Classifying Chemicals with Description Graphs and Logic Programming
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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 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 Classifying Chemicals with Description Graphs and Logic Programming Presentation Transcript

  • 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
  • O UTLINE 1 M OTIVATION 2 DGLP S , I MPLEMENTATION AND OVERVIEW1
  • M ODELLING C HEMICALS WITH OWL OWL used for the representation of molecular structures2
  • M ODELLING C HEMICALS WITH OWL OWL used for the representation of molecular structures Classification of chemical compounds [Villanueva-Rosales & Dumontier, OWLED 2007]2
  • 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
  • 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
  • T HE C H EBI O NTOLOGY OWL ontology Chemical Entities of Biological Interest3
  • T HE C H EBI O NTOLOGY OWL ontology Chemical Entities of Biological Interest Freely accessible dictionary of ‘small’ molecular entities3
  • 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
  • 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
  • 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
  • AUTOMATE C HEMICAL C LASSIFICATION ChEBI is manually incremented4
  • AUTOMATE C HEMICAL C LASSIFICATION ChEBI is manually incremented Currently contains approx. 28,000 fully annotated entities4
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • (M IS )R EPRESENTING R INGS WITH OWL Chemical compounds with rings are highly frequent5
  • (M IS )R EPRESENTING R INGS WITH OWL Chemical compounds with rings are highly frequent Fundamental inability of OWL to represent cycles5
  • (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
  • (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
  • (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
  • (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
  • (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
  • (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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • R ESULTS OVERVIEW Key idea:7
  • R ESULTS OVERVIEW Key idea: Switch from first-order logic to logic programming semantics7
  • R ESULTS OVERVIEW Key idea: Switch from first-order logic to logic programming semantics Replace classical negation with negation-as-failure7
  • R ESULTS OVERVIEW Key idea: Switch from first-order logic to logic programming semantics Replace classical negation with negation-as-failure Double benefit:7
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • O UTLINE 1 M OTIVATION 2 DGLP S , I MPLEMENTATION AND OVERVIEW8
  • W HAT IS A DGLP O NTOLOGY ? The syntactic objects of a DGLP ontology:9
  • W HAT IS A DGLP O NTOLOGY ? The syntactic objects of a DGLP ontology: Description graphs9
  • 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
  • W HAT IS A DGLP O NTOLOGY ? The syntactic objects of a DGLP ontology: Description graphs Function-free FOL Horn rules9
  • 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
  • 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
  • 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
  • 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
  • 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
  • E NCODING D ESCRIPTION G RAPHS Translate DGs into logic programs with function symbols10
  • E NCODING D ESCRIPTION G RAPHS Translate DGs into logic programs with function symbols E XAMPLE10
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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≤i<j≤4 → MoleculeWith4MemberedRing(x)12
  • 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≤i<j≤4 → MoleculeWith4MemberedRing(x) C C C C12
  • 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≤i<j≤4 → MoleculeWith4MemberedRing(x) Does cyclobutane contain a C C four-membered ring?  C C12
  • U NDECIDABILITY Logic programs with function symbols can axiomatise infinitely large structures13
  • U NDECIDABILITY Logic programs with function symbols can axiomatise infinitely large structures Reasoning with DGLP ontologies is trivially undecidable13
  • 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
  • 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
  • ACYCLICITY C ONDITIONS Formalisms extensively studied, e.g. Datalog±14
  • ACYCLICITY C ONDITIONS Formalisms extensively studied, e.g. Datalog± Various syntax-based acyclicity conditions14
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • E MPIRICAL E VALUATION Data extracted from ChEBI in Molfile format15
  • E MPIRICAL E VALUATION Data extracted from ChEBI in Molfile format XSB logic programming engine15
  • E MPIRICAL E VALUATION Data extracted from ChEBI in Molfile format XSB logic programming engine Chemical classes:15
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • OVERVIEW AND F UTURE D IRECTIONS 1 Expressive and decidable formalism for representation of structured objects16
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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