ICBOInternational Conference onBiomedical OntologyBuffalo, NY. July 20-26, 2009http://icbo.buffalo.edu1
2Why OntologyEngineering needsPhilosophyBarry SmithUniversity at Buffalohttp://ontology.buffalo.edu/smith
3Why Biomedical Scienceneeds OntologicalEngineeringBarry SmithUniversity at Buffalohttp://ontology.buffalo.edu/smith
Multiple kinds of data in multiplekinds of silosLab / pathology dataElectronic Health Record dataClinical trial dataPatien...
Example ontologiesGene Ontology (GO)Environment Ontology (EnvO)Infectious Disease Ontology (IDO)Cell Ontology (CL)Sequence...
Uses of ‘ontology’ in PubMed abstracts6
MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVH...
8Gene Ontologyca. 25,000 nodesorganized in alogical hierarchy
9
Why is the Gene Ontology so usefulin counteracts silos in biomedicalresearch where so many otherontologies have failed?1. ...
11Smith, et al., “Coordinated Evolution ofOntologies to Support Biomedical DataIntegration”, Nature Biotechnology, 25, 200...
12male courtship behavior,orientation prior to legtapping and wing vibrationGene Ontologyca. 25,000 nodes
What is an ontology?universal vs. particularclass vs. instance(catalog vs. inventory)(science text vs. diary)(human being ...
The central distinctionuniversal vs. particularclass vs. instance(catalog vs. inventory)(science text vs. diary)(human bei...
are representations of universalsin reality= representations of what isgeneral in realityScience texts, theories
An ontology is a representationof universalsaka kinds, types, categories,species, genera, ...in reality16What is an Ontology
siamesemammalcatorganismsubstanceanimalinstancesfroguniversals17
An ontology is a representation ofuniversalsWe learn about universals fromexamining the results of scientificexperimentsEx...
Whether something is an instance or auniversal is not a matter of arbitrary choice19
You can’t take a photograph of auniversal20
21Why, oh Why, OntologyEngineering needsPhilosophy
The standard engineering methodology• Pragmatics (‘usefulness’) iseverything• Usefulness = we get to writesoftware which r...
• It is easier to write useful software if oneworks with a simplified model• (“…we can’t know what reality is like inany c...
The standard engineering methodologyPragmatics (‘usefulness’) is everythingOntology engineering undermines thevery promise...
‘agent’ontologiesfrom theDAML/OILontologycatalog
ontologyengineeringneeds adultsupervision
Ontology Development 101: A Guide toCreating Your First OntologyNatalya Noy and Deborah McGuinnessExample: The Wine Ontolo...
28red = instances, black = classes, io = instance of
29Why the Wine OntologyEngineering needsPhilosophy
Terminological problemsClasses describe concepts in the domain. Forexample, a class of wines represents allwines. Specific...
Creating Instances… we can create an individual instance Chateau-Morgon-Beaujolais to represent a specific type ofBeaujola...
The definition of an instance of the Beaujolais classThe instance is Chateaux Morgon Beaujolais fromthe Beaujolais region,...
instance of the class Wine grape33
An instance or a class?Deciding whether a particularconcept [e.g. the Bourgogne region]is a class in an ontology or anindi...
Wines are instancespairing wine with food  Sterling VineyardsMerlot as instance in our knowledge baseinventory  individu...
What about wine regions“we may define main wine regions, such asFrance, United States, Germany, and soon, as classes and s...
However, we would also like to say that theCotes d’Or region is a Bourgogne region.Therefore, Bourgogne region must be acl...
From the Protégé glossary:Instance: Concrete occurrence ofinformation about a domain that is enteredinto a knowledge base....
39Barry SmithUniversity at Buffalohttp://ontology.buffalo.edu/smithWhy OntologyEngineering needsPhilosophy
Why build scientific ontologies?“There are many ways to createontologies …”Multiple ontologies simply make our datasilo pr...
Ontological (scientific) realism• Ontology is ineluctably a multi-disciplinary enterprise – it cannot beleft to knowledge ...
International Conference onBiomedical OntologyBuffalo, NY. July 20-26, 2009http://icbo.buffalo.edu42
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Ontology (Science)

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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
  • Ontology (Science)

    1. 1. ICBOInternational Conference onBiomedical OntologyBuffalo, NY. July 20-26, 2009http://icbo.buffalo.edu1
    2. 2. 2Why OntologyEngineering needsPhilosophyBarry SmithUniversity at Buffalohttp://ontology.buffalo.edu/smith
    3. 3. 3Why Biomedical Scienceneeds OntologicalEngineeringBarry SmithUniversity at Buffalohttp://ontology.buffalo.edu/smith
    4. 4. Multiple kinds of data in multiplekinds of silosLab / pathology dataElectronic Health Record dataClinical trial dataPatient historiesMedical imagingMicroarray dataProtein chip dataFlow cytometry4
    5. 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. 6. Uses of ‘ontology’ in PubMed abstracts6
    7. 7. MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTAHow to do biology across the genome?
    8. 8. 8Gene Ontologyca. 25,000 nodesorganized in alogical hierarchy
    9. 9. 9
    10. 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. 11. 11Smith, et al., “Coordinated Evolution ofOntologies to Support Biomedical DataIntegration”, Nature Biotechnology, 25, 2007Why OntologyEngineering needsPhilosophy
    12. 12. 12male courtship behavior,orientation prior to legtapping and wing vibrationGene Ontologyca. 25,000 nodes
    13. 13. What is an ontology?universal vs. particularclass vs. instance(catalog vs. inventory)(science text vs. diary)(human being vs. Arnold Schwarzenegger)13
    14. 14. The central distinctionuniversal vs. particularclass vs. instance(catalog vs. inventory)(science text vs. diary)(human being vs. Arnold Schwarzenegger)14
    15. 15. are representations of universalsin reality= representations of what isgeneral in realityScience texts, theories
    16. 16. An ontology is a representationof universalsaka kinds, types, categories,species, genera, ...in reality16What is an Ontology
    17. 17. siamesemammalcatorganismsubstanceanimalinstancesfroguniversals17
    18. 18. An ontology is a representation ofuniversalsWe learn about universals fromexamining the results of scientificexperimentsExperiments are performed always oninstances18
    19. 19. Whether something is an instance or auniversal is not a matter of arbitrary choice19
    20. 20. You can’t take a photograph of auniversal20
    21. 21. 21Why, oh Why, OntologyEngineering needsPhilosophy
    22. 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. 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. 24. The standard engineering methodologyPragmatics (‘usefulness’) is everythingOntology engineering undermines thevery promise of ontology to solve thesilo problem24
    25. 25. ‘agent’ontologiesfrom theDAML/OILontologycatalog
    26. 26. ontologyengineeringneeds adultsupervision
    27. 27. Ontology Development 101: A Guide toCreating Your First OntologyNatalya Noy and Deborah McGuinnessExample: The Wine Ontology27
    28. 28. 28red = instances, black = classes, io = instance of
    29. 29. 29Why the Wine OntologyEngineering needsPhilosophy
    30. 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. 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. 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. 33. instance of the class Wine grape33
    34. 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. 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. 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. 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. 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. 39. 39Barry SmithUniversity at Buffalohttp://ontology.buffalo.edu/smithWhy OntologyEngineering needsPhilosophy
    40. 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. 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. 42. International Conference onBiomedical OntologyBuffalo, NY. July 20-26, 2009http://icbo.buffalo.edu42

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