Extended RDF: Computability and Complexity Issues

ERDF stable model semantics is a recently proposed semantics for ERDF ontologies and a faithful extension of RDFS semantics on RDF graphs. In this paper, we elaborate on the computability and complexity issues of the ERDF stable model semantics. Based on the undecidability result of ERDF stable model semantics, decidability under this semantics cannot be achieved, unless ERDF ontologies of restricted syntax are considered. Therefore, we propose a slightly modified semantics for ERDF ontologies, called ERDF #n- stable model semantics. We show that entailment under this semantics is, in general, decidable and also extends RDFS entailment. Equivalence statements between the two semantics are provided. Additionally, we provide algorithms that compute the ERDF #n-stable models of syntax-restricted and general ERDF ontologies. Further, we provide complexity results for the ERDF #nstable model semantics on syntax-restricted and general ERDF ontologies. Finally, we provide complexity results for the ERDF stable model semantics on syntax-restricted ERDF ontologies

Using multiple reference ontologies: Managing composite annotations

There are a growing number of reference ontologies available across a variety of biomedical domains and current research focuses on their construction, organization and use. An important use case for these ontologies is annotation—where users create metadata that access concepts and terms in reference ontologies. We draw on our experience in physiological modeling to present a compelling use case that demonstrates the potential complexity of such annotations. In the domain of physiological biosimulation, we argue that most annotations require the use of multiple reference ontologies. We suggest that these “composite” annotations should be retained as a repository of knowledge about post-coordination that promotes sharing and interoperation across biosimulation models

Unsupervised Terminological Ontology Learning based on Hierarchical Topic Modeling

In this paper, we present hierarchical relationbased latent Dirichlet allocation (hrLDA), a data-driven hierarchical topic model for extracting terminological ontologies from a large number of heterogeneous documents. In contrast to traditional topic models, hrLDA relies on noun phrases instead of unigrams, considers syntax and document structures, and enriches topic hierarchies with topic relations. Through a series of experiments, we demonstrate the superiority of hrLDA over existing topic models, especially for building hierarchies. Furthermore, we illustrate the robustness of hrLDA in the settings of noisy data sets, which are likely to occur in many practical scenarios. Our ontology evaluation results show that ontologies extracted from hrLDA are very competitive with the ontologies created by domain experts

Conceptual modelling and the quality of ontologies: A comparison between object-role modelling and the object paradigm

Ontologies are key enablers for sharing precise and machine-understandable semantics among different applications and parties. Yet, for ontologies to meet these expectations, their quality must be of a good standard. The quality of an ontology is strongly based on the design method employed. This paper addresses the design problems related to the modelling of ontologies, with specific concentration on the issues related to the quality of the conceptualisations produced. The paper aims to demonstrate the impact of the modelling paradigm adopted on the quality of ontological models and, consequently, the potential impact that such a decision can have in relation to the development of software applications. To this aim, an ontology that is conceptualised based on the Object Role Modelling (ORM) approach is re-engineered into a one modelled on the basis of the Object Paradigm (OP). Next, the two ontologies are analytically compared using the specified criteria. The conducted comparison highlights that using the OP for ontology conceptualisation can provide more expressive, reusable, objective and temporal ontologies than those conceptualised on the basis of the ORM approach

Conceptual Modelling and The Quality of Ontologies: Endurantism Vs. Perdurantism

Ontologies are key enablers for sharing precise and machine-understandable semantics among different applications and parties. Yet, for ontologies to meet these expectations, their quality must be of a good standard. The quality of an ontology is strongly based on the design method employed. This paper addresses the design problems related to the modelling of ontologies, with specific concentration on the issues related to the quality of the conceptualisations produced. The paper aims to demonstrate the impact of the modelling paradigm adopted on the quality of ontological models and, consequently, the potential impact that such a decision can have in relation to the development of software applications. To this aim, an ontology that is conceptualised based on the Object-Role Modelling (ORM) approach (a representative of endurantism) is re-engineered into a one modelled on the basis of the Object Paradigm (OP) (a representative of perdurantism). Next, the two ontologies are analytically compared using the specified criteria. The conducted comparison highlights that using the OP for ontology conceptualisation can provide more expressive, reusable, objective and temporal ontologies than those conceptualised on the basis of the ORM approach

Context-based task ontologies for clinical guidelines

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned in the WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up

Towards automatic construction of domain ontologies: Application to ISA88 and assessment

Process Systems Engineering has shown a growing interest on ontologies to develop knowledge models, organize information, and produce software accordingly. Although software tools supporting the structure of ontologies exist, developing a PSE ontology is a creative procedure to be performed by human experts from each specific domain. This work explores the opportunities for automatic construction of domain ontologies. Specialised documentation can be selected and automatically parsed; next pattern recognition methods can be used to extract concepts and relations; finally, supervision is required to validate the automatic outcome, as well as to complete the task. The bulk of the development of an ontology is expected to result from the application of systematic procedures, thus the development time will be significantly reduced. Automatic methods were prepared and applied to the development of an ontology for batch processing based on the ISA88 standard. Methods are described and commented, and results are discussed from the comparison with a previous ontology for the same domain manually developed.Postprint (published version

Supporting public decision making in policy deliberations: An ontological approach

This is the post-print version of the Paper. The official published version can be accessed from the link below - Copyright @ 2011 SpringerSupporting public decision making in policy deliberations has been a key objective of eParticipation which is an emerging area of eGovernment. EParticipation aims to enhance citizen involvement in public governance activities through the use of information and communication technologies. An innovative approach towards this objective is exploiting the potentials of semantic web technologies centred on conceptual knowledge models in the form of ontologies. Ontologies are generally defined as explicit human and computer shared views on the world of particular domains. In this paper, the potentials and benefits of using ontologies for policy deliberation processes are discussed. Previous work is then extended and synthesised to develop a deliberation ontology. The ontology aims to define the necessary semantics in order to structure and interrelate the stages and various activities of deliberation processes with legal information, participant stakeholders and their associated arguments. The practical implications of the proposed framework are illustrated.This work is funded by the European Commission under the 2006/1 eParticipation call

Modelling data intensive web sites with OntoWeaver

This paper illustrates the OntoWeaver modelling approach, which relies on a set of comprehensive site ontologies to model all aspects of data intensive web sites and thus offers high level support for the design and development of data-intensive web sites. In particular, the OntoWeaver site ontologies comprise two components: a site view ontology and a presentation ontology. The site view ontology provides meta-models to allow for the composition of sophisticated site views, which allow end users to navigate and manipulate the underlying domain databases. The presentation ontology abstracts the look and feel for site views and makes it possible for the visual appearance and layout to be specified at a high level of abstractio