Historical Introduction to Ontologies Barry Smith

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Historical Introduction to OntologiesBarry Smith
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A brief history of ontology

• Aristotle Ontology is first philosophy
• Realist theory of categories based on
• substances and accidents
• universals and particulars
• Epistemological optimism

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Porphyrian Hierarchy
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Linnaean Hierarchy
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Epistemological pessimism

• Descartes Sceptical doubt, epistemology is first
  philosophy, we can only know our own minds
• Kant Reality in itself is unknowable all we can
  ever know is our own concepts

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The 20th Century

• Frege, Russell, Wittgenstein
• invention of first-order logic
• Logic is first philosophy
• Vienna Circle (1922 1938)
• Schlick, Neurath, Gödel, Carnap ...
• Universal science
• Joseph Woodger, The Axiomatic Method in Biology
  (1937)

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Primitive classes Primitive relations
cell male gamete female gamete whole organism organized unity genetic property part of earlier than derives by division or fusion from environment of

primitive classes and relations in Woodger
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sample page from Woodger
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Analytical metaphysics

• Quine
• Ontological commitment (study not what there is,
  but what sciences believe there is when
  logically formalized)
• Nominalism no universals or types, just generic
  predicates
• Analytical metaphysics (from ca. 1980) Chisholm,
  Armstrong, Fine, Lowe, rediscovery of
  metaphysics as first philosophy
• Realist theory of universals

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Applied Ontology, 5 (2010), 79108
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Lord and Stevens

• There are now over 60 ontologies in active use,
  increasingly developed as large, international
  collaborations. There are, however, many opinions
  on how ontologies should be authored ...
  Recently, a common opinion has been the realist
  approach that places restrictions upon the style
  of modelling considered to be appropriate.

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Lord and Stevens

• ... realism appears to be over-simplistic
  which, perversely, results in overly complex
  ontological models. We suggest that it is
  impossible to avoid compromise in modelling
  ontology a clearer understanding of these
  compromises will better enable appropriate
  modelling ...

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Two methodologies

• Logical conceptualism (Gary Merrill, Phil Lord,
  Robert Stevens, ...)
• using received FOL, or OWL, each group should
  formalize the sentences they need, using the
  attributes they need (tolerance),
• and then coordinate later to resolve forking
  problems
• Ontological realism (OBO Foundry)
• prospective standardization based on something
  like Basic Formal Ontology

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Argument in favor of tolerance

• Scientists need flexibility
• For any proposed top-level ontological axiom
  for example that the world is divided into
  continuants and occurrents there are entrenched
  views both pro and contra.

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Arguments against tolerance 1. the need to
prevent forking.

• Integrity is assured because users of OBO
  Foundry ontologies are focused on one and the
  same biological reality
• Take care of flexibility through
• constant updates
• competing consortia
• user interfaces / views
• application ontologies built on a common core
  of reference ontologies

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Arguments against tolerance 2. secondary
uses.

• The lessons of the GO and the FMA

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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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Hierarchical view representing relations between
represented types
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Most successful ontology venture thus far

• 100 mill. invested in literature and database
  curation using the Gene Ontology (GO)
• based on the idea of annotation
• over 11 million annotations relating gene
  products (proteins) described in the UniProt,
  Ensembl and other databases to terms in the GO
• multiple secondary uses because the ontology
  was not built to meet one specific set of
  requirements

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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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Sample Gene Array Data
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semantic annotation of data
where in the cell ?
what kind of molecular function ?
what kind of biological process?
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natural language labels
to make the data cognitively accessible to human
beings
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compare legends for maps
compare legends for maps
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compare legends for diagrams
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ontologies are legends for data
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compare legends for maps
compare legends for maps
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ontologies are legends for images
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what lesion ?
what brain function ?
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ontologies are legends for databases
GlyProt
MouseEcotope
sphingolipid transporter activity
DiabetInGene
GluChem
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annotation using common ontologies yields
integration of databases
GlyProt
MouseEcotope
Holliday junction helicase complex
DiabetInGene
GluChem
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annotation using common ontologies can support
comparison of data
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annotation with Gene Ontology

• supports reusability of data
• supports search of data by humans
• supports comparison of data
• supports aggregation of data
• supports reasoning with data by humans and
  machines

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The goal virtual science

• consistent (non-redundant) annotation
• cumulative (additive) annotation
• yielding, by incremental steps, a virtual map of
  the entirety of reality that is accessible to
  computational reasoning

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This goal is realizable if we have a common
ontology framework

• data is retrievable
• data is comparable
• data is integratable
• only to the degree that it is annotated using a
  common controlled vocabulary
• compare the role of seconds, meters, kilograms
  in unifying science

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To achieve this end we have to engage in
something like philosophy (?)
is this the right way to organize the top level
of this portion of the GO? how does the top level
of this ontology relate to the top levels of
other, neighboring ontologies?
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Strategy for doing this

• see the world as organized via
  types/universals/categories which are
  hierarchically organized
• and in relation to which statements can be
  formulated which are universally true of all
  instances
• cell membrane part_of cell

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Anatomical Space
Anatomical Structure
Organ Cavity Subdivision
Organ Cavity
Organ
Serous Sac
Organ Component
Serous Sac Cavity
Tissue
Serous Sac Cavity Subdivision
is_a
Pleural Sac
Pleura(Wall of Sac)
Pleural Cavity
part_of
Parietal Pleura
Visceral Pleura
Interlobar recess
Mediastinal Pleura
Mesothelium of Pleura
Foundational Model of Anatomy Ontology
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species, genera
mammal
frog
instances
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Aristotles metaphysics is focused on objects
(things, substances, organisms)

• The most important universals in his ontology
  are substance universals
• cow man rock planet
• which pertain to what a thing is at all times at
  which it exists
• Substance universals form trees of greater and
  lesser generality

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For Aristotle, the world contains also accidents

• which pertain to how a thing is at some time at
  which it exists
• what holds of a substance per accidens

red hot suntanned spinning
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Accidents, too, instantiate genera and species

• Thus accidents, too, form trees of greater and
  lesser generality

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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)
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Substances are the bearers of accidents
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Aristotles 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
Universal
Particular
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In fact however we need more than the ontological
squareNot everything in reality is either a
substance or an accident
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Positive and negative parts
negative part
or hole
(not made of matter)
positive part
(made of matter)
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Different kinds of holes
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Cerebral Cortex
Different kinds of boundaries
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Different levels of granularity

• An organism is a totality of atoms
• An organism is a totality of molecules
• An organism is a totality of cells
• An organism is a single unitary substance
• ... all of these express veridical partitions of
  one and the same reality

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Beyond Aristotle
an ontology of substances processes qualities,
functions, roles holes, cavities fiat and
bona fide boundaries ... information
artifacts multiple granularities
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Ontology requires multiple transparent partitions

• at different levels of granularity
• operating with species-genus hierarchies and
  with an ontology of substances and accidents
  along the lines described by Aristotle
• substances and accidents reappear in the
  microscopic and macroscopic worlds of e.g. of
  chemistry and evolutionary biology

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Periodic Table
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