The Information-Flow Approach to Ontology-Based Semantic Integration

In this article we argue for the lack of formal foundations for ontology-based semantic alignment. We analyse and formalise the basic notions of semantic matching and alignment and we situate them in the context of ontology-based alignment in open-ended and distributed environments, like the Web. We then use the mathematical notion of information flow in a distributed system to ground three hypotheses that enable semantic alignment. We draw our exemplar applications of this work from a variety of interoperability scenarios including ontology mapping, theory of semantic interoperability, progressive ontology alignment, and situated semantic alignment

Biomedical ontology alignment: An approach based on representation learning

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results

A formal foundation for ontology alignment interaction models

Ontology alignment foundations are hard to find in the literature. The abstract nature of the topic and the diverse means of practice makes it difficult to capture it in a universal formal foundation. We argue that such a lack of formality hinders further development and convergence of practices, and in particular, prevents us from achieving greater levels of automation. In this article we present a formal foundation for ontology alignment that is based on interaction models between heterogeneous agents on the Semantic Web. We use the mathematical notion of information flow in a distributed system to ground our three hypotheses of enabling semantic interoperability and we use a motivating example throughout the article: how to progressively align two ontologies of research quality assessment through meaning coordination. We conclude the article with the presentation---in an executable specification language---of such an ontology-alignment interaction model

Ontology mapping: the state of the art

Ontology mapping is seen as a solution provider in today's landscape of ontology research. As the number of ontologies that are made publicly available and accessible on the Web increases steadily, so does the need for applications to use them. A single ontology is no longer enough to support the tasks envisaged by a distributed environment like the Semantic Web. Multiple ontologies need to be accessed from several applications. Mapping could provide a common layer from which several ontologies could be accessed and hence could exchange information in semantically sound manners. Developing such mapping has beeb the focus of a variety of works originating from diverse communities over a number of years. In this article we comprehensively review and present these works. We also provide insights on the pragmatics of ontology mapping and elaborate on a theoretical approach for defining ontology mapping

Institutionalising Ontology-Based Semantic Integration

We address what is still a scarcity of general mathematical foundations for ontology-based semantic integration underlying current knowledge engineering methodologies in decentralised and distributed environments. After recalling the first-order ontology-based approach to semantic integration and a formalisation of ontological commitment, we propose a general theory that uses a syntax-and interpretation-independent formulation of language, ontology, and ontological commitment in terms of institutions. We claim that our formalisation generalises the intuitive notion of ontology-based semantic integration while retaining its basic insight, and we apply it for eliciting and hence comparing various increasingly complex notions of semantic integration and ontological commitment based on differing understandings of semantics

Cognitive context and arguments from ontologies for learning

The deployment of learning resources on the web by different experts has resulted in the accessibility of multiple viewpoints about the same topics. In this work we assume that learning resources are underpinned by ontologies. Different formalizations of domains may result from different contexts, different use of terminology, incomplete knowledge or conflicting knowledge. We define the notion of cognitive learning context which describes the cognitive context of an agent who refers to multiple and possibly inconsistent ontologies to determine the truth of a proposition. In particular we describe the cognitive states of ambiguity and inconsistency resulting from incomplete and conflicting ontologies respectively. Conflicts between ontologies can be identified through the derivation of conflicting arguments about a particular point of view. Arguments can be used to detect inconsistencies between ontologies. They can also be used in a dialogue between a human learner and a software tutor in order to enable the learner to justify her views and detect inconsistencies between her beliefs and the tutor’s own. Two types of arguments are discussed, namely: arguments inferred directly from taxonomic relations between concepts, and arguments about the necessary an