New Features and Rationale

W3C Editor's Draft 28 November 2008

This version:

http://www.w3.org/2007/OWL/draft/ED-owl2-new-features-20081128/

Latest editor's draft:

http://www.w3.org/2007/OWL/draft/owl2-new-features/

Previous version:

http://www.w3.org/2007/OWL/draft/ED-owl2-new-features-20081126/ (color-coded diff)

Authors:

Christine Golbreich, University of Versailles Saint-Quentin

Evan K. Wallace, NIST

Contributors:

Vipul Kashyap, Partners Health System, Inc.

Elisa Kendall, Sandpiper Software

Deborah McGuinness, Rensselaer Polytechnic Institute

Bijan Parsia, The University of Manchester

Note: The complete list of contributors is being compiled and will be included in the next draft.

This document is also available in these non-normative formats: PDF version.

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Copyright © 2008 W3C^® (MIT, ERCIM, Keio), All Rights Reserved. W3C liability, trademark and document use rules apply.

Abstract

Status of this Document

May Be Superseded

This section describes the status of this document at the time of its publication. Other documents may supersede this document. A list of current W3C publications and the latest revision of this technical report can be found in the W3C technical reports index at http://www.w3.org/TR/.

Set of Documents

This document is being published as one of a set of 11 documents:

1. Structural Specification and Functional-Style Syntax
2. Direct Semantics
3. RDF-Based Semantics
4. Conformance and Test Cases
5. Mapping to RDF Graphs
6. XML Serialization
7. Profiles
8. Quick Reference Guide
9. New Features and Rationale (this document)
10. Manchester Syntax
11. rdf:text: A Datatype for Internationalized Text

Please Comment By 2008-12-01

The OWL Working Group seeks public feedback on these Working Drafts. Please send your comments to public-owl-comments@w3.org (public archive). If possible, please offer specific changes to the text that would address your concern. You may also wish to check the Wiki Version of this document for internal-review comments and changes being drafted which may address your concerns.

No Endorsement

Publication as a Working Draft does not imply endorsement by the W3C Membership. This is a draft document and may be updated, replaced or obsoleted by other documents at any time. It is inappropriate to cite this document as other than work in progress.

Patents

This document was produced by a group operating under the 5 February 2004 W3C Patent Policy. W3C maintains a public list of any patent disclosures made in connection with the deliverables of the group; that page also includes instructions for disclosing a patent. An individual who has actual knowledge of a patent which the individual believes contains Essential Claim(s) must disclose the information in accordance with section 6 of the W3C Patent Policy.

This document is an Overview of the main new features that have been added to OWL 2 and of their rationale. These features are based on real applications, user and tool developer experience, much of which was documented and discussed as part of the OWLED Workshop Series. For each new feature, the document informaly introduces its meaning, as specified in the [Direct Semantics] document, and also its syntax, as defined in the [Syntax] document. It provides an explanation of the fundamental reasons that have motivated the design of these features, from a theoretical and implementation perspective. Furthermore, each feature is illustrated by simple examples from various applications, which are referred in an Appendix including some Use Cases (among others) that motivated these extensions. Finally, two synthetic tables resume the links between the use cases, requirements, and examples provided for illustration of the new features.

• a brief sentence explaining why the new feature is required
• a feature description including: a short informal sentence defining its meaning - with a link to the Semantics document, followed by its syntax - with a link to the Syntax document - and simple illustrative example(s) issued from the Use Cases.
• the rationale from a theoretical and implementation perspectives that led to the changes to OWL 1 seen in OWL 2.
• links to related use cases of the bibliography in the Appendix.

In addition, Section 2.7 discusses structural differences from OWL 1 that manifest themselves in the abstract syntax of OWL 2.

Depending on his profile (e.g., user, theoretician, implementor) the reader can focus on what he is more interested in this document thanks to different buttons that allow to Hide and Show the feature Examples, Theory or Implementation perspectives, respectively.

2.1.1 F1: DisjointUnion

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. This feature has been required as a shortcoming given the common use of such satements in domain models.

Feature

DisjointUnion defines a class as the union of other classes, all of which are pair-wise disjoint. It is a shorthand for owl:disjointWith statements used in combination with owl:unionOf to define a complete superclass from a set of mutually disjoint subclasses. [Syntax] [Semantics]

Use cases

Use Case #1 Use Case #2 Use Case #3 Use Case #4

2.1.2 F2: DisjointClasses

While OWL 1 provides means to state that two subclasses are disjoint, stating that several subclasses are pair-wise disjoint cannot be done concisely. This shortand has been required given the common use of such disjointness statements by many applications.

Feature

DisjointClasses states that all classes from the set are pair-wise disjoint. It is a shorthand for several owl:disjointWith statements to define a set of mutually disjoint subclasses. [Syntax] [Semantics]

Use cases

Use Case #1 Use Case #2

2.1.3 F3: NegativeObjectPropertyAssertion NegativeDataPropertyAssertion

While OWL 1 provides means to assert values of a property for an individual, asserting that a property has not some values is impossible. This requires the ability to assert facts about an individual stating property values that it does not have.

Feature

OWL 2 provides the shortands NegativeObjectPropertyAssertion and NegativeDataPropertyAssertion for asserting negative facts. While an ObjectPropertyAssertion (resp. DataPropertyAssertion) axiom states that a given property holds for the given individuals, a NegativeObjectPropertyAssertion (resp. NegativeDataPropertyAssertion) axiom states that a given property does not hold for the given individuals. [Syntax] [Semantics]

Use cases

Use Case #9

2.2.1 F4: Self Restriction

OWL 1 does not allow to define subclasses of objects that are related to themselves by a given property, for example the subclass of processes that auto-regulate themselves. Expressing this requires local reflexivity.

Feature

OWL 2 allows to assert restrictions on object properties by means of the new construct HasSelf. The class expression ObjectHasSelf defined using an HasSelf restriction on an object property denotes the class of all objects that are related to themselves via the given object property. It can be viewed as a kind of local reflexivity quality of the object property. [Syntax] [Semantics]

Use cases

Use Case #5 Use Case #3

OWL 2 allows to assert minimum, maximum or exact qualified cardinality restrictions on object or data properties by means of the new constructs MinCardinality MaxCardinality ExactCardinality. A qualified cardinality restriction (QCR) defines a restriction on the number of instances of the property and on its class or data range. The addition that qualified cardinality restriction brings to the initial OWL 1 constructs for cardinality restrictions is to allow defining restrictions not only on the number of instances of the property but also on the class or data range of the instances. In OWL 2, both qualified or unqualified cardinality restrictions are possible. An unqualified cardinality restriction is simply equivalent to a qualified one where the restricting class is owl:Thing. [Syntax] [Semantics]

2.2.2.1 Object Property Cardinality Restrictions

The class expressions ObjectMinCardinality, ObjectMaxCardinality, and ObjectExactCardinality defined using a MinCardinality, MaxCardinality or ExactCardinality restriction on an object property denotes the set of objects that are connected via the given object property to at least, at most, or exactly the given number of individuals of the given class:

• Minimum Cardinality

• Maximum Cardinality

• Exact Cardinality

2.2.2.2 Data Property Cardinality Restrictions

• Minimum Cardinality

• Maximum Cardinality

• Exact Cardinality

Use cases

Use Case #1 Use Case #2 Use Case #3, Use Case #4 Use Case #8

2.2.3 F6: Reflexive, Irreflexive, Asymmetric

While OWL 1 allows to assert that an object property is symmetric or transitive, it is impossible to assert that it is reflexive, irreflexive or assymetric. In mereology, the partOf relation is defined to be transitive (if x is a part of y and y is a part of z, then x is a part of z), reflexive (every object is a part of itself), and antisymmetric (if an object has a part which in turn has part itself, then they are the same). Many applications, particularly those where it is necessary to describe complex structures such as life science applications, require extensive use of part-whole relations, axiomatized according to these principles. Similarly, other relations encountered in ontology modeling require similar axiomatizations, possibly with different sets of characteristics (see, 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). Thus as illustrated by many use cases new charactersitics of properties, Reflexivity, Irreflexivity, Asymmetry, is a strong requirement.

[Syntax] [Semantics]

[Syntax] [Semantics]

[Syntax] [Semantics]

see F4 Theoretical Perspective above

Use cases

Use Case #5 Use Case #6 Use Case #8

2.2.4 F7: Disjoint properties

While OWL 1 provides means to state the disjointness of classes, it is impossible to state that properties are disjoint, that is OWL 1 does not provide means to assert that if the same pair of individuals is related by two different properties among a given set of properties, then the ontology is inconsistent.

Feature

OWL 2 provides the new construct DisjointProperties for asserting that several properties are incompatible (exclusive).

A disjoint properties axiom takes a set of object properties and states that all properties from the set are pair-wise disjoint; that is, no pair of individuals can at the same time be connected by two different properties of the set. [Syntax] [Semantics]

Use cases

Use Case #1 Use Case #2 Use Case #3

2.2.5 F8: Property chain inclusion

OWL 1 does not provide means to define properties as a composition of other properties. OWL 1 enables only the propagation of values via one property in asserting it transitive, but does not provide means to propagate a property (e.g.; isLocatedIn) along another property (e.g.; partOf), which is a very common requirement, specially in Life Sciences. Users cannot define properties as a chain of relations (as hasUncle).

Feature

OWL 2 allows to chain several object properties by means of the new construct PropertyChain.

A propertyExpressionChain expression defines a chain between several object properties by means of PropertyChain. [Syntax] [Semantics]

When used together with SubPropertyOf, an expression defined by PropertyChain provides a means to represent some types of rules. It allows in particular to express the propagation of one property along another property, e.g.; the propagation of a property from parts to whole, which is a very common requirement, specially in Life Sciences. However, the ontology set of axioms (involving SubObjectPropertyOf axioms with Property Chains) must satisfy some "Global Restrictions" in order to prevent cyclic definitions and to keep the language decidable.

In short, an axiom SubPropertyOf( PropertyChain( p₁ ... p_n ) p ) states that if an individual x is connected with an individual y by a chain of object properties p₁, ..., p_n, then x is also connected with y by the object property p. Such axioms are also known as complex role inclusions [SROIQ]. The full exact syntax of Property chain inclusion axioms is more precisely the following:

Use Cases

Use Case #1 Use Case #5 Use Case #7 Use Case #8

2.2.6 F9: Key

OWL 1 does not provide means to define keys. However, keys, aka inverse functional datatype properties (but limited to named individuals), 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.

Feature

OWL 2 allows to define Database style keys for a given class by means of the new construct HasKey. A 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 all the values of key properties, then these two individuals are the same. [Syntax] [Semantics]

Use cases

Use Case #2 Use Case #7 Use Case #9

• OWL 2 datatypes allow representing a) various kinds of numbers, e.g., integer, real, double, float, decimal, both adding support of a wider range of XML Schema Datatypes (double, float, decimal, positiveInteger etc.) and providing special datatypes e.g., owl:real b) strings with (or without) a Language Tag (using the rdf:text datatype) c) Boolean values, Binary Data, URIs, Time Instants, etc. Syntax
• It is possible to specify restrictions on datatypes by means of facets that restrain the range of values allowed for a given unary datataype. Constraining facets used in a DatatypeRestriction are one of the allowed facets defined in the Datatype Maps section, e.g., length, minLength, maxLength, pattern, minInclusive, minExclusive, maxInclusive, maxExclusive. They are denoted by an URI. The restriction value used in a DatatypeRestriction is a literal listed in the Datatype Maps section. [Syntax] [Semantics]

Use Cases

Use Case #9 Use Case #11 Use Case #12 Use Case #18 Use Case #19

Use Case #10 Use Case #11

Use Cases

Use Case #12 Use Case #13 Use Case #14 Use Case #15

2.5.1 F13: Annotation

OWL 1 allows to associate (metalogical) information, such as a label or a comment, like a textual description of the entity, to each ontology entity. But it is also useful to associate metalogical information to axioms. For example, one might want to keep information about who asserted an axiom or when. Therefore, it has been required to extend annotations to allow for the annotation of both entities and axioms.

Feature

OWL 2 provides for annotations on ontologies, entities (such as a class or individual, including anonymous individuals), and axioms. Even annotations of annotations are possible. Annotations however, have no semantic meaning in OWL 2.

• An annotation value is either a literal (e.g., string, integer, or any other OWL datatype), a URI, or an anonymous individual.
• A URI or an anonymous individual can be annotated with an annotation value by an annotation property. More precisely, the assertion AnnotationAssertion( P u v ) states that the URI or anonymous individual u is annotated with the annotation value v by the annotation property P.
• An axiom can be annotated with an annotation value by an annotation property. The axiom annotation Annotation( P v ) states that the axiom is annotated with the annotation value v by the annotation property P.
• There are only three axioms that can be used on annotation properties: AnnotationPropertyDomain, AnnotationPropertyRange and SubAnnotationPropertyOf axioms. These special annotation axioms have no semantics in OWL DL, but the normal semantics in OWL Full via their mapping to the standard RDF vocabulary. Syntax

Below extracts of the syntax used for annotating URIs or anonymous individuals and axioms, for example SubClassOf axioms, respectively, next followed by the related examples (for the complete syntax see Annotations in the Syntax document):

Use Cases

Use Case #5 Use Case #12 Use Case #19

2.6.1 F14: Declarations

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. As a consequence, it was deemed desirable that entities in an ontology could be declared — that is, they could be explicitly listed as being a part of an ontology.

Feature

A declaration axiom states that an entity is part of the vocabulary of an ontology. A declaration also associates an entity type (class, datatype, object property, data property, annotation property, individual, or a combination) to the declared entity. Declarations are optional for the most part.Syntax

Properties and classes should be declared in an ontology. Furthermore, declarations are also used during ontology parsing to disambiguate the productions of various syntaxes.

In addition, the OWL 2 specification provides the notion of declaration consistency which, roughly speaking, checks whether each entity used in an ontology also occurs in at least one declaration.

Use Cases

Use Case #17

2.6.2 F15: Profiles OWL 2 EL, OWL 2 QL, OWL 2 RL

Large Life Sciences ontologies like the FMA, NCI Thesaurus, SNOMED CT, Gene Ontology or other OBO ontologies are mainly concerned by scalability issues of the language and do not necessarily need the whole expressivity of OWL. On the other side, applications involving classical databases and also DBM system companies, are mainly concerned about interoperability of the language with standard relational DBMS. While other ones, such as the business rules community and rule companies, feel concerned about interoperability of the ontology language with rules and existing rule engines. Consequently, different profiles of language have emerged, been requested by different types of users - ontologists, DBMS or rule engine developpers - and correspond to various application scenarios:

• a scalable profile for large but (rather) simple ontologies that enables good time performance for ontology (TBox/schema) reasoning.
• a profile that can easily interoperate with relational database systems, useful for applications where scalable reasoning on large datasets is the most important task.
• a profile that can easily interoperate with rules engines and rule extended DBMS, useful for applications where query answering is the most important task.

Feature

OWL 2 defines several profiles, sublanguages with useful computational properties (e.g., reasoning complexity in range of LOGSPACE to PTIME) and implementation possibilities (e.g., fragments implementable using RDBs). These profiles are described in details in the Profile document.

OWL 2 EL

• Captures expressive power used by many large-scale ontologies, e.g.; SNOMED CT, the NCI thesaurus;
• Features include existential restrictions, intersection, subClass, equivalentClass, class disjointness, range and domain, object property inclusion (SubObjectPropertyOf), possibly involving property chains, and data property inclusion (SubDataPropertyOf)transitive properties, keys (HasKey) …;
• Missing features include value restrictions, cardinality restrictions (min, max and exact), disjunction and negation.

OWL 2 QL

• Captures expressive power of simple ontologies like thesauri, and (most of) expressive power of ER/UML schemas;
• Features include limited form of existential restrictions, subClass, equivalentClass, disjointness, range and domain, symmetric properties, …;
• Missing features include existential quantification to a class (ObjectSomeValuesFrom), self restriction (ObjectHasSelf), nominals (ObjectHasValue)(ObjectOneOf),universal quantification to a class (ObjectAllValuesFrom), ObjectMinCardinality, ObjectExactCardinality), disjunction (ObjectUnionOf, DisjointUnion) etc. cf. the Profile document for an exhaustive list missing features.
• Can be implemented on top of standard relational database.

OWL 2 RL

• Includes support for most OWL 2 features;
• But with restrictions placed on the syntax, for example it does not include existential on the right hand side of axioms (which often occurs in Life Sciences ontologies, e.g., SNOMED). Standard semantics only apply when they are used in a restricted way;
• Can be implemented on top of rule extended DBMS e.g., SQL (see Implementation Perspective).

Use Cases

Use Case #2 Use Case #3 Use Case #4 Use Case #8 Use Case #16

[OWL Use Cases and Requirements]

OWL Web Ontology Language: Use Cases and Requirements Jeff Heflin, ed. W3C Recommendation, 10 February 2004, http://www.w3.org/TR/2004/REC-webont-req-20040210/. Latest version available at http://www.w3.org/TR/webont-req/.

[SROIQ]

The Even More Irresistible SROIQ. Ian Horrocks, Oliver Kutz, and Uli Sattler. In Proc. of the 10th Int. Conf. on Principles of Knowledge Representation and Reasoning (KR 2006). AAAI Press, 2006.

[SHOIQ]

A Tableaux Decision Procedure for SHOIQ. Horrocks, I., and Sattler, U. In Proc. of 19th International Joint Conference on Artificial Intelligence (IJCAI 2005) (2005), Morgan Kaufmann, Los Altos.).

[Next Steps]

Next Steps to OWL. B. Cuenca Grau, I. Horrocks, B. Parsia, P. Patel-Schneider, and U. Sattler. In Proc. of OWL: Experiences and Directions, CEUR, 2006.

[Syntax Problem]

Problem with OWL Syntax. Boris Motik and I. Horrocks, OWLED 2006, 2006.

Reusing Ontological Background Knowledge in Semantic Wikis Denny Vrandecic, Markus Krötzsch, Proceedings 1st Workshop on Semantic Wikis. Budva, Montenegro, June 2006 .

[CEL]

CEL—A Polynomial-time Reasoner for Life Science Ontologies. F. Baader, C. Lutz, and B. Suntisrivaraporn. In U. Furbach and N. Shankar, editors, Proceedings of the 3rd International Joint Conference on Automated Reasoning (IJCAR'06), volume 4130 of Lecture Notes in Artificial Intelligence, pages 287–291. Springer-Verlag, 2006.

[SNOMED EL+]

Replacing SEP-Triplets in SNOMED CT using Tractable Description Logic Operators. B. Suntisrivaraporn, F. Baader, S. Schulz, K. Spackman, AIME 2007

[EL++]

Pushing the EL Envelope. Franz Baader, Sebastian Brandt, and Carsten Lutz. In Proc. of the 19th Joint Int. Conf. on Artificial Intelligence (IJCAI 2005), 2005.

[EL++ Update]

Pushing the EL Envelope Further. Franz Baader, Sebastian Brandt, and Carsten Lutz. In Proc. of the Washington DC workshop on OWL: Experiences and Directions (OWLED08DC), 2008.

[DL-Lite]

Tractable Reasoning and Efficient Query Answering in Description Logics: The DL-Lite Family. Diego Calvanese, Giuseppe de Giacomo, Domenico Lembo, Maurizio Lenzerini, Riccardo Rosati. J. of Automated Reasoning 39(3):385–429, 2007.

[DLP]

Description Logic Programs: Combining Logic Programs with Description Logic. Benjamin N. Grosof, Ian Horrocks, Raphael Volz, and Stefan Decker. in Proc. of the 12th Int. World Wide Web Conference (WWW 2003), Budapest, Hungary, 2003. pp.: 48–57

[pD*]

Completeness, decidability and complexity of entailment for RDF Schema and a semantic extension involving the OWL vocabulary. Herman J. ter Horst. J. of Web Semantics 3(2–3):79–115, 2005.

[OWLPrime]

Implementing an Inference Engine for RDFS/OWL Constructs and User-Defined Rules in Oracle. Zhe Wu Eadon, G. Das, S. Chong, E.I. Kolovski, V. Annamalai, M. Srinivasan, J. Oracle, Nashua, NH; Data Engineering, 2008. ICDE 2008. IEEE 24th International Conference on, pages 1239-1248, Cancun, 2008.

[Metamodeling]

On the Properties of Metamodeling in OWL. Boris Motik. On the Properties of Metamodeling in OWL. Journal of Logic and Computation, 17(4):617–637, 2007.

[Datatype]

OWL Datatypes: Design and Implementation. Boris Motik, Ian Horrocks, ISWC 2008, Karlsruhe, Deutshland, 2008.

Example for: Disjoint Union

• E.g.; Lobe is a disjoint union of FrontalLobe ParietalLobe TemporalLobe OccipitalLobe and LimbicLobe.

References: [MEDICAL REQ] [Ontology with rules] [Brain Imaging ]

Example for: Disjoint Classes

• E.g.; Nothing can be both a Leftlung and a RightLung.

References: [FMA]

Example for: Local reflexivity

• E.g.; A RingMolecule is a Molecule that connectedTo itself.

References: [Chemistry]

Example for: Qualified Cardinality

• E.g.; the class of automobile having exactly 2 rear doors.

References: [Auto]

Example for: Asymmetric

• E.g.; if p is a proper part of q then q cannot be a proper part of p.

References: [OBO] [RO] [OBO2OWL]

Example for: Irreflexive

• E.g.; Nothing flows into itself.

References: [Ordnance]

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

• E.g.; anything located in a part is located in the whole

References: [SNOMED REQ]

Example for: Reflexive

• E.g.; a frontal lobe is part of a brain memisphere or a car is part of a car

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]

Example for: Negative Property Assertion

• E.g.; This patient is not 5 years old.

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 protcols 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 enrollment 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 datatype

• E.g.; the enrollment date of a clinical trial participant should be within 30 days after the patient has been started on a particular therapy

Overview: [N-ary] presents many Use cases that would benefit from various datatype extensions

Features: Datatypes restriction, N-Ary

Example for: N-ary datatype

• E.g.; datatypes restrictions like intervals, or N-Ary datatype with inequality such as needed in Use Case #10.

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 developpers 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 metamodelling 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, Metamodelling

Example for: N-ary datatype

• E.g.; adults are individuals whose age is greater than 18 years.

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 a:Service class. For each concrete service (i.e., for each instance of a:Service), the users wanted to state what the input to the service is. Here is an example of a service description:

(1) a:Service rdf:type owl:Class
(2) a:Person rdf:type owl:Class
(3) s1 rdf:type a:Service
(4) s1 a:input a:Person

s1 is an individual of the class a:Service due to (1) and (3), and a:Person is a class due to (2); hence, in (4) we have a relationship a: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: Metamodelling

Example for: Simple metamodelling

• E.g.; a class and an individual : Person may be used both for a class and an individual

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 organise ontological vocabulary. Examples are statements such as:

• "The property is_located_in is in the class Deprecated_Properties and was replaced by property has_location."
• "Objects of the class City should have a value for the property population." (expressed by relating class and property)

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 realised 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: Metamodelling

Example for: Simple metamodelling

• E.g.; a property and an individual: to make a statement asserting that a property is an individual of the class Deprecated_properties

References: [Wiki] [Punning]

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: Metamodelling

Example for: Simple metamodelling

• E.g.; an object property and a class: PersonCompany may be used both for an object property and a class.

References: [UML] [Punning]

Example for: Profiles

• E.g.; OWL 2 QL profile to easily query a federation of databases in a convivial way

References: [Who reads?]

Example for: Declaration

• E.g.; A person is declared to be a class of an ontology.

References: [TOOLS] [DIG2] [OWL API] [Syntax Problem]

Overview: 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

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. 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

• E.g.; the range for atmosphere is above 18000 and below 19600 [feet]

References: [VSTO]

Example for: Extended annotation to attach annotations

• E.g.; comments on axioms, such as a SubClass axiom, to express for instance that the the elements of the subclass are data generated by a log parser.

References: [NCAR]

[Medical Req]

Web ontology language requirements w.r.t expressiveness of taxononomy and axioms in medicine. Christine Golbreich, Olivier Dameron, Bernard Gibaud, Anita Burgun. In Proc. of ISWC 2003, 2003.

[Micro Theory]

[Creation and Usage of a "Micro Theory" for Long Bone Fractures: An Experience Report]. Howard Goldberg, Vipul Kashyap and Kent Spackman, Proceedings of KR-MED 2008.

[Ontology with Rules]

Ontology enriched by rules for identifying brain anatomical structures. Christine Golbreich, Olivier Dameron, Bernard Gibaud, Anita Burgun. In RIF 2004, Washington, 2004.

and Annex.

[Brain Imaging]

Towards an Hybrid System Using an Ontology Enriched by Rules for the Semantic Annotation of Brain MRI Images In Proc. of RR 2007

The Brain Anatomy Case Study Christine Golbreich, Olivier Bierlaire, Olivier Dameron, Bernard Gibaud. In Proc. of Protege 2005.

[FMA]

The Foundational Model of Anatomy A

The Foundational Model of Anatomy B

The Foundational Model of Anatomy C.

[Chemistry]

Describing chemical functional groups in OWL-DL for the classification of chemical compounds Natalia Villanueva-Rosales and Michel Dumontier..

Modelling Life Sciences knowledge with OWL1.1

[Auto]

An exploratory study in an automotive company.

[OBO]

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Barry Smith et al. .

[RO]

-8- Relations in Biomedical Ontologies. .

[OBO2OWL]

OBO to OWL: Go to OWL1.1!

OBO and OWL: Leveraging Semantic Web Technologies for the Life Sciences (ISWC 2007).

[Ordnance]

Experiences of using OWL at the Ordnance Survey.

[SNOMED REQ]

An examination of OWL and the requirements of a large health care terminology.

[Agence Biomedecine]

Changing Kidney Allocation Policy in France: the Value of Simulation.

[Transplant Ontology]

Construction of the dialysis and transplantation ontology.

[Little Web]

A little semantic web goes a long way in biology Wolstencroft, K., Brass, A., Horrocks, I., Lord, P., Sattler, U., Stevens, R., Turi, D.: In: Proceedings of the 2005 International Semantic Web Conference (ISWC 2005), pp. 786-800. Springer, Berlin Heidelberg New York (2005).

[Part Whole]

Simple part-whole relations in OWL Ontologies Alan Rector, Chris Welty. W3C Editor's Draft 11 Aug 2005 .

[TOOLS]

Supporting Early Adoption of OWL 1.1 with Protege-OWL and FaCT++. Matthew Horridge and Dmitry Tsarkov and Timothy Redmond. In OWL: Experiences and Directions (OWLED 06), Athens, Georgia.

[OWL API]

Igniting the OWL 1.1 Touch Paper: The OWL API Matthew Horridge and Sean Bechhofer and Olaf Noppens (2007). In OWL: Experiences and Directions (OWLED 07), Innsbruck, Austria.

[DIG2]

DIG 2.0 Reference Middleware Timo Weith¨oner, Thorsten Liebig, Marko Luther, and Sebastian B¨ohm In OWL: Experiences and Directions (OWLED 07), Innsbruck, Austria.

[Protege OWL]

The Protégé OWL Experience Holger Knublauch, Matthew Horridge, Mark Musen, Alan Rector, Robert Stevens, Nick Drummond, Phil Lord, Natalya F. Noy2, Julian Seidenberg, Hai Wang. In OWL: Experiences and Directions (OWLED 05), Galway, Ireland, 2005.

[N-ary]

N-ary Data predicate use case.

[Web Service]

Preference-based Selection of Highly Configurable Web Services Steffen Lamparter, Anupriya Ankolekar, Stephan Grimm, Rudi Studer: WWW-07, Banff, Canada, 2007.

[Wiki]

Reusing Ontological Background Knowledge in Semantic Wikis Denny Vrandecic, Markus Krötzsch, Proceedings 1st Workshop on Semantic Wikis. Budva, Montenegro, June 2006 .

[UML]

Association.

[Punning]

Punning Use Cases.

[Who reads?]

Who reads our documents?

NIF

NIF Data-Integration slides

[VSTO]

The Virtual Solar-Terrestrial Observatory: A Deployed Semantic Web Application Case Study for Scientific Research McGuinness, D.L., Fox, P., Cinquini, L., West, P., Garcia, J., Benedict, J.L., Middleton, D..

VSTO2.

VMO.

[NCAR]

Semantic Provenance Capture in Data Ingest Systems.