Relational Patterns in OWL and their application to OBO<br />Robert Hoehndorf1, Anika Oellrich1, Michel Dumontier2, <br />...
Ontology<br />Explicit specification of conceptualization <br />specify meaning of terms in vocabulary<br />formal ontolog...
Biomedical Ontologies<br />OBO - 100+ ontologies<br />OBO Foundry <br />common principles and criteria<br />format: OBOF o...
OBO Flatfile Format<br />Graph based language<br />Nodes [term] represent categories <br />[Term]<br />id: CL:0000028<br /...
OBOF examples<br />Edges [typedef] represent relations<br />[Typedef] <br />id: develops_from<br />is_transitive: true<br ...
OBO Relationship Ontology<br />Smith, 2005 <br />FOL definitions for common relations<br />C part_of C' if and only if: gi...
Horrocks OBO2OWL semantics<br />Fixed semantics via mapping to OWL<br />intersection, union, disjointness<br />R(C,D) maps...
Critique<br />Horrocks semantics does not use RO semantics <br />but RO must be used for OBO Foundry ontologies<br />Horro...
Problem statement<br />RO in FOL -> undecidable<br />RO not integrated in OBOF <br />no semantics for OBOF<br />static tra...
Proposal<br />Observation: relation between classes defined through relations between instances <br />		R(C,D) <-> Def(C,D...
Extended OBOF syntax:OWLDEF<br />[Typedef]<br />id: CC-has-part<br />name: has-part<br />owldef: ?X subClassOf: has-part s...
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 />...
OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />14<br />
OBO2OWL<br />prototype extends OWL API to convert OBOF to OWL with owldef statements<br />?X and ?Y from the owldef statem...
OWL2OBO<br />Extract relational patterns from OWL ontology <br />Naïve: replace ?X and ?Y with all combinations of named c...
Evaluation<br />Celltype Ontology<br />1253 is-a; 275 develops-from relations<br />identified 9,497 is-a and 124,420 devel...
Open Problems<br />intersection, union statements and relations have unclear semantics<br />[Term]<br />id: ID:A<br />inte...
Advanced Applications<br />n-ary relations between classes<br />introduce variables ?X1, ..., ?XN<br />example: <br />has-...
Advanced Applications 2<br />open patterns as meta-properties of ontologies<br />Consider the combinatorics of connecting ...
Future Research<br />integration with OPPL2 and use of OPPL2 to define relations<br />formalization of further relations<b...
Conclusion<br />pattern approach as a simple interface to complex definitions<br />flexible semantics based on conversion ...
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Relational Patterns in OWL and their application to OBO

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Directed acyclic graphs are commonly used to represent ontologies in the biomedical domain. They provide an intuitive means to formalize relations that hold between ontological categories. However, their semantics is usually not explicit. We provide a semantics for a part of the OBO Flatfile Format by extending OWL with a method to express relational patterns. These patterns are OWL axioms with variables for classes. The variables can only be filled with named classes. Additionally, we provide a semantics for open patterns in OWL. Our method is applicable to the OBO Flatfile Format, and provides a means to design OWL ontologies using complex ontology design patterns. Therefore, it leads not only to an integration of the OBO Flatfile Format and OWL, but extends OWL with an intuitive interface for designing ontologies us ing complex definition patterns. A prototypic implementation and test results are available at http://bioonto.de/obo2owl

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  • Typedef statements specify the kinds of edges in the DAG. They representthe relation that is intended to be established between two nodes when an edgeof a certain kind is used. An edge has an identier and a name. Additionally,properties for the edges can be asserted, such as transitivity.
  • An edge of type R between nodes A and B is usually given the semantics of the OWL statement A subClassOf R some B
  • We developed an extension to the OBO Flatfile Format and to the Manchester OWL Syntax [8] based on the assumption that any statement in OWL in which two variables for classes occur, determines a relation between these two classes. For example, we define the CC-has-part relation as ?X subClassOf: has-part some ?Y, where CC-has-part is a relation between classes and has- part a relation between individuals.
  • Relational Patterns in OWL and their application to OBO

    1. 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. 2.
    3. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 14. OWLED2010:San Francisco:Relational Patterns in OWL and their application to OBO<br />14<br />
    15. 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. 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. 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. 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. 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. 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. 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. 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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