Enhanced reproducibility of SADI web service workflows with Galaxy and Docke

Background: Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. Findings: This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. Conclusions: The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.

An Access Control Model for Protecting Provenance Graphs

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WormBase: network access to the genome and biology of Caenorhabditis elegans

WormBase (http://www.wormbase.org) is a web-based resource for the Caenorhabditis elegans genome and its biology. It builds upon the existing ACeDB database of the C.elegans genome by providing data curation services, a significantly expanded range of subject areas and a user-friendly front end.

The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).

trEST, trGEN and Hits: access to databases of predicted protein sequences

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent efficient and effective searches of HTG and EST data for protein sequence homologies by standard search methods. Here, we briefly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especially to biologists not having access to a powerful local bioinformatics environment. trEST and trGEN are regularly regenerated databases of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Hits is a web-based data retrieval and analysis system providing access to precomputed matches between protein sequences (including sequences from trEST and trGEN) and patterns and profiles from Prosite and Pfam. The three resources can be accessed via the Hits home page (http://hits.isb-sib.ch).

MEDLINEplus: building and maintaining the National Library of Medicine's consumer health Web service

MEDLINEplus is a Web-based consumer health information resource, made available by the National Library of Medicine (NLM). MEDLINEplus has been designed to provide consumers with a well-organized, selective Web site facilitating access to reliable full-text health information. In addition to full-text resources, MEDLINEplus directs consumers to dictionaries, organizations, directories, libraries, and clearinghouses for answers to health questions. For each health topic, MEDLINEplus includes a preformulated MEDLINE search created by librarians. The site has been designed to match consumer language to medical terminology. NLM has used advances in database and Web technologies to build and maintain MEDLINEplus, allowing health sciences librarians to contribute remotely to the resource. This article describes the development and implementation of MEDLINEplus, its supporting technology, and plans for future development.

A general proposal to multilingual information access based on syntactic-semantic patterns

In the last few years, there has been a wide development in the research on textual information systems. The goal is to improve these systems in order to allow an easy localization, treatment and access to the information stored in digital format (Digital Databases, Documental Databases, and so on). There are lots of applications focused on information access (for example, Web-search systems like Google or Altavista). However, these applications have problems when they must access to cross-language information, or when they need to show information in a language different from the one of the query. This paper explores the use of syntactic-sematic patterns as a method to access to multilingual information, and revise, in the case of Information Retrieval, where it is possible and useful to employ patterns when it comes to the multilingual and interactive aspects. On the one hand, the multilingual aspects that are going to be studied are the ones related to the access to documents in different languages from the one of the query, as well as the automatic translation of the document, i.e. a machine translation system based on patterns. On the other hand, this paper is going to go deep into the interactive aspects related to the reformulation of a query based on the syntactic-semantic pattern of the request.

Assessment of Web Content Accessibility Levels in Spanish Official Online Education Environments

Diversity-based designing, or the goal of ensuring that web-based information is accessible to as many diverse users as possible, has received growing international acceptance in recent years, with many countries introducing legislation to enforce it. This paper analyses web content accessibility levels in Spanish education portals according to the international guidelines established by the World Wide Web Consortium (W3C) and the Web Accessibility Initiative (WAI). Additionally, it suggests the calculation of an inaccessibility rate as a tool for measuring the degree of non-compliance with WAI Guidelines 2.0 as well as illustrating the significant gap that separates people with disabilities from digital education environments (with a 7.77% average). A total of twenty-one educational web portals with two different web depth levels (42 sampling units) were assessed for this purpose using the automated analysis tool Web Accessibility Test 2.0 (TAW, for its initials in Spanish). The present study reveals a general trend towards non-compliance with the technical accessibility recommendations issued by the W3C-WAI group (97.62% of the websites examined present mistakes in Level A conformance). Furthermore, despite the increasingly high number of legal and regulatory measures about accessibility, their practical application still remains unsatisfactory. A greater level of involvement must be assumed in order to raise awareness and enhance training efforts towards accessibility in the context of collective Information and Communication Technologies (ICTs), since this represents not only a necessity but also an ethical, social, political and legal commitment to be assumed by society.

Body Percussion and Team Building through the BAPNE Method

BAPNE Method is a method based on cognitive stimulation integrating music and movement through body percussion. The aim of this research is to explore its whole potential as a tool to build teams. Team building is a philosophy for work design, and since over two decades ago, it defends that obtaining a high performance and organizing efficiency is more useful to perceive employees as interdependent members in a team of work than individuals ones. From this viewpoint, this research advocates that BAPNE Method’s body percussion practice will have an impact on this vision of team work directly. For its own characteristics, body percussion stimulates ways of contact in movement, which ease social ties and, especially, promote group cohesion. Through social, body and, affective dimension; BAPNE Method is capable of developing a shared vision and a single aim, to stimulate team work identity and an atmosphere of trust; and finally, to improve individual communication and satisfaction levels in group tasks.

Open Season for Data Fishing on the Web: The Challenges of the US PRISM Programme for the EU. CEPS Policy Brief No. 293, 18 June 2013

The revelation of the top-secret US intelligence-led PRISM Programme has triggered wide-ranging debates across Europe. Press reports have shed new light on the electronic surveillance ‘fishing expeditions’ of the US National Security Agency and the FBI into the world’s largest electronic communications companies. This Policy Brief by a team of legal specialists and political scientists addresses the main controversies raised by the PRISM affair and the policy challenges that it poses for the EU. Two main arguments are presented: First, the leaks over the PRISM programme have undermined the trust that EU citizens have in their governments and the European institutions to safeguard and protect their privacy; and second, the PRISM affair raises questions regarding the capacity of EU institutions to draw lessons from the past and to protect the data of its citizens and residents in the context of transatlantic relations. The Policy Brief puts forward a set of policy recommendations for the EU to follow and implement a robust data protection strategy in response to the affair.