Technical support for Life Sciences communities on a production grid infrastructure

Production operation of large distributed computing infrastructures (DCI) still requires a lot of human intervention to reach acceptable quality of service. This may be achievable for scientific communities with solid IT support, but it remains a show-stopper for others. Some application execution environments are used to hide runtime technical issues from end users. But they mostly aim at fault-tolerance rather than incident resolution, and their operation still requires substantial manpower. A longer-term support activity is thus needed to ensure sustained quality of service for Virtual Organisations (VO). This paper describes how the biomed VO has addressed this challenge by setting up a technical support team. Its organisation, tooling, daily tasks, and procedures are described. Results are shown in terms of resource usage by end users, amount of reported incidents, and developed software tools. Based on our experience, we suggest ways to measure the impact of the technical support, perspectives to decrease its human cost and make it more community-specific.Comment: HealthGrid'12, Amsterdam : Netherlands (2012

Mapping-based SPARQL access to a MongoDB database

Accessing legacy data as virtual RDF stores is a key issue in the building of the Web of Data. In recent years, the MongoDB database has become a leader in the NoSQL market and the management of very large datasets, making it a significant potential contributor to the Web of Linked Data. Therefore, in this paper we address the research question of how to access arbitrary MongoDB documents with SPARQL.We propose a two-step method to (i) translate a SPARQL query into a pivot abstract query under MongoDB-to-RDF mappings represented in the xR2RML language, then (ii) translate the pivot query into a concrete MongoDB query. We elaborate on the discrepancy between the expressiveness of SPARQL and the MongoDB query language, and we show that we can always come up with a rewriting that shall produce all certain answers

A survey of RDB to RDF translation approaches and tools

ISRN I3S/RR 2013-04-FR 24 pagesRelational databases scattered over the web are generally opaque to regular web crawling tools. To address this concern, many RDB-to-RDF approaches have been proposed over the last years. In this paper, we propose a detailed review of seventeen RDB-to-RDF initiatives, considering end-to-end projects that delivered operational tools. The different tools are classified along three major axes: mapping description language, mapping implementation and data retrieval method. We analyse the motivations, commonalities and differences between existing approaches. The expressiveness of existing mapping languages is not always sufficient to produce semantically rich data and make it usable, interoperable and linkable. We therefore briefly present various strategies investigated in the literature to produce additional knowledge. Finally, we show that R2RML, the W3C recommendation for describing RDB to RDF mappings, may not apply to all needs in the wide scope of RDB to RDF translation applications, leaving space for future extensions

xR2RML: Relational and Non-Relational Databases to RDF Mapping Language

This document describes xR2RML, a language for expressing customized mappings from various types of databases (XML, object-oriented, NoSQL) to RDF datasets. xR2RML flexibly adapts to heterogeneous query languages and data models while remaining free from any specific language or syntax. It extends R2RML, the W3C recommendation for the mapping of relational databases to RDF, and relies on RML for the handling of various data representation formats.Web version available at: http://i3s.unice.fr/~fmichel/xr2rml_specification_v5.htm

Translation of Heterogeneous Databases into RDF, and Application to the Construction of a SKOS Taxonomical Reference

International audienceWhile the data deluge accelerates, most of the data produced remains locked in deep Web databases. For the linked open data to benefit from the potential represented by this huge amount of data, it is crucial to come up with solutions to expose heterogeneous databases as linked data. The xR2RML mapping language is an endeavor towards this goal: it is designed to map various types of databases to RDF, by flexibly adapting to heterogeneous query languages and data models while remaining free from any specific language. It extends R2RML, the W3C recommendation for the mapping of relational databases to RDF, and relies on RML for the handling of various data formats. In this paper we present xR2RML, we analyse data models of several modern databases as well as the format in which query results are returned , and we show how xR2RML translates any result data element into RDF, relying on existing languages such as XPath and JSONPath when necessary. We illustrate some features of xR2RML such as the generation of RDF collections and containers, and the ability to deal with mixed data formats. We also describe a real-world use case in which we applied xR2RML to build a SKOS thesaurus aimed at supporting studies on History of Zoology, Archaeozoology and Conservation Biology

Alcohol Dependence Associated with Increased Utilitarian Moral Judgment: A Case Control Study

Recent studies indicate that emotional processes, mediated by the ventromedial prefrontal cortex (VMPC), are of great importance for moral judgment. Neurological patients with VMPC dysfunction have been shown to generate increased utilitarian moral judgments, i.e. are more likely to endorse emotionally aversive actions in order to maximize aggregate welfare, when faced with emotionally salient personal moral dilemmas. Patients with alcohol dependence (AD) also exhibit impairments in functions mediated by the prefrontal cortex, but whether they exhibit increased utilitarian moral reasoning has not previously been investigated. The aim of this study was to investigate moral judgment in AD patients (n = 20) compared to healthy controls (n = 20) matched by sex, age and education years. Each subject responded to a battery of 50 hypothetical dilemmas categorized as non-moral, moral impersonal and moral personal. They also responded to a questionnaire evaluating explicit knowledge of social and moral norms. Results confirmed our hypothesis that AD patients generated increased utilitarian moral judgment compared to controls when faced with moral personal dilemmas. Crucially, there was no difference in their responses to non-moral or impersonal moral dilemmas, nor knowledge of explicit social and moral norms. One possible explanation is that damage to the VMPC, caused by long term repeated exposure to alcohol results in emotional dysfunction, predisposing to utilitarian moral judgment. This work elucidates a novel aspect of the neuropsychological profile of AD patients, namely a tendency to generate utilitarian moral judgment when faced with emotionally salient moral personal dilemmas

Attention-deficit/hyperactivity disorder and risk for substance use disorders in relatives

BACKGROUND: Previous research indicates that attention-deficit/hyperactivity disorder (ADHD) is highly associated with substance use disorders (SUD). However, these studies have failed to clarify the nature of the overlap. The main aim of this study was to explore whether the overlap between ADHD and SUD could be explained by shared genetic and environmental factors or by harmful effects of ADHD medication. METHODS: We employed a matched cohort design across different levels of family relatedness recorded from 1973-2009. By linking longitudinal Swedish national registers, 62,015 ADHD probands and first-degree and second-degree relatives were identified and matched 1:10 with control subjects without ADHD and their corresponding relatives. Any record of SUD was defined by discharge diagnoses of the International Classification of Diseases or a purchase of any drug used in the treatment of SUD. RESULTS: First-degree relatives of ADHD probands were at elevated risk for SUD (odds ratios 2.2 and 1.8) compared with relatives of control subjects. The corresponding relative risk in second-degree relatives was substantially lower (odd ratios 1.4 and 1.4). The familial aggregation patterns remained similar for first-degree and second-degree relatives after excluding individuals with coexisting disorders such as schizophrenia, bipolar disorder, depression, and conduct disorder. CONCLUSIONS: Our findings suggest that the co-occurrence of ADHD and SUD is due to genetic factors shared between the two disorders, rather than to a general propensity for psychiatric disorders or harmful effects of ADHD medication.The Regional Agreement On Medical Training And Clinical Research (ALF) between Stockholm County Council and Karolinska InstitutetThe Swedish Research CouncilThe Swedish Initiative for Research on Microdata in the Social And Medical Sciences (SIMSAM)Accepte