Realism for Scientific Ontologies
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Realism for Scientific Ontologies

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Science aims to develop an accurate understanding of reality through a ...

Science aims to develop an accurate understanding of reality through a
variety of rigorously empirical and formal methods. Ontologies are used to formalize
the meaning of terms within a domain of discourse. The Basic Formal Ontology
is an ontology of particular importance in the biomedical domains, where it provides
the top-level for numerous ontologies, including those admitted as part of the
OBO Foundry collection. The Basic Formal Ontology requires that all classes in an
ontology are actually instantiated in reality. Despite the fact that it is hard to show
whether entities of some kind exist or do not exist in reality (especially for unobservable
entities like elementary particles), this criterion fails to satisfy the need of
scientists to communicate their findings and theories unambiguously. We discuss
the problems that arise due to the Basic Formal Ontology’s realism criterion and
suggest viable alternatives.

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  • A stunning critique of the realism criterion being applied to OBO Foundry ontologies, which is damaging to the advancement of science. Ultimately, the choice is to drop the criterion or ignore it altogether.
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Realism for Scientific Ontologies Realism for Scientific Ontologies Presentation Transcript

  • Realism for Scientific Ontologies Michel Dumontier and Robert Hoehndorf Carleton University and European Bioinformatics Institute 6th International Conference on Formal Ontology in Information Systems Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 1 / 34
  • Introduction Introduction Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 2 / 34
  • Introduction Introduction Summary 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 Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 3 / 34
  • Introduction Introduction What is science? Science is the concerted human effort to understand, or to understand better, the history of the natural world and how the natural world works, with observable physical evidence as the basis of that understanding (E.O. Wilson). Science is not truth. Science is not certainty. Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 4 / 34
  • Introduction Introduction The scientific method collection of data through observation formulation of hypotheses and theories inference and prediction experimentation Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 5 / 34
  • Introduction Introduction The 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 predicted instances of a type. Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 6 / 34
  • Ontologies in biomedicine Biomedical ontologies Database 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 Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 7 / 34
  • Ontologies in biomedicine Biomedical ontologies Gene Ontology three branches: cellular components, biological processes, molecular functions vocabulary organized as directed acyclic graph edges labelled is-a, part-of, regulates textual definitions for all terms goal: integration of model organism databases Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 8 / 34
  • Ontologies in biomedicine Biomedical ontologies Open Biomedical Ontologies (OBO) about 100 domain ontologies designed as vocabularies for database interoperability common principles: openness, common syntax, definitions and documentation, orthogonality Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 9 / 34
  • Ontologies in biomedicine Biomedical ontologies Which 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 and experiments Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 10 / 34
  • Ontologies in biomedicine Biomedical ontologies OBO 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? Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 11 / 34
  • Realism Realism Types of realism Realism does not say how things are but only that there is a way that they are. [Searle] Realism about the world Modal realism Scientific realism Realism about universals Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 12 / 34
  • Realism Realism Types of realism Realism does not say how things are but only that there is a way that they are. [Searle] Realism about the world Modal realism Scientific realism Realism about universals Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 13 / 34
  • Realism Realism Realism about universals: Aristotle universals exist independently from minds universals exist in things (in re) something identical in all instances dependent on particulars Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 14 / 34
  • Realism Realism BFO and OBO Foundry Realism in BFO and OBO Foundry: all classes in an ontology must be based 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) Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 15 / 34
  • Realism Realism Scientific theories: the Standard Model Standard Model in particle physics: theory of the strong, electromagnetic and weak interaction between elementary 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, magnetic photon, X boson, Y boson, ... the meaning of Higgs boson (X, Y boson, graviton, ...) is undisputed Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 16 / 34
  • Realism Realism Scientific theories: Higgs boson Electron can be a class in OBO Foundry/BFO Higgs boson cannot be a class in an OBO Foundry/BFO based ontology until instances are found theories and hypotheses about Higgs boson exist in “reality” How can the ontology of the Standard Model be made available for scientists? Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 17 / 34
  • Realism Realism Information, 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 ∃is about.Entity Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 18 / 34
  • Realism Realism Information IAO: ICE ∃is about.Entity Entity (BFO) is equivalent to Particular Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 19 / 34
  • Realism Realism Information IAO: ICE ∃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 Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 19 / 34
  • Realism Realism Information IAO: ICE ∃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 ∃is about.HiggsBoson HBT ∃is about.{HiggsBoson} Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 19 / 34
  • Realism Realism Information IAO: ICE ∃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 ∃is about.HiggsBoson HBT ∃is about.{HiggsBoson} no instances of HiggsBoson in “reality” therefore no HiggsBoson class in BFO/OBO Foundry no HBT class definition in BFO/OBO Foundry Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 19 / 34
  • Realism Realism Information HiggsBoson may not be an Aristotelian universal. Electron probably is. Consequence only experimentally supported predictions of the SM can be represented in BFO/OBO Foundry only information about supported predictions Can experiments be described using BFO/OBO Foundry? Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 20 / 34
  • Realism Realism Experimentation 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 to describe what the experiment and interpretation is about. Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 21 / 34
  • Realism Realism Experimentation 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 to describe what the experiment and interpretation is about. Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 22 / 34
  • Realism Realism Plans [I]t would be an error to include in a scientific ontology of drugs terms referring to pharmaceutical products which do not yet (and may never) exist, solely on the basis of plans and descriptions. Rather, such terms should be included precisely at the point where the corresponding instances do indeed exist in reality [...] [Smith et al., 2006] Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 23 / 34
  • Realism Realism Limiting research results De Silva et al. What is the smallest saturated acyclic alkane that cannot be made? J. Chem. Inf. Model, 45(1):81–87, 2005. Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 24 / 34
  • Realism What are chemical structures and their relations? Original example: Hastings et al., 2010 the CU, which has instances individual chemical entities BetaFarnesene Farnesene BetaFarnesene ≡ ∃hasSpecification.BetaFarneseneCG the connectivity, which exists in many individual molecules BetaFarneseneConnectivityME ME the chemical graph representation of the connectivity, which is an information artifact, concretized in a particular file on the computer BetaFarneseneCG InformationContentEntity BetaFarneseneCG ∀isAbout.BetaFarneseneConnectivityME Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 25 / 34
  • Realism What are chemical structures and their relations? Critique BetaFarnesene ≡ ∃hasSpecification.BetaFarneseneCG something must have a chemical graph specification to be a beta farnesene no MEs in BFO mathematical graphs become irrelevant no relation between mathematical graphs and molecules Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 26 / 34
  • Realism What are chemical structures and their relations? Application to C17 C 17 Molecule not allowed Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 27 / 34
  • Realism What are chemical structures and their relations? Application to C17 C 17 Molecule not allowed C 17CG ICE C 17CG ∀isAbout.C 17ME Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 27 / 34
  • Realism What are chemical structures and their relations? Application to C17 C 17 Molecule not allowed C 17CG ICE C 17CG ∀isAbout.C 17ME ∃hasSpecification.C 17CG Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 27 / 34
  • Realism What are chemical structures and their relations? Application to C17 C 17 Molecule not allowed C 17CG ICE C 17CG ∀isAbout.C 17ME ∃hasSpecification.C 17CG C 17 ≡ ∃hasSpecification.C 17CG not allowed Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 27 / 34
  • Realism Realism Alternative scientific theories Perpetual Motion Machine (first kind) Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 28 / 34
  • Realism Formal Ontology Which 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 in scientific discourse Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 29 / 34
  • Realism Formal Ontology An 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) Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 30 / 34
  • Conclusions Conclusions Summary 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 Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 31 / 34
  • Conclusions Conclusions Summary 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 Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 32 / 34
  • Conclusions Acknowledgements Heinrich Herre Janna Hastings Phillip Lord Philippe Rocca-Serra Robert Stevens Susanna-Assunta Sansone Janet Kelso Helen Parkinson Frank Loebe James Malone Nico Adams Jennifer Fostel Dietrich Anika Oellrich Rebholz-Schuhmann Darius Sulskus Maria Laikata Christoph Grabmueller Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 33 / 34
  • Conclusions Thank you! Robert Hoehndorf (EBI) Realism for Scientific Ontologies FOIS2010 34 / 34