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Classifying Chemicals with Description Graphs and Logic Programming

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OWL 2 is widely used to describe complex objects such as chemical molecules; however, OWL 2 axioms cannot represent `structural' features of chemical entities such as having a ring. A combination of OWL 2, rules and \emph{description graphs} (DGs) has been suggested as a possible solution, but an attempt to apply this formalism in a chemical Semantic Web application has revealed several drawbacks. Based on this experience, we present a radically different approach to modelling complex objects via a novel formalism that we call Description Graph Logic Programs. At the syntactic level, our approach combines DGs, rules, and OWL 2 RL axioms, but we give semantics to our formalism via a translation into logic programs interpreted under stable model semantics. The result is an expressive formalism that is well suited for modelling objects with complex structure, that captures the OWL 2 RL profile, and that thus fits naturally into the Semantic Web landscape. Additionally, we test the practical feasibility of our approach by means of a prototypical implementation which provides encouraging results.

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Classifying Chemicals with Description Graphs and Logic Programming

  1. 1. C LASSIFYING C HEMICALS U SING D ESCRIPTION G RAPHS AND L OGIC P ROGRAMMING Despoina Magka, Boris Motik and Ian Horrocks Department of Computer Science, University of Oxford May 28, 2012
  2. 2. O UTLINE 1 M OTIVATION 2 DGLP S , I MPLEMENTATION AND OVERVIEW1
  3. 3. M ODELLING C HEMICALS WITH OWL OWL used for the representation of molecular structures2
  4. 4. M ODELLING C HEMICALS WITH OWL OWL used for the representation of molecular structures Classification of chemical compounds [Villanueva-Rosales & Dumontier, OWLED 2007]2
  5. 5. M ODELLING C HEMICALS WITH OWL OWL used for the representation of molecular structures Classification of chemical compounds [Villanueva-Rosales & Dumontier, OWLED 2007] Chemical information integration [Konyk et al., DILS, 2008 ]2
  6. 6. M ODELLING C HEMICALS WITH OWL OWL used for the representation of molecular structures Classification of chemical compounds [Villanueva-Rosales & Dumontier, OWLED 2007] Chemical information integration [Konyk et al., DILS, 2008 ] Subsumptions between molecules and chemical classes [Hastings et al., OWLED, 2010]2
  7. 7. T HE C H EBI O NTOLOGY OWL ontology Chemical Entities of Biological Interest3
  8. 8. T HE C H EBI O NTOLOGY OWL ontology Chemical Entities of Biological Interest Freely accessible dictionary of ‘small’ molecular entities3
  9. 9. T HE C H EBI O NTOLOGY OWL ontology Chemical Entities of Biological Interest Freely accessible dictionary of ‘small’ molecular entities High quality annotation and taxonomy of chemicals3
  10. 10. T HE C H EBI O NTOLOGY OWL ontology Chemical Entities of Biological Interest Freely accessible dictionary of ‘small’ molecular entities High quality annotation and taxonomy of chemicals Interoperability between researchers3
  11. 11. T HE C H EBI O NTOLOGY OWL ontology Chemical Entities of Biological Interest Freely accessible dictionary of ‘small’ molecular entities High quality annotation and taxonomy of chemicals Interoperability between researchers Drug discovery and elucidation of metabolic pathways3
  12. 12. AUTOMATE C HEMICAL C LASSIFICATION ChEBI is manually incremented4
  13. 13. AUTOMATE C HEMICAL C LASSIFICATION ChEBI is manually incremented Currently contains approx. 28,000 fully annotated entities4
  14. 14. AUTOMATE C HEMICAL C LASSIFICATION ChEBI is manually incremented Currently contains approx. 28,000 fully annotated entities Grows at a rate of ~1,500 entities per curator per year4
  15. 15. AUTOMATE C HEMICAL C LASSIFICATION ChEBI is manually incremented Currently contains approx. 28,000 fully annotated entities Grows at a rate of ~1,500 entities per curator per year Biologically interesting entities possibly > 1,000,0004
  16. 16. AUTOMATE C HEMICAL C LASSIFICATION ChEBI is manually incremented Currently contains approx. 28,000 fully annotated entities Grows at a rate of ~1,500 entities per curator per year Biologically interesting entities possibly > 1,000,000 Each new molecule is subsumed by several chemical classes4
  17. 17. AUTOMATE C HEMICAL C LASSIFICATION ChEBI is manually incremented Currently contains approx. 28,000 fully annotated entities Grows at a rate of ~1,500 entities per curator per year Biologically interesting entities possibly > 1,000,000 Each new molecule is subsumed by several chemical classes Is dinitrogen inorganic?4
  18. 18. AUTOMATE C HEMICAL C LASSIFICATION ChEBI is manually incremented Currently contains approx. 28,000 fully annotated entities Grows at a rate of ~1,500 entities per curator per year Biologically interesting entities possibly > 1,000,000 Each new molecule is subsumed by several chemical classes Is dinitrogen inorganic? Does cyclobutane contain a four-membered ring?4
  19. 19. AUTOMATE C HEMICAL C LASSIFICATION ChEBI is manually incremented Currently contains approx. 28,000 fully annotated entities Grows at a rate of ~1,500 entities per curator per year Biologically interesting entities possibly > 1,000,000 Each new molecule is subsumed by several chemical classes Is dinitrogen inorganic? Does cyclobutane contain a four-membered ring? Is acetylene a hydrocarbon?4
  20. 20. AUTOMATE C HEMICAL C LASSIFICATION ChEBI is manually incremented Currently contains approx. 28,000 fully annotated entities Grows at a rate of ~1,500 entities per curator per year Biologically interesting entities possibly > 1,000,000 Each new molecule is subsumed by several chemical classes Is dinitrogen inorganic? Does cyclobutane contain a four-membered ring? Is acetylene a hydrocarbon? Does benzaldehyde contain a benzene ring?4
  21. 21. AUTOMATE C HEMICAL C LASSIFICATION ChEBI is manually incremented Currently contains approx. 28,000 fully annotated entities Grows at a rate of ~1,500 entities per curator per year Biologically interesting entities possibly > 1,000,000 Each new molecule is subsumed by several chemical classes Is dinitrogen inorganic? Does cyclobutane contain a four-membered ring? Is acetylene a hydrocarbon? Does benzaldehyde contain a benzene ring? Speed up curating tasks with automated reasoning tools4
  22. 22. AUTOMATE C HEMICAL C LASSIFICATION ChEBI is manually incremented Currently contains approx. 28,000 fully annotated entities Grows at a rate of ~1,500 entities per curator per year Biologically interesting entities possibly > 1,000,000 Each new molecule is subsumed by several chemical classes Is dinitrogen inorganic? Yes Does cyclobutane contain a four-membered ring? Yes Is acetylene a hydrocarbon? Yes Does benzaldehyde contain a benzene ring? Yes Speed up curating tasks with automated reasoning tools4
  23. 23. (M IS )R EPRESENTING R INGS WITH OWL Chemical compounds with rings are highly frequent5
  24. 24. (M IS )R EPRESENTING R INGS WITH OWL Chemical compounds with rings are highly frequent Fundamental inability of OWL to represent cycles5
  25. 25. (M IS )R EPRESENTING R INGS WITH OWL Chemical compounds with rings are highly frequent Fundamental inability of OWL to represent cycles At least one tree-shaped model for each consistent OWL knowledge base5
  26. 26. (M IS )R EPRESENTING R INGS WITH OWL Chemical compounds with rings are highly frequent Fundamental inability of OWL to represent cycles At least one tree-shaped model for each consistent OWL knowledge base E XAMPLE Cyclobutane ∃(= 4)hasAtom.(Carbon ∃(= 2)hasBond.Carbon) C C C C5
  27. 27. (M IS )R EPRESENTING R INGS WITH OWL Chemical compounds with rings are highly frequent Fundamental inability of OWL to represent cycles At least one tree-shaped model for each consistent OWL knowledge base E XAMPLE Cyclobutane ∃(= 4)hasAtom.(Carbon ∃(= 2)hasBond.Carbon) C C C C5
  28. 28. (M IS )R EPRESENTING R INGS WITH OWL Chemical compounds with rings are highly frequent Fundamental inability of OWL to represent cycles At least one tree-shaped model for each consistent OWL knowledge base E XAMPLE Cyclobutane ∃(= 4)hasAtom.(Carbon ∃(= 2)hasBond.Carbon) C C C C5
  29. 29. (M IS )R EPRESENTING R INGS WITH OWL Chemical compounds with rings are highly frequent Fundamental inability of OWL to represent cycles At least one tree-shaped model for each consistent OWL knowledge base E XAMPLE Cyclobutane ∃(= 4)hasAtom.(Carbon ∃(= 2)hasBond.Carbon) C C C C OWL-based reasoning support5
  30. 30. (M IS )R EPRESENTING R INGS WITH OWL Chemical compounds with rings are highly frequent Fundamental inability of OWL to represent cycles At least one tree-shaped model for each consistent OWL knowledge base E XAMPLE Cyclobutane ∃(= 4)hasAtom.(Carbon ∃(= 2)hasBond.Carbon) C C C C OWL-based reasoning support Does cyclobutane contain a four-membered ring? Does benzaldehyde contain a benzene ring? 5
  31. 31. OWL E XTENSIONS Limitation of OWL to represent cycles (partially) remedied by extension of OWL with Description Graphs and rules [Motik et al., 2009]6
  32. 32. OWL E XTENSIONS Limitation of OWL to represent cycles (partially) remedied by extension of OWL with Description Graphs and rules [Motik et al., 2009] A Description Graph represents structures by means of a directed labeled graph6
  33. 33. OWL E XTENSIONS Limitation of OWL to represent cycles (partially) remedied by extension of OWL with Description Graphs and rules [Motik et al., 2009] A Description Graph represents structures by means of a directed labeled graph E XAMPLE Cyclobutadiene 1 C C Carbon 2 3 Carbon C C Carbon 5 4 Carbon6
  34. 34. OWL E XTENSIONS Limitation of OWL to represent cycles (partially) remedied by extension of OWL with Description Graphs and rules [Motik et al., 2009] A Description Graph represents structures by means of a directed labeled graph E XAMPLE Cyclobutadiene 1 C C Carbon 2 3 Carbon C C Carbon 5 4 Carbon6
  35. 35. OWL E XTENSIONS Limitation of OWL to represent cycles (partially) remedied by extension of OWL with Description Graphs and rules [Motik et al., 2009] A Description Graph represents structures by means of a directed labeled graph E XAMPLE Cyclobutadiene 1 C C Carbon 2 3 Carbon C C Carbon 5 4 Carbon Does cyclobutadiene have a conjugated four-membered ring?6
  36. 36. OWL E XTENSIONS Limitation of OWL to represent cycles (partially) remedied by extension of OWL with Description Graphs and rules [Motik et al., 2009] A Description Graph represents structures by means of a directed labeled graph E XAMPLE Cyclobutadiene 1 C C Carbon 2 3 Carbon C C Carbon 5 4 Carbon Does cyclobutadiene have a conjugated four-membered ring? 6
  37. 37. OWL E XTENSIONS Limitation of OWL to represent cycles (partially) remedied by extension of OWL with Description Graphs and rules [Motik et al., 2009] A Description Graph represents structures by means of a directed labeled graph E XAMPLE Cyclobutadiene 1 Oxygen C C Carbon 2 3 Carbon C C Carbon 5 4 Carbon6
  38. 38. OWL E XTENSIONS Limitation of OWL to represent cycles (partially) remedied by extension of OWL with Description Graphs and rules [Motik et al., 2009] A Description Graph represents structures by means of a directed labeled graph E XAMPLE Cyclobutadiene 1 Oxygen C C Carbon 2 3 Carbon C C Carbon 5 4 Carbon ∀hasAtom.(Carbon Hydrogen) Hydrocarbon6
  39. 39. OWL E XTENSIONS Limitation of OWL to represent cycles (partially) remedied by extension of OWL with Description Graphs and rules [Motik et al., 2009] A Description Graph represents structures by means of a directed labeled graph E XAMPLE Cyclobutadiene 1 Oxygen C C Carbon 2 3 Carbon C C Carbon 5 4 Carbon ∀hasAtom.(Carbon Hydrogen) Hydrocarbon Is cyclobutadiene a hydrocarbon?6
  40. 40. OWL E XTENSIONS Limitation of OWL to represent cycles (partially) remedied by extension of OWL with Description Graphs and rules [Motik et al., 2009] A Description Graph represents structures by means of a directed labeled graph E XAMPLE Cyclobutadiene 1 Oxygen C C Carbon 2 3 Carbon C C Carbon 5 4 Carbon ∀hasAtom.(Carbon Hydrogen) Hydrocarbon Is cyclobutadiene a hydrocarbon? 6
  41. 41. R ESULTS OVERVIEW Key idea:7
  42. 42. R ESULTS OVERVIEW Key idea: Switch from first-order logic to logic programming semantics7
  43. 43. R ESULTS OVERVIEW Key idea: Switch from first-order logic to logic programming semantics Replace classical negation with negation-as-failure7
  44. 44. R ESULTS OVERVIEW Key idea: Switch from first-order logic to logic programming semantics Replace classical negation with negation-as-failure Double benefit:7
  45. 45. R ESULTS OVERVIEW Key idea: Switch from first-order logic to logic programming semantics Replace classical negation with negation-as-failure Double benefit: 1 Encode chemical classes based on the absence of information7
  46. 46. R ESULTS OVERVIEW Key idea: Switch from first-order logic to logic programming semantics Replace classical negation with negation-as-failure Double benefit: 1 Encode chemical classes based on the absence of information (e.g. hydrocarbons, inorganic molecules, saturated compounds,. . . )7
  47. 47. R ESULTS OVERVIEW Key idea: Switch from first-order logic to logic programming semantics Replace classical negation with negation-as-failure Double benefit: 1 Encode chemical classes based on the absence of information (e.g. hydrocarbons, inorganic molecules, saturated compounds,. . . ) 2 Represent rings with adequate precision7
  48. 48. R ESULTS OVERVIEW Key idea: Switch from first-order logic to logic programming semantics Replace classical negation with negation-as-failure Double benefit: 1 Encode chemical classes based on the absence of information (e.g. hydrocarbons, inorganic molecules, saturated compounds,. . . ) 2 Represent rings with adequate precision (e.g. cycloalkanes, benzene rings,. . . )7
  49. 49. R ESULTS OVERVIEW Key idea: Switch from first-order logic to logic programming semantics Replace classical negation with negation-as-failure Double benefit: 1 Encode chemical classes based on the absence of information (e.g. hydrocarbons, inorganic molecules, saturated compounds,. . . ) 2 Represent rings with adequate precision (e.g. cycloalkanes, benzene rings,. . . ) Expressive decidable logic-based formalism for modelling structured entities: Description Graph Logic Programs (DGLPs)7
  50. 50. R ESULTS OVERVIEW Key idea: Switch from first-order logic to logic programming semantics Replace classical negation with negation-as-failure Double benefit: 1 Encode chemical classes based on the absence of information (e.g. hydrocarbons, inorganic molecules, saturated compounds,. . . ) 2 Represent rings with adequate precision (e.g. cycloalkanes, benzene rings,. . . ) Expressive decidable logic-based formalism for modelling structured entities: Description Graph Logic Programs (DGLPs) Prototypical implementation of a logic-based chemical classification software7
  51. 51. O UTLINE 1 M OTIVATION 2 DGLP S , I MPLEMENTATION AND OVERVIEW8
  52. 52. W HAT IS A DGLP O NTOLOGY ? The syntactic objects of a DGLP ontology:9
  53. 53. W HAT IS A DGLP O NTOLOGY ? The syntactic objects of a DGLP ontology: Description graphs9
  54. 54. W HAT IS A DGLP O NTOLOGY ? The syntactic objects of a DGLP ontology: Description graphs E XAMPLE Cyclobutane 1 O O Dioxygen 1 C C Carbon 2 3 Carbon C C Carbon 5 4 Carbon Oxygen 2 3 Oxygen9
  55. 55. W HAT IS A DGLP O NTOLOGY ? The syntactic objects of a DGLP ontology: Description graphs Function-free FOL Horn rules9
  56. 56. W HAT IS A DGLP O NTOLOGY ? The syntactic objects of a DGLP ontology: Description graphs Function-free FOL Horn rules E XAMPLE Bond(x, y) → Bond(y, x) SingleBond(x, y) → Bond(x, y)9
  57. 57. W HAT IS A DGLP O NTOLOGY ? The syntactic objects of a DGLP ontology: Description graphs Function-free FOL Horn rules E XAMPLE Bond(x, y) → Bond(y, x) SingleBond(x, y) → Bond(x, y) Rules with negation-as-failure9
  58. 58. W HAT IS A DGLP O NTOLOGY ? The syntactic objects of a DGLP ontology: Description graphs Function-free FOL Horn rules E XAMPLE Bond(x, y) → Bond(y, x) SingleBond(x, y) → Bond(x, y) Rules with negation-as-failure E XAMPLE HasAtom(x, y) ∧ Carbon(y) → HasCarbon(x) Molecule(x)∧ not HasCarbon(x) → Inorganic(x)9
  59. 59. W HAT IS A DGLP O NTOLOGY ? The syntactic objects of a DGLP ontology: Description graphs Function-free FOL Horn rules E XAMPLE Bond(x, y) → Bond(y, x) SingleBond(x, y) → Bond(x, y) Rules with negation-as-failure E XAMPLE HasAtom(x, y) ∧ Carbon(y) → HasCarbon(x) Molecule(x)∧ not HasCarbon(x) → Inorganic(x) Facts9
  60. 60. W HAT IS A DGLP O NTOLOGY ? The syntactic objects of a DGLP ontology: Description graphs Function-free FOL Horn rules E XAMPLE Bond(x, y) → Bond(y, x) SingleBond(x, y) → Bond(x, y) Rules with negation-as-failure E XAMPLE HasAtom(x, y) ∧ Carbon(y) → HasCarbon(x) Molecule(x)∧ not HasCarbon(x) → Inorganic(x) Facts E XAMPLE Cyclobutane(c1 ), Dinitrogen(c2 ), . . .9
  61. 61. E NCODING D ESCRIPTION G RAPHS Translate DGs into logic programs with function symbols10
  62. 62. E NCODING D ESCRIPTION G RAPHS Translate DGs into logic programs with function symbols E XAMPLE10
  63. 63. E NCODING D ESCRIPTION G RAPHS Translate DGs into logic programs with function symbols E XAMPLE Cyclobutane(x) →Gcb (x, f1 (x), f2 (x), f3 (x), f4 (x)) Gcb (x, y1 , y2 , y3 , y4 ) →Cyclobutane(x) ∧ Carbon(y1 ) ∧ Carbon(y2 ) ∧ Carbon(y3 ) ∧ Carbon(y4 ) ∧ HasAtom(x, y1 ) ∧ Bond(y1 , y2 ) ∧ HasAtom(x, y2 ) ∧ Bond(y2 , y3 ) ∧ HasAtom(x, y3 ) ∧ Bond(y3 , y4 ) ∧ HasAtom(x, y4 ) ∧ Bond(y4 , y1 )10
  64. 64. E NCODING D ESCRIPTION G RAPHS Translate DGs into logic programs with function symbols E XAMPLE Cyclobutane(x) →Gcb (x, f1 (x), f2 (x), f3 (x), f4 (x)) Gcb (x, y1 , y2 , y3 , y4 ) →Cyclobutane(x) ∧ Carbon(y1 ) ∧ Carbon(y2 ) ∧ Carbon(y3 ) ∧ Carbon(y4 ) ∧ HasAtom(x, y1 ) ∧ Bond(y1 , y2 ) ∧ HasAtom(x, y2 ) ∧ Bond(y2 , y3 ) ∧ HasAtom(x, y3 ) ∧ Bond(y3 , y4 ) ∧ HasAtom(x, y4 ) ∧ Bond(y4 , y1 ) Function symbols allow for schema-level reasoning10
  65. 65. C LASSIFYING C HEMICALS E XAMPLE Molecule(x) ∧ HasAtom(x, y) ∧ not Carbon(y) ∧ not Hydrogen(y) → NotHydroCarbon(x) Molecule(x) ∧ not NotHydroCarbon(x) → HydroCarbon(x)11
  66. 66. C LASSIFYING C HEMICALS E XAMPLE Molecule(x) ∧ HasAtom(x, y) ∧ not Carbon(y) ∧ not Hydrogen(y) → NotHydroCarbon(x) Molecule(x) ∧ not NotHydroCarbon(x) → HydroCarbon(x) C C C C11
  67. 67. C LASSIFYING C HEMICALS E XAMPLE Molecule(x) ∧ HasAtom(x, y) ∧ not Carbon(y) ∧ not Hydrogen(y) → NotHydroCarbon(x) Molecule(x) ∧ not NotHydroCarbon(x) → HydroCarbon(x) Is cyclobutane a C C hydrocarbon? C C11
  68. 68. C LASSIFYING C HEMICALS E XAMPLE Molecule(x) ∧ HasAtom(x, yi ) ∧ Bond(yi , yi+1 ) ∧ 1≤i≤4 1≤i≤3 Bond(y4 , y1 ) not yi = yj 1≤ij≤4 → MoleculeWith4MemberedRing(x)12
  69. 69. C LASSIFYING C HEMICALS E XAMPLE Molecule(x) ∧ HasAtom(x, yi ) ∧ Bond(yi , yi+1 ) ∧ 1≤i≤4 1≤i≤3 Bond(y4 , y1 ) not yi = yj 1≤ij≤4 → MoleculeWith4MemberedRing(x) C C C C12
  70. 70. C LASSIFYING C HEMICALS E XAMPLE Molecule(x) ∧ HasAtom(x, yi ) ∧ Bond(yi , yi+1 ) ∧ 1≤i≤4 1≤i≤3 Bond(y4 , y1 ) not yi = yj 1≤ij≤4 → MoleculeWith4MemberedRing(x) Does cyclobutane contain a C C four-membered ring? C C12
  71. 71. U NDECIDABILITY Logic programs with function symbols can axiomatise infinitely large structures13
  72. 72. U NDECIDABILITY Logic programs with function symbols can axiomatise infinitely large structures Reasoning with DGLP ontologies is trivially undecidable13
  73. 73. U NDECIDABILITY Logic programs with function symbols can axiomatise infinitely large structures Reasoning with DGLP ontologies is trivially undecidable We are only interested in finite structures13
  74. 74. U NDECIDABILITY Logic programs with function symbols can axiomatise infinitely large structures Reasoning with DGLP ontologies is trivially undecidable We are only interested in finite structures E XAMPLE Carboxyl O AceticAcid Carboxyl Carbonyl 1 1 C Methyl Hydroxyl 2 3 2 3 CH3 OH Methyl Carboxyl Carbonyl Hydroxyl13
  75. 75. ACYCLICITY C ONDITIONS Formalisms extensively studied, e.g. Datalog±14
  76. 76. ACYCLICITY C ONDITIONS Formalisms extensively studied, e.g. Datalog± Various syntax-based acyclicity conditions14
  77. 77. ACYCLICITY C ONDITIONS Formalisms extensively studied, e.g. Datalog± Various syntax-based acyclicity conditions weak acyclicity [Fagin et al., ICDT, 2002] super-weak acyclicity [Marnette, PODS, 2009] joint acyclicity [Krötzsch and Rudolph, IJCAI, 2011]14
  78. 78. ACYCLICITY C ONDITIONS Formalisms extensively studied, e.g. Datalog± Various syntax-based acyclicity conditions weak acyclicity [Fagin et al., ICDT, 2002] super-weak acyclicity [Marnette, PODS, 2009] joint acyclicity [Krötzsch and Rudolph, IJCAI, 2011] rule out naturally-arising nested structures14
  79. 79. ACYCLICITY C ONDITIONS Formalisms extensively studied, e.g. Datalog± Various syntax-based acyclicity conditions weak acyclicity [Fagin et al., ICDT, 2002] super-weak acyclicity [Marnette, PODS, 2009] joint acyclicity [Krötzsch and Rudolph, IJCAI, 2011] rule out naturally-arising nested structures E XAMPLE Carboxyl O AceticAcid Carboxyl Carbonyl 1 1 C Methyl Hydroxyl 2 3 2 3 CH3 OH Methyl Carboxyl Carbonyl Hydroxyl14
  80. 80. ACYCLICITY C ONDITIONS Formalisms extensively studied, e.g. Datalog± Various syntax-based acyclicity conditions weak acyclicity [Fagin et al., ICDT, 2002] super-weak acyclicity [Marnette, PODS, 2009] joint acyclicity [Krötzsch and Rudolph, IJCAI, 2011] rule out naturally-arising nested structures Novel semantic acyclicity condition14
  81. 81. ACYCLICITY C ONDITIONS Formalisms extensively studied, e.g. Datalog± Various syntax-based acyclicity conditions weak acyclicity [Fagin et al., ICDT, 2002] super-weak acyclicity [Marnette, PODS, 2009] joint acyclicity [Krötzsch and Rudolph, IJCAI, 2011] rule out naturally-arising nested structures Novel semantic acyclicity condition checks for generation of unbounded structures on the fly14
  82. 82. ACYCLICITY C ONDITIONS Formalisms extensively studied, e.g. Datalog± Various syntax-based acyclicity conditions weak acyclicity [Fagin et al., ICDT, 2002] super-weak acyclicity [Marnette, PODS, 2009] joint acyclicity [Krötzsch and Rudolph, IJCAI, 2011] rule out naturally-arising nested structures Novel semantic acyclicity condition checks for generation of unbounded structures on the fly modelling of molecules that contain functional groups14
  83. 83. ACYCLICITY C ONDITIONS Formalisms extensively studied, e.g. Datalog± Various syntax-based acyclicity conditions weak acyclicity [Fagin et al., ICDT, 2002] super-weak acyclicity [Marnette, PODS, 2009] joint acyclicity [Krötzsch and Rudolph, IJCAI, 2011] rule out naturally-arising nested structures Novel semantic acyclicity condition checks for generation of unbounded structures on the fly modelling of molecules that contain functional groups O Carbonyl C Methyl Hydroxyl CH3 OH Carboxyl14
  84. 84. E MPIRICAL E VALUATION Data extracted from ChEBI in Molfile format15
  85. 85. E MPIRICAL E VALUATION Data extracted from ChEBI in Molfile format XSB logic programming engine15
  86. 86. E MPIRICAL E VALUATION Data extracted from ChEBI in Molfile format XSB logic programming engine Chemical classes:15
  87. 87. E MPIRICAL E VALUATION Data extracted from ChEBI in Molfile format XSB logic programming engine Chemical classes: Hydrocarbons Inorganic molecules Molecules with exactly two carbons Molecules with a four-membered ring Molecules with a benzene15
  88. 88. E MPIRICAL E VALUATION Data extracted from ChEBI in Molfile format XSB logic programming engine Chemical classes: Hydrocarbons Inorganic molecules Molecules with exactly two carbons Molecules with a four-membered ring Molecules with a benzene Preliminary evaluation ranging from 10 to 70 molecules15
  89. 89. E MPIRICAL E VALUATION Data extracted from ChEBI in Molfile format XSB logic programming engine Chemical classes: Hydrocarbons Inorganic molecules Molecules with exactly two carbons Molecules with a four-membered ring Molecules with a benzene Preliminary evaluation ranging from 10 to 70 molecules Results:15
  90. 90. E MPIRICAL E VALUATION Data extracted from ChEBI in Molfile format XSB logic programming engine Chemical classes: Hydrocarbons Inorganic molecules Molecules with exactly two carbons Molecules with a four-membered ring Molecules with a benzene Preliminary evaluation ranging from 10 to 70 molecules Results: All DGLP ontologies were found acyclic15
  91. 91. E MPIRICAL E VALUATION Data extracted from ChEBI in Molfile format XSB logic programming engine Chemical classes: Hydrocarbons Inorganic molecules Molecules with exactly two carbons Molecules with a four-membered ring Molecules with a benzene Preliminary evaluation ranging from 10 to 70 molecules Results: All DGLP ontologies were found acyclic Molecules classified as expected15
  92. 92. E MPIRICAL E VALUATION Data extracted from ChEBI in Molfile format XSB logic programming engine Chemical classes: Hydrocarbons Inorganic molecules Molecules with exactly two carbons Molecules with a four-membered ring Molecules with a benzene Preliminary evaluation ranging from 10 to 70 molecules Results: All DGLP ontologies were found acyclic Molecules classified as expected Suite of subsumption tests for largest ontology performed in few minutes15
  93. 93. OVERVIEW AND F UTURE D IRECTIONS 1 Expressive and decidable formalism for representation of structured objects16
  94. 94. OVERVIEW AND F UTURE D IRECTIONS 1 Expressive and decidable formalism for representation of structured objects 2 Novel acyclicity condition for logic programs with restricted use of function symbols16
  95. 95. OVERVIEW AND F UTURE D IRECTIONS 1 Expressive and decidable formalism for representation of structured objects 2 Novel acyclicity condition for logic programs with restricted use of function symbols 3 Prototype for the automated classification of chemicals16
  96. 96. OVERVIEW AND F UTURE D IRECTIONS 1 Expressive and decidable formalism for representation of structured objects 2 Novel acyclicity condition for logic programs with restricted use of function symbols 3 Prototype for the automated classification of chemicals Is dinitrogen inorganic? Does cyclobutane contain a four-membered ring? Is acetylene a hydrocarbon? Does benzaldehyde contain a benzene ring?16
  97. 97. OVERVIEW AND F UTURE D IRECTIONS 1 Expressive and decidable formalism for representation of structured objects 2 Novel acyclicity condition for logic programs with restricted use of function symbols 3 Prototype for the automated classification of chemicals Is dinitrogen inorganic? Does cyclobutane contain a four-membered ring? Is acetylene a hydrocarbon? Does benzaldehyde contain a benzene ring? 16
  98. 98. OVERVIEW AND F UTURE D IRECTIONS 1 Expressive and decidable formalism for representation of structured objects 2 Novel acyclicity condition for logic programs with restricted use of function symbols 3 Prototype for the automated classification of chemicals Is dinitrogen inorganic? Does cyclobutane contain a four-membered ring? Is acetylene a hydrocarbon? Does benzaldehyde contain a benzene ring? Future directions:16
  99. 99. OVERVIEW AND F UTURE D IRECTIONS 1 Expressive and decidable formalism for representation of structured objects 2 Novel acyclicity condition for logic programs with restricted use of function symbols 3 Prototype for the automated classification of chemicals Is dinitrogen inorganic? Does cyclobutane contain a four-membered ring? Is acetylene a hydrocarbon? Does benzaldehyde contain a benzene ring? Future directions: Datalog rules with existentials in the head16
  100. 100. OVERVIEW AND F UTURE D IRECTIONS 1 Expressive and decidable formalism for representation of structured objects 2 Novel acyclicity condition for logic programs with restricted use of function symbols 3 Prototype for the automated classification of chemicals Is dinitrogen inorganic? Does cyclobutane contain a four-membered ring? Is acetylene a hydrocarbon? Does benzaldehyde contain a benzene ring? Future directions: Datalog rules with existentials in the head User-friendly surface syntax16
  101. 101. OVERVIEW AND F UTURE D IRECTIONS 1 Expressive and decidable formalism for representation of structured objects 2 Novel acyclicity condition for logic programs with restricted use of function symbols 3 Prototype for the automated classification of chemicals Is dinitrogen inorganic? Does cyclobutane contain a four-membered ring? Is acetylene a hydrocarbon? Does benzaldehyde contain a benzene ring? Future directions: Datalog rules with existentials in the head User-friendly surface syntax Fully-fledged chemical classification system16
  102. 102. OVERVIEW AND F UTURE D IRECTIONS 1 Expressive and decidable formalism for representation of structured objects 2 Novel acyclicity condition for logic programs with restricted use of function symbols 3 Prototype for the automated classification of chemicals Is dinitrogen inorganic? Does cyclobutane contain a four-membered ring? Is acetylene a hydrocarbon? Does benzaldehyde contain a benzene ring? Future directions: Datalog rules with existentials in the head User-friendly surface syntax Fully-fledged chemical classification system Thank you for listening. Questions?16

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