VT

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VT
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The First Industrial-Strength Philosophy
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IFOMIS

• Institute for Formal Ontology
• and Medical Information Science
• http//ifomis.de

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Medicine

• needs to find a way to enable the huge amounts
  of data resulting from formal trials and from
  informal clinical practice
• to be (f)used together

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The problem

• Different communities of medical researchers use
  different and often incompatible category systems
  in expressing the results of their work

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Example Medical Nomenclature

• MeSH (Medical Subject Headings) blood is a
  tissue
• SNoMed (Systematized Nomenclature of Medicine)
• blood is a fluid

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The solution

• ONTOLOGY
• Remover Ontology Impedance
• But what does ontology mean?

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Two alternative readings

• Ontologies are oriented around terms or concepts
  currently popular IT conception
• Ontologies are oriented around the entities in
  reality traditional philosophical conception,
  embraced also by IFOMIS

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Ontology as a branch of philosophy

• seeks to establish
• the science of the kinds and structures of
  objects, properties, events, processes and
  relations in every domain of reality

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Ontology a kind of generalized chemistry or
zoology

• (Aristotles ontology grew out of biological
  classification)

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Aristotle
worlds first ontologist

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Worlds first ontology (from Porphyrys
Commentary on Aristotles Categories)
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Linnaean Ontology
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Medical Diagnostic Ontology
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Ontology is distinguished from the special
sciences
it seeks to study all of the various types of
entities existing at all levels of granularity
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and to establish how they hang together to form a
single whole (reality or being)
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Sources for ontological theorizing

• the study of ancient texts
• thought experiments (we are philosophers, after
  all)
• the development of formal theories
• the results of natural science
• now also
• working with computers

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The existence of computers

• and of large databases
• allows us to express old philosophical problems
  in a new light

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Example The Gene Ontology (GO)

• hormone GO0005179
• digestive hormone GO0046659
• peptide hormone GO0005180 adrenocorticotrop
  in GO0017043 glycopeptide hormone
  GO0005181 follicle-stimulating hormone
  GO0016913
• subsumption (lower term is_a higher term)

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as tree

• hormone
• digestive hormone peptide hormone
• adrenocorticotropin
  glycopeptide hormone
• 
  follicle-stimulating hormone

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GO

• is very useful for purposes of standardization in
  the reporting of genetic information
• but it is not much more than a telephone
  directory of standardized designations organized
  into hierarchies

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GO deals with such basic ontological notions very
haphazardly

• GOs three main term-hierarchies are
• component, function and process
• But GO confuses functions with structures, and
  also with executions of functions
• and has no clear account of the relation between
  functions and processes

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Moreover,

• GO can in practice be used only by trained
  biologists
• whether a GO-term stands in the subsumption
  relationship

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A still more important problem

• There exist multiple databases
• GDB
• Genome Database of Human Genome Project
• GenBank
• National Center for Biotechnology Information,
  Washington DC
• etc.

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What is a gene?

• GDB a gene is a DNA fragment that can be
  transcribed and translated into a protein
• GenBank a gene is a DNA region of biological
  interest with a name and that carries a genetic
  trait or phenotype
• GO uses gene in its term hierarchy,
• but it does not tell us which of these
  definitions is correct

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How resolve such incompatibilities?

• The Semantic Web Initiative
• (Tim Berners-Lee, the inventor of the internet)
  
• enforce terminological compatibility via
  standardized term hierarchies, with standardized
  definitions of terms
• applied as meta-tags to websites

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The Semantic Web

• The Web is a vast edifice of heterogeneous data
  sources
• Needs the ability to query and integrate across
  different conceptual systems

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Metadata the new Silver Bullet

• We agree on a metadata standard for washing
  machines as concerns size, capacity, energy
  consumption, water consumption, price
• We create machine-readable databases of our
  inventories and put them on the net
• A consumer can then query multiple sites
  simultaneously
• and thereby search the Internet for highly
  specific, reliable, context-sensitive results

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Cary Doctorow

• A world of exhaustive, reliable metadata would
  be a utopia.

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Problem 1 People lie

• Meta-utopia is a world of reliable metadata.
• But poisoning the well can confer benefits to
  the poisoners
• Metadata exists in a competitive world. Some
  people are crooks. Some people are cranks.

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Problem 2 People are lazy

• Half the pages on Geocities are called Please
  title this page

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Problem 3 People are stupid

• The vast majority of the Internet's users
• (even those who are native speakers of English)
• cannot spell or punctuate
• Will internet users suddenly and en masse learn
  to accurately categorize their information
  according to whatever DL-hierarchy they're
  supposed to be using?

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Problem 4 Metrics influence results

• raw MHz scores privilege Intel's CISC chips over
  Motorola's RISC chips.
• Every player in a metadata standards body will
  want to emphasize their high-scoring axes

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Problem 5 Multiple descriptions

• We impart information
• He chatters
• They gossip
• Requiring everyone to use the same vocabulary to
  describe their material denudes the cognitive
  landscape, enforces homogeneity in ideas.

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Problem 6 Ontology Impedance

• semantic mismatch between ontologies being
  merged
• This problem recognized in Semantic Web
  literature
• http//ontoweb.aifb.uni-karlsruhe.de/About/Deliver
  ables/ontoweb-del-7.6-swws1.pdf

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Solution 1 treat it as (inevitable) impedance

• and learn to find ways to cope with the
  disturbance which it brings
• Suggested here
• http//ontoweb.aifb.uni-karls-ruhe.de/Ab-out/Deliv
  erables/ontoweb-del-7.6-swws1.pdf

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Solution 2 resolve the impedance problem on a
case-by-case basis

• Suppose two databases are put on the web.
• Someone notices that "where" in the friends
  table and "zip" in a places table mean the same
  thing.
• http//www.w3.org/DesignIssues/Semantic.html

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Both solutions fail

• treating mismatches as impedance inappropriate
  in an area like medicine
• and ignores the problem of error propagation
• 2. resolving impedance on a case-by-case basis
  defeats the very purpose of the Semantic Web

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Problem 5 Multiple descriptions

• Requiring everyone to use the same vocabulary to
  describe their material not always practicable
  especially in the medical domain

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Clinicians

• often do not use category systems at all they
  use unstructured text
• from which useable data has to be extracted in a
  further step
• Reasons for this every case is different, much
  patient data is context-dependent

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Proposed IFOMIS solution

• distinguish two separate tasks
• - the task of developing computer applications
  capable of running in real time
• the task of developing an expressively rich
  framework of a sort which will allow us to
  resolve incompatibilities between definitions

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different terminology systems
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need not interconnect at all
for example they may relate to entities of
different granularity
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we cannot make incompatible terminology-systems
interconnect
just by looking at concepts, or knowledge or
language
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we cannot make incompatible terminology-systems
interconnect
or by staring at the terminology systems
themselves
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to decide which of a plurality of competing
definitions to accept
we need some tertium quid
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we need, in other words,
to take the world itself into account
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BFO

• basic formal ontology

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BFO

• ontology is defined not as the standardization
  or specification of conceptualizations
• (not as a branch of knowledge or concept
  engineering)
• but as an inventory of the entities existing in
  reality

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The BFO framework

• will solve the problem of ontological impedance
  and provide tools for quality-control on the
  output of computer applications

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BFO not a computer application

• but a Reference Ontology
• (something like old-fashioned metaphysics)

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Reference Ontology

• a theory of a domain of entities in the world
• based on realizing the goals of maximal
  expressiveness and adequacy to reality
• sacrificing computational tractability for the
  sake of representational adequacy

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Reference Ontology

• a theory of the tertium quid
• called reality
• needed to hand-callibrate database/terminology
  systems

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Methodology

• Get ontology right first
• (realism descriptive adequacy rather powerful
  logic)
• solve tractability problems later

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A reference ontology

• is a theory of reality
• But how is this possible?
• How can we get beyond our concepts?

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Answer

• draw on 2 millennia of philosophical research
• pertaining to realism, scepticism, error, theory
  change, and the language/concept/world relation
• pertaining to the structure of reality itself at
  different levels of granularity
• APPLY THE RESULTS TO THE DOMAIN OF MEDICAL REALITY

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try to find ways to look at the same objects at
different levels of granularity
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and also

• look not at concepts, representations, of a
  passive observer
• but rather at agents (clinicians) acting in the
  world
• taking account of the tacit knowledge of reality
  which the domain experts possess
• GO useable only by biologists, because only they
  know how given terms function in given contexts

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The Reference Ontology Community

• IFOMIS (Leipzig)
• Laboratories for Applied Ontology (Trento/Rome,
  Turin)
• Foundational Ontology Project (Leeds)
• Ontology Works (Baltimore)
• Ontek Corporation (Buffalo/Leeds)
• Language and Computing (LC) (Belgium/Philadelphia
  )

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Domains of Current Work

• IFOMIS Leipzig Medicine, Bioinformatics
• Laboratories for Applied Ontology
• Trento/Rome Ontology of Cognition/Language
• Turin Law
• Foundational Ontology Project Space, Physics
• Ontology Works Genetics, Molecular Biology
• Ontek Corporation Biological Systematics
• Language and Computing Natural Language
  Understanding

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Recall

• GDB a gene is a DNA fragment that can be
  transcribed and translated into a protein
• Genbank a gene is a DNA region of biological
  interest with a name and that carries a genetic
  trait or phenotype

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Ontology

• fragment, region, name, carry, trait,
  type
• ... part, whole, function, inhere,
  substance
• are ontological terms in the sense of traditional
  (philosophical) ontology

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BFO

• not just a system of categories
• but a formal theory
• with definitions, axioms, theorems
• designed to provide the resources for reference
  ontologies for specific domains
• of sufficient richness that terminological
  incompatibilities can be resolved intelligently
  rather than by brute force

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Two basic oppositions

• Granularity (of molecules, genes, cells, organs,
  organisms ...)
• SNAP vs. SPAN

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SNAP vs. SPAN

• Two different ways of existing in time
• continuing to exist (of organisms, their
  qualities, roles, functions, conditions)
• occurring (of processes)
• SNAP vs. SPAN Anatomy vs. Physiology

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SNAP Entities existing in toto at a time
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Three kinds of SNAP entities

1. Independent Substances, Objects, Things
2. Dependent Qualities, Functions, Conditions,
   Roles
3. Spatial regions

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SNAP Dependent
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SNAP-Spatial Region
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SNAP-Independent
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SPAN Entities occurring in time
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SPAN Dependent (Processes)
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SPAN Spatiotemporal Regions
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Realization (SNAP-SPAN)

• the execution of a plan
• the expression of a function
• the exercise of a role
• the realization of a disposition
• the course of a disease
• the application of a therapy

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SNAP dependent entities and their SPAN
realizations

• plan
• function
• role
• disposition
• disease
• therapy

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SNAP dependent entities and their SPAN
realizations

• execution
• expression
• exercise
• realization
• course
• application

SPAN
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More examples

• performance of a symphony
• projection of a film
• expression of an emotion
• utterance of a sentence
• increase of body temperature
• spreading of an epidemic
• extinguishing of a forest fire
• movement of a tornado

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BFO SNAP/SPAN Theory of Granular Partitions

• theory of universals and instances
• theory of part and whole
• theory of boundaries
• theory of functions, powers, qualities, roles
• theory of environments, contexts
• theory of spatial and spatiotemporal regions

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MedO medical domain ontology

• universals and instances and normativity
• theory of part and whole and absence
• theory of boundaries/membranes
• theory of functions, powers, qualities, roles,
  (mal)functions, bodily systems
• theory of environments inside and outside the
  organism
• theory of spatial and spatiotemporal regions
  anatomical mereotopology

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MedO medical domain ontology

• theory of granularity relations between
• molecule ontology
• gene ontology
• cell ontology
• anatomical ontology
• etc.

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IFOMIS project

• collaborate with LC to show how an ontology
  constructed on the basis of philosophical
  principles can help in overhauling and validating
  LCs large terminology-based medical ontology
  LinkBase

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Testing the BFO/MedO approach

• within a software environment for NLP of
  unstructured patient records
• collaborating with
• Language and Computing nv (www.landcglobal.be)

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LC

• LinKBase worlds largest terminology-based
  ontology
• with mappings to UMLS, SNOMED, etc.
• LinKFactory suite for developing and managing
  large terminology-based ontologies

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LinKBase

• LinKBase still lacking a formal theory
• BFO and MedO designed to add better reasoning
  capacity
• by tagging LinKBase domain-entities with
  corresponding BFO/MedO categories
• by constraining links within LinKBase according
  to the theory of granular partitions

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LCs long-term goal

• Transform the mass of unstructured patient
  records into a gigantic medical experiment

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IFOMISs long-term goal

• Build a robust high-level BFO-MedO framework
• THE WORLDS FIRST INDUSTRIAL-STRENGTH PHILOSOPHY
• which can serve as the basis for an
  ontologically coherent unification of medical
  knowledge and terminology

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END

• http//ontologist.com