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- 1. Relational Patterns in OWL and their application to OBO<br />Robert Hoehndorf1, Anika Oellrich1, Michel Dumontier2, <br />Janet Kelso4, Heinrich Herre3, and Dietrich Rebholz-Schuhmann1<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />1<br />1European Bioinformatics Institute, 2Carleton University,<br /> 3University of Leipzig, 4Max Planck Institute for Evolutionary Anthropology<br />
- 2.
- 3. Ontology<br />Explicit specification of conceptualization <br />specify meaning of terms in vocabulary<br />formal ontology uses languages with explicit semantics to specify meaning<br />axioms in FOL, OWL, etc<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />3<br />
- 4. Biomedical Ontologies<br />OBO - 100+ ontologies<br />OBO Foundry <br />common principles and criteria<br />format: OBOF or OWL <br />must use OBO Relation Ontology<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />4<br />
- 5. OBO Flatfile Format<br />Graph based language<br />Nodes [term] represent categories <br />[Term]<br />id: CL:0000028<br />name: CNS neuron (sensuNematoda and Protostomia)<br />is_a: CL:0000540 ! neuron<br />relationship: develops_from CL:0000338<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />5<br />
- 6. OBOF examples<br />Edges [typedef] represent relations<br />[Typedef] <br />id: develops_from<br />is_transitive: true<br />OBOF semantics not explicit<br />One solution uses tailored FOL semantics<br />Another uses fixed semantics for relations and relational statements<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />6<br />
- 7. OBO Relationship Ontology<br />Smith, 2005 <br />FOL definitions for common relations<br />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. <br />weak axioms (reflexivity, transitivity, etc.) <br />use of FOL and ternary relations: mapping to (decidable) OWL problematic<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />7<br />
- 8. Horrocks OBO2OWL semantics<br />Fixed semantics via mapping to OWL<br />intersection, union, disjointness<br />R(C,D) maps to<br /> C subClassOf R some D <br />OBOF<br />[Term]<br />name: mouse<br />relationship: has-part tail<br />OWL<br />mouse subClassOf has-part some tail<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />8<br />
- 9. Critique<br />Horrocks semantics does not use RO semantics <br />but RO must be used for OBO Foundry ontologies<br />Horrocks semantics sometimes inadequate <br />Tailless-Mouse <br />subClassOf lacks-part some Tail<br />Should instead be:<br />Tailless-Mouse <br />subClassOf not(has-part some Tail)<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />9<br />
- 10. Problem statement<br />RO in FOL -> undecidable<br />RO not integrated in OBOF <br />no semantics for OBOF<br />static translation of relations to OWL <br />C subClassOf R some D-> inadequate<br />develop OBOF semantics, preferably using decidable logic (OWL)<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />10<br />
- 11. Proposal<br />Observation: relation between classes defined through relations between instances <br /> R(C,D) <-> Def(C,D) <br />C and D occur as variables in Def <br />Idea: Pattern Definitions in OWL<br />extend OWL with variables for classes<br />use Manchester OWL syntax<br />formulate relations using extended OWL syntax <br />similar to OWL Pre-Processing Language (OPPL)<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />11<br />
- 12. Extended OBOF syntax:OWLDEF<br />[Typedef]<br />id: CC-has-part<br />name: has-part<br />owldef: ?X subClassOf: has-part some ?Y<br />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.<br />[Term]<br />id: Mouse<br />relationship: has-part Tail<br />gives:<br /> Mouse subClassOf has-part some Tail<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />12<br />
- 13. integral-part-of<br />integral-part-of(?X, ?Y): ?X part-of ?Y and ?Y has-part ?X <br />Produces two OWL class axioms<br />?X subClassOf part-of some ?Y <br />?Y subClassOf has-part some ?X <br />Which are transformed to one<br />(?X and not (part-of some ?Y)) or<br />(?Y and not (has-part some ?X))<br />subClassOfNothing<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />13<br />
- 14. OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />14<br />
- 15. OBO2OWL<br />prototype extends OWL API to convert OBOF to OWL with owldef statements<br />?X and ?Y from the owldef statement are replaced by the corresponding term names<br />inline axiom parser generates an OWL axiom<br />API and web-interface at http://bioonto.de/obo2owl<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />15<br />
- 16. OWL2OBO<br />Extract relational patterns from OWL ontology <br />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<br />Hermit used to prove axioms; keep track of those which could be inferred from asserted axioms<br />Obtain list of theorems that can be added to OBO file<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />16<br />
- 17. Evaluation<br />Celltype Ontology<br />1253 is-a; 275 develops-from relations<br />identified 9,497 is-a and 124,420 develops-from<br />Malaria Ontology<br />3 realized-by<br />Identified 56 realized-by<br />Sequence Ontology<br />Added 1 exonintegral-part-of transcript<br />Now: all exons are part-of transcript and all transcripts has-partexon<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />17<br />Results @ http://bioonto.de/obo2owl<br />
- 18. Open Problems<br />intersection, union statements and relations have unclear semantics<br />[Term]<br />id: ID:A<br />intersection_of: ID:B<br />intersection_of: integral-part-of ID:C<br />OWL class axiom (integral-part-of) intersected with class description -> invalid <br />(A subClassOf B) intersected with C: is C intersected with A, B, both?<br />no obvious solution: inherent problem in OBOF, needs to be addressed (by OBOF developers)<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />18<br />
- 19. Advanced Applications<br />n-ary relations between classes<br />introduce variables ?X1, ..., ?XN<br />example: <br />has-quality-with-value(?X1, ?X2, ?X3): ?X1 subClassOf has-quality some <br /> (?X2 and has-value some ?X3)<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />19<br />
- 20. Advanced Applications 2<br />open patterns as meta-properties of ontologies<br />Consider the combinatorics of connecting chemical groups to base groups for high throughput chemical synthesis<br />assert ?X subClassOf is-connected-to some ?Y<br />semantics: all named classes in ontology satisfy the pattern: all classes can be connected to all other classes<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />20<br />
- 21. Future Research<br />integration with OPPL2 and use of OPPL2 to define relations<br />formalization of further relations<br />repository of frequently used relation definitions<br />efficient conversion from OWL to OBO<br />integration with OWL: use of annotation properties<br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />21<br />
- 22. Conclusion<br />pattern approach as a simple interface to complex definitions<br />flexible semantics based on conversion to OWL<br />we implemented OBO RO in OWL <br />current approaches have shortcomings <br />open issues with intersection, union, etc<br />http://bioonto.de/obo2owl <br />OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />22<br />

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