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.

Transforming meteorological data into linked data

This paper describes the process followed in order to make some of the public meterological data from the Agencia Estatal de Meteorología (AEMET, Spanish Meteorological Office) available as Linked Data. The method followed has been already used to publish geographical, statistical, and leisure data. The data selected for publication are generated every ten minutes by the 250 automatic stations that belong to AEMET and that are deployed across Spain. These data are available as spreadsheets in the AEMET data catalog, and contain more than twenty types of measurements per station. Spreadsheets are retrieved from the website, processed with Python scripts, transformed to RDF according to an ontology network about meteorology that reuses the W3C SSN Ontology, published in a triple store and visualized in maps with Map4rdf.

A Keyword-driven approach for generating OWL DL conformance test data

The conformance of semantic technologies has to be systematically evaluated to measure and verify the real adherence of these technologies to the Semantic Web standards. Currente valuations of semantic technology conformance are not exhaustive enough and do not directly cover user requirements and use scenarios, which raises the need for a simple, extensible and parameterizable method to generate test data for such evaluations. To address this need, this paper presents a keyword-driven approach for generating ontology language conformance test data that can be used to evaluate semantic technologies, details the definition of a test suite for evaluating OWL DL conformance using this approach,and describes the use and extension of this test suite during the evaluation of some tools.

Combining data mining and ontology engineering to enrich ontologies and linked data

In this position paper, we claim that the need for time consuming data preparation and result interpretation tasks in knowledge discovery, as well as for costly expert consultation and consensus building activities required for ontology building can be reduced through exploiting the interplay of data mining and ontology engineering. The aim is to obtain in a semi-automatic way new knowledge from distributed data sources that can be used for inference and reasoning, as well as to guide the extraction of further knowledge from these data sources. The proposed approach is based on the creation of a novel knowledge discovery method relying on the combination, through an iterative ?feedbackloop?, of (a) data mining techniques to make emerge implicit models from data and (b) pattern-based ontology engineering to capture these models in reusable, conceptual and inferable artefacts.

SRBench: A streaming RDF/SPARQL benchmark

We introduce SRBench, a general-purpose benchmark primarily designed for streaming RDF/SPARQL engines, completely based on real-world data sets from the Linked Open Data cloud. With the increasing problem of too much streaming data but not enough tools to gain knowledge from them, researchers have set out for solutions in which Semantic Web technologies are adapted and extended for publishing, sharing, analysing and understanding streaming data. To help researchers and users comparing streaming RDF/SPARQL (strRS) engines in a standardised application scenario, we have designed SRBench, with which one can assess the abilities of a strRS engine to cope with a broad range of use cases typically encountered in real-world scenarios. The data sets used in the benchmark have been carefully chosen, such that they represent a realistic and relevant usage of streaming data. The benchmark defines a concise, yet omprehensive set of queries that cover the major aspects of strRS processing. Finally, our work is complemented with a functional evaluation on three representative strRS engines: SPARQLStream, C-SPARQL and CQELS. The presented results are meant to give a first baseline and illustrate the state-of-the-art.

Workflow-centric research objects: First class citizens in scholarly discourse.

A workflow-centric research object bundles a workflow, the provenance of the results obtained by its enactment, other digital objects that are relevant for the experiment (papers, datasets, etc.), and annotations that semantically describe all these objects. In this paper, we propose a model to specify workflow-centric research objects, and show how the model can be grounded using semantic technologies and existing vocabularies, in particular the Object Reuse and Exchange (ORE) model and the Annotation Ontology (AO).We describe the life-cycle of a research object, which resembles the life-cycle of a scienti?c experiment.

Characterising emergent semantics in Twitter lists

Twitter lists organise Twitter users into multiple, often overlapping, sets. We believe that these lists capture some form of emergent semantics, which may be useful to characterise. In this paper we describe an approach for such characterisation, which consists of deriving semantic relations between lists and users by analyzing the cooccurrence of keywords in list names. We use the vector space model and Latent Dirichlet Allocation to obtain similar keywords according to co-occurrence patterns. These results are then compared to similarity measures relying on WordNet and to existing Linked Data sets. Results show that co-occurrence of keywords based on members of the lists produce more synonyms and more correlated results to that of WordNet similarity measures.

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.

Demo paper: tablet-based visualization of transportation data in Madrid using SPARQLStream

In this demo paper we describe an iOS-based application that allows visualizing live bus transport data in Madrid from static and streaming RDF endpoints, reusing the Web services provided by the bus transport authority in the city and wrapping them using SPARQLStream

KATS: A Knowledge Acquisition Tool Based on Electronic Document Processing

This paper describes a particular knowledge acquisition tool for the construction and maintenance of the knowledge model of an intelligent system for emergency management in the field of hydrology. This tool has been developed following an innovative approach directed to end-users non familiarized in computer oriented terminology. According to this approach, the tool is conceived as a document processor specialized in a particular domain (hydrology) in such a way that the whole knowledge model is viewed by the user as an electronic document. The paper first describes the characteristics of the knowledge model of the intelligent system and summarizes the problems that we found during the development and maintenance of such type of model. Then, the paper describes the KATS tool, a software application that we have designed to help in this task to be used by users who are not experts in computer programming. Finally, the paper shows a comparison between KATS and other approaches for knowledge acquisition.

Estudio de las posibilidades de los datos abiertos enlazados (Linked Open Data) para la realización de mashups de ámbito geográfico.

La web ha sufrido una drástica transformación en los últimos años, debido principalmente a su popularización y a la enorme cantidad de información que alberga. Debido a estos factores se ha dado el salto de la denominada Web de Documentos, a la Web Semántica, donde toda la información está relacionada con otra. Las principales ventajas de la información enlazada estriban en la facilidad de reutilización, accesibilidad y disponibilidad para ser encontrada por el usuario. En este trabajo se pretende poner de manifiesto la utilidad de los datos enlazados aplicados al ámbito geográfico y mostrar como pueden ser empleados hoy en día. Para ello se han explotado datos enlazados de carácter espacial provenientes de diferentes fuentes, a través de servidores externos o endpoints SPARQL. Además de eso se ha trabajado con un servidor privado capaz de proporcionar información enlazada almacenada en un equipo personal. La explotación de información enlazada se ha implementado en una aplicación web en lenguaje JavaScript, tratando de abstraer totalmente al usuario del tratamiento de los datos a nivel interno de la aplicación. Esta aplicación cuenta además con algunos módulos y opciones capaces de interactuar con las consultas realizadas a los servidores, consiguiendo un entorno más intuitivo y agradable para el usuario. ABSTRACT: In recent years the web has suffered a drastic transformation because of the popularization and the huge amount of stored information. Due to these factors it has gone from Documents web to Semantic web, where the data are linked. The main advantages of Linked Data lie in the ease of his reuse, accessibility and availability to be located by users. The aim of this research is to highlight the usefulness of the geographic linked data and show how can be used at present time. To get this, the spatial linked data coming from several sources have been managed through external servers or also called endpoints. Besides, it has been worked with a private server able to provide linked data stored in a personal computer. The use of linked data has been implemented in a JavaScript web application, trying completely to abstract the internally data treatment of the application to make the user ignore it. This application has some modules and options that are able to interact with the queries made to the servers, getting a more intuitive and kind environment for users.

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.

A linked data approach to sentiment and emotion analysis of twitter in the financial domain

Sentiment analysis has recently gained popularity in the financial domain thanks to its capability to predict the stock market based on the wisdom of the crowds. Nevertheless, current sentiment indicators are still silos that cannot be combined to get better insight about the mood of different communities. In this article we propose a Linked Data approach for modelling sentiment and emotions about financial entities. We aim at integrating sentiment information from different communities or providers, and complements existing initiatives such as FIBO. The ap- proach has been validated in the semantic annotation of tweets of several stocks in the Spanish stock market, including its sentiment information.