Transcript Pax Terminologica

Basic Formal Ontology
Barry Smith
1
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
How to know how to build an ontology for a
new domain that will integrate well with
ontologies built by others for neighboring
domains
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Integration, in biomedicine
– across different species
– across levels of granularity (organ,
organism, cell, molecule)
– across different perspectives (physical,
chemical, biological, clinical)
– within and across disciplines and
specialisms
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NIH Mandates for Sharing of
Research Data
Investigators submitting an NIH
application seeking $500,000 or more in
any single year are expected to include a
plan for data sharing
(http://grants.nih.gov/grants/policy/data_sharing)
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Types of ontologies
Upper-level
integrating
ontologies
Domain
ontologies
Ontologies in
support of
science
Administrative
ontologies
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Types of ontologies
Ontologies in
support of
science
Administrative
ontologies
(e-commerce,
etc.)
Upper-level
integrating
ontologies
Domain
ontologies
BFO (Basic Formal
Ontology)
DOLCE, SUMO
GO
FMA
SNOMED
FOAF top level:
HL7 RIM
Amazon.com
ontology
Library of Congress
Catalog
6
Administrative ontologies
• Highly task-dependent – reusability and
compatibility not (always) important
• Entities may be brought into existence by
the ontology itself. (Convention, fiat ...)
• Can be secret
• Can be bought and sold
• Are comparable to software artifacts
• Need not be mutually interoperable
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For local, administrative purposes, goals
may be met if each organization creates its
own controlled terminologies
In science we must go further
Science is global
Science is public
Science is not steerable by fiat
Science is seamless
Science is open
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Why build scientific ontologies?
There are many ways to create
terminologies
Multiple terminologies will not solve data
silo problems
 We need to constrain terminologies so
that they converge
9
Evidence-based terminology
development
Q:
A1:
A2:
A3:
What is to serve as constraint?
Authority / Fiat ?
First in field (Founder effect) ?
Best candidate terminology ?
But what does ‘best’ mean?
A4: Voting ?
But then on what grounds should people vote?
A5: Reality, as revealed, incrementally, by
experimentally-based science
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http://ifomis.org/bfo
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http://ifomis.org/bfo
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Ontologies
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AFO Foundational Ontology
BioTop: A Biomedical Top-Domain Ontology
Cell Ontology (CL)
Chemical Entities of Biological Interest (ChEBI)
Common Anatomy Reference Ontology (CARO)
Drug Interaction Ontology (DIO)
Foundational Model of Anatomy (FMA)
Gene Ontology (GO)
Infectious Disease Ontology (IDO)
Neuroscience Information Framework Standard (NIFSTD) Ontology
Ontology for Biomedical Investigations (OBI)
Phenotypic Quality Ontology (PaTO)
Protein Ontology (PRO)
Sequence Ontology (SO)
Universal Core Semantic Layer (UCore SL)
Subcellular Anatomy Ontology (SAO)
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Zebrafish Anatomical Ontology (ZAO)
Institutions and Groups
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AstraZeneca - Clinical Information Science
BioPAX-OBO
BIRN Ontology Task Force (BIRN OTF)
Computer Task Group Inc.
Dumontier Lab
INRIA Lorraine Research Unit
Language and Computing
medicognos
National Center for Multi-Source Information Fusion
Ontology Works Inc.
OpenEHR
REMINE
Science Commons - Neurocommons
University of Texas Southwestern Medical Center
US Army Net-Centric Data Strategy Center of Excellence
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The History of BFO
BFO 1.0 2004
BFO 1.1: add generically dependent
continuants
BFO: 2.0: incorporate the top-level relation
from the OBO Relation Ontology into BFO
1.1, and ensure that all relations internal to
BFO (e.g. dependence) are included
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OBO Relation Ontology 1.0
Foundational
is_a
part_of
Spatial
located_in
contained_in
adjacent_to
Temporal
transformation_of
derives_from
preceded_by
Participation
has_participant
has_agent
“Relations in Biomedical Ontologies”,
Genome Biology, April 2005
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Kinds of relations
<universal, universal>: is_a, part_of, ...
<instance, universal>: this explosion
instance_of the universal explosion
<instance, instance>: Mary’s heart
part_of Mary
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Strategy of many ontology
initiatives e.g. in biomedicine
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Painting the Emperor´s Palace is
hard
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therefore
we will not try to paint the Palace at all
instead, we will be satisfied with a
grainy snapshot of some other building
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Strategy of ontological realism
get real ontology right first
and then investigate ways in which this real
ontology can be translated into computeruseable form later
not allow issues of computer-tractability to
determine the content of the ontology
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The methodology of ontological
realism
• Find out what the world is like by doing
science, talking to other scientists (SMEs) and
working continuously with them to ensure that
you don’t go wrong
• Create ontologies adequate to this world, not
to some simplified model in your laptop
• Build representations of entities in the world,
not of of the concepts in your colleagues’
heads or of the webpages in their servers
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For scientific ontologies
openness, reusability and
compatibility with neighboring scientific
ontologies are crucial
• Scientific ontologies must evolve gracefully
• Scientific ontologies are comparable to
scientific theories
• Scientific ontologies must be evidencebased, which means: based in the
observation of instances in the laboratory
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Science texts are
representations of what is
general in reality
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Scientific ontologies have a special
feature
Every term in the ontology must be such that
the developers of the ontology believe it to
refer to some general entity (type, universal,
class) in reality on the basis of the best
current scientific evidence
Entities in reality include also information
artifacts, scientific experiments, organizations
…
26
The central distinction
universal vs. instance
(catalog vs. inventory)
(science text vs. diary)
(human being vs. Arnold Schwarzenegger)
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Ontologies are
representations of
universals in reality
aka kinds, types, categories,
species, genera, ...
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instances
A
B
C
515287
521683
521682
DC3300 Dust Collector Fan
Gilmer Belt
Motor Drive Belt
universals29
For scientific ontologies
it is generalizations (universals) that are
important
For databases it is (normally) instances
that are important
= particulars in reality:
• patient #0000000001
• headache #000000004
• MRI image #23300014, etc.
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universals
substance
organism
animal
mammal
cat
siamese
frog
instances
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Each term in an ontology represents
exactly one universal
For this reason ontology terms should be
singular nouns
headache
human being
drug administration
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A photographic image is a
representation of an instance
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Three Levels to Keep Straight
• Level 1: the entities in reality, both
instances and universals
• Level 2: cognitive representations of this
reality e.g. on the part of scientists ...
• Level 3: publicly accessible concretizations
of these cognitive representations in textual
and graphical artifacts
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Ontology development
starts with: Level 2 = the cognitive
representations of practitioners or
researchers in the relevant domain
results in: Level 3 representational artifacts
(comparable to maps, science texts,
dictionaries)
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We can’t take photographs of universals
But we can create cartoons and diagrams
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Anatomical
Structure
Anatomical Space
Organ Cavity
Subdivision
Organ
Cavity
Organ
Serous Sac
Cavity
Subdivision
Serous Sac
Cavity
Serous Sac
Organ
Component
Organ
Subdivision
Pleural Sac
Pleural
Cavity
Parietal
Pleura
Interlobar
recess
Organ Part
Mediastinal
Pleura
Tissue
Pleura(Wall
of Sac)
Visceral
Pleura
Mesothelium
of Pleura
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The Gene
Ontology
is_a ─
part_of ─
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How do we know which general
terms designate universals?
Roughly: terms used in a plurality of
sciences to designate entities about
which we have a plurality of different
kinds of testable propositions / laws
(compare: cell, electron, membrane ...)
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universals vs. their extensions
The extension of the universal A is the class
of A’s instances
universals
{a,b,c,...}
collections of particulars
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Extension =def
the collection of all particular A’s, where ‘A’
is the name of a universal
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Class =def.
a maximal collection of particulars referred to by a
general term
the class A =def. the collection of all particular A’s
where ‘A’ is a general term (e.g. ‘brother of Elvis fan’,
‘cell’)
Classes are on the same level as the instances which
they contain
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Problem
The same general term can be used to
refer both to universals and to
collections of particulars.
HIV is an infectious retrovirus
HIV is spreading very rapidly through Asia
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Not all classes correspond to
universals
universals
extensions of universals
classes
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a spectrum of cases
cell
membrane
retina
lung
brother of Elvis fan
chemical whose
name begins with ‘B’
thing owned by the
emperor
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universals vs. classes
universals
defined classes
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(Scientific) Ontology =def.
a representational artifact whose representational
units (which may be drawn from a natural or from
some formalized language) are intended to
represent
1. universals [+ some defined classes] in reality
2. those relations between these universals which
obtain universally (= for all instances)
lung is_a anatomical structure
lobe of lung part_of lung
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Contemporary top-level
ontologies
DOLCE = Domain Ontology for Linguistic
and Cognitive Engineering
SUMO = Suggested Upper Merged
Ontology
BFO = Basic Formal Ontology
have many common roots
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BFO is a very small ontology to
support integration of scientific
research data
DOLCE is tilted towards objects of general
thought and communication (fiction,
mythology, ...)
SUMO contains many portions which are
more properly conceived of as domain
ontologies (airports, bacteria, ...); overlaps
inconveniently with science
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DOLCE and BFO draw on
Aristotle’s Ontological Square
Particular
Universal
Substantial
Accidental
Second substance Second accident
man
headache
cat
sun-tan
ox
dread
First substance
First accident
this man
this headache
this cat
this sun-tan
this ox
this dread
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For BFO, universals are admitted
only if they have instances in reality
Fictions (‘unicorn’) do not have instances
‘Average salary’ does not have instances
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Basic Formal Ontology
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•
•
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a true upper level ontology
no interference with domain ontologies
no interference with issues of cognition
no putative fictions
 a small subset of DOLCE but with a
clearer treatment of instances, universals,
relations and qualities, time
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Realist Perspectivalism: The
philosophical basis of BFO
Ontologies are windows on reality
There is a multiplicity of windows
(perspectives), all equally veridical
i.e. transparent to reality
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The Time Problem
The tumor developed in John’s lung over
25 years
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The Time Problem
____ developed in _____ over 25 years
process
occurrent
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The Time Problem
The tumor developed in the lung over 25 years
substances
things
objects
continuants
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The Problem
The tumor developed in the lung over 25 years
what is it that participates in this process of
tumor development?
parthood here not determinate
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The Problem
The tumor developed in the lung over 25 years
substances
process
gluing these two types of entities together yields
ontological monsters
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Continuants vs occurrents
process
substance
In preparing an inventory of reality, we
keep track of these two different kinds of
entities in two different ways
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BFO: the very top
Continuant
Occurrent
dependence
relation
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Two Orthogonal, Complementary
Perspectives
stocks and flows
commodities and services
products and processes
anatomy and physiology
drug and drug administration
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t
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Snapshot
ontology
Video
ontology
process
substance
Continuants and Occurrents
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continuants continue to exist
Note that, while, the views are
instantaneous, the objects viewed endure
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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
Continuant
Independent
Continuant
Occurrent
(always dependent
on one or more
independent
continuants)
Dependent
Continuant
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Dependent continuants:
one-place:
your temperature, color, height
my knowledge of French
the whiteness of this cheese
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relational dependent continuants
stand in relations of one-sided dependence
to a plurality of substances simultaneously
love
specific dependence
John
Mary
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Dependent continuants
Functions, capabilities, dispositions,
roles, qualities …
plans, shapes, disorders, states, data
entries, ontologies, diseases, the
boundary of your hacienda ...
the Olympic flame …
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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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Relational (n-place) processes
kissings, thumpings, conversings, dancings, …
join their carriers together into collectives of greater
or lesser duration
dancing
John
Mary
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An epidemic
(Continuant)
The spread of an epidemic
(Occurrent)
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Three dichotomies
• instance vs. universal
• continuant vs. occurrent
• dependent vs. independent
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Aristotle’s Ontological Square
Particular
Universal
Substantial
Accidental
Second substance Second accident
man
headache
cat
sun-tan
ox
dread
First substance
First accident
this man
this headache
this cat
this sun-tan
this ox
this dread
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The (Aristotelian) Ontological Sextet
Substances
Universals
Particulars
Qualities, Roles,
Functions, ….
Dependent
SubstanceContinuantuniversals
universals,
Dependent
SubstanceContinuantinstances
instances
Processes
Processuniversals
Processinstances
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BFO
Continuant
Independent
Continuant
Dependent
Continuant
(molecule,
(quality,
cell, organ,
organism)
function,
disease)
Occurrent
(Process)
Functioning
Side-Effect,
Stochastic
Process, ...
..... ..... .... .....
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Instances
..... ..... .... .....
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BFO
Continuant
Independent
Continuant
Dependent
Continuant
(molecule,
(quality,
cell, organ,
organism)
function,
disease)
Occurrent
(Process)
Functioning
Side-Effect,
Stochastic
Process, ...
..... ..... .... .....
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BFO
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 also windows on the
instances in reality
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RELATION
TO TIME
CONTINUANT
INDEPENDENT
OCCURRENT
DEPENDENT
GRANULARITY
ORGAN AND
ORGANISM
CELL AND
CELLULAR
COMPONENT
MOLECULE
Organism
(NCBI
Taxonomy)
Cell
(CL)
Anatomical
Organ
Entity
Function
(FMA,
(FMP, CPRO) Phenotypic
CARO)
Quality
(PaTO)
Cellular
Component
(FMA, GO)
Molecule
(ChEBI, SO,
RNAO, PRO)
Biological
Process
(GO)
Cellular
Function
(GO)
Molecular Function
(GO)
Molecular Process
(GO)
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RELATION TO
TIME
GRANULARITY
INDEPENDENT
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
CELL AND
CELLULAR
COMPONENT
Cell
(CL)
MOLECULE
CONTINUANT
DEPENDENT
Anatomical
Organ
Entity
Function
(FMA,
(FMP, CPRO) Phenotypic
CARO)
Quality
(PaTO)
Cellular
Cellular
Component Function
(FMA, GO)
(GO)
Molecule
(ChEBI, SO,
RNAO, PRO)
OCCURRENT
Molecular Function
(GO)
Organism-Level
Process
(GO)
Cellular Process
(GO)
Molecular
Process
(GO)
rationale of OBO Foundry coverage
(homesteading principle)
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RELATION
TO TIME
CONTINUANT
INDEPENDENT
GRANULARITY
ORGAN AND
ORGANISM
CELL AND
CELLULAR
COMPONENT
MOLECULE
Family, Community,
Deme, Population
Organism
(FMA,
(NCBI
CARO)
Taxonomy)
Cell
(CL)
Cell Component
(FMA,
GO)
Molecule
(ChEBI, SO,
RnaO, PrO)
DEPENDENT
ENVIRONMENT
COMPLEX OF
ORGANISMS
OCCURRENT
Organ
Function
(FMP,
CPRO)
Population
Phenotype
Population
Process
Phenotypic
Quality
(PaTO)
Biological
Process
(GO)
Cellular
Function
(GO)
Molecular Function
(GO)
Molecular
Process
(GO)
86
The Gene Ontology (GO)
Continuant
Occurrent
biological process
Independent
Continuant
Dependent
Continuant
cell component
molecular function
Kumar A., Smith B, Borgelt C. Dependence relationships between Gene Ontology
terms based on TIGR gene product annotations. CompuTerm 2004, 31-38.
Bada M, Hunter L. Enrichment of OBO Ontologies. J Biomed Inform. 2006 Jul 26
87
Function and Functioning
Continuant
Independent
Continuant
Dependent
Continuant
Occurrent
Functioning
Side-Effect,
Stochastic
Process, ...
Function
88
Blinding Flash of the Obvious
Continuant
Independent
Continuant
Dependent
Continuant
thing
quality
Occurrent
process
quality depends
on bearer
.... ..... .......
89
Phenotype Ontology
Continuant
Independent
Continuant
(molecule,
cell, organ,
organism)
PATO
phenotypic
quality
ontology
Occurrent
(Process)
Functioning
Side-Effect,
Stochastic
Process, ...
..... ..... .... .....
90
An example of a quality
• The particular redness of the left eye of a
single individual fly
– An instance of a quality universal
• The color ‘red’
– A quality universal
• Note: the eye does not instantiate ‘red’
• PATO represents quality universals: color,
temperature, texture, shape …
91
Qualities are dependent entities
• Qualities require (depend on) bearers,
which are independent continuants
Example:
– A shape requires a physical object as its bearer
– If the physical object ceases to exist (e.g. it
decomposes), then the shape ceases to exist
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the universal red
instantiates
the particular case
of redness (of a
particular fly eye)
the universal eye
instantiates
an instance of an
depends_on
eye (in a particular
fly)
93
color
is_a
red
instantiates
the particular case
of redness (of a
particular fly eye)
anatomical structure
is_a
eye
instantiates
an instance of an
depends on
eye (in a particular
fly)
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3 kinds of binary relations
Between universals (types):
• human is_a mammal
• cell nucleus part_of cell
Between an instance and a universal
• this human instance_of the universal human
• this human allergic_to the universal penicillin
Between instances:
• Mary’s heart part_of Mary
• Mary’s aorta connected_to Mary’s heart
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color
is_a
red
instantiates
the particular case
of redness (of a
particular fly eye)
anatomical structure
is_a
eye
instantiates
an instance of an
depends on
eye (in a particular
fly)
96
Definitions of type-level relations presuppose
underlying instance-level relations
A is_a B =def. all instances of A are
instances of B
presupposes instance_of
A part_of B =def. every instance of A are
instance-level-parts-of some instance of B
presupposes instance-level-part-of
97
Rule: relations in BFO should be included
only if the can support reasoning
If A R B and B R C, we want to be able to
infer something about the relation between
As and Cs.
Reasoning is impossible with relations like ‘is
somehow related to’, ‘is associated with’, …
98
Universal-universal relations
Only something that holds of all As will be an
assertion that holds of the universal A
Hence the All-Some rule
A part_of B =def. all instances of A are
instance-level-parts-of some instance of B
99
Rule for including relations in BFO
In every case we need to check, before we add
a relation A R B, that, for some representative
collection of instances of A and B, we have data
about the As and data about the Bs which is
such that
all the instances of A stand in R to some B
e.g. all the instances of cell membrane stand in
part_of to some instance of cell
100
The crucial role of the all-some
structure
If you know A part_of B, and B part_of C
then whichever A you choose, the
instance of B of which it is a part will be
included in some C, which will include as
part also the A with which you began
The same principle applies to the other
relations in BFO such as located_at,
transformation_of, derived_from,
adjacent_to, …
101
Benefits of well-defined
relationships
Reasoning should be able cascade from one
relational assertion (A R1 B) to the next (B R2 C).
Find all DNA binding proteins should also find all
transcription factor proteins because
– Transcription factor is_a DNA binding protein
Only the All-Some structure guarantees such
cascading of relational assertions
102
Some-some relations
Some_some relations are important, for example
where we have only data concerning likelihood of
associations, e.g. in text-mining contexts
We should not include some-some relations in an
ontology, because they do not support reasoning
Rather, we should incorporate the relevant
instance-level relations, and explore various
approaches to defining probabilistic relations at the
type level in their terms
103
Rule for including relations in BFO
Before including a type-level relation in
BFO ask yourself first whether the relation
can be easily defined in terms of existing
BFO relations plus domain-specific terms
e.g. can we define ‘synaptic connection’ in
terms of is_connected_to, is_a and the
univeral synapse ?
104
A part_of B, B part_of C ...
The all-some structure of the definitions
in the BFO allows cascading of
inferences
(i) within ontologies
(ii) between ontologies
(iii) between ontologies and EHR
repositories of instance-data
105
Anatomical
Structure
Anatomical Space
Organ Cavity
Subdivision
Organ
Cavity
Organ
Serous Sac
Cavity
Subdivision
Serous Sac
Cavity
Serous Sac
Organ
Component
Organ
Subdivision
Pleural Sac
Pleural
Cavity
Parietal
Pleura
Interlobar
recess
Organ Part
Mediastinal
Pleura
Tissue
Pleura(Wall
of Sac)
Visceral
Pleura
Mesothelium
of Pleura
Foundational
FMA Model of Anatomy
106
TLR2:MyD88
complex
TLR2-MyD88
binding
TIR-TIR
binding
TLR2
has_disposition
LTA binding
MyD88
process
has_participant
has_part
has_lower_level_granularity
TLR2-TLR2
ligand
binding
has_participant
TIR domain
TLR-2 signalling pathway
with thanks to Lindsay Cowell
107
How does BFO deal with negative
entities?
John has_a
SNOMED 311497003 : Acquired absent testis
108
Lacks
• Instance-type level
John lacks nipple with respect to part_of at
time t =def. there is no instance u of the
universal nipple such that u part_of John at t.
• Type-type level
male human lacks ovary with respect to
part_of =def. for all c,t, if c instance of male
human at t then c lacks ovary with respect to
part_of at time t.
109
Lacks
• Instance-type level
p lacks U with respect to r at time t =def.
there is no instance u of U such that p stands
in r to u at t.
• Type-type level
C1 lacks C2 with respect to r =def. for all c,t, if
c instance of C1 at t then c lacks C2 with
respect to r at time t.
110
How link continuants and occurrents
together on the instance level?
via other formal relations such as:
• dependence
• participation
• realization
111
Realization
the execution of a plan, algorithm
the expression of a function
the exercise of a role
the realization of a disposition
112
Material examples
performance of a symphony
projection of a film
expression of an emotion
utterance of a sentence
application of a therapy
course of a disease
increase of temperature
113
Realizable dependent entities
plan
function
role
disposition
algorithm
continuants
114
Their realizations
execution
expression
exercise
realization
application
course
occurrents
115
Continuant  Occurrent
Participation
Independent Continuant  Process
John swims
Realization
Dependent Continuant  Process
The plan is being realized
116
Continuant
Independent
Continuant
Dependent
Continuant
Non-realizable
Dependent
Continuant
(quality)
Realizable
Dependent
Continuant
(function, role,
disposition)
..... .....
117
Role (Externally-Grounded
Realizable Entity)
role =def. a realizable entity
• which exists because the bearer is in
some special physical, social, or
institutional set of circumstances in which
the bearer does not have to be, and
• is not such that, if it ceases to exist, then
the physical make-up of the bearer is
thereby changed.
118
Disposition (Internally-Grounded
Realizable Entity)
disposition =def.
a realizable entity which if it ceases to
exist, then its bearer is physically
changed, and
whose realization occurs when this
bearer is in some special physical
circumstances, in virtue of the bearer’s
physical make-up
119
Capability (A Good Disposition)
capability =def.
a disposition that
exists in virtue of the bearer’s physical
make-up, and
enables the entity in which it inheres to
participate in events of a certain kind
120
Function (A Good, Designed
Disposition)
function =def.
a capability that
exists in virtue of the bearer’s physical make-up,,
and
this physical make-up is something the bearer
possesses because it came into being, either
through evolution (in the case of natural biological
entities) or through intentional design (in the case
of artifacts), in order to realize processes of a
certain kind.
121
The parts of the organism have
functions
They are designed to ensure that the
events transpiring inside the organism
remain within the spectrum of allowed
values and to respond when they move
outside this spectrum of allowed values
122
Functions are associated with certain
characteristic process shapes
Screwdriver: rotates and simultaneously
moves forward simultaneously transferring
torque from hand and arm to screw
Heart: performs a contracting movement
inwards and an expanding movement
outwards
123
Functions and Prototypes
In its functioning, a
heart creates a fourdimensional process
shape.
Good hearts create
other process
shapes than sick
hearts do.
124
the canonical human life (plan)
birth
infancy
teenagerdom
early adulthood maturity
late adulthood
death
For all animals the canonical life plan includes:
canonical embryological development
canonical growth
canonical reproduction
canonical aging
canonical death
125
For humans
first, mewling and puking
then creeping like snail unwillingly to school
then sighing like furnace with woeful ballad made to
his mistress' eyebrow
then a soldier full of strange oaths
then justice in fair round belly
then the lean and slipper'd pantaloon
then second childishness and mere oblivion, sans
teeth, sans eyes, sans taste, sans everything.
As You Like It, II.vii.139-166
126
Family
Work
Money
Adoption
Aging
Birth
Child care
Death
Disability
Divorce
Domestic Violence
Driving
Elder Care
Empty Nesting
Health
Illness
Kids
Marriage
Parenting
Retirement
Schooling
Teenagers
Travelling FirstGov
Employment
Injury
Job Seeking
Re-employment
Small Business
Self-employment
Telecommuting
Unemployment
Volunteering
Workplace Violence
Bankruptcy
Budgeting
Charitable Contributions
College
Credit
Disasters
Home Improvement
Home Purchase
Home Selling
Insurance
Investing
IRS Audit
Lawsuits
Mortgage
Property
Renting
Saving
Taxes
Trusts
Wills
Life Events Taxonomy
127
What does every human canonical
life involve?
9 months of development
...
cycles of waking, sleeping; eating and not
eating; drinking and not drinking
...
death
128
Iberall and McCulloch 20 action modes:
Action Modes
Sleeps
Eats
Drinks
Voids
Sexes
Works
Rests (no motor activity, indifferent internal sensory flux)
Talks
Attends (indifferent motor activity, involved sensory activity)
Motor practices (runs, walks, plays, etc.)
Angers
Escapes (negligible motor and sensory input)
“Anxioius-es”
”Euphorics”
Laughs
Aggresses
Fears, fights, flights
Interpersonally attends (body, verbal or sensory contact)
Envies
Greeds
Total:
% of time
30
5
1
1
3
25
3
5
4
4
1
1
2
2
1
1
1
8
1
1
100% +/- 20% of time involvement
129
Improved version
an entity has a biological function if and
only if it is part of an organism and has
a disposition to act reliably in such a
way as to contribute to the organism’s
realization of the canonical life plan for
an organism of that type
130
What is disease?
functions are, roughly, good dispositions
relevant to the realization of the
canonical life plan for an organism of
the relevant type
diseases are (even more roughly)
counterpart bad dispositions
131
Continuant
Independent
Continuant
Occurrent
Dependent
Continuant
Realizable
Dependent
Continuant
Quality
Disposition
Disease
Function
Role
Functioning
132
Information objects
pdf file
poem
symphony
algorithm
symbol
sequence
molecular structure
133
Specifically Dependent Continuants
Specifically
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
Quality, Pattern
Realizable
Dependent
Continuant
134
Generically Dependent Continuants
Generically
Dependent
Continuant
if one bearer ceases to exist, then
the entity can survive, because
there are other bearers
(copyability)
the pdf file on my laptop
Information
Object
Sequence
the DNA (sequence) in this
chromosome
135
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)
136
Information entities exist in a
way which makes them
dependent on provenance,
and on processors, in a way in
which types are not
137
138
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
139
Generically dependent continuants
do not require specific media (paper,
silicon, neuron …)
140
What is a datum?
Continuant
Independent
Continuant
laptop, book
Dependent
Continuant
Occurrent
process
datum: a pattern in some
quality
medium with a certain
kind of provenance
.... ..... .......
14
1
Continuant
Independent
Continuant
Occurrent
Dependent
Continuant
Information
Entity
Action
creating a datum
.... ..... .......
14
2
Generically Dependent Continuants
Generically
Dependent
Continuant
Information
Artifact
.pdf file
Gene
Sequence
.doc file
instances
14
3
Information Entity (science)
protocol
database
theory
ontology
gene list
publication
result
...
14
4
Information Entity (labeling)
serial number
batch number
grant number
person number
name
address
email address
URL
...
14
5
Type or instance
Continuant
Independent
Continuant
human being,
protocol
document
Dependent
Continuant
pattern of
ink marks
Occurrent
(Process)
Applying
the protocol
Side-Effect …
... .. ..... .... .....
14
6
Continuant
Independent
Continuant
Occurrent
Dependent
Continuant
Information
Entity
Action
creating a datum
.... ..... .......
14
7
What is a work of literature?
Is War and Peace a type or an
instance?
•
If War and Peace were a type, and the
copies of War and Peace in my library and
in your library were instances, then
there would be many War(s) and
Peaces.
Hence War and Peace is an instance.
14
8
There are not two Declarations of
Independence
There can be two copies of the US
Declaration of Independence
There cannot be two US Declarations of
Independence
There cannot be subtypes of the US
Declaration of Independence
Hence the US Declaration of Independent
is an instance and not a type.
14
9
Rule for types
Their names are pluralizable
There can be three people
There cannot be three Michelle Obamas.
Information Entities = entities which can exist
in many perfect copies
15
0
Generically dependent continuants
are distinct from types
they have a different kind of
provenance
◦ Aspirin as product of Bayer GmbH
◦ aspirin as molecular structure
15
1
Generically Dependent Continuants
Generically
Dependent
Continuant
Information
Entity
.pdf file
Sequence
.doc file
instances
15
2
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
15
3
Generically dependent continuants
do not require specific media (paper,
silicon, neuron …)
15
4