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Ontology (Science)

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Paderborn, October 2008

Paderborn, October 2008

Published in: Education, Spiritual

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  • http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=116006492 sequence of X chromosome in baker’s yeast
  • http://www.fi.edu/learn/heart/vessels/images/large_xray-of-kidneys-and-aorta.jpg
  • http://www.fi.edu/learn/heart/vessels/images/large_xray-of-kidneys-and-aorta.jpg
  • protege.stanford.edu/doc/users_guide/glossary.html
  • Transcript

    • 1. ICBOInternational Conference onBiomedical OntologyBuffalo, NY. July 20-26, 2009http://icbo.buffalo.edu1
    • 2. 2Why OntologyEngineering needsPhilosophyBarry SmithUniversity at Buffalohttp://ontology.buffalo.edu/smith
    • 3. 3Why Biomedical Scienceneeds OntologicalEngineeringBarry SmithUniversity at Buffalohttp://ontology.buffalo.edu/smith
    • 4. Multiple kinds of data in multiplekinds of silosLab / pathology dataElectronic Health Record dataClinical trial dataPatient historiesMedical imagingMicroarray dataProtein chip dataFlow cytometry4
    • 5. Example ontologiesGene Ontology (GO)Environment Ontology (EnvO)Infectious Disease Ontology (IDO)Cell Ontology (CL)Sequence Ontology (SO)Protein Ontology (PRO)Common Anatomy Reference Ontology(CARO)5
    • 6. Uses of ‘ontology’ in PubMed abstracts6
    • 7. MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTAHow to do biology across the genome?
    • 8. 8Gene Ontologyca. 25,000 nodesorganized in alogical hierarchy
    • 9. 9
    • 10. Why is the Gene Ontology so usefulin counteracts silos in biomedicalresearch where so many otherontologies have failed?1. it was built by biologists2. philosophers play a role in its evolution10
    • 11. 11Smith, et al., “Coordinated Evolution ofOntologies to Support Biomedical DataIntegration”, Nature Biotechnology, 25, 2007Why OntologyEngineering needsPhilosophy
    • 12. 12male courtship behavior,orientation prior to legtapping and wing vibrationGene Ontologyca. 25,000 nodes
    • 13. What is an ontology?universal vs. particularclass vs. instance(catalog vs. inventory)(science text vs. diary)(human being vs. Arnold Schwarzenegger)13
    • 14. The central distinctionuniversal vs. particularclass vs. instance(catalog vs. inventory)(science text vs. diary)(human being vs. Arnold Schwarzenegger)14
    • 15. are representations of universalsin reality= representations of what isgeneral in realityScience texts, theories
    • 16. An ontology is a representationof universalsaka kinds, types, categories,species, genera, ...in reality16What is an Ontology
    • 17. siamesemammalcatorganismsubstanceanimalinstancesfroguniversals17
    • 18. An ontology is a representation ofuniversalsWe learn about universals fromexamining the results of scientificexperimentsExperiments are performed always oninstances18
    • 19. Whether something is an instance or auniversal is not a matter of arbitrary choice19
    • 20. You can’t take a photograph of auniversal20
    • 21. 21Why, oh Why, OntologyEngineering needsPhilosophy
    • 22. The standard engineering methodology• Pragmatics (‘usefulness’) iseverything• Usefulness = we get to writesoftware which runs on ourmachines• People will pay us for writing newontologies22
    • 23. • It is easier to write useful software if oneworks with a simplified model• (“…we can’t know what reality is like inany case; we only have our concepts…”)• This looks like a useful model to me• (One week goes by:) This other thinglooks like a useful model to him• Data in Pittsburgh does not interoperatewith data in PaderbornThe standard engineering methodology
    • 24. The standard engineering methodologyPragmatics (‘usefulness’) is everythingOntology engineering undermines thevery promise of ontology to solve thesilo problem24
    • 25. ‘agent’ontologiesfrom theDAML/OILontologycatalog
    • 26. ontologyengineeringneeds adultsupervision
    • 27. Ontology Development 101: A Guide toCreating Your First OntologyNatalya Noy and Deborah McGuinnessExample: The Wine Ontology27
    • 28. 28red = instances, black = classes, io = instance of
    • 29. 29Why the Wine OntologyEngineering needsPhilosophy
    • 30. Terminological problemsClasses describe concepts in the domain. Forexample, a class of wines represents allwines. Specific wines are instances of thisclass. The Bordeaux wine in the glass in frontof you … is an instance of the class ofBordeaux wines.30
    • 31. Creating Instances… we can create an individual instance Chateau-Morgon-Beaujolais to represent a specific type ofBeaujolais wine.Chateau-Morgon-Beaujolais is an instance of the classBeaujolais representing all Beaujolais wines. Thisinstance has the following slot values defined• Body: light, Color: red, Flavor: delicate, Tannin level:low• Grape: Gamay (instance of the Wine grape class)• Maker: Chateau-Morgon (instance of the Winery class)• Region: Beaujolais (instance of the Wine-Region class)31
    • 32. The definition of an instance of the Beaujolais classThe instance is Chateaux Morgon Beaujolais fromthe Beaujolais region, produced from the Gamaygrape by the Chateau Morgon winery.32
    • 33. instance of the class Wine grape33
    • 34. An instance or a class?Deciding whether a particularconcept [e.g. the Bourgogne region]is a class in an ontology or anindividual instance depends on whatthe potential applications of theontology are.34
    • 35. Wines are instancespairing wine with food  Sterling VineyardsMerlot as instance in our knowledge baseinventory  individual bottles as instancesrecord different properties for each vintage Sterling Vineyards Merlot 1993 asinstance35
    • 36. What about wine regions“we may define main wine regions, such asFrance, United States, Germany, and soon, as classes and specific wine regionswithin these large regions as instances.( Bourgogne is an instance of France).36
    • 37. However, we would also like to say that theCotes d’Or region is a Bourgogne region.Therefore, Bourgogne region must be aclass … However, making Bourgogneregion a class and Cotes d’Or region aninstance of Bourgogne region seemsarbitrary: it is very hard to clearly distinguishwhich regions are classes and which areinstances. Therefore, we define all wineregions as classes. ( Cote d’Or is a class)37
    • 38. From the Protégé glossary:Instance: Concrete occurrence ofinformation about a domain that is enteredinto a knowledge base. For example, FranSmith might be an instance for a Name slot.An instances is entered via a formgenerated by Protégé-2000.38
    • 39. 39Barry SmithUniversity at Buffalohttp://ontology.buffalo.edu/smithWhy OntologyEngineering needsPhilosophy
    • 40. Why build scientific ontologies?“There are many ways to createontologies …”Multiple ontologies simply make our datasilo problems worseQ: What is to serve as constraint?A: Reality as revealed by matureexperimentally-based science40
    • 41. Ontological (scientific) realism• Ontology is ineluctably a multi-disciplinary enterprise – it cannot beleft to knowledge engineers• Find out what the world is like bydoing science• Build representations adequate to thisworld, not to some simplified model inyour laptop41
    • 42. International Conference onBiomedical OntologyBuffalo, NY. July 20-26, 2009http://icbo.buffalo.edu42