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

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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

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.

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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

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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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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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