The Six Category Ontology: Basic Formal Ontology and Its Applications

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Basic Formal Ontology (BFO) is a small, domain-neutral, upper-level ontology that is used to support integration of domain-specific ontologies in scientific, military, clinical and other areas.

Like Lowe's 4CO, BFO divides reality into particulars and universals. But it replaces 4CO's dichotomy of substantials and non-substantials with a trichotomy of independent continuants, dependent continuants, and occurrents.

I will sketch the BFO ontology and show how it is being used as a starting point for the creation of domain ontologies to support data integration in scientific research.

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  • from Gerard Christman
  • The Six Category Ontology: Basic Formal Ontology and Its Applications

    1. 1. The Six Category Ontology:BFO and Its ApplicationsBarry SmithDurham, May 21, 2013
    2. 2. FantologyThe doctrine, usually tacit, according towhich „Fa‟ (and „Rab‟) is the key to theontological structure of realityThe syntax of first-order predicate logic is amirror of reality (a Leibnizian universalcharacteristic)http://ontology.buffalo.edu/bfo/Against_Fantology.pdf2
    3. 3. 3For the fantologist“F(a)”, “R(a, … , b)” is the language forontologyThis language reflects the structure ofrealityThe fantologist sees reality as being madeup of individuals (a, b, c, …) plus abstract(1- and n-place) „properties‟ or „attributes‟
    4. 4. FantologyWittgenstein: Propositions show the logicalform of reality. They display it. (4.121)Russell: logic is concerned with the realworld just as truly as zoology, though withits more abstract and general features.(1919)Armstrong: the spreadsheet ontology** “Vérités et vérifacteurs” (2004) 4
    5. 5. 5F G H I J K L M N O P Q R S T U Vabcdefghijk
    6. 6. 6F G H I J K L M N O P Q R S T U Va x x x x xbcdefghijk
    7. 7. 7F G H I J K L M N O P Q R S T U Va x x x x xb x x x x xcdefghijk
    8. 8. 8F G H I J K L M N O P Q R S T U Va x x x x xb x x x x xc x x x x xd x xefghijkand so on …
    9. 9. 9Fantologytends to make you believe in some futurestate of „total science‟when the values of „F‟ and „a‟, all of them,will be revealed to the electAll true ontology is the ontology of a futureperfected physics of ultimate atoms(Armstrong: all examples proving myontology is wrong will be shown tobelong merely to the „manifest image‟)
    10. 10. 10Varieties of fantology„F‟ stands for a property„a‟ stands for an individualPlatonistic: the Fs belong to somethinglike the Platonic realm of formsSet-theoretic: the Fs are sets ofindividuals which FNominalistic: „F‟ is just a predicate
    11. 11. 11The Spreadsheet OntologySubstances AttributesUniversals PropertiesParticulars Particulars
    12. 12. 12A slightly more sophisticatedArmstrongian viewSubstances AttributesUniversalsProperties andRelationsParticulars Particulars
    13. 13. 13Generic FantologyIndividuals AttributesAttributesF( ), G( ),R( , ... , )Individualsa, b, cthis, thatUniversalParticular
    14. 14. 14QuineIndividuals AttributesAttributesF( ), G( ), R( , ... , )(no ontological status)Individualsa, b, cthis, thatUniversalParticular
    15. 15. 15Nominalist Fantology (1CO)To understand properties is to understandpredicationIf John is white, there is no extra entity,John„s whitenessIf John is a man, there is no extra entity,John„s humanity-- modes and kinds and attributes are allontologically in the same boat
    16. 16. 16Bicategorial Nominalism(Peter Simons)Substantial AccidentalFirst substancethis manthis catthis oxTropesthis headachethis sun-tanthis dreadUniversalParticular
    17. 17. 17Aristotle’s Ontological Square(Husserl, Lowe, …)Substantial AccidentalSecond substancemancatoxSecond accidentheadachesun-tandreadFirst substancethis manthis catthis oxFirst accidentthis headachethis sun-tanthis dreadUniversalParticular
    18. 18. 18Aristotle’s two kinds ofpredicationPredication in the category of substance:• John is a man, Henry is an oxPredication in the category of accident:• John is hungry, Henry is asleep, Johnis wise
    19. 19. 19For Fantologythese two types of predication are oftenconfusedFor Armstrong: property universals are allwe needno need for kind universals(Armstrong‟s four-dimensionalism impliesthat there are no substances)
    20. 20. Husserl, Lowe, etc., tell us thatthere is a third kind of predicationJohn is a manJohn is hungryJohn has a headache (John has this headache)20
    21. 21. Husserl, Lowe, etc., tell us thatthere is a third kind of predicationJohn is a manJohn is hungryJohn has a headache (John has this headache)21
    22. 22. Husserl, Lowe, etc., tell us thatthere is a third kind of predicationJohn is a manJohn is hungryJohn has a headache (John has this headache)22
    23. 23. Husserl, Lowe, etc., tell us thatthere is a third kind of predicationJohn is a manJohn is hungryJohn has a headache (John has this headache)23
    24. 24. From 4CO to 6CO24
    25. 25. Three FOL ways of treatingtemporally indexed predication„F holds of a at t‟:(1) F holds-at-t of object a (the copula isindexed by times; F holds t-ly) (adverbialview)(2) F is a relation between object a and time t;(3) F holds of a new special entity called „at‟or„a-at-t‟ (an object stage or phase or slice)(four-dimensionalism)25
    26. 26. I agree with Jonathan in accepting theadverbial alternative (1)Lowe*: (1) has “been overlooked, at least byphilosophers trained to think in terms ofthe categories of modern quantification orpredicate logic, as it is called. For suchlogic simply has no place for adverbs.”* A Survey of Metaphysics, 2002, p. 4726
    27. 27. But now Jonathan himself seemsto do too little justice to the waysadverbs, other than t-ly, are usedin natural language27
    28. 28. 4CO plus temporal indexing stillcannot deal with adverbsConsider a simple change of property in anordinary object:a ball undergoes a change of shape.At t1 there is one shape-modeAt t2 there is another shape-mode.Cf. Johansson, Review of Lowe, Dialectica 60 (4)28
    29. 29. 4CO cannot deal with changeLowe can assert: both these modes instantiateshape universals and inhere in the same ball, andas a two-plurality the modes instantiate thetemporal relation „coming after‟.But more must be said: a simple sum of relations ofinstantiations of shapes, inherences of shapemodes, and the external relation of coming-afterlacks the temporal unity characteristic ofchanges and other processes (such assqueezings, surgical procedures, heart attacks,conversations, ontology lectures …).29
    30. 30. 4+2COEvent talk is common in natural language… but there is no fundamental category ofbeing called „event‟… if events exist at all, then they superveneon talk about objects and modes changingThe two extra categories in what followsshould be interpreted by Lowe-ists in thisspirit30
    31. 31. 31A better view6CO = there are objects, qualities andprocesses at the level of both universals andinstancesProcesses, like qualities, are dependent onsubstances• one-place processes:getting warmer, getting hungrier• relational processes:kissings, thumpings, conversations, dances
    32. 32. 326CO (Ellis, BFO)Substances Quality entities ProcessesUniversalsSubstance-universalsQuality-universalsProcess-universalsParticularsIndividualSubstancesQuality-instances(Tropes…)Process-instancesprovides resources to understandimportant ontological alternatives
    33. 33. 33Process nominalism(Heraclitus, Whitehead, …)Substances Qualities ProcessesUniversalsParticulars Flux
    34. 34. 34Trope nominalism(Simons, again)Substances Qualities ProcessesUniversalsParticulars Tropes, bundles
    35. 35. 35QuineIndividuals AttributesPredicatesF( ), G( ),R( , ... , )Individualsa, b, cthis, thatUniversalParticular
    36. 36. 36DavidsonSubstances Qualities ProcessesUniversalsPredicates (includingadverbial predicates):F( ), G( ), R( , ... , )Particulars Objects Events
    37. 37. 41For extreme fantologists ‘a’ leaves noroom for ontological complexityFrom this it follows:that fantology cannot do justice to theexistence of different levels of granularity ofrealitymore generally, that fantology is conducive toand conduced by reductionism in philosophy
    38. 38. from “Against Fantology”, in: M. E. Reicher, J. C. Marek (Eds.),Experience and Analysis, 2005, Vienna: ÖBV-HPT, 153-17059
    39. 39. one problem with 4CO60
    40. 40. “Against Fantology”, in: M. E. Reicher, J. C. Marek (Eds.),Experience and Analysis, Vienna, 2005,http://ontology.buffalo.edu/bfo/Against_Fantology.pdf 61
    41. 41. 6CO AppliedBasic Formal Ontology72
    42. 42. Applied Ontology 1. BiologyPlant Ontology“Ontologies as Integrative Tools for Plant Science”,American Journal of Botany, 99(8): 2012.Protein Ontology“The Protein Ontology: A StructuredRepresentation of Protein Forms andComplexes”, Nucleic Acids Research, 39: 2011.Cell Ontology“Logical development of the Cell Ontology”, BMCBioinformatics 12(6): 2011.73
    43. 43. FMAPleuralCavityInterlobarrecessMesotheliumof PleuraPleura(Wallof Sac)VisceralPleuraPleural SacParietalPleuraAnatomical SpaceOrganCavitySerous SacCavityAnatomicalStructureOrganSerous SacMediastinalPleuraTissueOrgan PartOrganSubdivisionOrganComponentOrgan CavitySubdivisionSerous SacCavitySubdivisionFoundational Model of Anatomy74
    44. 44. Applied Ontology 2. MedicineInfectious Disease Ontology“Infectious Disease Ontology”, in Sintchenko (ed.),Infectious Disease Informatics, Springer, 2009.Foundational Model of Anatomy“A Reference Ontology for Bioinformatics: TheFoundational Model of Anatomy”, Journal of BiomedicalInformatics, 36, 2003.Mental Disease Ontology“Foundations for a Realist Ontology of Mental Disease”,Journal of Biomedical Semantics, 1(10), 201075
    45. 45. Applied Ontology 3. FinanceXBRL = eXtensible Business ReportingLanguagegovernment mandated syntax for allreports to SECextensibility defeats comparability of data76http://financialreportontology.wikispaces.com/
    46. 46. Financial Report Ontology (FRO)77
    47. 47. Applied Ontology 4. DefenseUS Army Intelligence and InformationWarfare Directorate (I2WD)“Ontology for the Intelligence Analyst”, CrossTalk:The Journal of Defense Software Engineering,November/December, 2012, 18-25.78
    48. 48. 79
    49. 49. 80
    50. 50. Why do people in the military thinkthey need lexicons• Training• Compiling lessons learned from former engagements• Compiling results of testing, e.g. of proposed newdoctrine• Collective inferencing• Official reporting• Doctrinal development• Joint operations• Standard operating procedures• People need to share data• People need to (ensure that they) understand eachother
    51. 51. But each community produces its own ontology,this will merely create new, semantic siloesFireSupportLogisticsAirOperationsIntelligenceCivil-MilitaryOperationsTargetingManeuver&BlueForceTracking82
    52. 52. The problem with (actually existing)lexicons• They promote the development of silos (roachmotels for data)• They do not allow us to exploit today’stechnologies• They do not combine natural languageunderstandability with computationaladequacy• They do not scale83
    53. 53. 84
    54. 54. 85
    55. 55. US DoD Civil Affairs strategy for non-classifiedinformation sharing86
    56. 56. Military is 10 years behind the times when itcomes to resolving data interoperabilityproblems– where the problems of Big Data inbiomedicine were recognized already in 199887
    57. 57. The Gene Ontology (1999)response to the massive opportunitiescreated by the success of the HumanGenome Projectfor cross-organism biologyfor intra-organism biologyfor the biology of environments88
    58. 58. The Gene OntologyMouseEcotope GlyProtDiabetInGeneGluChem89
    59. 59. The Gene OntologyMouseEcotope GlyProtDiabetInGeneGluChemsphingolipidtransporteractivity90
    60. 60. The Gene OntologyMouseEcotope GlyProtDiabetInGeneGluChemHolliday junctionhelicase complex91
    61. 61. The Gene OntologyMouseEcotope GlyProtDiabetInGeneGluChemsphingolipidtransporteractivity92
    62. 62. International System of Units93
    63. 63. How to find your data?How to reason with data when you find it?How to understand the significance of the datayou collected 3 years earlier?How to integrate with other people’s data?Part of the solution must involve consensus-based, standardized terminologies and codingschemes94
    64. 64. Unifying goal: integration of biologicaland clinical data– within and across domains– across different species– across levels of granularity (organ,organism, cell, molecule)– across different perspectives (physical,biological, clinical)96
    65. 65. Ontologies• are computer-tractable representations oftypes in specific areas of reality• are more and less general (upper and lowerontologies)– upper = organizing ontologies– lower = domain ontologies97
    66. 66. Ontologies must be comparable• if we have multiple, redundant ontologies fora given domain, then this will recreate thevery problem of siloes which ontologytechnology was designed to• to ensure non-redundancy, ontologies mustbe comparable• to enhance comparability ontologies shouldshare a common upper level architecture98
    67. 67. Anatomy Ontology(FMA*, CARO)EnvironmentOntology(EnvO)InfectiousDiseaseOntology(IDO*)BiologicalProcessOntology (GO*)CellOntology(CL)CellularComponentOntology(FMA*, GO*) PhenotypicQualityOntology(PaTO)Subcellular Anatomy Ontology (SAO)Sequence Ontology(SO*) MolecularFunction(GO*)Protein Ontology(PRO*)Extension Strategy + Modular Organization 99top levelmid-leveldomainlevelInformation ArtifactOntology(IAO)Ontology forBiomedicalInvestigations(OBI)Spatial Ontology(BSPO)Basic Formal Ontology (BFO)
    68. 68. Continuant OccurrentIndependentContinuantDependentContinuantcell componentbiological processmolecular functionBasic Formal Ontology100
    69. 69. Anatomy Ontology(FMA*, CARO)EnvironmentOntology(EnvO)InfectiousDiseaseOntology(IDO*)BiologicalProcessOntology (GO*)CellOntology(CL)CellularComponentOntology(FMA*, GO*) PhenotypicQualityOntology(PaTO)Subcellular Anatomy Ontology (SAO)Sequence Ontology(SO*) MolecularFunction(GO*)Protein Ontology(PRO*)OBO Foundry: Downward Population from BFOtop levelmid-leveldomainlevelInformation ArtifactOntology(IAO)Ontology forBiomedicalInvestigations(OBI)Spatial Ontology(BSPO)Basic Formal Ontology (BFO)101/24
    70. 70. Example: The Cell Ontology
    71. 71. continuantindependentcontinuantportion ofmaterialobjectfiat objectpartobjectaggregateobjectboundarysitedependentcontinuantgenericallydependentcontinuantinformationartifactspecificallydependentcontinuantqualityrealizableentityfunctionroledispositionspatialregion0D-region1D-region2D-region3D-regionBFO:continuant
    72. 72. occurrentprocessualentityprocessfiat processpartprocessaggregateprocessboundaryprocessualcontextspatiotemporalregionscatteredspatiotemporalregionconnectedspatiotemporalregionspatiotemporalinstantspatiotemporalintervaltemporalregionscatteredtemporalregionconnectedtemporalregiontemporalinstanttemporalintervalBFO:occurrent
    73. 73. More than 100 Ontologyprojects using BFOhttp://www.ifomis.org/bfo/usersOne argument against 4COand 8CO: BFO has more users
    74. 74. Some Ontologies Built from BFO• AFO Foundational Ontology• US Army Biometrics Ontology• BioTop: A Biomedical Top-Domain Ontology• Cell Ontology (CL)• Chemical Entities of Biological Interest (ChEBI)• Common Anatomy Reference Ontology (CARO)• Drug Interaction Ontology (DIO)• Foundational Model of Anatomy (FMA)• Gene Ontology (GO)• Infectious Disease Ontology (IDO)• Neuroscience Information Framework Standard (NIFSTD) Ontology• Ontology for Biomedical Investigations (OBI)• Protein Ontology (PRO)• Sequence Ontology (SO)• Universal Core Semantic Layer (UCore SL)• Subcellular Anatomy Ontology (SAO)• Zebrafish Anatomical Ontology (ZAO) 106
    75. 75. DOLCE, SUMO, CycDOLCE: 6CO (largely) compatible with BFO,but built to support „linguistic and cognitiveengineering‟ – there to describe people‟sassumptions people have about reality(ethno-Quineanism)SUMO: 2CO (no diabetes, no temperatureinstances); SUMO has its own tiny biology(„body-covering‟, „fruit-Or-vegetable‟); not atrue top levelCyc: Allows inconsistent microtheories(embraces chaos) 107
    76. 76. Cyc:ConceivingSomething_BiologicalReproductionEvent =def a collection of events; asub-collection of BiologicalReproductionEvent. Ineach conceivingSomething_BiologicalReproductionEvent, someone becomes pregnant.Cyc:The immaculate conception =def. TheConceivingSomething_BiologicalReproductionEventin which Mary_MotherOfJesus was conceived.Catholic dogma holds that Mary (unlike Jesus) wasconceived by conventional biological means, butthat GodOfAbrahamIsaacAndJacob interceded atthe time of her conception to keep her free from thestain of original sin, or „immaculate‟.108
    77. 77. Basic Formal OntologyContinuant Occurrentprocess, eventIndependentContinuantthingDependentContinuantquality.... .... .......typesinstances165432
    78. 78. Blinding Flash of the ObviousContinuant Occurrentprocess, eventIndependentContinuantthingDependentContinuantquality.... ..... .......quality dependson bearer
    79. 79. Blue Force OverwatchContinuant Occurrentprocess, eventIndependentContinuantthingDependentContinuantquality, ….... ..... .......event dependson participant
    80. 80. Occurrents depend on participantsinstances15 May bombing5 April insurgency attackoccurrent typesbombingattackparticipant continuant typesexplosive deviceterrorist group
    81. 81. General rules for ontology developmentincorporated into BFOCommon traffic lawsLessons learned and disseminated ascommon guidelines – all developers aredoing it the same wayTools built for BFO ontologies can be re-used by othersExpertise developed in working with oneBFO ontology can be-used with others
    82. 82. Basic Formal Ontology (Top Level)http://www.ifomis.org/bfo/Continuant OccurrentIndependentContinuantDependentContinuantAnatomicalStructureProcessStageQuality114
    83. 83. this particular caseof redness (of aparticular fly eye)the universal redinstantiatesan instance of eye(in a particular fly)the universal eyeinstantiatesdepends_on115Phenotype Ontology (PATO)
    84. 84. the particular caseof redness (of aparticular fly eye)redinstantiatesan instance of aneye (in a particularfly)eyeinstantiatesdependsoncolor anatomical structureis_a is_a116
    85. 85. independentcontinuantdependentcontinuantqualitytemperatureorganismJohnJohn’stemperatureoccurrentprocesslife of anorganismJohn’slife117
    86. 86. A chart representing howJohn’s temperature changes118
    87. 87. A chart representing howJohn’s temperature changing119
    88. 88. temperatureJohn’s temperature12037ºC 37.1ºC 37.5ºC37.2ºC 37.3ºC 37.4ºCinstantiatesat t1instantiatesat t2instantiatesat t3instantiatesat t4instantiatesat t5instantiatesat t6
    89. 89. temperatureJohn’s temperature (exists continuously)12137ºC 37.1ºC 37.5ºC37.2ºC 37.3ºC 37.4ºCinstantiatesat t1instantiatesat t2instantiatesat t3instantiatesat t4instantiatesat t5instantiatesat t6in nature, no sharpboundaries herein nature, no sharpboundaries here
    90. 90. diseasecoronaryheart diseasegenetic heartdiseasedispositioninfectiveendocarditisrealizabledependent continuant
    91. 91. coronary heartdiseaseJohn’s coronary heart disease (exists continuously)123asymptomatic(„silent‟)infarctionearly lesionsand smallfibrous plaquesstableanginasurfacedisruption ofplaqueunstableanginainstantiatesat t1instantiatesat t2instantiatesat t3instantiatesat t4instantiatesat t5time
    92. 92. independentcontinuantdependentcontinuantdispositionheartdiseaseorganismJohnJohn’sheart diseaseoccurrentprocessheart diseasecourseJohn’sheart disease course124
    93. 93. So why not 8CO (à la Schneider)?125Substances Qualities ProcessesProcessqualitiesUniversalsSubstance-universalsQuality-universalsProcess-universalsProcessqualitiesParticularsIndividualSubstancesQuality-instances(Tropes…)Process-instancesProcessqualityinstances
    94. 94. independentcontinuantdependentcontinuantdispositionheartdiseaseorganismJohnJohn’sheart diseaseoccurrentprocessheart diseasecourseJohn’sheart disease course126processpattern
    95. 95. independentcontinuantdependentcontinuantdispositionheartdiseaseorganismJohnJohn’sheart diseaseoccurrentprocessheart diseasecourseJohn’sheart diseasecourse127processpatternJohn’sheart diseasecourse pattern?
    96. 96. independentcontinuantdependentcontinuantdispositionheartdiseaseorganismJohnJohn’sheart diseaseoccurrentprocessheartdiseasecourseJohn’sheart disease course128processpatternchronicprocesspatternchronic heartdiseasecourse pattern
    97. 97. 129occurrentprocessheartdiseasecourseJohn’sheartdiseasecourse 129processpatternchronicprocesspatternchronic heartdiseasecourse patternoccurrentprocessheartdiseasecourseJohn’sheart disease courseprocesspatternchronicprocesspatternchronic heartdiseasecourse patternJohn’s chronicheartdiseasecourse pattern
    98. 98. occurrentprocessheartdiseasecourseJohn’sheartdiseasecourseprocessqualitychronicprocessqualitychronic heartdiseasecourse qualityoccurrentprocessheartdiseasecourseJohn’sheart disease courseprocessqualitychronicprocessqualitychronic heartdiseasecourse qualityJohn’s chronicheartdiseasecourse quality
    99. 99. DependentContinuantQualityRealizable131Different subtypes ofBFO:dependent continuantfunctionrole disposition
    100. 100. Roles pertain not to what a thing enduringly is,but to the part it plays, e.g. in some operationContinuantOccurrentprocess, eventIndependentContinuantthingRealizableDependentContinuant(e.g. chef role).... ..... .......realization-of

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