OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists’ toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. Results We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy’s capability for enriching, modifying and querying biomedical ontologies. Conclusions Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses.

Comparison of Mesh Adaptation Using the Adjoint Methodology and Truncation Error Estimates

Mesh adaptation based on error estimation has become a key technique to improve th eaccuracy o fcomputational-fluid-dynamics computations. The adjoint-based approach for error estimation is one of the most promising techniques for computational-fluid-dynamics applications. Nevertheless, the level of implementation of this technique in the aeronautical industrial environment is still low because it is a computationally expensive method. In the present investigation, a new mesh refinement method based on estimation of truncation error is presented in the context of finite-volume discretization. The estimation method uses auxiliary coarser meshes to estimate the local truncation error, which can be used for driving an adaptation algorithm. The method is demonstrated in the context of two-dimensional NACA0012 and three-dimensional ONERA M6 wing inviscid flows, and the results are compared against the adjoint-based approach and physical sensors based on features of the flow field.

Estimación del error de discretización con principios variacionales multicampo: II. Flexión de placas

Desarrollos recientes para encajar dentro de un marco variacional la llamada Formulación Libre sugieren la posibilidad de introducir un nuevo tipo de estimador de error para cálculos por elementos finitos. Este estimador se basa en una diferencia entre ciertos funcionales multicampo, que toman el mismo valor para la solución exacta del problema. En el presente artículo, dividido en dos partes, se introduce la formulación del estimador para problemas de elasticidad y de flexión de placas según las hipótesis clásicas de Kirchhoff. Se presentan también algunos ejemplos para dar idea de los comportamientos numéricos observados.

SSONDE: Semantic Similarity On liNked Data Entities

Linked data offers a promising setting to encode, publish and share metadata of resources. As the matter of fact, it is already adopted by data producers such as European Environment Agency, US and some EU Governs, whose first ambition is to share (meta)data making their processes more effective and transparent. Such as an increasing interest and involvement of data providers surely represents a genuine witness of the web of data success, but in a longer perspective, frameworks supporting linked data consumers in their decision making processes will be a compelling need. In this respect, the talk is introducing SSONDE, a framework enabling in detailed comparison, ranking and selection of linked data resources through the analysis of their RDF ontology driven metadata. SSONDE implements an instance similarity especially designed to support in resource selection, namely the process stakeholders engage to choose a set of resources suitable for a given analysis purpose: (i) it deploys an asymmetric similarity assessment to emphasize information about gains and losses the stakeholders get adopting a resource in place of another; (ii) it relies on an explicit formalization of contexts to tailor the similarity assessment with respect to specific user-defined selection goals. The talk aims at providing an insight on SSONDE instance similarity and it will briefly describe some examples of SSONDE deployment in the context of linked data consumption.

Adding semantic annotations into (Geospatial) RESTful services

In this paper the authors present an approach for the semantic annotation of RESTful services in the geospatial domain. Their approach automates some stages of the annotation process, by using a combination of resources and services: a cross-domain knowledge base like DBpedia, two domain ontologies like GeoNames and the WGS84 vocabulary, and suggestion and synonym services. The authors’ approach has been successfully evaluated with a set of geospatial RESTful services obtained from ProgrammableWeb.com, where geospatial services account for a third of the total amount of services available in this registry.

A core ontological model for semantic sensor web infrastructures

Semantic Sensor Web infrastructures use ontology-based models to represent the data that they manage; however, up to now, these ontological models do not allow representing all the characteristics of distributed, heterogeneous, and web-accessible sensor data. This paper describes a core ontological model for Semantic Sensor Web infrastructures that covers these characteristics and that has been built with a focus on reusability. This ontological model is composed of different modules that deal, on the one hand, with infrastructure data and, on the other hand, with data from a specific domain, that is, the coastal flood emergency planning domain. The paper also presents a set of guidelines, followed during the ontological model development, to satisfy a common set of requirements related to modelling domain-specific features of interest and properties. In addition, the paper includes the results obtained after an exhaustive evaluation of the developed ontologies along different aspects (i.e., vocabulary, syntax, structure, semantics, representation, and context).

Enabling query technologies for the semantic sensor web

Sensor networks are increasingly being deployed in the environment for many different purposes. The observations that they produce are made available with heterogeneous schemas, vocabularies and data formats, making it difficult to share and reuse this data, for other purposes than those for which they were originally set up. The authors propose an ontology-based approach for providing data access and query capabilities to streaming data sources, allowing users to express their needs at a conceptual level, independent of implementation and language-specific details. In this article, the authors describe the theoretical foundations and technologies that enable exposing semantically enriched sensor metadata, and querying sensor observations through SPARQL extensions, using query rewriting and data translation techniques according to mapping languages, and managing both pull and push delivery modes.

Enabling folksonomies for knowledge extraction: A semantic grounding approach

Folksonomies emerge as the result of the free tagging activity of a large number of users over a variety of resources. They can be considered as valuable sources from which it is possible to obtain emerging vocabularies that can be leveraged in knowledge extraction tasks. However, when it comes to understanding the meaning of tags in folksonomies, several problems mainly related to the appearance of synonymous and ambiguous tags arise, specifically in the context of multilinguality. The authors aim to turn folksonomies into knowledge structures where tag meanings are identified, and relations between them are asserted. For such purpose, they use DBpedia as a general knowledge base from which they leverage its multilingual capabilities.

Problem-based learning supported by semantic techniques

Problem-based learning has been applied over the last three decades to a diverse range of learning environments. In this educational approach, different problems are posed to the learners so that they can develop different solutions while learning about the problem domain. When applied to conceptual modelling, and particularly to Qualitative Reasoning, the solutions to problems are models that represent the behaviour of a dynamic system. The learner?s task then is to bridge the gap between their initial model, as their first attempt to represent the system, and the target models that provide solutions to that problem. We propose the use of semantic technologies and resources to help in bridging that gap by providing links to terminology and formal definitions, and matching techniques to allow learners to benefit from existing models.

The SSN ontology of the W3C semantic sensor network incubator group

The W3C Semantic Sensor Network Incubator group (the SSN-XG) produced an OWL 2 ontology to describe sensors and observations ? the SSN ontology, available at http://purl.oclc.org/NET/ssnx/ssn. The SSN ontology can describe sensors in terms of capabilities, measurement processes, observations and deployments. This article describes the SSN ontology. It further gives an example and describes the use of the ontology in recent research projects.

A novel context ontology to facilitate interoperation of semantic services in environments with wearable devices

The LifeWear-Mobilized Lifestyle with Wearables (Lifewear) project attempts to create Ambient Intelligence (AmI) ecosystems by composing personalized services based on the user information, environmental conditions and reasoning outputs. Two of the most important benefits over traditional environments are 1) take advantage of wearable devices to get user information in a nonintrusive way and 2) integrate this information with other intelligent services and environmental sensors. This paper proposes a new ontology composed by the integration of users and services information, for semantically representing this information. Using an Enterprise Service Bus, this ontology is integrated in a semantic middleware to provide context-aware personalized and semantically annotated services, with discovery, composition and orchestration tasks. We show how these services support a real scenario proposed in the Lifewear project.

Towards a lightweight mobile semantic-based approach for enhancing interaction with smart objects

This work describes a semantic extension for a user-smart object interaction model based on the ECA paradigm (Event-Condition-Action). In this approach, smart objects publish their sensing (event) and action capabilities in the cloud and mobile devices are prepared to retrieve them and act as mediators to configure personalized behaviours for the objects. In this paper, the information handled by this interaction system has been shaped according several semantic models that, together with the integration of an embedded ontological and rule-based reasoner, are exploited in order to (i) automatically detect incompatible ECA rules configurations and to (ii) support complex ECA rules definitions and execution. This semantic extension may significantly improve the management of smart spaces populated with numerous smart objects from mobile personal devices, as it facilitates the configuration of coherent ECA rules.

Some reflections on the IT challenges for a multilingual semantic web

Many attempts have been made to provide multilinguality to the Semantic Web, by means of annotation properties in Natural Language (NL), such as RDFs or SKOS labels, and other lexicon-ontology models, such as lemon, but there are still many issues to be solved if we want to have a truly accessible Multilingual Semantic Web (MSW). Reusability of monolingual resources (ontologies, lexicons, etc.), accessibility of multilingual resources hindered by many formats, reliability of ontological sources, disambiguation problems and multilingual presentation to the end user of all this information in NL can be mentioned as some of the most relevant problems. Unless this NL presentation is achieved, MSW will be restricted to the limits of IT experts, but even so, with great dissatisfaction and disenchantment

Quantity and degree assessment in an RDF.based semantic language

This paper introduces a semantic language developed with the objective to be used in a semantic analyzer based on linguistic and world knowledge. Linguistic knowledge is provided by a Combinatorial Dictionary and several sets of rules. Extra-linguistic information is stored in an Ontology. The meaning of the text is represented by means of a series of RDF-type triples of the form predicate (subject, object). Semantic analyzer is one of the options of the multifunctional ETAP-3 linguistic processor. The analyzer can be used for Information Extraction and Question Answering. We describe semantic representation of expressions that provide an assessment of the number of objects involved and/or give a quantitative evaluation of different types of attributes. We focus on the following aspects: 1) parametric and non-parametric attributes; 2) gradable and non-gradable attributes; 3) ontological representation of different classes of attributes; 4) absolute and relative quantitative assessment; 5) punctual and interval quantitative assessment; 6) intervals with precise and fuzzy boundaries

Deriving semantic sensor metadata from raw measurements

Sensor network deployments have become a primary source of big data about the real world that surrounds us, measuring a wide range of physical properties in real time. With such large amounts of heterogeneous data, a key challenge is to describe and annotate sensor data with high-level metadata, using and extending models, for instance with ontologies. However, to automate this task there is a need for enriching the sensor metadata using the actual observed measurements and extracting useful meta-information from them. This paper proposes a novel approach of characterization and extraction of semantic metadata through the analysis of sensor data raw observations. This approach consists in using approximations to represent the raw sensor measurements, based on distributions of the observation slopes, building a classi?cation scheme to automatically infer sensor metadata like the type of observed property, integrating the semantic analysis results with existing sensor networks metadata.