Ontology Design Patterns Research Articles

A set of ontology design patterns for reengineering SBVR statements into OWL/SWRL ontologies

The work presents a set of ontology design patterns.Patterns provide a way to obtain an OWL/SWRL ontology from a SBVR specification.Translations from SBVR to SWRL fill the gap in the expressive power of SBVR and OWL.Patterns are readily usable for business people or software developers.Patterns are illustrated by means of an example depicting a fictitious company. The interest in the use of ontologies for creating more intelligent and effective enterprise information systems has increased considerably in recent years. The most critical aspects during the development of these systems are: (1) to identify the ontology concepts and (2) to make explicit the business rules by means of the ontology axioms.In order to address these issues, mappings of business rules expressions to ontology statements based on different languages were proposed. Despite the efforts made in this area, some work remain to be done.This work presents a set of ontology design patterns providing a way to obtain an OWL/SWRL ontology by applying metamodel transformation rules over the SBVR specification of a business domain. Patterns are rooted in the structural specification of the standards, providing a set of mappings readily usable for business people or developers concerned with the implementation of a mapping tool. Moreover, translations from SBVR to SWRL language are presented in order to fill the gap in the expressive power of SBVR and OWL. The theoretical expressions of patterns are illustrated by means of an example depicting the core structure of a fictitious company.

How Can Ontology Design Patterns Help Ontology Refinement?

How Can Ontology Design Patterns Help Ontology Refinement?

Political Roles Ontology (PRoles): Enhancing Archival Authority Records through Semantic Web Technologies

In this paper we present the Political Roles (PRoles) ontology, an OWL 2 DL ontology for the description of political relationships between persons. Building upon existing ontological models, such as the Publishing Roles Ontology (PRO), the Provenance Ontology (PROV-O) and the N-ary Participation ontology design pattern, PRoles provides a clear ontological characterisation of political roles and related events, establishing a link between the description of such concepts and the documents from which this information is distilled.

A MAUT APPROACH FOR REUSING DOMAIN ONTOLOGIES ON THE BASIS OF THE NeOn METHODOLOGY

Knowledge resource reuse is becoming a widespread approach in the ontology engineering field because it can speed up the ontology development process. In this context, the NeOn Methodology specifies some guidelines for reusing different types of knowledge resources (ontologies, nonontological resources, and ontology design patterns). These guidelines prescribe how to perform the different activities involved in any of the diverse types of reuse processes. One such activity is to select the best knowledge resources for reuse in an ontology development. This selection activity is a complex decision-making problem involving conflicting objectives, like understandability, integration or reliability. We propose a multi-attribute utility theory (MAUT) approach to deal with the selection of the best domain ontologies for reuse, stressing the identification of attributes to measure ontology performances. We take advantage of the sensitivity analysis tools provided by the GMAA system, a PC-based decision support system based on an additive multi-attribute utility model, to exploit imprecise information on the inputs. An example concerning the selection of a subset of ontologies for reuse in the development of a new ontology in the sports domain illustrates the approach.

Pattern languages: addressing the challenges

Pattern languages: addressing the challenges

Ontologies for interaction: Enabling serendipitous interoperability in smart environments

The thesis describes the design and development of an ontology and software framework to support user interaction in ubiquitous computing scenarios. The key goal of ubiquitous computing is serendipitous interoperability, where devices that were not necessarily designed to work together should be able to discover each other’s functionality and be able to make use of it. Future ubiquitous computing scenarios involve hundreds of devices. Therefore, anticipating all the different types of devices and usage scenarios a priori is an unmanageable task. An iterative approach was followed during the design process, with three design iterations documented in the thesis. The work was done in close cooperation with designers and other project partners, in order to elicit requirements and maintain a more holistic view of the various application areas. The thesis describes an interaction model that shows the various concepts that are involved in user interaction in a smart space, including how these concepts work together. Based in the interaction model, a theory of semantic connections is introduced that focuses on the meaning of the connections between the different entities in a smart environment. Ontologies are formal representations of concepts in a domain of interest and the relationships between these concepts. They are used to enable the exchange of information without requiring up-front standardisation. The ontology described in the thesis helps developers to focus on modelling the interaction capabilities of smart objects and inferring the possible connections between these objects, making it easier to build smart objects and enable device interoperability on a semantic level. Rather than just describing the low-level hardware input event that triggered an action, interaction events in the ontology are modelled as high-level input actions which report the intent of the user’s action directly. This allows developers to write software that respond to these high-level events, without having to support every kind of device that could have generated that event. The event hierarchy can be inferred using semantic reasoning. The software architecture implements the publish/subscribe messaging paradigm, enabling smart objects to subscribe to changes in data, represented in triple form, and be notified every time these triples are updated, added or removed. Semantic reasoning is performed on an information broker, simplifying the implementation on the smart objects. A pilot deployment, composed of heterogeneous smart objects designed and manufactured by a range of companies and institutions, was used to validate the design. A performance evaluation was performed, where the results indicated acceptable response times for a networked user interface. A usability analysis of the ontology and system implementation was performed using a developer questionnaire based on an existing usability framework. Various ontology design patterns were identified during the course of the design, and are documented in the thesis. The resulting design artefact is an ontology for user interaction with devices in a smart environment, where devices are able to share interaction events and make use of each other’s functionality.

A PATTERN SYSTEM FOR DESCRIBING THE SEMANTICS OF STRUCTURED MULTIMEDIA DOCUMENTS

Today's metadata models and metadata standards often focus on a specific media type only, lack combinability with other metadata models, or are limited with respect to the features they support. Thus they are not sufficient to describe the semantics of rich, structured multimedia documents. To overcome these limitations, we have developed a comprehensive model for representing multimedia metadata, the Multimedia Metadata Ontology (M3O). The M3O has been developed by an extensive analysis of related work and abstracts from the features of existing metadata models and metadata standards. It is based on the foundational ontology DOLCE+DnS Ultralight and makes use of ontology design patterns. The M3O serves as generic modeling framework for integrating the existing metadata models and metadata standards rather than replacing them. As such, the M3O can be used internally as semantic data model within complex multimedia applications such as authoring tools or multimedia management systems. To make use of the M3O in concrete multimedia applications, a generic application programming interface (API) has been implemented based on a sophisticated persistence layer that provides explicit support for ontology design patterns. To demonstrate applicability of the M3O API, we have integrated and applied it with our SemanticMM4U framework for the multi-channel generation of semantically annotated multimedia documents.

Improving procedural modeling with semantics in digital architectural heritage

We first introduce three challenges in the procedural modeling of digital architectural heritages and then present a general framework, which integrates several machine intelligence and semantic techniques, e.g., the ontology design approach, pattern mining, auto-annotating and rule reduction, to improve the procedural methods in architectural modeling. Several evaluations and experiments are also presented. The experimental results illustrate the improvements following our approach.

Proposed actions are no actions: re-modeling an ontology design pattern with a realist top-level ontology.

BackgroundOntology Design Patterns (ODPs) are representational artifacts devised to offer solutions for recurring ontology design problems. They promise to enhance the ontology building process in terms of flexibility, re-usability and expansion, and to make the result of ontology engineering more predictable. In this paper, we analyze ODP repositories and investigate their relation with upper-level ontologies. In particular, we compare the BioTop upper ontology to the Action ODP from the NeOn an ODP repository. In view of the differences in the respective approaches, we investigate whether the Action ODP can be embedded into BioTop. We demonstrate that this requires re-interpreting the meaning of classes of the NeOn Action ODP in the light of the precepts of realist ontologies.ResultsAs a result, the re-design required clarifying the ontological commitment of the ODP classes by assigning them to top-level categories. Thus, ambiguous definitions are avoided. Classes of real entities are clearly distinguished from classes of information artifacts. The proposed approach avoids the commitment to the existence of unclear future entities which underlies the NeOn Action ODP. Our re-design is parsimonious in the sense that existing BioTop content proved to be largely sufficient to define the different types of actions and plans.ConclusionsThe proposed model demonstrates that an expressive upper-level ontology provides enough resources and expressivity to represent even complex ODPs, here shown with the different flavors of Action as proposed in the NeOn ODP. The advantage of ODP inclusion into a top-level ontology is the given predetermined dependency of each class, an existing backbone structure and well-defined relations. Our comparison shows that the use of some ODPs is more likely to cause problems for ontology developers, rather than to guide them. Besides the structural properties, the explanation of classification results were particularly hard to grasp for 'self-sufficient' ODPs as compared with implemented and 'embedded' upper-level structures which, for example in the case of BioTop, offer a detailed description of classes and relations in an axiomatic network. This ensures unambiguous interpretation and provides more concise constraints to leverage on in the ontology engineering process.

Ontology patterns for service‐oriented software development

SUMMARYModern software often uses ontologies as its key component to store data and their relationships. This is different from using an ontology as a stand‐alone tool for knowledge sharing and representation. The ontology component needs to work with other software components and needs to evolve as the software evolves. Ontology design has been a research topic for years; however, most of these studies focus on using ontologies as stand‐alone applications. This paper studies ontology patterns that can be applied to design ontologies as an integral part of a service‐oriented application. The paper first briefly reviews various ontology design issues including a brief survey of existing ontology design patterns. The paper then outlines general principles for using ontologies in software applications, including the needs to incorporate ontology design process as a part of software development processes, design ontologies as a component of an overall software architecture, and use ontologies to enhance software evolution and the role that ontologies can play in software validation. The paper then proposes some common ontology patterns that can be used to design ontologies in service‐oriented applications. This is followed by examining two international projects, SENSEI and FCINT, where ontologies are used in service‐oriented applications and several ontology design patterns are used. Copyright © 2011 John Wiley & Sons, Ltd.

Unintended consequences of existential quantifications in biomedical ontologies.

BackgroundThe Open Biomedical Ontologies (OBO) Foundry is a collection of freely available ontologically structured controlled vocabularies in the biomedical domain. Most of them are disseminated via both the OBO Flatfile Format and the semantic web format Web Ontology Language (OWL), which draws upon formal logic. Based on the interpretations underlying OWL description logics (OWL-DL) semantics, we scrutinize the OWL-DL releases of OBO ontologies to assess whether their logical axioms correspond to the meaning intended by their authors.ResultsWe analyzed ontologies and ontology cross products available via the OBO Foundry site http://www.obofoundry.org for existential restrictions (someValuesFrom), from which we examined a random sample of 2,836 clauses.According to a rating done by four experts, 23% of all existential restrictions in OBO Foundry candidate ontologies are suspicious (Cohens' κ = 0.78). We found a smaller proportion of existential restrictions in OBO Foundry cross products are suspicious, but in this case an accurate quantitative judgment is not possible due to a low inter-rater agreement (κ = 0.07). We identified several typical modeling problems, for which satisfactory ontology design patterns based on OWL-DL were proposed. We further describe several usability issues with OBO ontologies, including the lack of ontological commitment for several common terms, and the proliferation of domain-specific relations.ConclusionsThe current OWL releases of OBO Foundry (and Foundry candidate) ontologies contain numerous assertions which do not properly describe the underlying biological reality, or are ambiguous and difficult to interpret. The solution is a better anchoring in upper ontologies and a restriction to relatively few, well defined relation types with given domain and range constraints.

Scalable representations of diseases in biomedical ontologies

BackgroundThe realm of pathological entities can be subdivided into pathological dispositions, pathological processes, and pathological structures. The latter are the bearer of dispositions, which can then be realized by their manifestations — pathologic processes. Despite its ontological soundness, implementing this model via purpose-oriented domain ontologies will likely require considerable effort, both in ontology construction and maintenance, which constitutes a considerable problem for SNOMED CT, presently the largest biomedical ontology.ResultsWe describe an ontology design pattern which allows ontologists to make assertions that blur the distinctions between dispositions, processes, and structures until necessary. Based on the domain upper-level ontology BioTop, it permits ascriptions of location and participation in the definition of pathological phenomena even without an ontological commitment to a distinction between these three categories. An analysis of SNOMED CT revealed that numerous classes in the findings/disease hierarchy are ambiguous with respect to process vs. disposition. Here our proposed approach can easily be applied to create unambiguous classes. No ambiguities could be defined regarding the distinction of structure and non-structure classes, but here we have found problematic duplications.ConclusionsWe defend a judicious use of disjunctive, and therefore ambiguous, classes in biomedical ontologies during the process of ontology construction and in the practice of ontology application. The use of these classes is permitted to span across several top-level categories, provided it contributes to ontology simplification and supports the intended reasoning scenarios.

ANEMONE: An environment for modular ontology development

Many real-world ontologies contain thousands of terms and are developed by multiple participants. The use of monolithic ontologies can cause problems that affect various stages of the ontology life cycle. Thus, there is an urgent need for tools and methodologies that facilitate modular ontology design. The benefits of a modular approach include division of labor, scalability, partial reuse, and broadened participation. This article presents a methodology for modular ontology development. The main idea is to facilitate an interoperable hierarchical network of ontology modules. Modules are designed as a combination of more abstract modules in higher levels of the hierarchy. This methodology differs from previous methodologies in the way that it defines concrete development steps, to facilitate use by both naive and expert ontology developers. This methodology is also supported by ontology design patterns and a prototypical ontology development tool.

Ontology Patterns for Complex Topographic Feature Types

Complex feature types are defined as integrated relations between basic features for a shared meaning or concept. The shared semantic concept is difficult to define in commonly used geographic information systems (GIS) and remote sensing technologies. The role of spatial relations between complex feature parts was recognized in early GIS literature, but had limited representation in the feature or coverage data models of GIS. Spatial relations are more explicitly specified in semantic technology. In this paper, semantics for topographic feature ontology design patterns (ODP) are developed as data models for the representation of complex features. In the context of topographic processes, component assemblages are supported by resource systems and are found on local landscapes. The topographic ontology is organized across six thematic modules that can account for basic feature types, resource systems, and landscape types. Types of complex feature attributes include location, generative processes and physical description. Node/edge networks model standard spatial relations and relations specific to topographic science to represent complex features. To demonstrate these concepts, data from The National Map of the U. S. Geological Survey was converted and assembled into ODP.

Ontology design patterns to disambiguate relations between genes and gene products in GENIA

MotivationAnnotated reference corpora play an important role in biomedical information extraction. A semantic annotation of the natural language texts in these reference corpora using formal ontologies is challenging due to the inherent ambiguity of natural language. The provision of formal definitions and axioms for semantic annotations offers the means for ensuring consistency as well as enables the development of verifiable annotation guidelines. Consistent semantic annotations facilitate the automatic discovery of new information through deductive inferences.ResultsWe provide a formal characterization of the relations used in the recent GENIA corpus annotations. For this purpose, we both select existing axiom systems based on the desired properties of the relations within the domain and develop new axioms for several relations. To apply this ontology of relations to the semantic annotation of text corpora, we implement two ontology design patterns. In addition, we provide a software application to convert annotated GENIA abstracts into OWL ontologies by combining both the ontology of relations and the design patterns. As a result, the GENIA abstracts become available as OWL ontologies and are amenable for automated verification, deductive inferences and other knowledge-based applications.AvailabilityDocumentation, implementation and examples are available from http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/.

Theoretical foundations and engineering tools for building ontologies as reference conceptual models

Perhaps the most fundamental notion underlying the desiderata for a successful Semantic Web is Semantic Interoperability. In this context, ontologies have been more and more recognized as one of the enabling technologies. This paper defends the view that an approach which neglects the role of ontologies as reference conceptual models cannot meet the requirements for full semantic interoperability. The paper starts by offering an engineering view on ontology engineering, discussing the relation between ontologies as conceptual models and ontologies as codification artifacts. Furthermore, it discusses the importance of foundational theories and principles to the design of ontology (conceptual) modeling languages and models, emphasizing the fundamental role played by true ontological notions in this process. Finally, it elaborates on the need for proper tools to handle the complexity of ontology engineering in industrial scenarios and complex domains. These tools include ontological design patterns as well as well-founded computational environments to support ontology creation, verification and validation (via model simulation).

Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language

AbstractAs ontologies are developed there is a common need to transform them, especially from those that are axiomatically lean to those that are axiomatically rich. Such transformations often require large numbers of axioms to be generated that affect many different parts of the ontology. This paper describes the Ontology Pre-Processor Language (OPPL), a domain-specific macro language, based in the Manchester OWL Syntax, for manipulating ontologies written in OWL. OPPL instructions can add/remove entities, and add/remove axioms (semantics or annotations) to/from entities in an OWL ontology. OPPL is suitable for applying the same change to different ontologies or at different development stages, and for keeping track of the changes made (e.g. in pipelines). It is also suitable for defining independent modelling macros (e.g. Ontology Design Patterns) that can be applied at will and systematically across an ontology. The presented OPPL Instruction Manager is a Java library that processes OPPL instructions making the changes to an OWL ontology. A reference implementation that uses the OPPL Instruction Manager is also presented. The use of OPPL has been demonstrated in the Cell Cycle Ontology

Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language

As ontologies are developed there is a common need to transform them, especially from those that are axiomatically lean to those that are axiomatically rich. Such transformations often require large numbers of axioms to be generated that affect many different parts of the ontology. This paper describes the Ontology Pre-Processor Language (OPPL), a domain-specific macro language, based in the Manchester OWL Syntax, for manipulating ontologies written in OWL. OPPL instructions can add/remove entities, and add/remove axioms (semantics or annotations) to/from entities in an OWL ontology. OPPL is suitable for applying the same change to different ontologies or at different development stages, and for keeping track of the changes made (e.g. in pipelines). It is also suitable for defining independent modelling macros (e.g. Ontology Design Patterns) that can be applied at will and systematically across an ontology. The presented OPPL Instruction Manager is a Java library that processes OPPL instructions making the changes to an OWL ontology. A reference implementation that uses the OPPL Instruction Manager is also presented. The use of OPPL has been demonstrated in the Cell Cycle Ontology

The Cell Cycle Ontology: an application ontology supporting the study of cell cycle control

AbstractThe Cell Cycle Ontology (CCO) is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process by combining, interlinking and enriching knowledge from various sources. CCO uses Semantic Web technologies, and it is accessible via the web for browsing, visualising, advanced querying, and computational reasoning. CCO facilitates a detailed analysis of cell cycle related molecular network components. Through querying and automated reasoning, it may provide new hypotheses to help steer a systems biology approach to biological network building. The ontology is available on "http://www.cellcycleontology.org":http://www.cellcycleontology.org. Visual exploration can be done via the BioPortal, the Ontology Lookup Service, the Ontology Online service, or the DIAMONDS platform.*The Cell Cycle Ontology*The Cell Cycle Ontology captures detailed information (in terms and relationships) of the cell cycle process by combining representations from several, public sources.1 CCO supports four model organisms (H. sapiens, A. thaliana, S. pombe and S. cerevisiae) with separate ontologies and one integrated ontology. It is an application ontology that is supplied as an integrated turnkey system for exploratory analysis, advanced querying, and automated reasoning.CCO holds more than 13,000 concepts and 30 types of relationships. CCO comprises data from existing resources such as the Gene Ontology (GO), the Relations Ontology (RO), the IntAct database (MI), the NCBI taxonomy, the UniProt Knowledge Base as well as orthology data. An automatic pipeline builds CCO from scratch periodically: initially some existing ontologies (GO, RO, MI, in-house ones) are automatically fetched, integrated and merged, producing a core cell cycle ontology. Then, organism-specific protein and gene data are added from UniProt and from the GO Annotation files, generating four organism-specific ontologies. Those four ontologies are merged and more terms are included from an ontology built automatically from the OrthoMCL execution on the cell cycle proteins.*Formats and queries*CCO is built in the OBOF format with ONTO-PERL and exported to other formats later.2 CCO is available in: OBOF, RDF, XML, OWL, GML, and DOT. The Semantic Web formats RDF and OWL allow queries on CCO. In a SPARQL endpoint complex queries on the RDF format can be formulated, such as “retrieve all the core cell cycle proteins in S. cerevisiae that are located in the cytoplasm and that have a hydrolysisrelated function”.Relational closures are pre-inferenced in the RDF triple store, by operating SPARUL update queries over CCO and Metarel. This allows for very simple and responsive queries over long chains of relations in CCO.Finally, during the maintenance phase, a semantic improvement on the OWL version is carried out: Ontology Design Patterns are included using the Ontology Pre-Processor Language. The resulting CCO is designed to provide a richer view of the cell cycle regulatory process, in particular by accommodating the intrinsic dynamics of this process.*References*1. Antezana E, Egaña M, Blondé W et al. The Cell Cycle Ontology: An application ontology for the representation and integrated analysis of the cell cycle process, Genome Biology, 2009, 10:52. Antezana E, Egaña M, De Baets B, Kuiper M, Mironov V. ONTO-PERL: an api supporting the development and analysis of bio-ontologies. Bioinformatics, 2008, pp. 885–887.

Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology

BackgroundBio-ontologies are key elements of knowledge management in bioinformatics. Rich and rigorous bio-ontologies should represent biological knowledge with high fidelity and robustness. The richness in bio-ontologies is a prior condition for diverse and efficient reasoning, and hence querying and hypothesis validation. Rigour allows a more consistent maintenance. Modelling such bio-ontologies is, however, a difficult task for bio-ontologists, because the necessary richness and rigour is difficult to achieve without extensive training.ResultsAnalogous to design patterns in software engineering, Ontology Design Patterns are solutions to typical modelling problems that bio-ontologists can use when building bio-ontologies. They offer a means of creating rich and rigorous bio-ontologies with reduced effort. The concept of Ontology Design Patterns is described and documentation and application methodologies for Ontology Design Patterns are presented. Some real-world use cases of Ontology Design Patterns are provided and tested in the Cell Cycle Ontology. Ontology Design Patterns, including those tested in the Cell Cycle Ontology, can be explored in the Ontology Design Patterns public catalogue that has been created based on the documentation system presented ().ConclusionsOntology Design Patterns provide a method for rich and rigorous modelling in bio-ontologies. They also offer advantages at different development levels (such as design, implementation and communication) enabling, if used, a more modular, well-founded and richer representation of the biological knowledge. This representation will produce a more efficient knowledge management in the long term.