Bioinformatics service reconciliation by heterogeneous schema transformation

This paper focuses on the problem of bioinformatics service reconciliation in a generic and scalable manner so as to enhance interoperability in a highly evolving field. Using XML as a common representation format, but also supporting existing flat-file representation formats, we propose an approach for the scalable semi-automatic reconciliation of services, possibly invoked from within a scientific workflows tool. Service reconciliation may use the AutoMed heterogeneous data integration system as an intermediary service, or may use AutoMed to produce services that mediate between services. We discuss the application of our approach for the reconciliation of services in an example bioinformatics workflow. The main contribution of this research is an architecture for the scalable reconciliation of bioinformatics services

vSPARQL: A View Definition Language for the Semantic Web

Translational medicine applications would like to leverage the biological and biomedical ontologies, vocabularies, and data sets available on the semantic web. We present a general solution for RDF information set reuse inspired by database views. Our view definition language, vSPARQL, allows applications to specify the exact content that they are interested in and how that content should be restructured or modified. Applications can access relevant content by querying against these view definitions. We evaluate the expressivity of our approach by defining views for practical use cases and comparing our view definition language to existing query languages

The Case for Dynamic Models of Learners' Ontologies in Physics

In a series of well-known papers, Chi and Slotta (Chi, 1992; Chi & Slotta, 1993; Chi, Slotta & de Leeuw, 1994; Slotta, Chi & Joram, 1995; Chi, 2005; Slotta & Chi, 2006) have contended that a reason for students' difficulties in learning physics is that they think about concepts as things rather than as processes, and that there is a significant barrier between these two ontological categories. We contest this view, arguing that expert and novice reasoning often and productively traverses ontological categories. We cite examples from everyday, classroom, and professional contexts to illustrate this. We agree with Chi and Slotta that instruction should attend to learners' ontologies; but we find these ontologies are better understood as dynamic and context-dependent, rather than as static constraints. To promote one ontological description in physics instruction, as suggested by Slotta and Chi, could undermine novices' access to productive cognitive resources they bring to their studies and inhibit their transition to the dynamic ontological flexibility required of experts.Comment: The Journal of the Learning Sciences (In Press

Challenges in Bridging Social Semantics and Formal Semantics on the Web

This paper describes several results of Wimmics, a research lab which names stands for: web-instrumented man-machine interactions, communities, and semantics. The approaches introduced here rely on graph-oriented knowledge representation, reasoning and operationalization to model and support actors, actions and interactions in web-based epistemic communities. The re-search results are applied to support and foster interactions in online communities and manage their resources

Knowledge Management for Public Administrations: Technical Realizations of an Enterprise Attention Management System

The improvement of governments’ efficiency has gained great importance and validity especially in the current times of economic downturn. E-Government constitutes the most contemporary techno-managerial proposition in the track of possible interventions. The paper addresses, more specifically, empowerments necessitated by Public Administration (PA) organizations. Anchored on the needs of three real-life cases, the paper describes the conception and the realization of an IT artefact together with its methodological appeals aiming at improving information access and delivery and thus PAs’ decision making capacity. Our proposition constitutes a novel approach for managing users’ attention in knowledge intensive organizations which goes beyond informing a user about changes in relevant information towards proactively supporting the user to react on changes. The approach is based on an expressive attention model, which is realized by combining ECA (Event-Condition-Action) rules with ontologies. The technical realizations described in the paper constitute the underlying infrastructure of an Enterprise Attention Management System

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

An ontological approach for recovering legacy business content

Legacy Information Systems (LIS) pose a challenge for many organizations. On one hand, LIS are viewed as aging systems needing replacement; on the other hand, years of accumulated business knowledge have made these systems mission-critical. Current approaches however are often criticized for being overtly dependent on technology and ignoring the business knowledge which resides within LIS. In this light, this paper proposes a means of capturing the business knowledge in a technology agnostic manner and transforming it in a way that reaps the benefits of clear semantic expression - this transformation is achieved via the careful use of ontology. The approach called Content Sophistication (CS) aims to provide a model of the business that more closely adheres to the semantics and relationships of objects existing in the real world. The approach is illustrated via an example taken from a case study concerning the renovation of a large financial system and the outcome of the approach results in technology agnostic models that show improvements along several dimensions