Bijan Parsia

The University of Manchester · School of Computer Science

In this paper, we introduce the problem of rewriting finite formal languages using syntactic macros such that the rewriting is minimal in size. We present polynomial-time algorithms to solve variants of this problem and show their correctness. To demonstrate the practical relevance of the proposed problems and the feasibility and effectiveness of o...

We present algorithms for computing definitions and concept descriptions that agents can use to restrict and adapt their knowledge with respect to signature shared with other agents. This ensures that knowledge shared is understood by the communication partners. We focus on agents that make use of description logic ontologies to represent their exp...

For OWL ontologies, classification is the central reasoning task, and several highly-optimised reasoners have been designed for different fragments of OWL. Some of these exploit different notions of modularity, including the atomic decomposition (AD), to further optimise their performance, but this is a complex task due to ontology modules overlapp...

With the growth of ontologies used in diverse application areas, the need for module extraction and modularisation techniques has risen. The notion of the modular structure of an ontology, which comprises a suitable set of base modules together with their logical dependencies, has the potential to help users and developers in comprehending, sharing...

It is sometimes claimed that adding inferred axioms, e.g. the inferred class hierarchy (ICH), to an ontology can improve reasoning performance or an ontology’s usability in practice. While such beliefs may have an effect on how ontologies are published, there is no conclusive empirical evidence to support them. To develop an understanding of the im...

Successful exams require a balance of easy, medium, and difficult questions. Question difficulty is generally either estimated by an expert or determined after an exam is taken. The latter provides no utility for the generation of new questions and the former is expensive both in terms of time and cost. Additionally, it is not known whether expert...

While exam-style questions are a fundamental educational tool serving a variety of purposes, manual construction of questions is a complex process that requires training, experience, and resources. This, in turn, hinders and slows down the use of educational activities (e.g. providing practice questions) and new advances (e.g. adaptive testing) tha...

Ontology Design Patterns (ODP) have been proposed to facilitate ontology engineering. Despite numerous conceptual contributions for over more than a decade, there is little empirical work to support the often claimed benefits provided by ODPs. Determining ODP use from ontologies alone (without interviews or other supporting documentation) is challe...

Designing good multiple choice questions (MCQs) for education and assessment is time consuming and error-prone. An abundance of structured and semi-structured data has led to the development of automatic MCQ generation methods. Recently, ontologies have emerged as powerful tools to enable the automatic generation of MCQs. However, current question...

The OWL Reasoner Evaluation competition is an annual competition (with an associated workshop) that pits OWL 2 compliant reasoners against each other on various standard reasoning tasks over naturally occurring problems. The 2015 competition was the third of its sort and had 14 reasoners competing in six tracks comprising three tasks (consistency,...

SNOMED International is working on a query language specification for SNOMED CT, which we call here SCTQL. SNOMED CT is the leading terminology for use in Electronic Health Records (EHRs). SCTQL can contribute to effective retrieval and reuse of clinical information within EHRs. This paper analyses the functional capabilities needed for SCTQL and p...

In order to provide support for the construction of MCQs, there have been recent efforts to generate MCQs with controlled difficulty from OWL ontologies. Preliminary evaluation suggests that automatically generated questions are not field ready yet and highlight the need for further evaluations. In this study, we have presented an extensive evaluat...

The OWL Reasoner Evaluation (ORE) Competition is an annual competition (with an associated workshop) which pits OWL 2 compliant reasoners against each other on various standard reasoning tasks over naturally occurring problems. The 2015 competition was the third of its sort and had 14 reasoners competing in six tracks comprising three tasks (consis...

Available at http://ceur-ws.org/Vol-1586/

With the growing interest in using ontologies in semantically-enabled applications, the interest in enhancing the quality of such ontologies has grown as well. Standard reasoning services focus on certain obvious dimensions of quality, e.g., to detect inconsistencies and incoherence. In addition, bespoke tools have been presented to address the com...

SKOS and OWL are quite different but complimentary languages. SKOS is targeted at “cognitive” or “navigational” representations, that is, thesauri, controlled vocabularies, and the like. OWL is targeted at logical representations of conceptual knowledge. To a first approximation, SKOS vocabularies try to capture useful relations between concepts, w...

Multiple choice questions (MCQs) are considered highly useful (being easy to take or mark) but quite difficult to create and large numbers are needed to form valid exams and associated practice materials. The idea of re-using an existing ontology to generate MCQs almost suggests itself and has been explored in various projects. In this project, we...

OWL 2 DL is a complex logic with reasoning problems that have a high worst case complexity. Modern reasoners perform mostly very well on naturally occurring ontologies of varying sizes and complexity. This performance is achieved through a suite of complex optimisations (with complex interactions) and elaborate engineering. While the formal basis o...

Ontology-based Multiple Choice Question (MCQ) generation has a relatively short history. Many attempts have been carried out to develop methods to generate MCQs from ontologies. However, there is still a need to understand the applicability of these methods in real educational settings. In this paper, we present an empirical evaluation of ontology-...

Several attempts have been already made to develop similarity measures for ontologies. We noticed that some existing similarity measures are ad-hoc and unprincipled. In addition, there is still a need for similarity measures which are applicable to expressive Description Logics and which are terminological. To address these requirements, we have de...

The World Health Organisation is using OWL as a key technology to develop ICD-11 - the next version of the well-known International Classification of Diseases. Besides providing better opportunities for data integration and linkages to other well-known ontologies such as SNOMED-CT, one of the main promises of using OWL is that it will enable variou...

The quality, and therefore, the usability and reliability of data in digital libraries depends on author disambiguation, i.e., the correct assignment of publications to a particular person. Author disambiguation aims to resolve name ambiguity, i.e., synonyms (the same author publishing under different names), and polysemes (different authors with t...

The Atomic Decomposition of an ontology is a succinct representation of the logic-based modules in that ontology. Ultimately, it reveals the modular structure of the ontology. Atomic Decompositions appear to be useful for both user and non-user facing services. For example, they can be used for ontology comprehension and to facilitate reasoner opti...

OWL 2 Full remains a " catch all " language in the sense that it treats as well formed any legal RDF graph. In contrast, OWL 2 DL, and its sub profiles, exclude large classes of RDF graphs as malformed and thus meaningless. Many ontology documents on the web appear to fall under OWL Full. However, not all ways of being OWL Full are indicative of mo...

Ontologies published on the web can be quite large, from a couple of megabytes to more than a gigabyte. Deploying, importing and using such ontologies can be a problem, both in terms of bandwidth and load time over the web, and in terms of physically storing them. Some ontologies in BioPortal for example are shipped in their compressed form (via th...

Tool development for and empirical experimentation in OWL ontology research require a wide variety of suitable ontologies as input for testing and evaluation purposes and detailed characterisations of real on-tologies. Findings of surveys and results of benchmarking activities may be biased, even heavily, towards manually assembled sets of " someho...

http://ceur-ws.org/Vol-1162/

We present a domain specific ontology editor for viewing, updating and managing a clinical documentation knowledge base. The editor is designed to allow clinical content specialists, who do not have a working knowledge of OWL, Semantic Web technologies or knowledge engineering, to quickly generate ontologies that describe clinical documentation tem...

Clinical assessment scales, such as the Glasgow coma scale, are a core part of Electronic Health Records (EHRs). However, fully representing them in an OWL ontology is challenging: In particular, the determination of a score from patient's observations and clinical findings requires forms of aggregation and addition which are either tedious in OWL...

Medical vocabulary is complex, and convoluted not least because of large numbers of compound terms. Formalized medical terminologies such as SNOMED-CT and ICD-10 take one of two strategies when representing medical language: so-called pre-coordination where valid compound terms are included explicitly and post-coordination where the terminology con...

Very expressive Description Logics in the SH family have worst case complexity ranging from EXPTIME to double NEXPTIME. In spite of this, they are very popular with modellers and serve as the foundation of the Web Ontology Language (OWL), a W3C standard. Highly optimised reasoners handle a wide range of naturally occurring ontologies with relative...

Justifications are the dominant form of explanation for entailments of OWL ontologies, with popular OWL ontology editors, such as Protege 4, providing justification-based explanation facilities. A justification is a minimal subset of an ontology which is sufficient for an entailment to hold; they correspond to the premises of a proof. Unlike proofs...

Given the high expressivity of the Web Ontology Language OWL 2, there is a potential for great diversity in the logical content of OWL ontologies. The fact that many naturally occurring entailments of such ontologies have multiple justifications indicates that ontologies often overdetermine their consequences, suggesting a diversity in supporting r...

Tool development for and empirical experimentation in OWL ontology engineering require a wide variety of suitable ontologies as input for testing and evaluation purposes and detailed characterisations of real ontologies. Empirical activities often resort to (somewhat arbitrarily) hand curated corpora available on the web, such as the NCBO BioPortal...

For ontology reuse and integration, a number of approaches have been devised that aim at identifying modules, i.e., suitably small sets of “relevant” axioms from ontologies. Here we consider three logically sound notions of modules: MEX modules, only applicable to inexpressive ontologies; modules based on semantic locality, a sound approximation of...

The OWL reasoner evaluation (ORE) workshop brings together reasoner developers and ontology engineers in order to discuss and evaluate the performance and robustness of modern reasoners on OWL ontologies. In addition to paper submissions, the workshop featured a live and offline reasoner competition where standard reasoning tasks were tested: class...

The OWL reasoner evaluation (ORE) workshop brings together reasoner developers and ontology engineers in order to discuss and evaluate the performance and robustness of modern reasoners on OWL ontologies. In addition to paper submissions, the workshop featured a live and offline reasoner competition where standard reasoning tasks were tested: class...

In spite of the recent renaissance in lightweight description logics (DLs), many prominent DLs, such as that underlying the Web Ontology Language (OWL), have high worst case complexity for their key inference services. Modern reasoners have a large array of optimization, tuned calculi, and implementation tricks that allow them to perform very well...

Tool development for and empirical experimentation in OWL ontology engineering require a wide variety of suitable ontologies as input for testing and evaluation purposes. Empirical activities often resort to (somewhat arbitrarily) hand curated corpora available on the web, such as the NCBO BioPortal and the TONES Repository, or manually select a se...

http://ceur-ws.org/Vol-999/

Understanding ontology evolution is becoming an active topic of interest for ontology engineers, e.g., there exist large collaboratively-developed ontologies but, unlike in software engineering, comparatively little is understood about the dynamics of historical changes, especially at a fine level of granularity. Only recently has there been a syst...

In this paper we present the diff tool ecco, which detects changes to both axioms and concepts between OWL ontologies. Furthermore, the tool aligns axiom changes between each other, according to a fine-grained change categorisation, and subsequently aligns axiom changes with the concepts that each of those directly affect. The diff is open source,...

This paper analyzes the probabilistic description logic P-\(\mathcal{SROIQ}\) as a fragment of well-known first-order probabilistic logic (FOPL).P-\(\mathcal{SROIQ}\) was suggested as a language that is capable of representing and reasoning about different kinds of uncertainty in ontologies, namely generic probabilistic relationships between concep...

CADIAG-2 is a well known rule-based medical expert system aimed at providing support in medical diagnose in the field of internal medicine. Its knowledge base consists of a large collection of IF-THEN rules that represent uncertain relationships between distinct medical entities. Given this uncertainty and the size of the system, it has been challe...

Due to the high worst case complexity of the core reasoning problem for the expressive profiles of OWL 2, ontology engineers are often surprised and confused by the performance behaviour of reasoners on their ontologies. Even very experienced modellers with a sophisticated grasp of reasoning algorithms do not have a good mental model of reasoner pe...

This paper presents an evaluation of state of the art black box justification finding algorithms on the NCBO BioPortal ontology corpus. This corpus represents a set of naturally occurring ontologies that vary greatly in size and expressivity. The results paint a picture of the performance that can be expected when finding all justifications for ent...

Detecting, much less understanding, the difference between two description logic based ontologies is challenging for ontology engi-neers due, in part, to the possibility of complex, non-local logic effects of axiom changes. First, it is often quite difficult to even determine which concepts have had their meaning altered by a change. Second, once a...

FishBase is an important species data collection produced by the FishBase Information and Research Group Inc (FIN), a not-for-profit NGO with the aim of collecting comprehensive information (from the taxonomic to the ecological) about all the world's finned fish species. FishBase is exposed as a MySQL backed website (supporting a range of canned, a...

Different computational models for generating analogies of the form "A is to B as C is to D" have been proposed over the past 35 years. However, analogy generation is a challenging problem that requires further research. In this article, we present a new approach for generating analogies in Multiple Choice Question (MCQ) format that can be used for...

Extracting a subset of a given OWL ontology that captures all the ontology's knowledge about a specified set of terms is a well-understood task. This task can be based, for instance, on locality-based modules (LBMs). These come in two flavours, syntactic and semantic, and a syntactic LBM is known to contain the corresponding semantic LBM. For synta...

The detection and presentation of changes between OWL ontologies (in the form of a diff) is an important service for ontology engineering, being an active research topic. In this paper, we present a diff tool that incorporates structural and semantic techniques in order to, firstly, distinguish effectual and ineffectual changes between ontolo-gies...

In this paper, we propose a new approach to generate anal-ogy questions of the form "A is to B as ... is to ?" from ontologies. Analogy questions are widely used in multiple-choice tests such as SATs and GREs and are used to assess student's higher cognitive abilities. The design, implementation and evaluation of the new approach are pre-sented in...

Most ontology development environments (ODEs) are term oriented and take a frame-based view of the information in an ontology about a given term. Even tools, such as Protégé 4, designed for axiom oriented development preserve the frame-based view as the central mode of interaction with the ontology. The frame-based approach has a number of advantag...

This paper presents a characterisation of and definitions for the phenomenon of masking in the context of justifications for entailments in ontologies. In essence masking is present within a justification, over a set of justifications, or over a complete ontology when the number of justifications for an entailment does not reflect the number of rea...

The analysis of changes between OWL ontologies (in the form of a diff) is an important service for ontology engineering. A purely syntactic analysis of changes is insufficient to distinguish between changes that have logical impact and those that do not. The current state of the art in semantic diffing ignores logically ineffectual changes and lack...

The analysis of changes between OWL ontologies (in the form of a diff ) is an important service for ontology engineering. A purely syntactic analysis of changes is insufficient to distinguish between changes that have logical impact and those that do not. The current state of the art in semantic diffing ignores logically ineffectual changes and lac...

We present the first large scale investigation into the modular structure of a substantial collection of state-of-the-art biomedical ontolo-gies, namely those maintained in the NCBO BioPortal repository. 5 Using the notion of Atomic Decomposition, we partition BioPortal ontologies into logically coherent subsets (atoms), which are related to each o...

In this paper we examine several forms of modularity in logics as a basis for various conceptions of the topical structure of an ontology. Intuitively, a topic is a coherent fragment of the subject matter of the ontology. Different topics may play different roles: e.g., the main topic (or topics), side topics, or subtopics. If, at the lowest level,...

The National Cancer Institute (NCI) Thesaurus (NCIt) is a biomedical ontology which has been developed for over a decade. Nearly every month from 2003 through 2011, the NCI has published an updated version of the NCIt to the Web as an OWL ontology (as well as in other formats). We collected all 88 OWL versions of the NCIt available and conducted a...

Java is a widespread object-oriented programming language for implementing information systems because it provides means to express various domains of interest. Nevertheless, some fields like Health Care and Life Sciences are so complex that Java is not suited for their design. In comparison, the Web Ontology Language (OWL) provides various powerfu...

Information systems should be designed to allow users to express their information requests in a simple way and to retrieve information that they consider as relevant to these requests. In order to fulfil these requirements, information system designers face many challenges w.r.t. selecting appropriate technologies and deciding on a modelling appro...

Extracting a subset of a given ontology that captures all the ontology's knowledge about a specified set of terms is a well-understood task. This task can be based, for instance, on locality-based modules. However, a single module does not allow us to understand neither topicality, connectedness, structure, or superfluous parts of an ontology, nor...

The detection of changes between OWL ontologies is an important service for ontology engineering. There are several approaches to this problem, both syntactic and semantic. A purely syntactic analysis of changes is insufficient to detect changes with logical effect, while the current state of the art in semantic diffing ignores logically ineffectua...

The canonical standard description logic reasoning service is classification, that is, the generation of the set of atomic subsumptions which are entailed by some ontology. While this consequence relation is well defined and finite, there is significant variance in the composition of that set. For example, it is common (in tools and in discussion)...

Current ontology development tools offer debugging support by presenting justifications for entailments of OWL ontologies. While these minimal subsets have been shown to support debugging and understanding tasks, the occurrence of multiple justifications presents a significant cognitive challenge to users. In many cases even a single entailment may...

In this paper, we present an approach to determining the cognitive complexity of justifications for entailments of OWL ontologies. We introduce a simple cognitive complexity model and present the results of validating that model via experiments involving OWL users. The validation is based on test data derived from a large and diverse corpus of natu...

Extracting a subset of a given ontology that captures all the ontology's knowledge about a specified set of terms is a well-understood task. This task can be based, for instance, on locality-based modules. However, a single module does not allow us to understand neither topic-ality, connectedness, structure, or superfluous parts of an ontology, nor...

Information system designers face many challenges w.r.t. selecting appropriate semantic technologies and deciding on a modelling approach for their system. However, there is no clear methodology yet to evaluate "semantically enriched" information systems. In this paper we present a case study on different modelling approaches for annotating medical...

Analysing the performance of OWL reasoners on expressive OWL ontologies is an ongoing challenge. In this paper, we present a new approach to performance analysis based on justifications for entailments of OWL ontologies. Justifications are minimal subsets of an ontology that are sufficient for an entailment to hold, and are commonly used to debug O...

Justifications — that is, minimal entailing subsets of an ontology — are currently the dominant form of explanation provided by ontology engineering environments, especially those focused on the Web Ontology Language (OWL). Despite this, there are naturally occurring justifications that can be very difficult to understand. In essence, justification...

Efficiently extracting a module from a given ontology that captures all the ontology's knowledge about a set of specified terms is a well-understood task. This task can be based, for instance, on locality-based modules. In contrast, extracting all modules of an ontology is computationally difficult because there can be exponentially many. However,...

This paper presents a discussion on the phenomena of mask- ing in the context of justifications for entailments. Various types of mask- ing are introduced and a definition for each type is given.

The demonstration presents Pronto -a prototype of a non-monotonic probabilistic reasoner for very expressive Description Logics. Pronto is built on top of the OWL DL reasoner Pellet, and is capa-ble of performing default probabilistic reasoning in the Semantic Web. It can handle uncertainty in terminological and assertional DL axioms. The demonstra...

This paper presents a system description of Pronto — the first probabilistic Description Logic reasoner capable of processing knowl-edge bases containing about a thousand of probabilistic axioms. We de-scribe the design and architecture of the reasoner with an emphasis on the components that implement algorithms which are crucial for achiev-ing suc...

This paper analyzes the probabilistic description logic P-SHIQ as a fragment of first-order probabilistic logic (FOPL). P-SHIQ was suggested as a language that is capable of representing and reasoning about different kinds of uncertainty in ontologies, namely generic probabilistic relationships between concepts and probabilistic facts about individ...

Ontology-based data access has received a lot of attention recently, yet there is no clear methodology to evaluate a "semantically enriched" information system in general or an ontology based data ac-cess system in particular. The quality of such an information system clearly depends on how well your data fits your class-level ontology, and how wel...

Justifications play a central role as the basis for explaining entailments in OWL ontologies. While techniques for computing justifications for entailments in consistent ontologies are theoretically and practically well-understood, little is known about the practicalities of computing justifications for inconsistent ontologies. This is despite the...

The standardization of the Web Ontology Language, OWL, leaves (at least) two important issues for Web-based ontologies unsatisfactorily resolved, namely how to represent and reason with multiple distinct, but linked ontologies, and how to enable effective knowledge reuse and sharing on the Semantic Web. In this paper, we present a solution for thes...

In this paper, we describe an approach for ontology comprehension support called model exploration in which models for ontologies are generated and presented interactively. We also discuss the issues involved in using tableau reasoners for the generation of models for model exploration and report on a user study we conducted on our prototype implem...

This paper analyzes the probabilistic description logic P- SHIQ by looking at it as a fragment of probabilistic rst-order logic with semantics based on possible worlds. We argue that this is an ap- propriate way of investigating its properties and developing extensions. We show how the previously made arguments about dierent types of rst-order prob...

Medical research and clinical workflows often involve collaboration between various institutions. Therefore, ontologies such as SNOMED CT 1 or the Foundational Model of Anatomy (FMA) 2 have gained acceptance as an important tool for a common standard of communication. Medical images are often stored in

The current OWL2 specification provides mechanisms for im- porting whole ontologies. This paper discusses the import of only a mod- ule of an external ontology, which is specified by a set of terms (classes and properties) and defined in such a way that it contains "all knowledge" of the external ontology about these terms. We discuss possible desi...

The OWL 2 Web Ontology Language, informally OWL 2, is an ontology language for the Semantic Web with formally defined meaning. OWL 2 ontologies provide classes, properties, individuals, and data values and are stored as Semantic Web documents. OWL 2 ontologies can be used along with information written in RDF, and OWL 2 ontologies themselves are pr...