Automatically exposing OpenLifeData via SADI semantic Web Services

Background: Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier to collect and integrate by moving towards the harmonization of data syntax, descriptive vocabularies, and identifiers, as well as providing a standardized mechanism for data access. Second, Web Services, often linked together into workflows, normalize data access and create transparent, reproducible scientific methodologies that can, in principle, be re-used and customized to suit new scientific questions. Constructing queries that traverse semantically-rich Linked Data requires substantial expertise, yet traditional RESTful or SOAP Web Services cannot adequately describe the content of a SPARQL endpoint. We propose that content-driven Semantic Web Services can enable facile discovery of Linked Data, independent of their location. Results: We use a well-curated Linked Dataset - OpenLifeData - and utilize its descriptive metadata to automatically configure a series of more than 22,000 Semantic Web Services that expose all of its content via the SADI set of design principles. The OpenLifeData SADI services are discoverable via queries to the SHARE registry and easy to integrate into new or existing bioinformatics workflows and analytical pipelines. We demonstrate the utility of this system through comparison of Web Service-mediated data access with traditional SPARQL, and note that this approach not only simplifies data retrieval, but simultaneously provides protection against resource-intensive queries. Conclusions: We show, through a variety of different clients and examples of varying complexity, that data from the myriad OpenLifeData can be recovered without any need for prior-knowledge of the content or structure of the SPARQL endpoints. We also demonstrate that, via clients such as SHARE, the complexity of federated SPARQL queries is dramatically reduced.

A semantic middleware to enhance current multimedia retrieval systems with content-based functionalities

210 p. : graf.

SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing

12 p.

Exploring Semantic Textual Similarity

[EN]Measuring semantic similarity and relatedness between textual items (words, sentences, paragraphs or even documents) is a very important research area in Natural Language Processing (NLP). In fact, it has many practical applications in other NLP tasks. For instance, Word Sense Disambiguation, Textual Entailment, Paraphrase detection, Machine Translation, Summarization and other related tasks such as Information Retrieval or Question Answering. In this masther thesis we study di erent approaches to compute the semantic similarity between textual items. In the framework of the european PATHS project1, we also evaluate a knowledge-base method on a dataset of cultural item descriptions. Additionaly, we describe the work carried out for the Semantic Textual Similarity (STS) shared task of SemEval-2012. This work has involved supporting the creation of datasets for similarity tasks, as well as the organization of the task itself.

Semantic change

[ES] En este trabajo se define el cambio semántico, se analizan las causas de que se produzca y se especifican sus tipos en el griego antiguo.

Executing SADI services in Galaxy

Background: In recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension. The availability of Semantic Web-oriented tools in Galaxy, however, is limited. This is also the case for Semantic Web Services such as those provided by the SADI project, i.e. services that consume and produce RDF. Here we present SADI-Galaxy, a tool generator that deploys selected SADI Services as typical Galaxy tools. Results: SADI-Galaxy is a Galaxy tool generator: through SADI-Galaxy, any SADI-compliant service becomes a Galaxy tool that can participate in other out-standing features of Galaxy such as data storage, history, workflow creation, and publication. Galaxy can also be used to execute and combine SADI services as it does with other Galaxy tools. Finally, we have semi-automated the packing and unpacking of data into RDF such that other Galaxy tools can easily be combined with SADI services, plugging the rich SADI Semantic Web Service environment into the popular Galaxy ecosystem. Conclusions: SADI-Galaxy bridges the gap between Galaxy, an easy to use but "static" workflow system with a wide user-base, and SADI, a sophisticated, semantic, discovery-based framework for Web Services, thus benefiting both user communities.

RESTful Discovery and Eventing for Service Provisioning in Assisted Living Environments

Service provisioning in assisted living environments faces distinct challenges due to the heterogeneity of networks, access technology, and sensing/actuation devices in such an environment. Existing solutions, such as SOAP-based web services, can interconnect heterogeneous devices and services, and can be published, discovered and invoked dynamically. However, it is considered heavier than what is required in the smart environment-like context and hence suffers from performance degradation. Alternatively, REpresentational State Transfer (REST) has gained much attention from the community and is considered as a lighter and cleaner technology compared to the SOAP-based web services. Since it is simple to publish and use a RESTful web service, more and more service providers are moving toward REST-based solutions, which promote a resource-centric conceptualization as opposed to a service-centric conceptualization. Despite such benefits of REST, the dynamic discovery and eventing of RESTful services are yet considered a major hurdle to utilization of the full potential of REST-based approaches. In this paper, we address this issue, by providing a RESTful discovery and eventing specification and demonstrate it in an assisted living healthcare scenario. We envisage that through this approach, the service provisioning in ambient assisted living or other smart environment settings will be more efficient, timely, and less resource-intensive.

From Gods to men: A historical overview of the discovery of the chemical elements

To achieve the apparently simple Periodic Table of the Elements has implied tremendous efforts over thousands of years. In this paper we present a brief history of the discovery of the chemical elements from prehistory to the present day, revealing the controversies that arose on the way and claiming the important work performed by alchemists in the advancement of knowledge. This is especially important if we consider that alchemy had a period of existence of many thousands of years, while the "Chemistry", officially established as a science in the eighteenth century, has operated as such for only a few hundred years. Even so, if we consider the progress of discovery and isolation of chemical elements throughout history, it can be observed that the number of elements identified is achieved mainly in the nineteenth and twentieth centuries, reflecting the development of instrumental techniques, that facilitated this task.

Pio del Rio Hortega and the discovery of the oligodendrocytes

Rio del Rio Hortega (1882-1945) discovered microglia and oligodendrocytes (OLGs), and after Ramon y Cajal, was the most prominent figure of the Spanish school of neurology. He began his scientific career with Nicolas Achucarro from whom he learned the use of metallic impregnation techniques suitable to study non-neuronal cells. Later on, he joined Cajal's laboratory. and Subsequently, he created his own group, where he continued to develop other innovative modifications of silver staining methods that revolutionized the study of glial cells a century ago. He was also interested in neuropathology and became a leading authority on Central Nervous System (CNS) tumors. In parallel to this clinical activity, del Rio Hortega rendered the first systematic description of a major polymorphism present in a subtype of macroglial cells that he named as oligodendroglia and later OLGs. He established their ectodermal origin and suggested that they built the myelin sheath of CNS axons, just as Schwann cells did in the periphery. Notably, he also suggested the trophic role of OLGs for neuronal functionality, an idea that has been substantiated in the last few years. Del Rio Hortega became internationally recognized and established an important neurohistological school with outstanding pupils from Spain and abroad, which nearly disappeared after his exile due to the Spanish civil war. Yet, the difficulty of metal impregnation methods and their variability in results, delayed for some decades the confirmation of his great insights into oligodendrocyte biology until the development of electron microscopy and immunohistochemistry. This review aims at summarizing the pioneer and essential contributions of del Rio Hortega to the current knowledge of oligodendrocyte structure and function, and to provide a hint of the scientific personality of this extraordinary and insufficiently recognized man.