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This document provides an overview of the main new features of OWL 2 and their rationale. These features were determined based on real applications and user and tool-developer experience, some of which has been documented in the OWLED Workshop Series. The inclusion of the features is supported by use cases provided to the W3C OWL Working Group, some of which are listed in the Section 7. This document also describes and motivates some of the other design decisions that were made during the development of OWL 2 or purposefully retained from OWL Web Ontology Language (OWL 1), particularly the various concrete syntaxes for OWL 2, and the relationship of OWL 2 with RDF (Section 4). OWL 2 extends OWL 1 and inherits the language features, design decisions, and use cases for OWL 1. This document thus forms an extension of the Use Cases and Requirements that underlie OWL 1 [OWL Use Cases and Requirements].
OWL 2 adds several new features to OWL 1, including increased expressive power for properties, extended support for datatypes, simple metamodeling capabilities, extended annotation capabilities, and keys (Section 2). OWL 2 also defines several profiles – OWL 2 language subsets that may better meet certain performance requirements or may be easier to implement (Section 3).
The new features of OWL 2 are presented here, organized in the following categories:
Each feature is described in a common pattern as follows:
Readers may selectively Show or Hide the Examples and the Functional Syntax (FSS) or the RDF Syntax in the Examples by toggling the buttons below .
OWL 2 adds syntactic sugar to make some common patterns easier to write. Since all these constructs are simply shorthands they do not change the expressiveness, semantics, or complexity of the language. Implementations, however, may prefer to take special notice of these constructs for more efficient processing.
While OWL 1 provides means to define a set of subclasses as a disjoint and complete covering of a superclass by using several axioms, this cannot be done concisely.
DisjointUnion defines a class as the union of other classes, all of which are pairwise disjoint. It is a shorthand for separate axioms making the classes pairwise disjoint and one setting up the union class. Normative Syntax Direct Semantics RDF-Based Semantics
DisjointUnion ({ A } C CE1 ... CEn ) where C is a class, CEi, 1 ≤ i ≤ n are class expressions, and { A } zero or more annotations.
DisjointUnion(:BrainHemisphere :LeftHemisphere :RightHemisphere) (UC#2) | A :BrainHemisphere is exclusively either a :LeftHemisphere or :RightHemisphere and cannot be both of them. |
DisjointUnion(:Lobe :FrontalLobe :ParietalLobe :TemporalLobe :OccipitalLobe :LimbicLobe) (UC#1) | A :Lobe is exclusively either a :FrontalLobe, :ParietalLobe, :TemporalLobe, :OccipitalLobe or a :LimbicLobe and cannot be both of them. |
DisjointUnion(:AmineGroup :PrimaryAmineGroup :SecondaryAmineGroup :TertiaryAmineGroup )(UC#3) | An :AmineGroup is exclusively either a :PrimaryAmineGroup, :SecondaryAmineGroup or a :TertiaryAmineGroup and cannot be both of them. |
DisjointUnion(:CarDoor :FrontDoor :RearDoor :TrunkDoor) (UC#4) | A :CarDoor is exclusively either a :FrontDoor, a :RearDoor or a:TrunkDoor and not both of them. |
Use Case #1 Use Case #2 Use Case #3 Use Case #4
While OWL 1 provides means to state that two subclasses are disjoint, stating that several subclasses are pairwise disjoint cannot be done concisely.
DisjointClasses states that all classes from the set are pairwise disjoint. It is a shorthand for binary disjointness axioms between the classes. Normative Syntax Direct Semantics RDF-Based Semantics
DisjointClasses ({ A } CE1 ... CEn ) where CEi, 1 ≤ i ≤ n are class expressions, and { A } zero or more annotations.
DisjointClasses( :UpperLobeOfLung :MiddleLobeOfLung :LowerLobeOfLung ) (UC#2) | :UpperLobeOfLung :MiddleLobeOfLung :LowerLobeOfLung are pairwise exclusive. |
DisjointClasses( :LeftLung :RightLung ) (UC#2) | Nothing can be both a :LeftLung and a :RightLung. |
While OWL 1 provides means to assert values of a property for an individual, it does not provide a construct for directly asserting values of a property that an individual does not have (negative facts).
NegativeObjectPropertyAssertion (resp. NegativeDataPropertyAssertion) states that a given property does not hold for the given individuals. Normative Syntax Direct Semantics RDF-Based Semantics
NegativeObjectPropertyAssertion( { A } OPE a1 a2 ) where OPE is an object property expression, a1 a2 are individuals, and {A} zero or more annotations.
NegativeDataPropertyAssertion( { A } DPE a lt ) where DPE is a data property expression, a an individual, lt a literal, and {A} 0 or more annotations.
NegativeObjectPropertyAssertion( :livesIn :ThisPatient :IleDeFrance ) (UC#9) | :ThisPatient does not live in the :IleDeFrance region. |
NegativeDataPropertyAssertion( :hasAge :ThisPatient 5^^xsd:integer ) (UC#9) | :ThisPatient is not five years old. |
OWL 1 was mainly focused on constructs for expressing information about classes and individuals, and exhibited some weakness regarding expressiveness for properties. OWL 2 offers new constructs for expressing additional restrictions on properties, new characteristics of properties, incompatibility of properties, property chains and keys.
OWL 1 does not allow defining subclasses of objects that are related to themselves by a given property, for example the subclass of processes that auto-:regulate themselves. This local reflexivity is useful in many applications, particularly when global reflexivity does not hold for a property in general, but local reflexivity holds for a subset. The OWL 2 construct ObjectHasSelf allows asserting local reflexivity. Self restrictions are part of SROIQ [SROIQ], an extension of the description logic underlying OWL-DL (SHOIN) designed to provide additions requested by users, while not affecting its decidability and practicability. SROIQ has been supported by several reasoners, including FACT++ [TOOLS].
A class expression defined using an ObjectHasSelf restriction denotes the class of all objects that are related to themselves via the given object property. Normative Syntax Direct Semantics RDF-Based Semantics
ObjectHasSelf (OPE) where OPE is an object property expression.
SubClassOf( :AutoRegulatingProcess ObjectHasSelf( :regulate ) ) | Auto-regulating processes regulate themselves. |
SubClassOf( :Auto-Phosphorylating-Kinase ObjectHasSelf( :phosphorylate )) (UC#20) | Auto-Phosphorylating-Kinases phosphorylate themselves. |
While OWL 1 allows defining restrictions on the number of instances of a property, e.g. for defining persons that have at least three children, it does not provide means to restrain the class or data range of its instances (qualified cardinality restrictions), e.g. for specifying the class of persons that have at least three children who are girls. In OWL 2, both qualified or unqualified cardinality restrictions are possible. Qualified object and data cardinality are present in SROIQ and have been successfully implemented. They are already supported by various tools and reasoners (e.g.; Protégé 4, FACT++, PELLET, RACER, KAON2) [TOOLS] [OWL API].
ObjectMinCardinality, ObjectMaxCardinality, and ObjectExactCardinality (DataMinCardinality, DataMaxCardinality, and DataExactCardinality) allow asserting minimum, maximum or exact qualified cardinality restrictions, object (respectively, data) properties. Normative Syntax Direct Semantics RDF-Based Semantics
ObjectMinCardinality ( n OPE [ CE ] ) where n is a non negative integer, OPE an object property expression, and [ CE ] 0 or one class expression.
ObjectMaxCardinality ( n OPE [ CE ] ) where n is a non negative integer, OPE an object property expression, and [ CE ] 0 or one class expression.
ObjectExactCardinality ( n OPE [ CE ] ) where n is a non negative integer, OPE an object property expression, and [ CE ] 0 or one class expression.
ObjectMinCardinality( 5 :hasDirectPart owl:Thing ) | Class of objects having at least 5 direct part. |
ObjectExactCardinality( 1 :hasDirectPart :FrontalLobe ) (UC#1) | Class of objects having exactly one direct part of type frontal lobe. |
In OWL 1 it is possible to express that a Brain Hemisphere has at least 5 direct parts but not that it has exactly one direct part of each specific type frontal, parietal, temporal, occipital, limbic lobe, as needed in UC#1. In OWL 2 both statements are possible like in the examples above.
ObjectMaxCardinality( 3 :boundedTo :Hydrogen) (UC#3) | Class of objects bounded to at most three different :Hydrogen |
ObjectMaxCardinality( 5 :hasPart :Door ) (UC#4) | Class of objects having at most 5 :Door |
ObjectExactCardinality( 2 :hasPart :RearDoor ) (UC#4) | Class of objects having exactly 2 :RearDoor |
DataMinCardinality ( n DPE [ DR ] ) where n is a non negative integer, DPE a data property expression, and [ DR ] 0 or one or one data range.
DataMaxCardinality ( n DPE [ DR ] ) where n is a non negative integer, DPE a data property expression, and [ DR ] 0 or one or one data range.
DataExactCardinality ( n DPE [ DR ] ) where n is a non negative integer, DPE a data property expression, and [ DR ] 0 or one or one data range.
DataMaxCardinality( 1 :hasSSN ) | Each individual has at most one Social Security Number |
Use Case #1 Use Case #2 Use Case #3, Use Case #4 Use Case #8
While OWL 1 allows to assert that an object property is symmetric or transitive, it is impossible to assert that the property is reflexive, irreflexive or asymmetric.
The OWL 2 construct ReflexiveObjectProperty allows asserting that an object property expression is globally reflexive - that is the property holds for all the individuals. Normative Syntax Direct Semantics RDF-Based_Semantics
ReflexiveObjectProperty ( { A } OPE ) where OPE is an object property expression and { A } zero or more annotations.
ReflexiveObjectProperty( :sameBloodGroup ) (UC#9) | Everything has the same blood group as himself. |
ReflexiveObjectProperty( :part_of ) (UC#2) | Everything is :part_of itself |
Note: there are different interpretations of the mereological relations. For example OBO (Use Case #5) states that :part_of is reflexive while the mereological relation anatomicalPartOf between anatomical entities is asserted to be irreflexive in Use Case #1.
The OWL 2 construct IrreflexiveObjectProperty allows asserting that an object property expression is irreflexive - that is the property does not hold for any individual. Normative Syntax Direct Semantics RDF-Based_Semantics
IrreflexiveObjectProperty ( { A } OPE ) where OPE is an object property expression and { A } zero or more annotations.
IrreflexiveObjectProperty( :proper_part_of ) (UC#5) | Nothing can be a proper part of itself. |
IrreflexiveObjectProperty( :boundedBy ) (UC#1) | Nothing can be bounded by itself. |
IrreflexiveObjectProperty( :flowsInto )(UC#6) | Nothing can flow into itself. |
Note: the given examples corresponds to the statements about mereological and topological properties anatomicalPartOf :boundedBy in the given Use Cases, e.g.; Use Case #1. But other applications may use these terms for properties with different characteristics.
The OWL 2 construct AsymmetricObjectProperty allows asserting that an object property expression is asymmetric - that is if the property expression OPE holds between the individuals x and y, then it cannot hold between y and x. Normative Syntax Direct Semantics RDF-Based_Semantics
AsymmetricObjectProperty ( { A } OPE ) where OPE is an object property expression and { A } zero or more annotations.
AsymmetricObjectProperty( :proper_part_of )(UC#8) | The property :proper_part_of is asymmetric. |
These constructs are part of SROIQ and have been implemented in SROIQ reasoners, or can be easily added to SROIQ.
Use Case #5 Use Case #6 Use Case #8
Note: Many use cases illustrate the desirability for Reflexivity, Irreflexivity, Asymmetry or Local Relexivity. The usefulness of these features was explicitly mentioned by the Health Care and Life Sciences interest group in their last call comment. The Semantic Web Deployment Working Group (SWD) also explicitly mentioned the potential usefulness of reflexivity and asymmetry e.g., for specifying application-specific specializations of SKOS semantic relations (see comment from the SWD). For example, in mereology, the partOf relation is defined to be transitive, reflexive, and antisymmetric. Many applications, which describe complex structures, in life science or systems engineering, require extensive use of part-whole relations, axiomatized in that way. Other relations encountered in ontology modeling require such axiomatizations as well, possibly with different characteristics (e.g., [OBO] [RO]). Examples include proper part of and locative relations (typically transitive and irreflexive), causal relations (typically transitive and irreflexive) and membership relations (typically irreflexive). Another example is the skos:broader relationship. SKOS specification [SKOS] makes no statements regarding the reflexivity or irreflexivity of skos:broader to allow both interpretations: for example it should be considered reflexive for a direct translation of an inferred OWL subclass hierarchy, but irreflexive for most thesauri or classification schemes. OWL 2 reflexivity/irreflexivity allows to add one of these two features on demand. Self restrictions are even more fine grained, allowing to state that skos:broader should only be locally reflexive or irreflexive w.r.t. skos:Concept (via a SubClassOf axiom ) .
While OWL 1 provides means to state the disjointness of classes, it is impossible to state that properties are disjoint.
The OWL 2 construct DisjointObjectProperties allows asserting that several object properties are pairwise incompatible (exclusive); that is, two individuals cannot be connected by both two different properties of the set. This construct is part of SROIQ and has been implemented in SROIQ reasoners. Normative Syntax Direct Semantics RDF-Based Semantics
DisjointObjectProperties( { A } OPE1 ... OPEn ) where OPEi, 1 ≤ i ≤ n are object property expressions and { A } zero or more annotations.
DisjointObjectProperties( :connectedTo :contiguousTo ) (UC#1) | :connectedTo and :contiguousTo are exclusive properties. |
Note: Use Case #1 defines two anatomical entities related by a third anatomical entity as connected, while when they are adjacent, they are said contiguous.
DisjointDataProperties allows asserting that several data properties are pairwise incompatible (exclusive). Normative Syntax Direct Semantics RDF-Based Semantics
DisjointDataProperties( { A } DPE1 ... DPEn ) where DPEi, 1 ≤ i ≤ n are data property expressions and { A } zero or more annotations.
DisjointDataProperties( :startTime :endTime ) | Start time of something, e.g. surgery, must be different from its end time. |
Use Case #1 Use Case #2 Use Case #3
OWL 1 does not provide means to define properties as a composition of other properties, like uncle could be defined, hence, it is not possible to propagate a property (e.g.; is:locatedIn) along another property (e.g.; partOf). The OWL 2 construct ObjectPropertyChain in a SubObjectPropertyOf axiom allows defining a property as the composition of several properties. Such axioms are known as complex role inclusions in SROIQ, and if they meet certain regularity conditions have been implemented in SROIQ reasoners. Normative Syntax Direct Semantics RDF-Based Semantics
An axiom SubObjectPropertyOf ( ObjectPropertyChain( OPE1 ... OPEn ) OPE) states that any individual x connected with an individual y by a chain of object properties expressions OPE1, ..., OPEn is necessary connected with y by the object property OPE.
SubObjectPropertyOf ( { A } ObjectPropertyChain( OPE1 ... OPEn ) OPE ) where OPEi, 1 ≤ i ≤ n are object property and { A } zero or more annotations.
SubPropertyOf( ObjectPropertyChain( :locatedIn :partOf ) :locatedIn ) (UC#7) | If x is located in y and y is part of z then x is located in z, for example a disease located in a part is located in the whole. |
Use Case #1 Use Case #5 Use Case #7 Use Case #8
OWL 1 does not provide means to define keys. However, keys are clearly of vital importance to many applications in order to uniquely identify individuals of a given class by values of (a set of) key properties. The OWL 2 construct HasKey allows defining keys for a given class. While in OWL 2 key properties are not required to be functional or total properties, it is always possible to separately state that a key property is functional, if desired. Keys in OWL 2 are a form of DL Safe rule [DL-Safe]. They have been implemented in KAON2 and can be added to other reasoners.
An HasKey axiom states that each named instance of a class is uniquely identified by a (data or object) property or a set of properties - that is, if two named instances of the class coincide on values for each of key properties, then these two individuals are the same. Normative Syntax Direct Semantics RDF-Based Semantics
HasKey( { A } CE ( OPE1 ... 0PEm ) ( DPE1 ... DPEm ) ) where CE is a class expression, OPEi , 1 ≤ i ≤ m are object property expressions DPEj, 1 ≤ j ≤ n are data property expression and { A } zero or more annotations.
HasKey( :RegisteredPatient :hasWaitingListN ) | Each registered patient [on the ABM national organ waiting list], is uniquely identified by his waiting list number (UC#9) |
ClassAssertion( :RegisteredPatient :ThisPatient ) | :ThisPatient is a :RegisteredPatient. |
DataPropertyAssertion( :hasWaitingListN :ThisPatient "123-45-6789" ) | :ThisPatient has the the waiting list number "123-45-6789". |
In this example, since :hasWaitingListN is a key for the class :RegisteredPatient, the number "123-45-6789" uniquely identifies :ThisPatient. The axiom HasKey( :RegisteredPatient :hasWaitingListN ) only states that two different patients who have got a number assigned cannot have the same number on the waiting list: if the values of :hasWaitingListN were the same for two named instances of the class :RegisteredPatient, these two individuals would be equal. An HasKey axiom is similar to an InverseFunctionalProperty axiom, the main difference being that it is applicable only to individuals that are explicitly named. It does not state that each registered patient has at least or at most one value of :hasWaitingListN. The inference that each patient who has a :hasWaitingListN belongs to the class :RegisteredPatient cannot be drawn.
HasKey( :Transplantation :donorId :recipientId :ofOrgan ) | Each Transplantation is uniquely identified by a donor, a recipient, and an organ (UC#9) |
A set of several properties is needed to identify a transplantation: indeed a donor may provide several organs to a single person, e.g., a kidney and a liver, or the same organ to two recipients, e.g., a kidney, or different organs to different recipients.
Use Case #2 Use Case #7 Use Case #9
OWL 1 provides support for only integers and strings as datatypes and does not support any subsets of these datatypes. For example, one could state that every person has an age which is an integer but not to restrain the range of that datatype to say that adults have an age greater than 18. OWL 2 provides new capabilities for datatypes, supporting a richer set of datatypes and restrictions of datatypes by facets, as in XML Schema.
OWL 2 datatypes include a) various kinds of numbers, adding support for a wider range of XML Schema Datatypes (double, float, decimal, positiveInteger, etc.) and providing its own datatypes, e.g., owl:real; b) strings with (or without) a Language Tag (using the rdf:PlainLiteral datatype); and c) boolean values, binary data, IRIs, time instants, etc.
DatatypeRestriction makes it also possible to specify restrictions on datatypes by means of constraining facets that constrain the range of values allowed for a given datataype, by length (for strings) e.g. minLength, maxLength, and minimum/maximum value, e.g. minInclusive, maxInclusive. Extended datatypes are allowed in many description logics and are supported by several reasoners. Normative Syntax Direct Semantics RDF-Based Semantics
DatatypeRestriction( DT F1 lt1 ... Fn ltn ) where DT is a unary datatype, 1 ≤ i ≤ n ⟨ Fi lti ⟩ are pairs of constraining facet and literal.
DatatypeRestriction(xsd:integer minInclusive 18) (UC#9) | new datatype with a lower bound of 18 on the XML Schema datatype xsd:integer |
This datatype is needed for example to define patients under 18 (child) who depend on pediatric services at hospital while over 18 (adult) depend on adult services.
Use Case #9 Use Case #11 Use Case #12 Use Case #18 Use Case #19
In OWL 1 it is not possible to represent relationships between values for one object, e.g., a square is a rectangle whose length equals its width. N-ary datatype support was not added to OWL 2 because there were issues on just what support should be added. However, OWL 2 includes syntactic constructs needed for n-ary datatypes, to provide a common basis for extensions. The Data Range Extension: Linear Equations Note proposes an extension to OWL 2 for defining data ranges in terms of linear (in)equations with rational coefficients.
DataAllValuesFrom ( :admissionTemperature :currentTemperature DataComparison(Arguments(x y) leq( x y )))) (UC#11) | individuals whose :admissionTemperature is inferior to :currentTemperature. |
OWL 1 allows to define a new class by a class description but it does not offer means to explicitely define a new datatype. For ease of writing, reading, maintaining ontologies, OWL 2 provides a new construct to define datatypes that occur a couple of times in an ontology (like adult age, legal driving age etc.) .
DatatypeDefinition allows to explicitely name a new datatype. Normative Syntax Direct Semantics RDF-Based Semantics
DatatypeDefinition ( { A } DT DR ), where DT is a datatype, DR a data range and { A } zero or more annotations.
DatatypeDefinition( :adultAge DatatypeRestriction(xsd:integer minInclusive 18)(UC#9) | An adult age is defined as an integer with a lower bound of 18 on the XML Schema datatype xsd:integer |
While OWL 1 allows to construct a new class by combining classes, it does not provide means to construct a new datatype by combining other ones. In OWL 2 it is possible to define new datatypes by combination of datatypes.
In OWL 2, combinations of data ranges can be constructed using intersection (DataIntersectionOf), union ( DataUnionOf), and complement (DataComplementOf) of data ranges.
DataIntersectionOf ( { A } DR1 ... DRn ) where DRi where 1 ≤ i ≤ n, are data ranges and { A } zero or more annotations.
DataUnionOf ( { A } DR1 ... DRn ) where DRi where 1 ≤ i ≤ n, are data ranges and { A } zero or more annotations.
DataComplementOf ( { A } DR) where DRi where 1 ≤ i ≤ n, are data ranges and { A } zero or more annotations.
DataComplementOf( :adultAge ) | This data range contains all literals that are not a positive integer greater or equal to 18 |
OWL 1 DL required a strict separation between the names of, e.g., classes and individuals. OWL 2 DL relaxes this separation somewhat to allow different uses of the same term, e.g., Eagle, to be used for both a class, the class of all Eagles, and an individual, the individual representing the species Eagle belonging to the (meta)class of all plant and animal species. However OWL 2 DL still imposes certain restrictions: it requires that a name cannot be used for both a class and a datatype and that a name can only be used for one kind of property. The OWL 2 Direct Semantics treats the different uses of the same name as completely separate, as is required in DL reasoners.
Declaration( Class( :Person ) ) (UC#13) (1) | :Person is declared to be a class |
ClassAssertion( :Service :s1 ) (2) | :s1 is an individual of :Service. |
ObjectPropertyAssertion( :hasInput :s1 :Person )(3) | the individual :s1 is connected by :hasInput to the individual :Person. |
The same term ':Person' denotes both a class in (1) and an individual in (3). This is possible in OWL 2 thanks to punning (Class ↔ Individual).
Declaration( Class( :Deprecated_Properties ) ) (UC#14)(1) | :Deprecated_Properties is declared to be a Class |
Declaration( ObjectProperty( :is_located_in ) ) (2) | :is_located_in is declared to be an ObjectProperty |
ClassAssertion( :Deprecated_Properties :is_located_in ) (3) | :is_located_in is an individual of :Deprecated_Properties. |
The same term 'is_located_in' denotes both a property (2) and an individual (3). This is possible in OWL 2 thanks to punning (Property ↔ Individual).
Use Case #14 could also be represented using an annotation deprecated property on the property :is_located_in, which might be more intuitive or better modeling.
Declaration( Class( :Person ) ) Declaration( Class( :Company ) ) (UC#15) (1) | :Person and :Company are declared to be classes. |
SubClassOf ( :PersonCompany :Association) (2) | :PersonCompany denotes a subclass of an :Association used to model an association between classes :Person and Company as a class. |
ObjectPropertyDomain( :PersonCompany :Person )(3) | The domain of the property :PersonCompany is :Person. |
ObjectPropertyRange( :PersonCompany :Company )(4) | The range of the property :PersonCompany is :Company. |
The same term :PersonCompany denotes both a class (2) and an ObjectProperty(3 ; 4). This is possible in OWL 2 thanks to punning (Class ↔ ObjectProperty).
Use Case #12 Use Case #13 Use Case #14 Use Case #15
OWL 1 allows extralogical information, such as a label or a comment, to each ontology entity, but did not allow annotations on axioms, e.g., with information about who asserted an axiom or when. OWL 2 allows to annotate ontologies, entities, anonymous individuals, axioms, and annotations themselves.
OWL 2 provides the construct AnnotationAssertion for annotations of ontology entities (such as classes or properties) and anonymous individuals. These annotations carry no semantics in the OWL 2 Direct Semantics, allowing the direct use of DL reasoners.
AnnotationAssertion( { A } AP s v ) where AP is an annotation property, s is an IRI or an anonymous individual, v is a literal, an IRI, or an anonymous individual and {A} are 0 or more annotations (of the annotation assertion)
AnnotationAssertion (rdfs:label CARO:0000003 "anatomical structure" ) (UC#5) | The IRI CARO:0000003 of CARO ontology is annotated with the rdfs:label annotation property by the human-readable label "anatomical structure". |
AnnotationAssertion (FMA:UWDAID FMA:Heart 7088 ) (UC#2) | The IRI FMA:Heart of the FMA is annotated with the annotation property FMA:UWDAID by the integer 7088 (its FMA Id). |
OWL 2 provides the construct Annotation for annotations of axioms and ontologies. It can also be used for annotations of annotations themselves. These annotations carry no semantics in the OWL 2 Direct Semantics, allowing the direct use of DL reasoners.
Annotation( {A} AP v ) where AP is an annotation property, v is a literal, an IRI, or an anonymous individual and {A} are 0 or more annotations.
SubClassOf( Annotation( rdfs:comment "Middle lobe of lungs are necessary right lobe since left lung do not have middle lobe.") :MiddleLobe :RightLobe ) (UC#2) | The comment "Middle lobe of lungs are necessary right lobe" is an annotation of the subclass axiom which explains why :MiddleLobe is a subclass of :RightLobe. |
Use Case #2 Use Case #5 Use Case #12 Use Case #19
Annotation properties can be given domains (AnnotationPropertyDomain) and ranges (AnnotationPropertyRange) and participate in an annotation property hierarchy (SubAnnotationPropertyOf). These special axioms have no semantic meaning in the OWL 2 Direct Semantics, but carry the standard RDF semantics in the RDF-based Semantics (via their mapping to RDF vocabulary).
SubAnnotationPropertyOf( { A } AP1 AP2 ) where AP 1 and AP2 are annotation properties, and {A} are 0 or more annotations.
SubAnnotationPropertyOf (:narrow_synonym :synonym ) (UC#5) | The property :narrow synonym is a subproperty of :synonym.
OBO ontologies, in particular Gene Ontology, distinguish different kinds of synonyms: exact_synonym, narrow_synonym, broad_synonym. |
AnnotationPropertyDomain ( FMA:UWDAID FMA:AnatomicalEntity )(UC#2) | Only FMA: AnatomicalEntity can have an FMA:UWDAID (that is an FMA ID) |
AnnotationPropertyRange ( FMA:UWDAID xsd:positiveInteger ) (UC#2) | The ID of an FMA: AnatomicalEntity is a positive integer |
In OWL 1, an entity such as a class or an object property could be used in an ontology without any prior announcement, so there was no way of ensuring that entity names matched in different axioms. In practice, if an entity name was mistyped in an axiom, there was no way of catching the error. In OWL 2 a declaration signals that an entity is part of the vocabulary of an ontology. A declaration also associates an entity category (class, datatype, object property, data property, annotation property, or individual) to the declared entity. Declarations are not always necessary (see Syntax). Declarations do not affect the meaning of OWL 2 ontologies and thus do not have an effect on reasoning. Implementations may choose to check that every name is declared if desired.
Declaration( A E ) where A is an annotation and E an entity.
The following declarations state that the IRI :Person is used as a class and the IRI :Peter as an individual.
Declaration( Class( :Person ) ) (UC#17) | :Person is declared to be a class |
Declaration( NamedIndividual( :Peter ) ) | :Peter is declared to be an individual |
Declaration( Class( CARO:0000003 ) ) (UC#5) | CARO:0000003 is declared to be a class |
While OWL 1 had only top and bottom predefined entities for classes, the two classes owl:Thing and owl:Nothing, OWL 2 provides in addition top and bottom object and data properties, namely owl:topObjectProperty, owl:bottomObjectProperty, owl:topDataProperty, and owl:bottomDataProperty.
Uniform Resource Locators (URIs) were used in OWL 1 to identify classes, ontologies, and other ontology elements. URIs are strings formed using a subset of ASCII. This was quite limiting, particularly with respect to non-English language names as ASCII only included letters from the English alphabet. To support broad international needs, OWL 2 uses Internationalized Resource Identifiers (IRIs) [RFC3987] for identifying ontologies and their elements.
In OWL 1 ontologies can be stored as Semantic Web documents, and ontologies can import other ontologies. OWL 2 makes it clear that this importing is by the location of the ontology document.
OWL 2 also clears up the relationship between an ontology name (IRI) and its location and, in response to several requests, provides a simple versioning mechanism by means of version names (IRIs). Each OWL 2 ontology may have an ontology IRI, which is used to identify the ontology. An OWL 2 ontology may also have a version IRI, which is used to identify a particular version of the ontology.
An OWL 2 ontology is stored at its version IRI and one of the ontologies that have the ontology IRI is stored at the ontology IRI as well. If it does not matter which of the versions is desired then importing can use the ontology IRI, but if a particular version is desired then the version IRI is used.
Ontology ( [O [ V ]] { Import ( O' ) } { A } { AX } ) where [O] and [V] are 0 or one ontology and version IRIs, {Import(O')} are 0 or more imports, O' is an ontology IRI, {A} are 0 or more annotations and {AX} are 0 or more axioms.
The ontology is stored at its version IRI V. One of the versions using the ontology IRI O should also be stored at O; this is considered to be the current version of the ontology.
Some other changes have been introduced in the OWL 2 syntax, but these are not changes in the expressive power with respect to OWL 1.
In OWL 1, anonymous individuals were introduced as individuals without identifiers.
Individual(value( :city :Paris ) value( :region :IleDeFrance )) | This axiom does not contain an individual name for the address, so the introduced individual is an anonymous individual. |
In contrast, in OWL 2 anonymous individuals are identified using node IDs.
ObjectPropertyAssertion( :city _:a1 :Paris ) (UC#9) | This axiom introduces an explicit anonymous individual _:a1 for this unknown address which is in the city of Paris ... |
ObjectPropertyAssertion( :region _:a1 :IleDeFrance ) | and in the region of IleDeFrance |
This change was mainly motivated by a requirement related to the new functional syntax. While patterns using blank nodes could be specified without node IDs because of the (nested) frame structure of Abstract syntax constructions, this cannot be done in the functional syntax. There is no change in expressive capability. Nothing changed on the RDF side, and the treatment of anonymous individuals in OWL 2 is fully backwards compatible with that in OWL 1. In the example above, the "_:a1" simply represents a blank node in the RDF graph.
In OWL 1, all properties are atomic, but it is possible to assert that some object property is the inverse of another property. In OWL 2, property expressions such as ObjectInverseOf( P ) can be directly used in class expressions. This ease of writing ontologies spares from having to name an inverse.
An inverse object property expression ObjectInverseOf( P ) connects an individual a1 with a2 if and only if the object property P connects a2 with a1.
ObjectInverseOf( P ) where P is an object property.
ObjectInverseOf( :partOf ) | this expression represents the inverse property of :partOf |
An inverse object properties axiom InverseObjectProperties( OPE1 OPE2 ) states that two properties are inverse.
InverseObjectProperties( OPE1 OPE2 ) where OPE1 and OPE2 are object property expressions.
The following is an example of an OWL 1 inverse property axiom.
ObjectProperty( :hasPart inverse :partOf ) | :hasPart has an inverse property named :partOf. |
This can be represented in OWL 2 by the following axiom stating that :hasPart is an inverse of :partOf.
EquivalentProperties( :hasPart ObjectInverseOf( :partOf ) ) | :partOf is the same as the inverse property of :hasPart. |
As such axioms are quite common, OWL 2 provides the following syntactic shortcut as well.
InverseObjectProperties( :hasPart :partOf ) | :hasPart and :partOf are inverse properties. |
OWL 1 defined two major dialects, OWL DL and OWL Full, and one syntactic subset (OWL Lite). However, it turned out that it was not sufficient to address needs later enlightened by OWL ontologies and deployment.
OWL 2 defines three different profiles : OWL 2 EL, OWL 2 QL, and OWL 2 RL, sublanguages (syntactic subsets) of OWL 2 with useful computational properties (e.g., reasoning complexity in range of LOGSPACE to PTIME) or implementation possibilities (e.g., fragments implementable using RDBs). They are briefly described below, for an extensive description, see Profile.
OWL 2 EL captures expressive power used by many large-scale ontologies, e.g.; SNOMED CT, the NCI thesaurus;
OWL 2 EL places several syntactical restrictions on the language:
In return, respecting OWL 2 EL restrictions offers computational guarantees while not sacrificing too much expressive power OWL 2 EL is a language for which reasoning, including query answering, is known to be worst-case polynomial. It is related to the theory of [EL++] [EL++ Update]. OWL 2 EL enables efficient implementations , E.g., CEL [CEL] is the first reasoner for the description logic EL+; CEL implements a polynomial-time algorithm.
OWL 2 QL captures expressive power of simple ontologies like thesauri, and (most of) expressive power of ER/UML schemas;
OWL 2 QL places several syntactical restrictions on the language:
In return, respecting OWL 2 QL restrictions offers several benefits:
OWL 2 QL is a language for which reasoning, including query answering, is known to be worst case logspace (same as DB). OWL 2 QL can be implemented on top of standard relational database: the data can be left in the DBs, and query answering simply uses the ontology to rewrite the queries into equivalent SQL queries against the source DBs.
OWL 2 RL captures expressive power used by many large-scale ontologies, e.g.; SNOMED CT, the NCI thesaurus;
OWL 2 RL places several syntactical restrictions on the language:
In return, respecting OWL 2 RL restrictions offers several benefits:
OWL 2 RL allows for polynomial reasoning (consistency, classification, and instance checking) using rule-based technologies. It is related to the theory of DLP [DLP] and pD* [pD*]. OWL 2 RL can be implemented on top of rule extended DBMS, using rule-extended database technologies operating directly on RDF triples, E.g., Oracle’s OWL Prime implemented using forward chaining rules applied to triples of the RDF serialization in Oracle 11g (see ORACLE 11gR1 OWL Prime.) [OWL Prime].
Use Case #2 Use Case #3 Use Case #4 Use Case #8 Use Case #16
Ontology developers may consider which profile best suits their needs. The choice between the different profiles mainly depends on the expressiveness required by the application, the priority to reasoning on classes or data, the size and importance of scalability etc. For instance, those who look for
OWL 2 QL and OWL 2 RL are particularly suitable for applications where relatively lightweight ontologies are used with very large datasets, but while OWL 2 QL may be useful or necessary to access the data directly via relational queries (e.g., SQL), OWL 2 RL is useful or necessary to operate directly on data in the form of RDF triples.
While OWL 2 is fully backwards compatible with OWL 1, its conceptual design is slightly different, in particular regarding OWL 2 syntax.
There are various syntaxes available to serialize and exchange OWL 2 ontologies. The primary exchange syntax for OWL 2 is the RDF/XML Syntax [RDF/XML] which is the only syntax that MUST be supported by implementations. As explained below, the Functional Syntax main purpose is to specify the structure of the language. OWL/XML is an XML serialization motivated by the desire of better interoperability.
Normative syntax
The only required exchange syntax for OWL 2 ontologies is RDF/XML, as clearly stated in Section 2.1 of the Conformance and Test Cases document:
"Several syntaxes have been defined for OWL 2 ontology documents, some or all of which could be used by OWL 2 tools for exchanging documents. However, conformant OWL 2 tools that take ontology documents as input(s) must accept ontology documents using the RDF/XML serialization [OWL 2 Mapping to RDF Graphs], and conformant OWL 2 tools that publish ontology documents must, if possible, be able to publish them in the RDF/XML serialization if asked to do so (e.g., via HTTP content negotiation)."
Functional Syntax
The grammar of OWL 1 was defined by the Abstract Syntax (AS). The Functional Syntax (FS) plays a similar role for OWL 2: it defines the grammar of the language. But OWL 2 is specified not only in terms of a grammar but also of structure. Indeed, in addition to the Functional Syntax, OWL 2 has introduced the structural specification to precisely specify the conceptual structure of OWL 2 ontologies. The structural specification is defined using the Unified Modeling Language (UML). It uses a very simple form of UML diagrams that are expected to be easily understandable by readers familiar with object-oriented systems. The structural specification provides a normative abstract model for all the syntaxes of OWL 2, normative and non normative. It is independent of any concrete exchange syntaxes for OWL 2 ontologies. The Functional Syntax closely follows the structural specification. Clarity and readability of the syntax were important factors in the design of the Functional Syntax. The functional-style syntax has been introduced to allow for easy writing of OWL 2 axioms. Another benefit of the OWL 2 Functional Syntax is that it is closer to the syntax used in first order logic, which makes various specification issues as well as relating OWL 2 constructs to the general literature easier. It is one among several syntaxes for OWL 2 (e.g. RDF/XML, Manchestersyntax).
OWL 1 provides a frame-like syntax that allows several features of a class, property or individual to be defined in a single axiom at once. This may cause problems in practice. First, it bundles many different aspects of the given entity into a single axiom. While this may be convenient when ontologies are being designed, it is not convenient for manipulating them programmatically. In fact, most implementations of OWL 1 break such axioms apart into several "atomic" axioms, each dealing with only a single feature of the entity. However, this may cause problems with round-tripping, as the structure of the ontology may be destroyed in the process. Second, this type of axiom is often misinterpreted as a declaration and unique "definition" of the given entity. In OWL 1, however, entities may be used without being the subject of any such axiom, and there may be many such axioms relating to the same entity. OWL 2 has addressed these problems in several ways. First, the frame-like notation has been dropped in favor of a more fine-grained structure of axioms: each axiom describes just one feature of the given entity. Second, OWL 2 provides explicit declarations, and an explicit definition of the notion of structural consistency. Although OWL 2 is more verbose, this is not expected to lead to problems given that most OWL ontologies are created using ontology engineering tools.
The following is an example of an OWL 1 frame-like axiom.
ObjectProperty( :partOf ObjectInverseOf( :containedIn ) inverseFunctional transitive
Annotation( rdfs:comment "an object is a part of another object.")) | The property :partOf has an inverse property named containedIn, is an inverse functional and transitive property, and has the human-friendly comment "Specifies that an object is a part of another object." |
This can be represented in OWL 2 using the following axioms.
Declaration( ObjectProperty( :partOf ) ) | Declaration of the object property :partOf |
AnnotationAssertion( rdfs:comment :partOf "partOf means that an object is a part of another object." ) | This assertion provides a comment on the property :partOf which is "partOf means that an object is a part of another object." |
InverseObjectProperties( :partOf :containedIn ) | :partOf and :containedIn are inverse properties |
InverseFunctionalObjectProperty( :partOf ) | :partOf is an inverse functional property |
TransitiveObjectProperty( :partOf ) | :partOf is a transitive property |
Concerning the usability of the abstract syntax in OWL 2, if used as an exchange syntax then, OWL 1 ontologies written in AS may be input to OWL 2 tools and remain valid ontologies. But it should be emphasized that this is an issue of the tool providers: the only required exchange syntax for OWL 2 ontologies being RDF/XML, it is up to the tools to decide whether they would accept ontologies serialized in AS (or in FS, for that matter).
OWL/XML Syntax
The OWL Working Group has defined an XML syntax for OWL 2 based on XML Schema [XML Schema] called XML_Serialization OWL/XML. This syntax mirrors the structural specification of OWL 2 OWL 2 Structural Specification and Functional-Style Syntax. The XML syntax is motivated by the desire to support OWL users who want better interoperability with XML based tools and languages, for example WSDL, XSLT/XQuery/XPath, or schema aware editors. This is a standard format that OWL tool vendors may optionally support to provide access to the extensive tool chain available for XML schemas. Thus OWL tool developers and users using tools from these vendors will be be able to write XPath, XSLT, XQuery and CSS to work with OWL. This was very difficult to do using RDF/XML format which was the only XML format available for OWL 1. An additional benefit is that XML data can be exposed to RDF/OWL applications using GRDDL. The introduction of OWL/XML also provides a more comfortable avenue for the XML savvy user to understand OWL and makes OWL more appealing to those organizations and individuals who have made considerable investment in XML tooling and training. An open source toolkit is already available for conversion between this format and the required exchange form RDF/XML. Thus OWL/XML integrates with existing OWL 1 tooling and data, while not breaking interoperability among tools.
The overall structure of OWL 2 has not changed compared to OWL 1 — almost all the building blocks of OWL 2 were already present in OWL 1, albeit possibly under a different name.
The central role of RDF/XML as the only required exchange syntax for OWL 2 tools and the relationships between the Direct and RDF-Based semantics (i.e., the correspondence theorem) have not changed. More importantly, backwards compatibility with OWL 1 is complete, both syntactically and semantically.
This table provides a summary of the main new features with an example for each. It summarizes the relations between Use Cases (column 1), Features (column 2) and Examples (column 3). For each use case one specific feature, noted by name in bold, is selected. The corresponding example is given (column 3) and the reference from which it is issued appears in bold (column 4). The other features that the use case is concerned with are noted by numbers F1 to F15. (the choice done aims at conciliating an easy understandable illustration for each feature, a variety of domains, and real examples from papers available online).
Use Case | Feature(s) | Example | References |
---|---|---|---|
UC#1 | DisjointUnion F2 F5 F7 F8 F11 | DisjointUnion(:Lobe :FrontalLobe :ParietalLob :TemporalLobe :OccipitalLobe :LimbicLobe)
:Lobe is a disjoint union of :FrontalLobe :FrontalLobe :ParietalLob :TemporalLobe :OccipitalLobe :LimbicLobe | [MEDICAL REQ] |
UC#2 | DisjointClasses F1 F2 F5 F7 F9 | DisjointClasses( :LeftLung :RightLung )
a :Lung cannot be :LeftLung and :RightLung | [FMA] |
UC#20 | Local reflexivity | ObjectHasSelf( :phosphorylates)
class of all individuals that :phosphorylates themselves | [BIO] |
UC#4 | Qualified Cardinality F1 F15 | ExactCardinality( 2 :hasPart :RearDoor )
Class of objects having exactly 2 :RearDoor | [Auto] |
UC#5 | Asymmetric property F6 F8 F13 | AsymmetricProperty( :proper_part_of)
if p is a proper part of q then q cannot be a proper part of p | [OBO] |
UC#6 | Irreflexive property | IrreflexiveProperty( :flowsInto )
Nothing :flowsInto itself. | [Ordnance] |
UC#7 | Property chain F9 | SubPropertyOf( ObjectPropertyChain( :locatedIn :partOf ) :locatedIn )
anything :locatedIn a part is :locatedIn the whole, e.g. a disease. | [SNOMED REQ] |
UC#8 | Reflexive property F5 F8 | ReflexiveProperty( :partOf )
[Part Whole] argues about partOf as a reflexive property e.g. that a "car is a part of a car". | [Part Whole] |
UC#9 | Negative property F9 F10 | NegativePropertyAssertion( :hasAge :ThisPatient 5^^xsd:integer ) This patient is not five years old. | [Transplant Ontology] |
UC#10 | N-ary | AllValuesFrom( :testDate :enrollmentDate x > y + 30)
individuals whose :testDate is superior to their :enrollmentdate + 30. | [N-ary] |
UC#11 | N-ary F10 | AllValuesFrom( :admissionTemperature :currentTemperature x < y)
individuals whose :admissionTemperature is inferior to :currentTemperature. | [N-ary] |
UC#12 | Datatype restriction F5 F12 F13 | DatatypeRestriction(xsd:integer minInclusive 18)
new datatype with a lower bound of 18 on the XML Schema datatype xsd:integer, e.g. to describe the class Adult. | [Protege] |
UC#13 | metamodeling | Declaration( Class( :Person ) )
:Person is declared to be a class | [Web Service]
[Punning] |
UC#14 | metamodeling | Declaration( ObjectProperty( :is_located_in ) ) :is_located_in is declared to be an ObjectProperty | [Wiki]
[Punning] |
UC#15 | metamodeling | Declaration( Class( :Person ) ) Declaration( Class( :Company ) ) :Person and :Company are declared to be classes | [UML]
[Punning] |
UC#16 | Profiles | This Use Case motivates a profile e.g., OWL QL, where conjunctive query answering is implemented using conventional relational database systems | [Who reads?] |
UC#17 | Declaration | Declaration( Class( :Person ) ) :Person is declared to be a class. | [Syntax Problem] |
UC#18 | Datatype F5 | DatatypeRestriction( xsd:integer minInclusive "18000"^^xsd:integer maxExclusive "19600"^^xsd:integer ) The data range for atmosphere above 18000 [feet] and below 19600 [feet] | [VSTO] |
UC#19 | Annotation F10 | SubClassOf( rdfs:comment ("data generated by the LogParser using the ObserverLog") :LogInformation :Information) This is an example of an annotation of axioms | [NCAR] |
Legend:
F1 | F2 | F3 | F4 | F5 | F6 | F7 | F8 | F9 | F10 | F11 | F12 | F13 | F14 | F15 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Disjoint Union | Disjoint Classes | Negative Property Assertion | Local reflexivity | Qualified Cardinality | Reflexive, Irreflexive, Asymmetric | Disjoint properties | Property chain inclusion | Keys | Datatype restriction | N-ary datatype | Simple metamodeling capabilities | Extended annotations | Declarations | Profiles |
Use Case | Disjoint Union | Disjoint Classes | Negative property | Local reflexivity | Qualified Cardinality | Reflex., Irrefl., Asymm. | Disjoint properties | Property chain | Keys | Datatype restriction | N-ary datatype | Meta- modeling | Extend. annot. | Declarations | Profiles | Anonym. Individual |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
UC#1 | ||||||||||||||||
UC#2 | ||||||||||||||||
UC#3 | ||||||||||||||||
UC#4 | ||||||||||||||||
UC#5 | ||||||||||||||||
UC#6 | ||||||||||||||||
UC#7 | ||||||||||||||||
UC#8 | ||||||||||||||||
UC#9 | ||||||||||||||||
UC#10 | ||||||||||||||||
UC#11 | ||||||||||||||||
UC#12 | ||||||||||||||||
UC#13 | ||||||||||||||||
UC#14 | ||||||||||||||||
UC#15 | ||||||||||||||||
UC#16 | ||||||||||||||||
UC#17 | ||||||||||||||||
UC#18 | ||||||||||||||||
UC#19 |
The following list of Use Cases is not exhaustive. Use Cases included in that list are only some among many that motivated the OWL 2 new features - whatever user/implementor/theoretical reasons - that appear, at this time, accepted by the Working Group for OWL 2. Some other extensions pointed out in the papers (such as rules, default, etc.), possibly needed in the future, are indicated within brackets.
All use cases are presented using the following pattern: Overview, Features, Example for, References. The Overview only gives a general description of the use cases. Features lists several features required by the use case after the paper. Example points to a feature and short example which has been selected to illustrate a specific new feature of OWL 2. This same information can be seen in an abbreviated form in Table 3.2. For an easy access, References points to the related papers available online which URL is provided in the bibliography of the Appendix.
Overview: The system being developed concerns the preparation of surgical procedures in neurosurgery. Specifically, the aim is to assist a user in labelling the cortical gyri and sulci in the region surrounding a lesion whose resection is the primary objective. Providing anatomical landmarks, especially in eloquent cortex, is highly important for surgery. Brain image annotation is also useful for documentation of clinical cases, which then enables retrieval of similar cases for decision support in future procedures. A shared ontology of brain anatomy is also needed to integrate multiple distributed image sources indexed by anatomical features. This is useful for large-scale federated systems for statistical analysis of brain images of major brain pathologies.
Features: Disjoint Union, Disjoint Classes, Qualified Cardinality Restrictions, Disjoint Properties, Property chain inclusion axioms, [N-ary], [Rules]
Example for: Disjoint Union
References: [MEDICAL REQ] [Ontology with rules] [Brain Imaging ]
Overview: The Foundational Model of Anatomy (FMA) is the most comprehensive ontology of human 'canonical' anatomy. Anatomy plays a prominent role in biomedicine, and many biomedical ontologies and applications refer to anatomical entities. FMA is a tremendous resource in bioinformatics that facilitates sharing of information among applications that use anatomy knowledge. As its authors claim, the FMA is “ ... a reference ontology in biomedical informatics for correlating different views of anatomy, aligning existing and emerging ontologies in bioinformatics ...”. Anatomy, together with Gene and Disease reference ontologies constitute the backbone of the future Semantic Web for Life Sciences. But the FMA would benefit from new features of OWL to state that some properties are exclusive (e.g.; proper-part and bounded-by). Since many biomedical ontologies and applications refer to the FMA anatomical entities through cross-references, keys would also be useful.
Features: Disjoint Union, Disjoint Classes, Qualified Cardinality Restrictions, Disjoint Properties, Keys, Extended annotations, Profiles
Example for: Disjoint Classes
References: [FMA]
Overview: Functional groups describe the semantics of chemical reactivity in terms of atoms and their connectivity, which exhibit characteristic chemical behavior when present in a compound. In this use case the authors take a first step towards designing an OWL-DL ontology of functional groups for the classification of chemical compounds, and highlight the capabilities and limitations of OWL 1 and the proposed OWL 1.1 in terms of domain requirements. They also describe the application of expressive features in the design of an ontology of basic relations and how an upper level ontology can be used to guide the formulation of life science knowledge. They report on experiences to enhance existing ontologies so as to facilitate knowledge representation and question answering.
"Monocyclic and polycyclic ring structures are important parts of molecules that participate in several kinds of chemical reactions." A new OWL language feature such as qualified cardinality restriction, would be helpful to describe the number and types of functional groups.
Features: Disjoint Union, Disjoint Classes, Qualified Cardinality Restrictions, Profiles
Example for: Qualified Cardinality Restrictions
References: [Chemistry]
Overview: Large companies often store information and knowledge in multiple information systems using various models and formats. The key objective in this use case is the retrieval of relevant information from multiple data and knowledge sources for a large automotive company. For this application a language with a profile facilitating querying multiple databases and easy representation of Parts Library ISO 13584 Standard (PLIB) ontologies of Products, which is particularly used for e-business catalogues, would be helpful.
Features: Disjoint Union, Qualified Cardinality Restrictions, Profiles (OWL 2 QL)
Example for: Qualified Cardinality Restrictions
References: [Auto]
Overview: The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to facilitate the integration of biomedical data through their annotation using common controlled ontologies. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of OBO ontologies designed to be interoperable and to incorporate accurate representations of biological reality. Within that effort the OBO ontology of relations is designed to define a set of basic relations with their semantics. OBO qualifies each relation using characteristics of being transitive, symmetric, reflexive, anti-symmetric. More generally OBO format offers constructs such as is_reflexive, is_symmetric, is_cyclic, is_anti_symmetric, etc. that are used in the OBO obtologies. Converting OBO ontologies requires the new OWL 2 property axioms reflexive, irreflexive, asymmetric to map corresponding OBO constructs, otherwise they should be transformed into annotations.
Features: Local reflexivity, Reflexive, Irreflexive, Asymmetric, Property chain inclusion axioms, Declaration [Antisymmetric]
Example for: Asymmetric
References: [OBO] [RO] [OBO2OWL]
Overview: Ordnance Survey is Britain's National Mapping Agency. It currently maintains a continuously updated database of the topography of Great Britain. The database includes around 440 million man-made and natural landscape features. These features include everything from forests, roads and rivers down to individual houses, garden plots, and even pillar boxes. In addition to this topographic mapping, entire new layers of information are progressively being added to the database, such as aerial photographic images which precisely match the mapping; data providing the addresses of all properties; and integrated transport information. For topological and spatial relationships, and in many other places, “we need to be able to say whether a property is reflexive, irreflexive, asymmetric or antisymmetric in order to capture the true intentions of our axioms”.
Features: Reflexive, Irreflexive, Asymmetric, [Antisymmetric]
Example for: Irreflexive
References: [Ordnance]
Overview: The Systematized Nomenclature of Medicine, Clinical Terms (SNOMED CT) is a work of clinical terminology with broad coverage of the domain of health care, and it has been selected as a national standard for use in electronic health applications in many countries, including the U.S., U.K., Canada, Australia, Denmark, and others. SNOMED was originally published in 1976, while SNOMED CT became available in 2002 as a major expansion resulting from the merger of SNOMED RT with the U.K.'s Clinical Terms version 3. A major distinguishing feature differentiating it from prior editions is the use of description logic (DL) to define and organize codes and terms. Another major distinguishing feature of SNOMED is its size and complexity. With over 350,000 concept codes, each representing a different class, it is an order of magnitude larger than the next largest DL-based ontology of which we are aware.
Without property chain inclusion axioms, adoption of OWL by the SNOMED community would have required awkward workarounds with their attendant complications and complexities - effectively killing movement in that direction. With [them], we have a clear path to using OWL 2 for further development and integration with other biomedical ontologies. The required property chain inclusion axioms allow to encode inheritance of properties along another property, e.g., part-of, which is of utmost importance in anatomy. For example, with axioms such as has-location ◦ proper-part-of < has-location injury to finger can be inferred as injury to hand. As reported in [SNOMED EL+] by re-engineering SNOMED-CT in this way, the number of anatomical classes dropped from 54,380 to 18,125, and the time needed by the CEL reasoner [CEL] (version 0.94) from 900.15 seconds to 18.99 seconds.
Like the FMA, given the common use of cross-references between SNOMED and other biomedical ontologies via concepts ID, keys would be highly useful as well.
Features: Property chain inclusion axioms, Keys, Profiles (OWL 2 EL)
Example for: Property chain
References: [SNOMED REQ]
Overview: Representing part-whole relations is a very common issue for those developing ontologies for the Semantic Web. OWL does not provide any built-in primitives for part-whole relations (as it does for the subclass relation), but contains sufficient expressive power to capture most, but not all, of the common cases. The study of part-whole relations is an entire field in itself - "mereology" - this note is intended only to deal with straightforward cases for defining classes involving part-whole relations. Several extensions of whole needed for part-whole are discussed in this study, namely, needs of qualified cardinality restriction, reflexivity, propagation from parts to whole
Features: Qualified cardinality restriction, Reflexivity, Property chain inclusion
Example for: Reflexive
Note: according to the definition given in OBO, the whole is being considered as a part [Part Whole] but there are controversial opinions asserting that 'part of' is not reflexixe.
References: [Part Whole]
Overview: Allocation in France falls under the responsibility of the Agence de la biomedicine. It includes general rules such as: donor-recipient ABO blood group identity, unique registration on the national waiting list (a registration number is assigned at the registration of the waiting list which uniquely identifies a patient on the waiting list) and definition of some organ specific nation-wide allocation priorities. For each kidney recipient, minimal HLA matching and forbidden antigens can be specified. Pediatric recipients get a priority for pediatric donors. Kidneys are proposed by order of priority to (1) urgent patients, (2) patients with panel reactive antibodies level = 80% included in a specific acceptable antigen protocol or =1 HLA mismatch with the donor, then (3) zero mismatch patients, and (4) patients with low transplantation accessibility. Geographic criteria are involved: each region (of the transplant map), e.g., Ile de France, is supposed to take in charge only patients living in the region. This real-life application and allocation system show how distinguishing between adults and children has strong implications in health care: at hospital, patients under 18 (child) depend on pediatric services while over 18 (adult) depend on adult services; only children less than 16 years waiting for a transplant have a priority on the waiting list.
Features: Negative Property Assertion, Datatypes restriction, Keys
Example for: NegativePropertyAssertion
References: [Agence Biomedecine] [Transplant Ontology]
Overview: This use case is based on an ongoing W3C task force on Clinical Observations Interoperability where the goal is to enable re-use and sharing of clinical data created in healthcare delivery in the Clinical Trials context. In particular the first application chosen to demonstrate feasibility of the interoperability approach is that of patient recruitment. In this case, a sample set of clinical trial protocols available from http://www.clinicaltrials.gov each of which contains a list of eligibility (inclusion and exclusion criteria). These eligibility criteria are used for identify eligible patients and potentially form conditions in a SPARQL query or could be represented as OWL classes. They also need to be mapped as per the discussion in the use case above. A list of requirements based on an analysis of these clinical trial protocols is available from http://esw.w3.org/topic/HCLS/ClinicalObservationsInteroperability?action=AttachFile&do=get&target=FunctionalRequirements_v1.xls
In particular, one of the clinical trials requires that the enrolment date of a clinical trial participant be within 30 days after the patient has been started on a particular therapy. This motivated the need for N-ary datatypes with inequality expressions.
Features: [N-Ary]
Example for: N-ary Datatypes
Overview: [N-ary] presents many Use cases that would benefit from various datatype extensions
Features: Datatypes restriction, [N-Ary]
Example for: N-ary Datatypes
References: [N-ary]
Overview: [Protege] reported in 2005 on Protégé experiences with the development of OWL support, and on the experiences of the user community with OWL at that time. While the overall feedback from the community was positive, their experience suggested that there were considerable gaps between the user requirements, the expressivity of OWL, and users’ understanding of OWL. To summarize, based on their experiences, Protégé developers suggested a number of extensions to a future version of OWL namely, Integration of user-defined datatypes (esp. for numeric ranges), Qualified Cardinality Restrictions, Management of disjointness (owl:AllDisjoint), More flexible annotation properties (at least as best practices). This report underlined that one of the omissions in the OWL language that users complain about most often is poor representation of numeric expressions. Almost all groups, except for those developing traditional medical terminologies, sorely need to be able to express quantitative information. Typical examples include the length between 1mm and 2mm, age greater than 18 years, pressure in the range of 1030mb to 1035mb. Such range declarations are needed to classify individuals and to build class definitions such as Adult, and should therefore be supported by reasoners. User base points out that the current OWL datatype formalism is much too weak to support most real world applications and that many potential users therefore cannot adopt OWL. "The user communities anxiously await an extension to the OWL specification to represent user-defined datatypes with XML Schema facets such as xsd:minInclusive." It also points out some limitations related to annotations or metamodeling from an implementors perspective: "Despite the value of annotation properties, in OWL DL, properties that are declared as annotation properties are greatly limited in so far that they can neither have range or domain constraints, nor can they be arranged in sub-property hierarchies. This type of information about a property enables tools to control the values that annotation properties can acquire. Without range constraints it is difficult to provide the user with appropriate input widgets. In a similar sense, it is often helpful to declare meta-classes so that classes can be categorized into types and different interfaces be pro-vided for each type. Currently, using these features means that the ontology will be forced into OWL Full."
Features: Qualified cardinality restriction, Datatypes restriction, Annotations, metamodeling
Example for: Extra Datatypes
References: [Protege]
Overview: People often want to use a class to specify the value of some property. An example originating at the University of Karlsruhe [Web Service] is in service modeling. Services are modeled as instances of the :Service class. For each concrete service (i.e., for each instance of :Service), the users wanted to state what the input to the service is. Here is an example of a service description:
(1) :Service rdf:type owl:Class
(2) :Person rdf:type owl:Class
(3) s1 rdf:type :Service
(4) s1 :input :Person
s1 is an individual of the class :Service due to (1) and (3), and :Person is a class due to (2); hence, in (4) we have a relationship :input between an individual and a class. Hence, you need some kind of metamodeling to solve this problem. One way would be that the name 'Person' may refer both to Person as a class and as an individual denoting Person as a whole (Class ↔ Individual)
Features: metamodeling
Example for: Simple metamodeling
References: [Web Service] [Punning]
Overview: It can be useful to relate schema elements (classes/properties) with each other in order to capture pragmatic relationships between them. An example observed in applications of Semantic MediaWiki (a simple but widely used OWL-based semantic content management system with light-weight expressiveness) [OWL1.1 Wiki] is that users wish to relate schema elements to indicate domain-specific relationships, and generally to organize ontological vocabulary. Examples are statements such as:
These are merely pragmatic descriptions, and no logical relationship on schema-level is intended. However, in collaborative vocabulary creation, it is relevant that users can express such intended relationships. An important aspect of Semantic MediaWiki is that users can also query for semantic information, and this is currently realized as intended by punning. Semantic MediaWiki has already been extended by using off-the-shelf OWL reasoners, and it would be desirable if such systems would be able to deal with the use of punning in such simple cases; (Class/Property ↔ Individual)
Features: metamodeling
Example for: Simple metamodeling
Overview: The Unified Modeling Language (UML) includes a modeling element known as an Association Class which combines the features of a UML Class and a UML Association (UML's construct for defining class to class relationships Association). The Association Class, e.g., the association between classes Person and Company allows a modeler to define a relation as an association and reify it simultaneously. This is convenient when one wants to model attributes of relations themselves. One way to support such case might be Class and ObjectProperty punning (Class ↔ ObjectProperty).
Features: metamodeling
Example for: Simple metamodeling
Overview: Some life sciences application designer has been building a database federation scheme. The scheme involves designing an XML schema that describes the fields and values in a variety of databases, and associated query tools that, from a query interface, can write queries (in several variants of SQL) to databases that have relevant information. Those results are presented as a single integrated view. He hears that OWL and Semantic Web technologies might be a suitable technology for implementing the same functionality and making it available using Web standards, but doesn't know where to start. This application illustrates common needs of a wide community of users that would like to use their databases and can easily query them in a convivial way. This motivates a profile where conjunctive query answering is implemented using conventional relational database systems.
Features: Profiles (OWL 2 QL)
Example for: Profiles
References: [Who reads?]
Overview: A user adds an assertion to an ontology; however, he accidentally mistypes the IRI of an individual. It should be possible to detect this error by comparing the IRI of the individual in the axiom with the IRIs explicitly declared to be a part of the ontology: if the individual IRI has not been explicitly introduced as being in the ontology, the user should be given the opportunity to correct his error. Tools developers, such as those involved in the Protégé-OWL toolset architecture [TOOLS], have often expressed problems raised for e.g.; APIs [OWL API] due to lack of declarations. "The first problem is that OWL does not allow for explicit declarations—assertions that a certain class, property, or an individual exists in an ontology. This aspect of the OWL standard was often misinterpreted, which caused design errors in OWL APIs" [Syntax Problem].
Features: Declaration
Example for: Declaration
References: [Syntax Problem]
Overview: Numerous single discipline and multi-discipline virtual observatories (e.g., http://vsto.org , http://vmo.nasa.gov/ ) are beginning to use semantic technologies to provide data access and integration. A virtual observatory is a suite of software applications on a set of computers that allows users to uniformly find, access, and use resources (data, software, document, and image products and services using these) from a collection of distributed product repositories and service providers. A VO is a service that unites services and / or multiple repositories. from http://lwsde.gsfc.nasa.gov/VO_Framework_7_Jan_05.doc. Some Virtual Observatories are focusing quite heavily on provenance encoding at data ingest time (e.g., http://spcdis.hao.ucar.edu/ ). The Virtual Solar Terrestrial Observatory (VSTO) is a National Science Foundation and National Center for Atmospheric Research supported effort that allows researchers to find solar and solar-terrestrial data. It provides an ontology-enhanced interface to semantically-enhanced web services that help access a number of online repositories of scientific data. The background OWL ontology contains term descriptions for science terms including instruments, observatories, parameters, etc. Users essentially need to specify a description of the data they wish to retrieve which includes either a specific instrument class or a description of that class, a date range for the data taken, and the parameters. In order to specify that in relevant science terms, scientists need to be able to represent numerical ranges and comparisons going beyond the numeric support of OWL 1. The application also needs to expand to include spatial descriptions. It would use representational power if provided for spatial/geographic containment.
Requirements: Qualified Cardinality, Datatype restriction, [Defaults]
Example for: Datatype restriction
References: [VSTO]
Overview: In an effort to provide better search capabilities over meta information in addition to scientific data, the SPCDIS effort is providing infrastructure to capture declarative descriptions of scientific provenance information at data ingest time. The initial domain of the effort is solar coronal physics. This effort requires (among other things) extended annotations as well as datatype restriction.
Features: Datatype restriction, Extended Annotations
Example for: Extended annotation to attach annotations
References: [NCAR]
Overview: In Biochemistry, some biomolecules will chemical modify themselves in such a way that it has biologically important consequences. i) Protein kinases are enzymes capable of adding phosphate groups to certain amino acids found within target proteins. Some kinases, known as Auto-Phosphorylating Kinases, will add phosphate groups to certain target amino acids that are part of itself. ii) Ribozymes are catalytically active RNA molecules in which 7 natural types are known to cleave their own RNA sequences. Such cleavage may result in significant changes to viral replication, gene expression, and possibly the generation of different protein transcripts. Such catalytically active, self-cleaving RNA make up a subclass of ribozymes called Self-Cleaving Ribozymes. Such biochemical self-interaction can be captured by asserting local reflexivity of the properties.
Features: Local Reflexivity
Example for: Local reflexivity
References: [BIO]
The starting point for the development of OWL 2 was the OWL1.1 member submission, itself a result of user and developer feedback, and in particular of information gathered during the OWL Experiences and Directions (OWLED) Workshop series. The working group also considered postponed issues from the WebOnt Working Group.
This document has been produced by the OWL Working Group (see below), and its contents reflect extensive discussions within the Working Group as a whole. The editors extend special thanks to Elisa Kendall (Sandpiper Software), Peter F. Patel-Schneider (Bell Labs Research, Alcatel-Lucent) and Alan Ruttenberg (Science Commons) for their thorough reviews.
The regular attendees at meetings of the OWL Working Group at the time of publication of this document were: Jie Bao (RPI), Diego Calvanese (Free University of Bozen-Bolzano), Bernardo Cuenca Grau (Oxford University), Martin Dzbor (Open University), Achille Fokoue (IBM Corporation), Christine Golbreich (Université de Versailles St-Quentin and LIRMM), Sandro Hawke (W3C/MIT), Ivan Herman (W3C/ERCIM), Rinke Hoekstra (University of Amsterdam), Ian Horrocks (Oxford University), Elisa Kendall (Sandpiper Software), Markus Krötzsch (FZI), Carsten Lutz (Universität Bremen), Deborah L. McGuinness (RPI), Boris Motik (Oxford University), Jeff Pan (University of Aberdeen), Bijan Parsia (University of Manchester), Peter F. Patel-Schneider (Bell Labs Research, Alcatel-Lucent), Sebastian Rudolph (FZI), Alan Ruttenberg (Science Commons), Uli Sattler (University of Manchester), Michael Schneider (FZI), Mike Smith (Clark & Parsia), Evan Wallace (NIST), Zhe Wu (Oracle Corporation), and Antoine Zimmermann (DERI Galway). We would also like to thank past members of the working group: Jeremy Carroll, Jim Hendler, Vipul Kashyap.