1. OWL 2 in use

2. OWL 2 OWL 2 is a knowledge representation language, designed to formulate, exchange and reason with knowledge about a domain of interest. The basic notions of OWL 2 are: Axioms: the basic statements that an OWL ontology expresses Entities: elements used to refer to real-world objects Expressions: combinations of entities to form complex descriptions from basic ones We can also draw consequences from knowledge Reasoners – tools that can automatically compute consequences. PathoNGenTrace REST API workshop, January 2013 2

3. In general classes are used to group individuals that have something in common in order to refer to them. classes essentially represent sets of individuals. PathoNGenTrace REST API workshop, January 2013 3 Classes and Instances Isolate Species 0021/84 Neisseria_meni ngitidis rdf:type classes instances Ontology Level Data Level

4. In general classes are used to group individuals that have something in common in order to refer to them. classes essentially represent sets of individuals. PathoNGenTrace REST API workshop, January 2013 4 Classes and Instances <owl:NamedIndividual rdf:about="http://rest.phyloviz.net/ontology#Neisseria_meningitidis"> <owl:NamedIndividual rdf:about="http://rest.phyloviz.net/ontology#Neisseria_meningitidis"> Class Isolate Individual Neisseria_meningitidis

5. In OWL 2, this is done by a so-called subclass axiom: PathoNGenTrace REST API workshop, January 2013 5 Class Hierarchies MultiLocus MLST subClassOf What can be inferred with respect to Individuals? What can be inferred with respect to Individuals? Subclass relationship between classes is transitive e reflexive Do we have examples of transitivity in typon?

6. Equivalence: classes may effectively refer to the same sets of individuals. Disjointness: defines an incompatibility relationship between classes. PathoNGenTrace REST API workshop, January 2013 6 Equivalence and Disjoint Classes Are these classes disjoint ? MultiLocus MLST SingleLocus spaTyping ccrBTyping emmTyping

7. Specify how the individuals relate to other individuals. Order in which the individuals are written is important. PathoNGenTrace REST API workshop, January 2013 7 Object Properties <owl:ObjectProperty rdf:about=http://rest.phyloviz.net/ontology#belongsToSpecies> <owl:ObjectProperty rdf:about=http://rest.phyloviz.net/ontology#belongsToSpecies> And what is the order ?

8. PathoNGenTrace REST API workshop, January 2013 8 Domain and Range Restrictions Two axioms for defining the domain and range of properties (object or data) Having these two axioms and also What the reasoner can infer? Having these two axioms and also What the reasoner can infer?

9. OWL does not make the assumption that different names are names for different individuals. PathoNGenTrace REST API workshop, January 2013 9 Equality and Inequality of Individuals

10. These properties relate individuals to data values (instead of to other individuals), and many of the XML Schema datatypes can be used. Domain and range can also be stated for datatype properties as it is done for object properties PathoNGenTrace REST API workshop, January 2013 10 Datatype properties

11. Advanced Class Relationships -- Complex Classes PathoNGenTrace REST API workshop, January 2013 11 Named classes, properties, and individuals can be used as building blocks to define new classes Intersection of two classes consists of exactly those individuals which are instances of both classes Union of two classes contains every individual which is contained in at least one of these classes. Complement of a class corresponds to logical negation. Does Typon has examples using this constructors ?

12. Advanced Class Relationships -- Complex Classes PathoNGenTrace REST API workshop, January 2013 12 Union

13. Advanced Class Relationships -- Property Restrictions PathoNGenTrace REST API workshop, January 2013 13 Existential quantification: defines a class as the set of all individuals that are connected via a particular property to another individual which is an instance of a certain class Does Typon has examples of this restriction ? Let’s think about the object property hasSpecies.

14. Advanced Class Relationships -- Property Restrictions PathoNGenTrace REST API workshop, January 2013 14 Universal quantification: describe class of individuals for which all related individuals must be instances of a given class. Typon does not have this kind of restriction.

15. Advanced Class Relationships -- Property Restrictions PathoNGenTrace REST API workshop, January 2013 15 Cardinality restrictions: to specify the number of individuals involved in the restriction. Does Typon has examples of this restriction ? Let’s think about the object property isOfGene. //... 1

16. Advanced Use of Properties -- Property Restrictions PathoNGenTrace REST API workshop, January 2013 16 And more… Disjoint Reflexive Irreflexive Transitive Inverse property (inverseOf): one property is obtained by taking another property and changing its direction. Does Typon has this kind of restriction? Functional property (FunctionalProperty): every individual can be linked by the property to at most one other individual. Does Typon has this kind of restriction? Inverse Functional property (InverseFunctionalProperty): the inverse of the property is also functional Does Typon has this kind of restriction? Symmetric property (SymmetricProperty): the property and its inverse coincide. Asymetric property (AsymetricProperty): if the property connects entity A with entity B, then it can never connect B with A. Does Typon has these kind of restrictions?

17. RDF Schema: Language PathoNGenTrace REST API workshop, January 2013 17 Primitives of RDF(S) Resources: rdfs:Class - denotes sets of resources rdf:Property – the class of resources that links resources Properties: rdf:type rdfs:subClassOf rdfs:subPropertyOf rdfs:domain rdfs:range

18. OWL Syntax PathoNGenTrace REST API workshop, January 2013 18 OWL is an extension of RDF - S OWL primitives are related with RDF-S primitives Ex: owl:Class ⊆ rdfs:Class Equivalences, disjunctions and classes boolean expressions: Though specific properties in rdfs:Class ou rdf:Property (como rdf:subclassOf ) Boolean expressions such as: owl:unionOf, owl:complementOf, owl:intersectionOf ElementEquivalenceDisjunction classowl:equivalentClassowl:disjointWith propertyowl:equivalentProperty individualowl:sameAsowl:differentFrom

19. Relating Ontologies PathoNGenTrace REST API workshop, January 2013 19 equivalence partOf Possibly equivalent Importing other ontologies for reusing is a good practice. Since… -> A shared representation is essential for success in communication and interoperability Gene GeoReference Gene GeoReference Gene Geographic Information

20. OWL 2 profile PathoNGenTrace REST API workshop, January 2013 20 OWL 2 profiles (commonly called a fragment or a sublanguage in computational logic) is a trimmed down version of OWL 2 that trades some expressive power for the efficiency of reasoning. OWL 2 EL OWL 2 QL OWL 2 RL OWL 2 DL OWL 2 Full