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Stefan Schulz , Martin Boeker, Holger Stenzhorn

MIE 2008. How Granularity Issues Concern Biomedical Ontology Integration. Stefan Schulz , Martin Boeker, Holger Stenzhorn. University Medical Center Freiburg, Institute of Medical Biometry and Medical Informatics Freiburg, Germany.

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Stefan Schulz , Martin Boeker, Holger Stenzhorn

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  1. MIE 2008 How Granularity Issues Concern Biomedical Ontology Integration Stefan Schulz, Martin Boeker, Holger Stenzhorn University Medical Center Freiburg, Institute of Medical Biometry and Medical Informatics Freiburg, Germany

  2. IntroductionProblem 1 Problem 2 Problem 3 Conclusion

  3. Introduction Problem 1 Problem 2 Problem 3 Conclusion Introduction • Background: emerging biomedical ontologies: standard descriptions of types of bio(medical) entities • Challenge: interlink ontologies and enable interoperability • Goal: share data both within and across disciplinary boundaries • Proposal: BioTop, an integrative domain top level ontology for life science E Beisswanger, U Hahn, H Stenzhorn, S Schulz: BioTop: A Life Science Upper Domain Ontology. Forthcoming in Applied Ontology 2008

  4. Introduction Problem 1 Problem 2 Problem 3 Conclusion Biomedical Ontologies… …are artifacts whose representational units are intended to designate classes of biomedical entities, their properties, and their interrelations DomainOntologies

  5. Introduction Problem 1 Problem 2 Problem 3 Conclusion • Transcription • DNA-dependent transcription • antisense RNA transcription • mRNA transcription • rRNA transcription • tRNA transcription • … • (from Gene Ontology) Biomedical Ontologies… OBO (Gene Ontology, Sequence Ontology, Cell Ontology, OBI, ChEBI, Mouse Anatomy, FMA …) DomainOntologies

  6. Introduction Problem 1 Problem 2 Problem 3 Conclusion • Transcription • DNA-dependent transcription • antisense RNA transcription • mRNA transcription • rRNA transcription • tRNA transcription • … • (from Gene Ontology) Upper Ontologies… Onto-logies limited to domain-independent categories OBO (Gene Ontology, Sequence Ontology, Cell Ontology, OBI, ChEBI, Mouse Anatomy, FMA …) DomainOntologies

  7. Introduction Problem 1 Problem 2 Problem 3 Conclusion • Entity • Continuant • Dependent Continuant • Realizable Entity • Function • Role • Independent Continuant • Object • Object Aggregate • Occurrent DOLCE BFO • Transcription • DNA-dependent transcription • antisense RNA transcription • mRNA transcription • rRNA transcription • tRNA transcription • … • (from Gene Ontology) Upper Ontologies UpperOntology OBO (Gene Ontology, Sequence Ontology, Cell Ontology, OBI, ChEBI, Mouse Anatomy, FMA …) DomainOntologies

  8. Introduction Problem 1 Problem 2 Problem 3 Conclusion • Entity • Continuant • Dependent Continuant • Realizable Entity • Function • Role • Independent Continuant • Object • Object Aggregate • Occurrent DOLCE BFO • Organism • Body Part • Cell • Cell Component • Tissue • Protein • Nucleic Acid • DNA • RNA • Biological Function • Biological Process • Transcription • DNA-dependent transcription • antisense RNA transcription • mRNA transcription • rRNA transcription • tRNA transcription • … • (from Gene Ontology) Middle-level ? UpperOntology OBO (Gene Ontology, Sequence Ontology, Cell Ontology, OBI, ChEBI, Mouse Anatomy, FMA …) DomainOntologies

  9. Introduction Problem 1 Problem 2 Problem 3 Conclusion • Entity • Continuant • Dependent Continuant • Realizable Entity • Function • Role • Independent Continuant • Object • Object Aggregate • Occurrent DOLCE BFO • Organism • Body Part • Cell • Cell Component • Tissue • Protein • Nucleic Acid • DNA • RNA • Biological Function • Biological Process • Transcription • DNA-dependent transcription • antisense RNA transcription • mRNA transcription • rRNA transcription • tRNA transcription • … • (from Gene Ontology) Top Domain Ontologies UpperOntology OBO (Gene Ontology, Sequence Ontology, Cell Ontology, OBI, ChEBI, Mouse Anatomy, FMA …) DomainOntologies

  10. Introduction Problem 1 Problem 2 Problem 3 Conclusion Lower-level alignment DOLCE UpperOntology BFO Simple Bio Upper Ontology BioTop GFO-Bio Top DomainOntology GENIA Ontology OBO (Gene Ontology, Sequence Ontology, Cell Ontology, OBI, ChEBI, Mouse Anatomy, FMA …) DomainOntologies

  11. Introduction Problem 1 Problem 2 Problem 3 Conclusion Upper-level alignment BFO BioTop

  12. IntroductionProblem 1 Problem 2 Problem 3 Conclusion

  13. Introduction Problem 1 Problem 2 Problem 3 Conclusion Upper-level alignment BFO BioTop

  14. Continuant Introduction Problem 1 Problem 2 Problem 3 Conclusion Object or FiatObjectPart? FiatObjectPart IndependentContinuant BFO Object FiatObjectPart ObjectAggregate An independent continuant entity that is spatially extended, maximally self-connected and self-contained (the parts are not separated from each other by spatial gaps), and possesses an internal unity; the identity of substantial objects is independent of that of other entities and can be maintained through time and through loss and gain of parts and qualities. Examples: an organism, a chair, a cell, a lung, an apple. An independent continuant entity that is part of a object but is not demarcated by any physical discontinuities. Examples: upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Copenhagen, the lower right portion of a human torso.

  15. Continuant Introduction Problem 1 Problem 2 Problem 3 Conclusion Object or FiatObjectPart? FiatObjectPart IndependentContinuant Object FiatObjectPart ObjectAggregate ? Bodily Organ BioTop

  16. Introduction Problem 1 Problem 2 Problem 3 Conclusion Object or FiatObjectPart? Lung Surface vs.Pleural Space: Bona Fide Boundary(physical discontinuity) Lung Hilus: Entry of Bronchi, veins and arteries. Fiat Boundary(no physical discontinuity)

  17. Continuant Introduction Problem 1 Problem 2 Problem 3 Conclusion Object or FiatObjectPart? IndependentContinuant BFO Object FiatObjectPart ObjectAggregate SiameseTwin BioTop …before separation

  18. Continuant Introduction Problem 1 Problem 2 Problem 3 Conclusion Object or FiatObjectPart? IndependentContinuant BFO Object FiatObjectPart ObjectAggregate SiameseTwin BioTop …after separation

  19. IntroductionProblem 1 Problem 2 Problem 3 Conclusion Object vs. ObjectAggregate

  20. Continuant IntroductionProblem 1 Problem 2 Problem 3 Conclusion Object vs. ObjectAggregate IndependentContinuant BFO Object FiatObjectPart ObjectAggregate An independent continuant entity that is spatially extended, maximally self-connected and self-contained (the parts are not separated from each other by spatial gaps), and possesses an internal unity; the identity of substantial objects is independent of that of other entities and can be maintained through time and through loss and gain of parts and qualities. Examples: an organism, a chair, a cell, a lung, an apple. An independent continuant entity that is a mereological sum of separate objects. Examples: a heap of stones, a group of commuters on the subway, a collection of bacteria, a flock of geese, the patients in a hospital, a symphony orchestra.

  21. Continuant IntroductionProblem 1 Problem 2 Problem 3 Conclusion Object vs. ObjectAggregate IndependentContinuant BFO Object FiatObjectPart ObjectAggregate ? BiologicalObject BioTop

  22. IntroductionProblem 1 Problem 2 Problem 3 Conclusion Object vs. ObjectAggregate Object An independent continuant entity that is spatially extended, maximally self-connected and self-contained (the parts are not separated from each other by spatial gaps), and possesses an internal unity; the identity of substantial objects is independent of that of other entities and can be maintained through time and through loss and gain of parts and qualities. Examples: an organism, a chair, a cell, a lung, an apple. E.coli

  23. IntroductionProblem 1 Problem 2 Problem 3 Conclusion Object vs. ObjectAggregate Object ObjectAggregate E.coli

  24. IntroductionProblem 1 Problem 2 Problem 3 Conclusion Object vs. ObjectAggregate Object ObjectAggregate E.coli

  25. IntroductionProblem 1 Problem 2 Problem 3 Conclusion Object vs. ObjectAggregate Object ObjectAggregate H H H

  26. IntroductionProblem 1 Problem 2 Problem 3 Conclusion Object vs. ObjectAggregate! H H Object ObjectAggregate H H H H H H H H H H

  27. IntroductionProblem 1 Problem 2 Problem 3 Conclusion Every Biological Object is an ObjectAggregate! H Object ObjectAggregate H H H An independent continuant entity that is a mereological sum of separate objects. H H H H H 0,0001% nuclei 99,9999% empty space “filled” by probability distributions of electrons

  28. IntroductionProblem 1 Problem 2 Problem 3 Conclusion

  29. IntroductionProblem 1 Problem 2 Problem 3 Conclusion Problem 3: What are “separate objects”? Object ObjectAggregate An independent continuant entity that is spatially extended, maximally self-connected and self-contained (the parts are not separated from each other by spatial gaps), and possesses an internal unity; the identity of substantial objects is independent of that of other entities and can be maintained through time and through loss and gain of parts and qualities. Examples: an organism, a chair, a cell, a lung, an apple. An independent continuant entity that is a mereological sum of separate objects. Examples: a heap of stones, a group of commuters on the subway, a collection of bacteria, a flock of geese, the patients in a hospital, a symphony orchestra. E.coli E.coli

  30. IntroductionProblem 1 Problem 2 Problem 3 Conclusion Continuum of physical connection strength of connection Ionic PolarCovalent Non PolarCovalent Metallic Hydrogen Bridges Van-der-Waals mechanic adhesion electro-static adhesion surfaces chemical bonds

  31. IntroductionProblem 1 Problem 2 Problem 3 Conclusion

  32. IntroductionProblem 1 Problem 2 Problem 3 Conclusion BFO 3rd level categories challenged by • Granularity-dependent notion of self-containedness and unity of objects • Granularity-dependent view of objects as collection of particles • Continuum of physical connection • BFO uses ill-defined criteria of highest-level ontological distinctions

  33. IntroductionProblem 1 Problem 2 Problem 3 Conclusion Consequences for upper ontology integration • Critique of domain level ontology (BioTop) by applying the rigor of an upper level ontology • Critique of the upper level ontology by assessing the appropriateness of upper level categories from the perspective of the domain level • Practical conclusion for BioTop: exclude subclasses of BFO:IndependentContinuant

  34. Continuant IntroductionProblem 1 Problem 2 Problem 3 Conclusion Consequences for upper ontology integration IndependentContinuant BFO Object FiatObjectPart ObjectAggregate BioTop BioTop

  35. IntroductionProblem 1 Problem 2 Problem 3 Conclusion BioTop • Metrics: • BioTop is freely available at: http://purl.org/biotop • BioTop discussion forum: biotop@googlegroups.com • BootSTREP (FP6 - 028099 ) project: http://www.bootstrep.eu

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