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

Semantic Grounding Strategies for Tagbased Recommender Systems

Recommender systems usually operate on similarities between recommended items or users. Tag based recommender systems utilize similarities on tags. The tags are however mostly free user entered phrases. Therefore, similarities computed without their semantic groundings might lead to less relevant recommendations. In this paper, we study a semantic grounding used for tag similarity calculus. We show a comprehensive analysis of semantic grounding given by 20 ontologies from different domains. The study besides other things reveals that currently available OWL ontologies are very narrow and the percentage of the similarity expansions is rather small. WordNet scores slightly better as it is broader but not much as it does not support several semantic relationships. Furthermore, the study reveals that even with such number of expansions, the recommendations change considerably.Comment: 13 pages, 5 figure

Business Process Retrieval Based on Behavioral Semantics

This paper develops a framework for retrieving business processes considering search requirements based on behavioral semantics properties; it presents a framework called "BeMantics" for retrieving business processes based on structural, linguistics, and behavioral semantics properties. The relevance of the framework is evaluated retrieving business processes from a repository, and collecting a set of relevant business processes manually issued by human judges. The "BeMantics" framework scored high precision values (0.717) but low recall values (0.558), which implies that even when the framework avoided false negatives, it prone to false positives. The highest pre- cision value was scored in the linguistic criterion showing that using semantic inference in the tasks comparison allowed to reduce around 23.6 % the number of false positives. Using semantic inference to compare tasks of business processes can improve the precision; but if the ontologies are from narrow and specific domains, they limit the semantic expressiveness obtained with ontologies from more general domains. Regarding the perform- ance, it can be improved by using a filter phase which indexes business processes taking into account behavioral semantics propertie

Towards automated knowledge-based mapping between individual conceptualisations to empower personalisation of Geospatial Semantic Web

Geospatial domain is characterised by vagueness, especially in the semantic disambiguation of the concepts in the domain, which makes defining universally accepted geo- ontology an onerous task. This is compounded by the lack of appropriate methods and techniques where the individual semantic conceptualisations can be captured and compared to each other. With multiple user conceptualisations, efforts towards a reliable Geospatial Semantic Web, therefore, require personalisation where user diversity can be incorporated. The work presented in this paper is part of our ongoing research on applying commonsense reasoning to elicit and maintain models that represent users' conceptualisations. Such user models will enable taking into account the users' perspective of the real world and will empower personalisation algorithms for the Semantic Web. Intelligent information processing over the Semantic Web can be achieved if different conceptualisations can be integrated in a semantic environment and mismatches between different conceptualisations can be outlined. In this paper, a formal approach for detecting mismatches between a user's and an expert's conceptual model is outlined. The formalisation is used as the basis to develop algorithms to compare models defined in OWL. The algorithms are illustrated in a geographical domain using concepts from the SPACE ontology developed as part of the SWEET suite of ontologies for the Semantic Web by NASA, and are evaluated by comparing test cases of possible user misconceptions

Towards Analytics Aware Ontology Based Access to Static and Streaming Data (Extended Version)

Real-time analytics that requires integration and aggregation of heterogeneous and distributed streaming and static data is a typical task in many industrial scenarios such as diagnostics of turbines in Siemens. OBDA approach has a great potential to facilitate such tasks; however, it has a number of limitations in dealing with analytics that restrict its use in important industrial applications. Based on our experience with Siemens, we argue that in order to overcome those limitations OBDA should be extended and become analytics, source, and cost aware. In this work we propose such an extension. In particular, we propose an ontology, mapping, and query language for OBDA, where aggregate and other analytical functions are first class citizens. Moreover, we develop query optimisation techniques that allow to efficiently process analytical tasks over static and streaming data. We implement our approach in a system and evaluate our system with Siemens turbine data

A Survey of Volunteered Open Geo-Knowledge Bases in the Semantic Web

Over the past decade, rapid advances in web technologies, coupled with innovative models of spatial data collection and consumption, have generated a robust growth in geo-referenced information, resulting in spatial information overload. Increasing 'geographic intelligence' in traditional text-based information retrieval has become a prominent approach to respond to this issue and to fulfill users' spatial information needs. Numerous efforts in the Semantic Geospatial Web, Volunteered Geographic Information (VGI), and the Linking Open Data initiative have converged in a constellation of open knowledge bases, freely available online. In this article, we survey these open knowledge bases, focusing on their geospatial dimension. Particular attention is devoted to the crucial issue of the quality of geo-knowledge bases, as well as of crowdsourced data. A new knowledge base, the OpenStreetMap Semantic Network, is outlined as our contribution to this area. Research directions in information integration and Geographic Information Retrieval (GIR) are then reviewed, with a critical discussion of their current limitations and future prospects