9,138 research outputs found
Interoperability and FAIRness through a novel combination of Web technologies
Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs
Linked education: interlinking educational resources and the web of data
Research on interoperability of technology-enhanced learning (TEL) repositories throughout the last decade has led to a fragmented landscape of competing approaches, such as metadata schemas and interface mechanisms. However, so far Web-scale integration of resources is not facilitated, mainly due to the lack of take-up of shared principles, datasets and schemas. On the other hand, the Linked Data approach has emerged as the de-facto standard for sharing data on the Web and offers a large potential to solve interoperability issues in the field of TEL. In this paper, we describe a general approach to exploit the wealth of already existing TEL data on the Web by allowing its exposure as Linked Data and by taking into account automated enrichment and interlinking techniques to provide rich and well-interlinked data for the educational domain. This approach has been implemented in the context of the mEducator project where data from a number of open TEL data repositories has been integrated, exposed and enriched by following Linked Data principles
edge2vec: Representation learning using edge semantics for biomedical knowledge discovery
Representation learning provides new and powerful graph analytical approaches
and tools for the highly valued data science challenge of mining knowledge
graphs. Since previous graph analytical methods have mostly focused on
homogeneous graphs, an important current challenge is extending this
methodology for richly heterogeneous graphs and knowledge domains. The
biomedical sciences are such a domain, reflecting the complexity of biology,
with entities such as genes, proteins, drugs, diseases, and phenotypes, and
relationships such as gene co-expression, biochemical regulation, and
biomolecular inhibition or activation. Therefore, the semantics of edges and
nodes are critical for representation learning and knowledge discovery in real
world biomedical problems. In this paper, we propose the edge2vec model, which
represents graphs considering edge semantics. An edge-type transition matrix is
trained by an Expectation-Maximization approach, and a stochastic gradient
descent model is employed to learn node embedding on a heterogeneous graph via
the trained transition matrix. edge2vec is validated on three biomedical domain
tasks: biomedical entity classification, compound-gene bioactivity prediction,
and biomedical information retrieval. Results show that by considering
edge-types into node embedding learning in heterogeneous graphs,
\textbf{edge2vec}\ significantly outperforms state-of-the-art models on all
three tasks. We propose this method for its added value relative to existing
graph analytical methodology, and in the real world context of biomedical
knowledge discovery applicability.Comment: 10 page
UK utility data integration: overcoming schematic heterogeneity
In this paper we discuss syntactic, semantic and schematic issues which inhibit the integration of utility data in the UK. We then focus on the techniques employed within the VISTA project to overcome schematic heterogeneity. A Global
Schema based architecture is employed. Although automated approaches to Global Schema definition were attempted
the heterogeneities of the sector were too great. A manual approach to Global Schema definition was employed. The
techniques used to define and subsequently map source utility data models to this schema are discussed in detail. In order to ensure a coherent integrated model, sub and cross domain validation issues are then highlighted. Finally the proposed framework and data flow for schematic integration is introduced
Going Deeper with Semantics: Video Activity Interpretation using Semantic Contextualization
A deeper understanding of video activities extends beyond recognition of
underlying concepts such as actions and objects: constructing deep semantic
representations requires reasoning about the semantic relationships among these
concepts, often beyond what is directly observed in the data. To this end, we
propose an energy minimization framework that leverages large-scale commonsense
knowledge bases, such as ConceptNet, to provide contextual cues to establish
semantic relationships among entities directly hypothesized from video signal.
We mathematically express this using the language of Grenander's canonical
pattern generator theory. We show that the use of prior encoded commonsense
knowledge alleviate the need for large annotated training datasets and help
tackle imbalance in training through prior knowledge. Using three different
publicly available datasets - Charades, Microsoft Visual Description Corpus and
Breakfast Actions datasets, we show that the proposed model can generate video
interpretations whose quality is better than those reported by state-of-the-art
approaches, which have substantial training needs. Through extensive
experiments, we show that the use of commonsense knowledge from ConceptNet
allows the proposed approach to handle various challenges such as training data
imbalance, weak features, and complex semantic relationships and visual scenes.Comment: Accepted to WACV 201
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