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BASIC FORMAL ONTOLOGY

BASIC FORMAL ONTOLOGY. Robert Arp, Ph.D. Ontology Research Group (ORG) www.org.buffalo.edu National Center for Biomedical Ontology (NCBO) www.bioontology.org. I: Meanings of ‘Ontology’ II: Basic Formal Ontology III: Constructing a Domain Ontology.

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BASIC FORMAL ONTOLOGY

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  1. BASIC FORMAL ONTOLOGY Robert Arp, Ph.D. Ontology Research Group (ORG) www.org.buffalo.edu National Center for Biomedical Ontology (NCBO) www.bioontology.org

  2. I: Meanings of ‘Ontology’II: Basic Formal OntologyIII: Constructing a Domain Ontology

  3. Part I:Meanings of ‘Ontology’

  4. (1) Philosophical Ontology (2) Domain Ontology (3) Formal Ontology

  5. Philosophical Ontology • “...I can fit wholesale evolution and a creating god into my ontology without contradiction.” • “...just because it has mental existence doesn’t mean it has ontological existence.”

  6. - Ontos (being, existence)+ Logos (word, account, explanation) - The study of what is, of the kinds and structures of objects, properties, events, processes, and relations in every area of reality - “The branch of Metaphysics that studies the nature of existence.”Random House College Dictionary

  7. PORPHYRIAN TREE Compare: Linnean Taxonomy and Periodic Table

  8. To a certain extent, all of us are Philosophical Ontologists in that we naturally and automatically categorize any and all things in reality so as to understand, explain, control, dominate, and navigate reality.

  9. (1) Philosophical Ontology (2) Domain Ontology (3) Formal Ontology

  10. (2) Domain Ontology “...I’m working on an ontology for annelids.” “...the Gene Ontology has data on that HOX gene.”

  11. Representation of the entities and relations existing within a particular domain of reality such as medicine, geography, ecology, or law Gene Ontology (GO) • Foundational Model of Anatomy (FMA) Environment Ontology (EnvO) • - Opposed to ontology in the philosophical sense, which has all of reality as its subject matter • - Ideally, provides a controlled, structured vocabulary to annotate data in order to make it more easily searchable by human beings and processable by computers

  12. ONTOLOGY:“a representational artifact, comprising a taxonomy as its main part, whose representational units are intended to designate some combination of universals, defined classes, and certain relations between them.” ** Smith, B., Kusnierczyk, W., Schober, D., & Ceusters, W. (2006). Towards a reference terminology for ontology research and development in the biomedical domain. Proceedings of KR-MED 2006, 1, 1-14.

  13. REALISM-BASED ONTOLOGY:“…built out of representational units which are intended to refer exclusively to (real) universals, and corresponds to that part of the content of a scientific theory that is captured by its constituent general terms and the interrelations between the universals denoted by these terms.” (Smith et al., 2006)

  14. Method of Ontological Realism • Find out what the world is like by doing science, talking to other scientists, and working continuously with them to ensure that you don’t go wrong • Build representations adequate to this world, not to some simplified model in your laptop

  15. Informatics:The science of information collection, categorization, management, storage, processing, retrieval, and dissemination.“…the fundamental role of a domain ontology is to support knowledge sharing and reuse.” ** Domingue, J., & Motta, E. (1999). A knowledge-based news server supporting ontology-driven story enrichment and knowledge retrieval. In D. Fensel & R. Studer (Eds.), Knowledge acquisition, modeling and management (pp. 104-112). Berlin: Springer.

  16. Ontology characterized as a hybrid of: • - Taxonomy • Axiomatic • Theory Domain ontology contrasted with:- Database- Rule-Based Language - Thesaurus- Glossary- Catalogue- Inventory- Axiomatic Theory- Simple Taxonomy

  17. Domain Ontologies are representations ofuniversals in reality:kindstypescategoriesgeneraspecies

  18. The Central Distinction universalvs.instance (cataloguevs. inventory) (science textvs. diary) (human being vs. George Bush) (mouse brain vs. Mickey Mouse’s brain) (cytoplasm vs. this cytoplasm under the scope)

  19. substance organism animal cat instances siamese universals mammal frog

  20. Example Domain Ontology Mouse Trap

  21. Example Domain Ontology Beer

  22. BORROWED FROM: http://www.bio.davidson.edu/courses/genomics/2006/martens... 3DN A Gene Ontology Example: Glutathione

  23. A Gene Ontology Example: Cytokinesis

  24. is_a part_of A Gene Ontology Example

  25. Scientific Experiment Ontology http://technology.newscientist.com/article/dn9288-translator-lets-computers-understand-experiments-.html

  26. p/o = part_of is_a

  27. Part of a Lipid Ontology Being developed by: Low, H-S., Alexander, G., Baker, C., & Wenk, M. (2008). Lipid ontology Available at: http://MUS.12R.lipidontology.biochem.nus.edu.sg/lipidversion3.owl.

  28. Because of: • Varying perspectives, methodologies, ideas, and • Data • Extraordinary depth, magnitude of data… • Overwhelmed with data and information… • More information than humans can handle… A couple of problems result(there are more…)

  29. A Couple of Problems(there are more…) 1 How do you find your data? 2 THE SILO EFFECT

  30. How do you find your data? 1 - How do you understand the significance of the data you collected 3 years earlier? - How do you reason with the data when you find it? - How do you integrate your data with other people’s data?

  31. CHAOS

  32. Part of the solution seems to involve consensus-based- standardized terminologies - coding schemes

  33. THE SILO EFFECT 2 Many domains that are non-interoperable, non-communicative, isolated, insolated, encapsulated “silos” of data

  34. THE SILO EFFECT

  35. THE SILO EFFECT

  36. Informatics problems that contribute to SILO EFFECT: • - Dumb Beast • - Nonsense-In-Nonsense-Out • - Computer Solipsism • - Human Idiosyncrasy • Tower of Babel • Pressures from Insurance Companies • Legal Pressures • ** Human Error: Incorrect Thinking THE SILO EFFECT

  37. ** Human Error: Incorrect Thinking Three Levels to Keep Straight • Level 1: The entities in reality, both instances and universals • Level 2: Cognitive representations of this reality on the part of scientists • Level 3: Publicly accessible concretizations of these cognitive representations in textual, graphical, or computational representational artifacts

  38. Three Levels to Keep Straight Cognitive representations Representational artifacts Reality

  39. PROBLEM:DE-SILOING all of this domain data so that it may be found (!), queried effectively, shared, and re-used…

  40. PROBLEM:DE-SILOING all of this domain data so that it may be found (!), queried effectively, shared, and re-used… SOLUTION:Formal Ontology

  41. (1) Philosophical Ontology (2) Domain Ontology (3) Formal Ontology

  42. (3) Formal Ontology “...This upper-level ontology should help organize these domains.” “...IEEE just came out with the latest version of SUMO that may solve some of these problems.”

  43. Assists in making communication between and among domain ontologies possible by providing:-Common language-Common formal framework for reasoning

  44. Concerns, at least:- Adoption of a set of basic categories of objects- Discerning what kinds of entities fall within each of these categories of objects- Determining what relationships hold between the different categories in the domain ontology

  45. Formal Ontology is like a “backbone” or “spine” making communication, interoperability, and optimal dissemination of information possible between and among domain ontologies

  46. From this… To this…

  47. From this… To this…

  48. Program Announcement Number: PAR-07-425 Title: Data Ontologies for Biomedical Research (R01) NIH Blueprint for Neuroscience Research, (http://neuroscienceblueprint.nih.gov/)National Cancer Institute (NCI), (http://www.cancer.gov)National Center for Research Resources (NCRR), (http://www.ncrr.nih.gov/)National Eye Institute (NEI), (http://www.nei.nih.gov/)National Heart Lung and Blood Institute (NHLBI), (http://http.nhlbi.nih.gov )National Human Genome Research Institute (NHGRI), (http://www.genome.gov)National Institute on Alcohol Abuse and Alcoholism (NIAAA), (http://www.niaaa.nih.gov/)National Institute of Biomedical Imaging and Bioengineering (NIBIB), (http://www.nibib.nih.gov/)National Institute of Child Health and Human Development (NICHD), (http://www.nich.nih.gov/)National Institute on Drug Abuse (NIDA), (http://www.nida.nih.gov/)National Institute of Environmental Health Sciences (NIEHS), (http://www.niehs.nih.gov/)National Institute of General Medical Sciences (NIGMS), (http://www.nigms.nih.gov/)National Institute of Mental Health (NIMH), (http://www.nimh.nih.gov/)National Institute of Neurological Disorders and Stroke (NINDS), (http://www.ninds.nih.gov/)National Institute of Nursing Research (NINR), (http://www.ninr.nih.gov)

  49. PAR-07-425 Purpose “Optimal use of informatics tools… and (data) resources depends upon explicit understandings of concepts related to the data upon which they compute.” “This is typically accomplished by a tool or resource adopting a formal controlled vocabulary and ontology.”

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