Ontology: Not Just for Philosophers Anymore Robert Arp, Ph.D. - The Ontology Research Group (ORG) www.org.buffalo.edu - The National Center for Biomedical

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  • Slide 1
  • Ontology: Not Just for Philosophers Anymore Robert Arp, Ph.D. - The Ontology Research Group (ORG) www.org.buffalo.edu - The National Center for Biomedical Ontology (NCBO) www.bioontology.org Special thanks to Barry Smith and Werner Ceusters for comments and material from articles, books, and presentations. This work was funded by the National Institutes of Health through the NIH Roadmap for Biomedical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at: http://nihroadmap.nih.gov/bioinformatics.
  • Slide 2
  • Three Parts To Talk: I:Meanings of Ontology II:Basic Formal Ontology (BFO) III:The Vision and Mission of the Ontology Research Group (ORG)
  • Slide 3
  • Part I: Meanings of Ontology
  • Slide 4
  • (1) Philosophical Ontology I can fit wholesale evolution and a creating god into my ontology without contradiction. Just because it has mental existence doesnt mean it has ontological existence. (2) Domain Ontology Im working on an ontology for annelids. The Gene Ontology has data on that HOX gene. (3) Formal Ontology This upper level ontology should help organize these domains. IEEE just came out with the latest version of SUO that may solve some of these problems.
  • Slide 5
  • (1) Philosophical Ontology - 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. - Theoretical discipline concerned with accurately describing the taxonomy of all things that exist according to underlying entities and principles that make things: A) BEwhat they are. B) BE KNOWN ASwhat they are. - Synonymous with classical Metaphysics.
  • Slide 6
  • PORPHYRIAN TREE Cf. Linnean Taxonomy and The Periodic Table
  • Slide 7
  • 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.
  • Slide 8
  • Different Schools / Approaches to Philosophical Ontology We cant know reality because we cant get beyond our sensations, perceptions, and/or ideas of reality (Idealism) We can only know the theories, languages, concepts, or systems of beliefs about reality, and reality is what minds make it (Antirealism) We can know reality out there as a world beyond our minds, and reality, ultimately, is in no way (e)affected by our minds (Realism) Reality is one kind of thing: all mind (Mental Monism) Reality is one kind of thing: all matter (Material Monism) Reality is two kinds of things: mind and matter (Dualism) Only the Bible accurately depicts reality (Fundamentalism) Only science accurately depicts reality (Scientism)
  • Slide 9
  • (2) Domain Ontology - Representation of the entities and relations existing within a particular domain of reality such as medicine, geography, ecology, or law, e.g., GO, FMA, 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. - Synonymous (for some) with Reference Ontology. - Task or Application Ontology: runs, uses, exploits a domain ontology.
  • Slide 10
  • AN ONTOLOGY (Ontology Research Group) : 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. * E.G., The Gene Ontology (GO) The Foundational Model of Anatomy Ontology (FMA) The Environment Ontology (EnvO) * Smith et al., Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain, Proc KRMed 2006: http://ontology.buffalo.edu/bfo/Terminology_for_Ontologies.pdf
  • Slide 11
  • A REALISM-BASED ONTOLOGY: is 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. * (again, ORG definition) Contrasted with: - Idealism-Based Ontology - Antirealism-Based Ontology * Smith et al., Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain, Proc KRMed 2006: http://ontology.buffalo.edu/bfo/Terminology_for_Ontologies.pdf
  • Slide 12
  • Informatics: The science of information collection, categorization, management, storage, processing, retrieval, and dissemination. (Arps rendition)
  • Slide 13
  • Bioinformatics: A discipline of quantitative analysis of information relating to biological macro- molecules with the aid of computers. Jin Xiong, Essential Bioinformatics (Cambridge University Press, 2006), 3. developed in the space occupied with mathematical and computational biology, biometry and biostatistics, computer science, cybernetics, molecular evolution, genomics and proteomics, genetics, and molecular and cell biology. Polanski and Kimmel, Bioinformatics (Verlag: Springer, 2007), 2-3.
  • Slide 14
  • Domain ontology is contrasted with: - Database: stores data of ontology or whatever info. - Rule-based Language (e.g., XSD): tells you how to store, control, and describe an ontology or whatever info. - Thesaurus: taxonomy coupled with relations - Taxonomy: terms and glosses organized into subsumed hierarchical relations - Glossary: catalogue of glosses (translations) in a language - Catalogue: set of terms with meanings - Inventory: checklist of items, terms, entities - Axiomatic Theory: formal system with clear rules and semantics However, it is arguable that an Ontology can be characterized as a hybrid of a Taxonomy and an Axiomatic Theory.
  • Slide 15
  • Example Ontology
  • Slide 16
  • BORROWED FROM: http://www.bio.davidson.edu/courses/genomics/2 006/martens... 3DN A Gene Ontology Example
  • Slide 17
  • Genetics Diseases Ecology Evolution Primatology Cardiology The Information Age: A Sea of Information - Varying perspectives, methodologies, ideas, and DATA - More information than humans can handle - Extraordinary depth, magnitude, and CHAOS - Plenty of human error RESULT: - More DOMAINS that are non-interoperable, non-communicative, isolated, insolated, encapsulated silos of information - Lost at sea? In the sea?
  • Slide 18
  • Informatics Problems that Contribute to Being Lost at Sea: - Dumb Beast - Nonsense-In-Nonsense-Out - Computer Solipsism - Human Idiosyncrasy - Tower of Babel - Pressures from Insurance Companies - Legal Pressures - Human Error: Incorrect Thinking (IT)
  • Slide 19
  • IT: Simply Getting the Facts Wrong * FROM GO, SNOMED, BRIDG, and UMLS (1) extracellular region is_a cellular component (2) extrinsic to membrane part_of membrane (3) derives from confused with develops from (4) both testes is_a testis (5) Animal =Def. A non-person living entity (6) An ontology is the same thing as a database (7) An ontology is just a taxonomy * N.B. It may be the case that the examples of IT used in this presentation have been resolved. No matter, (sadly) there are legion examples of IT to be found.
  • Slide 20
  • IT: Lack of Clear and Coherent Definitions FROM NCIT, BRIDG, and SNOMED: (1) Try and Define: Cancer, Gene, Neuropathy, Disease, Infectious Disease, Bios Itself... admittedly difficult. (2) Disease Progression =Def. Cancer that continues to grow and spread, and Increase in size of tumor, and The worsening of a disease over time (3) Person =Def. Human being (4) European is_a ethnic group (5) Other European in New Zealand is_a ethnic group (6) Mixed ethnic census group is_a ethnic group
  • Slide 21
  • IT: Circular Definitions FROM GO and BRIDG (1) Hemolysis of red blood cells =Def. The processes by which an organism effects hemolysis Cf. Filtration of kidneys =Def. The processes by which an organism effects filtration (of kidneys) (2) Ingredient =Def. A substance that acts as an ingredient within a product. Note that ingredients may also have ingredients. (3) Protection from natural killer cell mediated cytolysis =Def. The process of protecting a cell from cytolysis by natural killer cells
  • Slide 22
  • IT: Examples Instead of Definitions FROM BRIDG (1) Adverse Event =Def. (a) toxic reaction (b) untoward occurrence in a subject administered a pharmaceutical product (c) An unfavorable and unintended reaction, symptom, syndrome, or disease encountered by a subject on a clinical trial (2) Defeasibility =Def. a line of communication that is terminated, boundaries for software Basic Mistakes in Definitions: 101 See Platos Euthyphro. Holiness is what Im doing in prosecuting my father At least one reason why we need Philosophers?
  • Slide 23
  • IT: Use-Mention Confusion FROM BIRN, MeSH, NCIT, and HL7 (1)Mouse =Def. Name for the species Mus musculus (2)National Socialism is_a MeSH Descriptor (3) Conceptual Entities =Def. An organizational header for concepts representing mostly abstract entities (4) Animal =Def. a subtype of Living Subject representing any animal-of-interest to the Personnel Management domain (5) living subject is_a code system
  • Slide 24
  • IT: Conception/Perception