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.

Ecient Inference-aware RDB2RDF Query Rewriting

RDB2RDF systems generate RDF from relational databases, operating in two di�erent manners: materializing the database content into RDF or acting as virtual RDF datastores that transform SPARQL queries into SQL. In the former, inferences on the RDF data (taking into account the ontologies that they are related to) are normally done by the RDF triple store where the RDF data is materialised and hence the results of the query answering process depend on the store. In the latter, existing RDB2RDF systems do not normally perform such inferences at query time. This paper shows how the algorithm used in the REQUIEM system, focused on handling run-time inferences for query answering, can be adapted to handle such inferences for query answering in combination with RDB2RDF systems.

Benchmarking federated SPARQL query engines: Are existing testbeds enough?

Testbeds proposed so far to evaluate, compare, and eventually improve SPARQL query federation systems have still some limitations. Some variables and con�gurations that may have an impact on the behavior of these systems (e.g., network latency, data partitioning and query properties) are not su�ciently de�ned; this a�ects the results and repeatability of independent evaluation studies, and hence the insights that can be obtained from them. In this paper we evaluate FedBench, the most comprehensive testbed up to now, and empirically probe the need of considering additional dimensions and variables. The evaluation has been conducted on three SPARQL query federation systems, and the analysis of these results has allowed to uncover properties of these systems that would normally be hidden with the original testbeds.

Digital libraries for the preservation of research methods and associated artifacts

New digital artifacts are emerging in data-intensive science. For example, scientific workflows are executable descriptions of scientific procedures that define the sequence of computational steps in an automated data analysis, supporting reproducible research and the sharing and replication of best-practice and know-how through reuse. Workflows are specified at design time and interpreted through their execution in a variety of situations, environments, and domains. Hence it is essential to preserve both their static and dynamic aspects, along with the research context in which they are used. To achieve this, we propose the use of multidimensional digital objects (Research Objects) that aggregate the resources used and/or produced in scientific investigations, including workflow models, provenance of their executions, and links to the relevant associated resources, along with the provision of technological support for their preservation and efficient retrieval and reuse. In this direction, we specified a software architecture for the design and implementation of a Research Object preservation system, and realized this architecture with a set of services and clients, drawing together practices in digital libraries, preservation systems, workflow management, social networking and Semantic Web technologies. In this paper, we describe the backbone system of this realization, a digital library system built on top of dLibra.

On correctness in RDF stream processor benchmarking

Two complementary benchmarks have been proposed so far for the evaluation and continuous improvement of RDF stream processors: SRBench and LSBench. They put a special focus on different features of the evaluated systems, including coverage of the streaming extensions of SPARQL supported by each processor, query processing throughput, and an early analysis of query evaluation correctness, based on comparing the results obtained by different processors for a set of queries. However, none of them has analysed the operational semantics of these processors in order to assess the correctness of query evaluation results. In this paper, we propose a characterization of the operational semantics of RDF stream processors, adapting well-known models used in the stream processing engine community: CQL and SECRET. Through this formalization, we address correctness in RDF stream processor benchmarks, allowing to determine the multiple answers that systems should provide. Finally, we present CSRBench, an extension of SRBench to address query result correctness verification using an automatic method.

Towards a systematic benchmarking of ontology-based query rewriting systems

Query rewriting is one of the fundamental steps in ontologybased data access (OBDA) approaches. It takes as inputs an ontology and a query written according to that ontology, and produces as an output a set of queries that should be evaluated to account for the inferences that should be considered for that query and ontology. Different query rewriting systems give support to different ontology languages with varying expressiveness, and the rewritten queries obtained as an output do also vary in expressiveness. This heterogeneity has traditionally made it difficult to compare different approaches, and the area lacks in general commonly agreed benchmarks that could be used not only for such comparisons but also for improving OBDA support. In this paper we compile data, dimensions and measurements that have been used to evaluate some of the most recent systems, we analyse and characterise these assets, and provide a unified set of them that could be used as a starting point towards a more systematic benchmarking process for such systems. Finally, we apply this initial benchmark with some of the most relevant OBDA approaches in the state of the art.

kyrie2: query rewriting under extensional constraints in ELHIO

In this paper we study query answering and rewriting in ontologybased data access. Specifically, we present an algorithm for computing a perfect rewriting of unions of conjunctive queries posed over ontologies expressed in the description logic ELHIO, which covers the OWL 2 QL and OWL 2 EL profiles. The novelty of our algorithm is the use of a set of ABox dependencies, which are compiled into a so-called EBox, to limit the expansion of the rewriting. So far, EBoxes have only been used in query rewriting in the case of DL-Lite, which is less expressive than ELHIO. We have extensively evaluated our new query rewriting technique, and in this paper we discuss the tradeoff between the reduction of the size of the rewriting and the computational cost of our approach.

Accessing and managing open medical resources in Africa over the Internet

Recent commentaries have proposed the advantages of using open exchange of data and informatics resources for improving health-related policies and patient care in Africa. Yet, in many African regions, both private medical and public health information systems are still unaffordable. Open exchange over the social Web 2.0 could encourage more altruistic support of medical initiatives. We have carried out some experiments to demonstrate the feasibility of using this approach to disseminate open data and informatics resources in Africa. After the experiments we developed the AFRICA BUILD Portal, the first Social Network for African biomedical researchers. Through the AFRICA BUILD Portal users can access in a transparent way to several resources. Currently, over 600 researchers are using distributed and open resources through this platform committed to low connections.

Estudio, definición e implementación de una ontología para la creación y consulta de una base de datos relacional sobre datos obtenidos del linaje de las parcelas catastrales.

En los últimos años la evolución de la información compartida por internet ha cambiado enormemente, llegando a convertirse en lo que llamamos hoy la Web Semántica. Este término, acuñado en 2004, muestra una manera más “inteligente” de compartir los datos, de tal manera que éstos puedan ser entendibles por una máquina o por cualquier persona en el mundo. Ahora mismo se encuentra en fase de expansión, prueba de ello es la cantidad de grupos de investigación que están actualmente dedicando sus esfuerzos al desarrollo e implementación de la misma y la amplitud de temáticas que tienen sus trabajos. Con la aparición de la Web Semántica, la tendencia de las bases de datos de nueva creación se está empezando a inclinar hacia la creación de ontologías más o menos sencillas que describan las bases de datos y así beneficiarse de las posibilidades de interoperabilidad que aporta. Con el presente trabajo se pretende el estudio de los beneficios que aporta la implementación de una ontología en una base de datos relacional ya creada, los trabajos necesarios para ello y las herramientas necesarias para hacerlo. Para ello se han tomado unos datos de gran interés y, como continuación a su trabajo, se ha implementado la ontología. Estos datos provienen del estudio de un método para la obtención automatizada del linaje de las parcelas registradas en el catastro español. Abstract: In the last years the evolution of the information shared on the Internet has dramatically changed, emerging what is called Semantic Web. This term appeared in 2004, defining a “smarter” way of sharing data. Data that could be understood by machines or by any human around the world. Nowadays, the Semantic Web is in expansion phase, as it can be probed by the amount of research groups working on this approach and the wide thematic range of their work. With the appearance of the Semantic Web, current database technologies are supported by the creation of ontologies which describe them and therefore get a new set of interoperability possibilities from them. This work focuses in the study of the benefits given by the implementation of an ontology in a created relational database, the steps to follow and the tools necessary to get it done. The study has been done by using data of considerable interest, coming from a study of the lineage of parcels registered in the Spanish cadaster. As a continuation of this work an ontology has been implemented.

Towards a Systematic benchmarking of ontology-based query rewriting systems

Query rewriting is one of the fundamental steps in ontologybased data access (OBDA) approaches. It takes as inputs an ontology and a query written according to that ontology, and produces as an output a set of queries that should be evaluated to account for the inferences that should be considered for that query and ontology. Different query rewriting systems give support to different ontology languages with varying expressiveness, and the rewritten queries obtained as an output do also vary in expressiveness. This heterogeneity has traditionally made it difficult to compare different approaches, and the area lacks in general commonly agreed benchmarks that could be used not only for such comparisons but also for improving OBDA support. In this paper we compile data, dimensions and measurements that have been used to evaluate some of the most recent systems, we analyse and characterise these assets, and provide a unified set of them that could be used as a starting point towards a more systematic benchmarking process for such systems. Finally, we apply this initial benchmark with some of the most relevant OBDA approaches in the state of the art.

Implementación de un recolector de RDF

La web semántica aporta un mayor conocimiento a los datos para que estos puedan ser procesados por las máquinas. Esto es posible gracias a estándares como por ejemplo Resource Framework Description (RDF). Éste, aporta un marco para que la información pueda ser representada de una manera más comprensible para las maquinas. Muchas veces la información no se encuentra codificada en RDF pero igualmente es interesante aprovecharse de sus características. Es por ello que surge la necesidad de crear una herramienta que permita consultas entre distintas fuentes de datos apoyándose en el estándar RDF independientemente del formato de origen de los datos. De esta manera se conseguirá realizar consultas entre las diversas fuentes, las cuales, sin la unificación en un estándar semántico, serían mucho más difíciles de conseguir.---ABSTRACT---The Semantic Web provides a new knowledge framework to data, therefore computers would become capable of analyzing the data. Standards, as Resource Framework Description (RDF), help to achieve it. RDF promotes the easier way for computers on how to describe data. Sometimes data are coded in a different way from RDF, nevertheless it would also be interesting to examine it. Accordingly, the need to create new software emerges. The software, based on RDF, would be able to combine information from different sources regardless of its format. Consequently, several sources, whatever their original formats were, could be queried on an easier way since a common semantic standard is available.

Knowledgeable Feedback via a Cast of Virtual Characters with Different Competences

DynaLearn (http://www.DynaLearn.eu) develops a cognitive artefact that engages learners in an active learning by modelling process to develop conceptual system knowledge. Learners create external representations using diagrams. The diagrams capture conceptual knowledge using the Garp3 Qualitative Reasoning (QR) formalism [2]. The expressions can be simulated, confronting learners with the logical consequences thereof. To further aid learners, DynaLearn employs a sequence of knowledge representations (Learning Spaces, LS), with increasing complexity in terms of the modelling ingredients a learner can use [1]. An online repository contains QR models created by experts/teachers and learners. The server runs semantic services [4] to generate feedback at the request of learners via the workbench. The feedback is communicated to the learner via a set of virtual characters, each having its own competence [3]. A specific feedback thus incorporates three aspects: content, character appearance, and a didactic setting (e.g. Quiz mode). In the interactive event we will demonstrate the latest achievements of the DynaLearn project. First, the 6 learning spaces for learners to work with. Second, the generation of feedback relevant to the individual needs of a learner using Semantic Web technology. Third, the verbalization of the feedback via different animated virtual characters, notably: Basic help, Critic, Recommender, Quizmaster & Teachable agen

Did you validate your ontology? OOPS!

The application of methodologies for building ontologies can im-prove ontology quality. However, such quality is not guaranteed because of the difficulties involved in ontology modelling. These difficulties are related to the inclusion of anomalies or bad practices within the ontology development. Sev-eral authors have provided lists of typical anomalies detected in ontologies dur-ing the last decade. In this context, our aim in this paper is to describe OOPS! (OntOlogy Pitfall Scanner!), a tool for detecting pitfalls in ontologies.

Using online presence to improve online collaborative learning

Social software tools have become an integral part of students? personal lives and their primary communication medium. Likewise, these tools are increasingly entering the enterprise world (within the recent trend known as Enterprise 2.0) and becoming a part of everyday work routines. Aiming to keep the pace with the job requirements and also to position learning as an integral part of students? life, the field of education is challenged to embrace social software. Personal Learning Environments (PLEs) emerged as a concept that makes use of social software to facilitate collaboration, knowledge sharing, group formation around common interests, active participation and reflective thinking in online learning settings. Furthermore, social software allows for establishing and maintaining one?s presence in the online world. By being aware of a student's online presence, a PLE is better able to personalize the learning settings, e.g., through recommendation of content to use or people to collaborate with. Aiming to explore the potentials of online presence for the provision of recommendations in PLEs, in the scope of the OP4L project, we have develop a software solution that is based on a synergy of Semantic Web technologies, online presence and socially-oriented learning theories. In this paper we present the current results of this research work.

Ontology Localization

In the context of the Semantic Web, resources on the net can be enriched by well-defined, machine-understandable metadata describing their associated conceptual meaning. These metadata consisting of natural language descriptions of concepts are the focus of the activity we describe in this chapter, namely, ontology localization. In the framework of the NeOn Methodology, ontology localization is defined as the activity of adapting an ontology to a particular language and culture. This adaptation mainly involves the translation of the natural language descriptions of the ontology from a source natural language to a target natural language, with the final objective of obtaining a multilingual ontology, that is, an ontology documented in several natural languages. The purpose of this chapter is to provide detailed and prescriptive methodological guidelines to support the performance of this activity.