IFOMIS Projects

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IFOMIS Projects

• Basic Formal Ontology
• 2. Ceusters
• 3. Medical Being

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1. Basic Formal Ontology

• mereotopology
• dependence
• granularity/partition theory
• SNAP/SPAN
• action/participation
• plans/functions/executions
• causality/powers/dispositions
• environment
• normativity

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2. Ceusters

• unstructured patient records as basis for a
  cosmic medical experiment
• We provide formal-ontological services for
  Ceusters
• He provides powerful software tools and
  influential support in our fight for good
  ontology in the medical informatics domain

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Rules for Good Ontology

• These are rules of thumb
• They represent ideals to be approximated to in
  practice
• (and often come with trade-offs)

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3. Medical Being

• MedO
• many MedOs
• BFO SNAPs, SPAN(s), granularity
• MedO SNAPs, SPAN(s), granularity
• different bodily systems
• total bodily system

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OUTPUT

• Basic Formal Ontology
• collaboration with B. Bennett re axiom systems
• conference presentations
• many publications in good journals
• 2. Ceusters
• ontology software tools for medical NLP
• 3. Medical Being
• a big book

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Medical Being

• mereotopology Schubert (anatomy with holes)
• dependence
• granularity/partition theory molecules, cells
• SNAP/SPAN anatomy, physiology
• action/participation doctor, patient
• plans/functions/executions therapy, application
  of therapy
• causality/powers/dispositions placebo effect
• normativity health, disease, normal liver
• environment environmental influences on disease

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Medical Being

• a book,
• a textbook of medical ontology
• for pedagogical purposes
• for testing purposes (applied formal ontology)
• as a showcase of good ontological methods

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Chapters

• Main Body Systems
• structural system
• bones, muscles, connective tissue
• skin and hair
• circulatory system
• heart, veins, arteries, blood
• digestive system
• intestinal system
• urinary system

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Chapters

• Main Body Systems (contd.)
• nervous system
• respiratory system
• immune system
• How do these systems relate together?
• (a medico-ontological analogue of the mind-body
  problem)

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Chapters

• Embryonic Development
• Sexual Reproduction
• Birth
• Childhood
• Adolescence
• Aging
• Coma
• Death

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Chapters

• Health
• Disease
• Infection
• Accident, Injury, Wound
• Epidemiology

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Chapters

• Sleep, anaesthesia, coma
• Pain, Consciousness, Empathy, Sympathy
• Mental illness
• Therapy (null therapy)
• Cure
• Drug
• Recuperation

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Chapters

• Antigens
• viruses
• bacteria
• Parasites
• Food
• Alcohol

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The ontologists job

• is not to mimic or replace or usurp science
• not to discover statistical or functional laws
• it is to establish the categories involved in
  given domains of reality and the relations
  between them
• via taxonomies
• and partonomies
• and by addressing NORMATIVE ISSUES such as what
  holds in the standard case

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Naturalness

• A good ontology should include in its basic
  category scheme only those categories which are
  instantiated by entities in reality (it should
  reflect nature at its joints)

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A good first test

• the categories in question should be reflected
  in TEE
• (for Technically Extended English
• English as extended by the various technical
  vocabularies of medical and scientific
  disciplines)

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Basic categories

• are reflected by morphologically simple terms
• dog
• pain
• foot
• blood
• hunger
• hot
• red
• diabetes

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No theoretical artifacts

• A good ontology should not include in its basic
  category scheme
• artifacts of logical, mathematical or
  philosophical theories (such as transfinite
  cardinals, instantaneous rabbit-slices,
  non-existent golden mountains, functions across
  possible worlds, and the like).

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Problem cases

• Fictional entities?
• Absences?
• Holes?

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A good category scheme

• should not be a mish-mash of natural and
  philosophical taxa
• (keep views separate
• basic views, domain-specific views,
• theoretical-artefactual views)

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Perspectivalism

• Perspectivalism

Different partitions may represent cuts through
the same reality which are skew to each other
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Ontology

• like cartography
• must work with maps at different scales and with
  maps picking out different dimensions of
  invariants

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Varieties of granular partitions

• Partonomies inventories of the parts of
  individual entities
• Maps partonomies of space
• Taxonomies inventories of the universals
  covering a given domain of reality

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Cheese-paring principle

• While a good ontology should use categories
  which reflect only TEE, it should also have the
  resources to do justice to the fact that the
  world can be sliced in many ways, including ways
  not reflected by TEE

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Example of cheese-paring
substance
action (relational process)
substance
agent (substance plus role)
patient (substance plus role)
linked by mutual dependence
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Always ask the question

• when is this proposition true?
• when does this entity exist?
• Different sorts of answers
• at ti (for SNAP entities)
• -------------------------------------------
• timelessly looking down on the order of time
  from the outside (for SPAN entities)
• -------------------------------------------
• through the time interval ti,tj ?

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John lived in Kansas for 25 years

• when is this proposition true?
• when does the entity which makes it true exist?
• The problem with states of affairs is that they
  are not mereologically determinate
• What are the parts of the state of affairs that
  John lived in Kansas for 25 years

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Against Sentences

• Nouns and verbs are in order as they stand
• The mereological indeterminacy of states of
  affairs goes hand in hand with the ontological
  perversity of the sentence

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Everything

• within SNAP is mereologically determinate
• Everything
• within SPAN is mereologically determinate

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Sums within SNAP are always mereologically
determinate

• John plus his role Major John
• John plus his quality hungry John
• John plus his disease diabetic John, John the
  case of diabetes

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Sums within SPAN are always mereologically
determinate

• The course of Johns disease plus the course of
  Johns treatment plus the course of Johns
  recuperation
• The first half of the match

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Double-Counting

• in realm of substances
• person
• ear, nose, throat, arm
• family, clinical trial population
• fiat parts and aggregates should be explicitly
  marked as involving double-counting

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Double-Counting

• in realm of processes
• process
• beginning, end, first phase
• series of clinical trials, World Cup
• fiat parts and aggregates on the same level of
  granularity should be explicitly marked as
  involving double-counting

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Rule Always mark cases of double-counting

• wherever this occurs within a single ontology.
• Double-counting is perfectly acceptable when we
  are using more than one ontologies simultaneously
  (yielding separate views of one and the same
  reality)
• Varzi An inventory of reality should involve no
  double-counting
• (this principle is unsustainable)

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SNAPshot ONTOLOGY
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SPAN ONTOLOGY
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SPAM ONTOLOGY
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Core Categories

• are those categories of an ontology which
  survive when all cases of double counting have
  been eliminated

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Rule No Crossing Categories

• If C is a core category then an instance of C is
  always an instance of C whichever view of C we
  take
• If C is a core category then an instance of C is
  always an instance of C whichever granularity we
  take
• If C is a core category then all parts and
  aggregates of instances of C are also instances
  of C

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Determinables and Determinates

• Determinable color
• Determinate this particular shade of redness
• (holds for tokens and for types)
• Determinable Johns temperature
• Determinate Johns temperature of 62 degrees
• (The value is changing all the time)

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Rule

• If x instances a category under any
  determinable, then it instances this category
  under all determinables
• Johns temperature is a quality (a SNAP entity)
• The value of Johns temperature at a time is a
  quality (a SNAP entity)
• (This is so even if this value is changing
  continuously)

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Rule Respect Granularity
spatial region
quality
substance
parts of spatial regions are always spatial
regions
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Respect Granularity
spatial region
quality
substance
parts of substances are always substances
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Respect Granularity
spatial region
quality
substance
parts of qualities are always qualities
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Relations crossing the SNAP/SPAN border are not
part-relations
Johns life
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Relations between entities at different
granularities

• are part relations
• Hence we have two sorts of part-relations
• within a granularity
• between granularities
• Where granularities start and stop is determined
• by the formation of scientific disciplines
• by fiat?

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Rule for Crossing Granularities

• For x and y instances of core categories
• If x is part of y, then x is of the same core
  category as y
• (if x is substantial, then y is substantial)
• (if x is a quality, then y is a quality)
• (if x is a process, then y is process)
• (if x is a spatial region, then y is a spatial
  region)
• (if x is a spatial boundary, then y is a spatial
  boundary)

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Rule for Crossing Granularities

• For x an instances of a basic category, x is
  always an instance of that category in every view
  or from every perspective
• (if x is substantial, then y is substantial)
• (if x is a quality, then y is a quality)
• (if x is a process, then y is process)
• (if x is a spatial region, then y is a spatial
  region)
• (if x is a spatial boundary, then y is a spatial
  boundary)

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How to treat cross-categorial structures?

• which ontology do they belong to?
• How to treat higher-order attributions
• Universals have instances
• Universal A depends for its instantiation on the
  instantiation of universal B
• Roughly these are meta-assertions
• (that they have special truthmakers of their own
  is an illusion of language)

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Universals have instances

• is not an extra assertion
• rather it is something which shows itself via the
  syntax of a good ontological language
• (cf. Wittgensteins Tractatus)

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Rules for good syntax in formalizing ontology

• entities of the same category should be
  represented by means of symbols of the same type
• some symbols will not represent entities at all
  (V, ?, , ?, etc.)

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Tools are just tools

• If specific logical or mathematical or
  conceptual tools are needed, for example for
  semantic purposes,
• then these should be clearly recognized as tools
  and thus not be seen as having consequences for
  basic ontology.
• (Possible worlds )

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Trade off between cheese-paring and sake-mongering

• We can cut the cheese in many ways
• But when we say
• For Pierres sake , for Ingvars sake
• then
• There are no sakes in this room
• And this is so however we cut the cheese

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Problems arise for partial ontologies

• only if they come along with the claim to be
  complete
• (reductionists are nearly always correct in what
  they hold to exist --
• but incorrect when they hold that nothing else
  exists)

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Even reductionists

• are right as far as they go
• (even their peculiar maps of reality,
• as consisting of processes,
• or of spacetime worms,
• are transparent to reality)
• The only problem with such maps is that they are
  not complete

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Rules Governing Taxonomies

• Every (coherent, tested) ontology for a given
  domain at a given level of granularity
• should be representable as a tree in the
  mathematical sense
• Problem cases shapes, colors ?

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Natural scientific classifications are principled
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Principled classifications satisfy the
no-diamonds rule

• A E
• F
  G
• B C D
• 
  H

Good
Bad
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Counterexample in the realm of artifacts ?
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Eliminating counter-examples
urban structures
buildings
parking areas
multi-story car-parks
Ontoclean
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Rule No others

• All category labels should be positive
• No category labels like
• entities which do not fall under the other
  categories

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Rule Representations

• A representation is never identical with the
  object which it is a representation of

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Rule Fallibilism

• Ontologists are seeking principles that are true
  of reality,
• but this does not mean that they have special
  powers for discovering the truth.
• Ontology is, like physics or chemistry, part of
  a piecemeal, on-going process of exploration,
  hypothesis-formation, testing and revision.

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Fallibilism

• Ontological claims advanced as true today may
  well be rejected tomorrow in light of further
  discoveries or of new and better arguments
• Ontology is like a small window on reality
  which, in fits and starts, gets bigger and more
  refined as we proceed

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Rule Adequatism

• A good ontology should be adequatist
• its taxonomies and partonomies should comprehend
  the entities in reality at all levels of
  aggregation,
• from the microphysical to the cosmological,
• and including also the middle world (the
  mesocosmos) of human-scale entities in between.
• Adequatists Aristotle, Ingarden, Chisholm
  Johansson, Smith

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Nothing in life is certain

• except
• death
• and taxes
• Fictionalism is always wrong
• Either an entity exists, or it does not exist
• Either an entity type exists, or it does not exist

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Quine is wrong

• There is no entity without identity
• We have no identity criteria for
• people
• taxes
• plans
• diseases

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Quine is wrong

• Quines slogan
• -- no entity without an identity criterion --
• represents a confusion of ontology and
  epistemology
• Compare no truth without a truth criterion

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A good category scheme

• should not be a mish-mash of individuals and
  universals
• Universals are not extra types of entities
• Types of entities ARE universals
• Boxes in category diagrams represent universals
• The instances are what the boxes contain

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SNAPshot ONTOLOGY
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SNAPshot ONTOLOGY
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Tree structure

• Higher nodes within the tree represent more
  general universals, lower nodes represent less
  general universals.

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• Branches connecting nodes represent the
  relations of inclusion of a lower category in a
  higher
• man is included in mammal
• mammal is included in animal
• and so on.

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An Ontology (Taxonomy) should be Principled

• Suppose that in counting off the cars passing
  beneath you on the highway, your checklist
  includes one box labeled red cars and another box
  labeled Chevrolets.
• The resultant inventory will be unprincipled
• you will almost certainly be guilty of counting
  some cars twice.
• Unprincipled the two modes of classification
  belong to two distinct classifications made for
  two distinct purposes

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An Ontology (Taxonomy) should be Principled

• Principled Constructed for a single purpose
• Principled Generative (recursive?)
• Principled Double-counting clearly marked
• Principled SNAP-SPAN opposition reflected (so
  mereological determinateness is guaranteed)
• Principled Clear rules when a new category must
  be admitted
• What else?
• CYC is not principled

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Tree structure implies

• A good ontology should satisfy certain
  well-formedness rules

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Well-formedness rule

• Each tree is unified
• in the sense that it has a single top-most or
  maximal node, representing the maximum category
• comprehending all the categories represented by
  the nodes lower down the tree

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Why trees?

• A taxonomy (ontology) with two maximal nodes
  would be in need of completion by some extra,
  higher-level node representing the union of these
  two maxima.
• Otherwise it would not be one taxonomy at all,
  but rather two separate taxonomies (e.g. SNAP and
  SPAN)

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Entity

• label for the highest-level category of
  ontology.
• Everything which exists is an entity
• Alternative top-level terms favored by different
  ontologists thing, object, item,
  element, existent.
• Use of entity is dangerous (see Frege)

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Rule Seek to establish a basis in minimal nodes
(leaves)

• Leaves of the tree represent the lowest
  categories (infima species)
• categories in which no sub-categories are
  included.
• Has a basis in minimal nodes the categories
  at the lowest level of the tree exhaust the
  maximum category

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Rule Aim for Exhaustiveness

• The chemical classification of the noble gases is
  exhausted by
• Helium, Neon, Argon, Krypton, Xenon and Radon.
• normally very hard to achieve

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For a taxonomy with a basis in minimal nodes

• every intermediate node in the tree is
  identifiable as a combination of minimal nodes.

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More well-formedness principles

• There should be a finite number of steps between
  the maximal category and each minimal category.
• There should be the same number of steps between
  the topmost node of the tree and all its
  lowest-level nodes.

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Well-Formedness

• The taxonomy as a whole is thereby divided into
  homogeneous levels,
• each level represents a jointly exhaustive and
  pairwise disjoint partition of the corresponding
  domain of categories on the side of objects in
  the world.

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Which rules satisfied by BFO?
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Types of Formal Relation

• Intracategorial
• Mereological (part)
• Topological (connected, temporally precedes)
• Dependency (e.g. functional ?)
• Intercategorial
• Inherence (quality of)
• Location
• Participation (agent)
• Dependency (of process on substance)

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Relations can also hold across granularities

• Microbial processes in the human body sustain the
  human body in existence
• Neurophysiological processes in the brain cause
  and provide the substratum for cognitive processes

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Trees of universals (species-genus hierarchies)

• capture the way the world is (realism)
• they depict the invariant structures/patterns/r
  egularities in reality

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BUT species-genus hierarchies

• may capture the way the world should be
• by depicting the structures/patterns/regulariti
  es in the realm of standards, ideal cases,
  recipes
• (a hierarchy of medical therapies)

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TEEcentric (Aristotelian) Realism

• The general terms of TEE (or many of them),
• including terms like Coca Cola,
• correspond to universals (species and genera,
  invariant patterns) in reality

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Two distinct realms of being
universals particulars
general individual
types tokens
species instances
essence fact
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species, genera
mammal
frog
instances
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Common nouns
common nouns proper names
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types
mammal
frog
tokens
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Accidents Species and instances
types
tokens
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There are universals

• both among substances (man, mammal)
• and among qualities (hot, red)
• and among processes (run, movement)
• There are universals also among spatial regions
  (triangle, room, cockpit)
• and among spatio-temporal regions (orbit)

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Substance universals

• pertain to what a thing is at all times at which
  it exists

cow man rock planet VW Golf
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Quality universals

• pertain to how a thing is at some time at which
  it exists

red hot suntanned spinning
Clintophobic Eurosceptic
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Process universals

• reflect invariants in the spatiotemporal world
  taken as an atemporal whole
• football match
• course of disease
• exercise of function
• (course of) therapy

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Processes and qualities, too, instantiate genera
and species

• Thus process and quality universals form trees

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Accidents Species and instances
quality
color
red
scarlet
R232, G54, B24
this individual accident of redness (this
token redness here, now)