realism for scientific ontologies

Realism for Scientific Ontologies

Michel Dumontier and Robert Hoehndorf

Carleton University and European Bioinformatics Institute

6th International Conference on Formal Ontology in InformationSystems

Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 1 / 34

Introduction

Introduction


Introduction

IntroductionSummary

Terms in an ontology should correspond to instances in reality.[...] Ontologies consist of representations of types in reality.

realism criteria for biomedical ontologies: all classes must be based on(Aristotelian) universals

no adequate representation of theories and hypotheses

no adequate representation of plans and descriptions

not suited for scientific discourse

harmful for many applications of ontologies in science


Introduction

IntroductionWhat is science?

Science is the concerted human effort to understand, or tounderstand better, the history of the natural world and how thenatural world works, with observable physical evidence as thebasis of that understanding (E.O. Wilson).

Science is not truth.

Science is not certainty.


Introduction

IntroductionThe scientific method

collection of data through observation

formulation of hypotheses and theories

inference and prediction

experimentation


Introduction

IntroductionThe role of ontology

In each step of the scientific method we require ontology:

to describe and classify collected data,

to formulate and express hypotheses and theories

to infer and predict outcomes,

to collect evidence through experimentation, e.g., to find predictedinstances of a type.


Ontologies in biomedicine

Biomedical ontologiesDatabase annotation

End of 1990s: genome projects

Large number of homologous genes

Data available and annotated in model organism databases

Different terms used to describe gene functions

Problem: integration and communication problem



Biomedical ontologiesGene Ontology

three branches: cellular components, biological processes, molecularfunctions

vocabulary organized as directed acyclic graph

edges labelled is-a, part-of, regulates

textual definitions for all terms

goal: integration of model organism databases



Biomedical ontologiesOpen Biomedical Ontologies (OBO)

about 100 domain ontologies

designed as vocabularies for database interoperability

common principles: openness, common syntax, definitions anddocumentation, orthogonality



Biomedical ontologiesWhich problem do we want to solve?

ontologies (in biology) intend to solve a communication problem

database integration by defining the terms used in databases

support scientific discourse

specify the meaning of terms in a vocabulary

terms refer to observations, hypotheses, theories, predictions andexperiments



Biomedical ontologiesOBO Foundry

“high-quality” ontologies for science

Relationship Ontology and Basic Formal Ontology (BFO)

“Terms in an ontology should correspond to instances in reality.”

“Ontologies consist of representations of types in reality.”

collection of realist ontologies

What is a realist ontology?


Realism

RealismTypes of realism

Realism does not say how things are but only that there is a waythat they are. [Searle]

Realism about the world

Modal realism

Scientific realism

Realism about universals


Realism

RealismRealism about universals: Aristotle

universals exist independently from minds

universals exist in things (in re)

something identical in all instances

dependent on particulars


Realism

RealismBFO and OBO Foundry

Realism in BFO and OBO Foundry: all classes in an ontology must bebased on Aristotelian universals.

no inconsistent classes

no classes which have no instances in “reality”

only represent types in “reality”

“ontology as reality representation” (Smith, 2004)


Realism

RealismScientific theories: the Standard Model

Standard Model in particle physics:

theory of the strong, electromagnetic and weak interaction betweenelementary particles

consistent with most high-energy physics experiments

predictive power: W and Z bosons, gluon, top and charm quarks,decay of Z bosons

Hypothetical and unconfirmed: Higgs boson, graviton, magneticphoton, X boson, Y boson, ...

the meaning of Higgs boson (X, Y boson, graviton, ...) is undisputed


Realism

RealismScientific theories: Higgs boson

Electron can be a class in OBO Foundry/BFO

Higgs boson cannot be a class in an OBO Foundry/BFO basedontology until instances are found

theories and hypotheses about Higgs boson exist in “reality”

How can the ontology of the Standard Model be made available forscientists?


Realism

RealismInformation, propositions, theories

Information Artifact Ontology (IAO) aims to represent:

documents, texts, data files

parts of documents: conclusions, introductions

numerals

scientific discourse

theories, propositions, statements

aboutness

ICE v ∃is about.Entity


Realism

RealismInformation

IAO: ICE v ∃is about.Entity

Entity (BFO) is equivalent to Particular

reify classes to refer to information about types

use BFO’s Generically Dependent Continuant class(BFO’s) universals are generically dependent on their instances

HBT v ∃is about.HiggsBoson

HBT v ∃is about.{HiggsBoson}no instances of HiggsBoson in “reality”

therefore

no HiggsBoson class in BFO/OBO Foundryno HBT class definition in BFO/OBO Foundry


Realism

RealismInformation






HBT v ∃is about.{HiggsBoson}

no instances of HiggsBoson in “reality”

therefore



Realism

RealismInformation






HBT v ∃is about.{HiggsBoson}no instances of HiggsBoson in “reality”

therefore



Realism

RealismInformation

HiggsBoson may not be an Aristotelian universal.

Electron probably is.

Consequence

only experimentally supported predictions of the SM can be representedin BFO/OBO Foundryonly information about supported predictions

Can experiments be described using BFO/OBO Foundry?


Realism

RealismExperimentation and interpretation

Ontology of Biomedical Investigations (OBI) aims to represent:

investigation, experimentation, documentation

scientific assays

plans and descriptions

outcomes and measurements

interpretation of results

But: to describe experimentation and interpretation, we must be able todescribe what the experiment and interpretation is about.


Realism

RealismPlans

[I]t would be an error to include in a scientific ontology of drugsterms referring to pharmaceutical products which do not yet(and may never) exist, solely on the basis of plans anddescriptions. Rather, such terms should be included precisely atthe point where the corresponding instances do indeed exist inreality [...] [Smith et al., 2006]


Realism

RealismLimiting research results

De Silva et al. What is the smallest saturated acyclic alkane that cannotbe made? J. Chem. Inf. Model, 45(1):81–87, 2005.


Realism

What are chemical structures and their relations?Original example: Hastings et al., 2010

the CU, which has instances individual chemical entities

BetaFarnesene v FarneseneBetaFarnesene ≡ ∃hasSpecification.BetaFarneseneCG

the connectivity, which exists in many individual molecules

BetaFarneseneConnectivityME v ME

the chemical graph representation of the connectivity, which is aninformation artifact, concretized in a particular file on the computer

BetaFarneseneCG v InformationContentEntityBetaFarneseneCG v ∀isAbout.BetaFarneseneConnectivityME


Realism

What are chemical structures and their relations?Critique

BetaFarnesene ≡ ∃hasSpecification.BetaFarneseneCG

something must have a chemical graph specification to be a betafarnesene

no MEs in BFO

mathematical graphs become irrelevant

no relation between mathematical graphs and molecules


Realism

What are chemical structures and their relations?Application to C17

C 17 v Molecule not allowed

C 17CG v ICE

C 17CG v ∀isAbout.C 17ME

∃hasSpecification.C 17CG

C 17 ≡ ∃hasSpecification.C 17CG not allowed


Realism

RealismAlternative scientific theories

Perpetual Motion Machine (first kind)


Realism

Formal OntologyWhich problem do ontologies solve?

ontologies to support scientific discourse and data integration

contain all terms used within scientific discourse

Unicorn is not used in scientific discourse

Higgs boson, Perpetual motion, impossible molecules, etc. are used inscientific discourse


Realism

Formal OntologyAn old solution

include all relevant terms within a domain/application

specify the meaning of terms: how a term refers

(need for possible worlds with contingent natural laws)


Conclusions

ConclusionsSummary

BFO/OBO Foundry: all classes in an ontology must have instances in“reality”

applied in some biomedical ontologies

cannot represent unconfirmed hypotheses, predictions, theories

unsuitable as foundation for scientific discourse and investigation


Conclusions

ConclusionsSummary

philosophy is useful to support scientific investigations

“You cannot do what you need because Aristotle said so” is not

realism criterion should not be applied


Conclusions

Acknowledgements

Heinrich Herre

Phillip Lord

Robert Stevens

Janet Kelso

Frank Loebe

Nico Adams

DietrichRebholz-Schuhmann

Maria Laikata

Janna Hastings

Philippe Rocca-Serra

Susanna-Assunta Sansone

Helen Parkinson

James Malone

Jennifer Fostel

Anika Oellrich

Darius Sulskus

Christoph Grabmueller


Conclusions

Thank you!


realism for scientific ontologies

Health & Medicine

realism realism realism

scientic ontologies

realism realism bfo

realism criteria

applications of ontologies

obo foundry realism

scientic ontologiesfois2010

databasessupport scientic