Relational Patterns in OWL and their application to OBO
Robert Hoehndorf1, Anika Oellrich1, Michel Dumontier2,
Janet Kelso4, Heinrich Herre3, and Dietrich Rebholz-Schuhmann1
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1European Bioinformatics Institute, 2Carleton University, 3University of Leipzig, 4Max Planck Institute for Evolutionary Anthropology
Ontology
• Explicit specification of conceptualization – specify meaning of terms in vocabulary
• formal ontology uses languages with explicit semantics to specify meaning– axioms in FOL, OWL, etc
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Biomedical Ontologies
• OBO - 100+ ontologies • OBO Foundry
– common principles and criteria– format: OBOF or OWL – must use OBO Relation Ontology
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OBO Flatfile Format
Graph based language• Nodes [term] represent categories
[Term]id: CL:0000028name: CNS neuron (sensu Nematoda and Protostomia)is_a: CL:0000540 ! neuronrelationship: develops_from CL:0000338
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OBOF examples
• Edges [typedef] represent relations
[Typedef] id: develops_fromis_transitive: true
OBOF semantics not explicit• One solution uses tailored FOL semantics• Another uses fixed semantics for relations and relational
statements
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OBO Relationship Ontology
• Smith, 2005 • FOL definitions for common relations
– C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t.
– weak axioms (reflexivity, transitivity, etc.) – use of FOL and ternary relations: mapping to
(decidable) OWL problematic
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Horrocks OBO2OWL semantics
• Fixed semantics via mapping to OWL– intersection, union, disjointness
• R(C,D) maps to C subClassOf R some D
• OBOF[Term]name: mouserelationship: has-part tail
• OWLmouse subClassOf has-part some tail
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Critique
• Horrocks semantics does not use RO semantics – but RO must be used for OBO Foundry ontologies
• Horrocks semantics sometimes inadequate
Tailless-Mouse subClassOf lacks-part some Tail
Should instead be:
Tailless-Mouse subClassOf not(has-part some Tail)
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Problem statement
• RO in FOL -> undecidable • RO not integrated in OBOF
– no semantics for OBOF• static translation of relations to OWL
C subClassOf R some D -> inadequate– develop OBOF semantics, preferably using
decidable logic (OWL)
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Proposal
• Observation: relation between classes defined through relations between instances
R(C,D) <-> Def(C,D) • C and D occur as variables in Def • Idea: Pattern Definitions in OWL
– extend OWL with variables for classes– use Manchester OWL syntax– formulate relations using extended OWL syntax – similar to OWL Pre-Processing Language (OPPL)
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Extended OBOF syntax:OWLDEF
[Typedef]id: CC-has-partname: has-partowldef: ?X subClassOf: has-part some ?Y• every use of the relation CC-has-part in the OBOF is expanded to
an OWL axiom in which the variables are filled by the classes between which the relation was asserted.
[Term]id: Mouserelationship: has-part Tailgives:
Mouse subClassOf has-part some Tail
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integral-part-of
integral-part-of(?X, ?Y): ?X part-of ?Y and ?Y has-part ?X
• Produces two OWL class axioms?X subClassOf part-of some ?Y ?Y subClassOf has-part some ?X
• Which are transformed to one(?X and not (part-of some ?Y)) or(?Y and not (has-part some ?X)) subClassOf Nothing
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OBO2OWL
• prototype extends OWL API to convert OBOF to OWL with owldef statements
• ?X and ?Y from the owldef statement are replaced by the corresponding term names
• inline axiom parser generates an OWL axiom• API and web-interface at
http://bioonto.de/obo2owl
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OWL2OBO
• Extract relational patterns from OWL ontology – Naïve: replace ?X and ?Y with all combinations of
named classes are generated to fill variables in the relation patterns and generate OWL axioms from binary class relations
– Hermit used to prove axioms; keep track of those which could be inferred from asserted axioms
– Obtain list of theorems that can be added to OBO file
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Evaluation
• Celltype Ontology– 1253 is-a; 275 develops-from relations– identified 9,497 is-a and 124,420 develops-from
• Malaria Ontology– 3 realized-by– Identified 56 realized-by
• Sequence Ontology– Added 1 exon integral-part-of transcript– Now: all exons are part-of transcript and all transcripts
has-part exon
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Results @ http://bioonto.de/obo2owl
Open Problems
• intersection, union statements and relations have unclear semantics
[Term]id: ID:Aintersection_of: ID:Bintersection_of: integral-part-of ID:C
• OWL class axiom (integral-part-of) intersected with class description -> invalid
• (A subClassOf B) intersected with C: is C intersected with A, B, both?
• no obvious solution: inherent problem in OBOF, needs to be addressed (by OBOF developers)
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Advanced Applications
• n-ary relations between classes• introduce variables ?X1, ..., ?XN• example:
has-quality-with-value(?X1, ?X2, ?X3): ?X1 subClassOf has-quality some
(?X2 and has-value some ?X3)
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Advanced Applications 2
• open patterns as meta-properties of ontologies• Consider the combinatorics of connecting
chemical groups to base groups for high throughput chemical synthesis
• assert ?X subClassOf is-connected-to some ?Y• semantics: all named classes in ontology satisfy
the pattern: all classes can be connected to all other classes
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Future Research
• integration with OPPL2 and use of OPPL2 to define relations
• formalization of further relations• repository of frequently used relation
definitions• efficient conversion from OWL to OBO• integration with OWL: use of annotation
properties
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Conclusion
• pattern approach as a simple interface to complex definitions
• flexible semantics based on conversion to OWL– we implemented OBO RO in OWL
• current approaches have shortcomings – open issues with intersection, union, etc
• http://bioonto.de/obo2owl
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