historical introduction to ontologies barry smith
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Historical Introduction to Ontologies
Barry Smith
A brief history of ontology
Aristotle: Ontology is first philosophy
Realist theory of categories based on
substances and accidents
universals and particulars
Epistemological optimism2
Porphyrian Hierarchy
3
Linnaean Hierarchy
4
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
5
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
primitive classes and relations in Woodger 7
sample page from Woodger
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Analytical metaphysicsQuine
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 9
Applied Ontology, 5 (2010), 79–108
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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 methodologiesLogical 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.
15
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
Arguments against tolerance : 1. the need to prevent forking
.
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The lessons of the GO and the FMA
Arguments against tolerance : 2. secondary uses
.
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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 20
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
21
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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where in the cell ?
what kind of molecular function ?
semantic annotation of data
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 mapscompare: 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 mapscompare: 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
MouseEcotope GlyProt
DiabetInGene
GluChem
sphingolipid transporter
activity
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annotation using common ontologies yields integration of databases
MouseEcotope GlyProt
DiabetInGene
GluChem
Holliday junction helicase complex
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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? 39
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 cell40
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
Foundational Model of Anatomy Ontology41
siamese
mammal
cat
organism
substancespecies, genera
animal
instances
frog
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Aristotle’s 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
this individual accident of redness (this token redness – here, now)
quality
color
red
scarlet
R232, G54, B24
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= relations of inherence(one-sided existential dependence)
John
hunger
Substances are the bearers of accidents
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Aristotle’s Ontological SquareSubstantial 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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In fact however we need more than the ontological square
Not everything in reality is either a substance or an accident
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Positive and negative parts
positivepart
negativepartor hole
(made of matter)
(not 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 53
Beyond Aristotle
an ontology ofsubstancesprocessesqualities, 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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