#10 instance_of generically dependent continuant type OBI:plan specification
#10 specifies how to create performance of #9.
#10 is concretized_in this network of subplan (complex realizable SDC) distributed across the minds of the conductor and members of this orchestra #11
#11 realized_in this performance #12
#12 “copied” in what you hear (a process inside your head)
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Two directions of fit
world-to-mind and mind-to-world
what begins as a plan, ends as a record (with truthmaker – if it is a true record – the journey you took)
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Are mental processes process profiles?
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