An Open Source, DDI-based Curation System for Social Science Data

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Building a Canadian Virtual Health Library Database / Création de la Bibliothèque virtuelle canadienne de santé

Introduction: Avec l’abondance d’information gratuite disponible en ligne, la tâche de trouver, de trier et d’acheminer de l’information pertinente à l’auditoire approprié peut s’avérer laborieuse. En décembre 2010, la Bibliothèque virtuelle canadienne de santé / Canadian Virtual Health Library (BVCS) a formé un comité d’experts afin d’identifier, d’évaluer, de sélectionner et d’organiser des ressources d’intérêt pour les professionnels de la santé. Méthodes: Cette affiche identifiera les décisions techniques du comité d’experts, incluant le système de gestion de contenus retenu, l’utilisation des éléments Dublin Core et des descripteurs Medical Subject Headings pour la description des ressources, et le développement et l’adaptation de taxonomies à partir de la classification MeSH. La traduction française des descripteurs MeSH à l’aide du portail CISMeF sera également abordée. Résultats: Au mois de mai 2011, le comité a lancé la base de données BVCS de ressources en ligne gratuites sur la santé, regroupant plus de 1600 sites web et ressources. Une variété de types de contenus sont représentés, incluant des articles et rapports, des bases de données interactives et des outils de pratique clinique. Discussion: Les bénéfices et défis d’une collaboration pancanadienne virtuelle seront présentés, ainsi que l’inclusion cruciale d’un membre francophone pour composer avec la nature bilingue de la base de données. En lien avec cet aspect du projet, l’affiche sera présentée en français et en anglais. Introduction: With the abundance of freely available online information, the task of finding, filtering and fitting relevant information to the appropriate audience, is daunting. In December 2010 the Canadian Virtual Health Library / Bibliothèque virtuelle canadienne de santé (CVHL) formed an expert committee to identify, evaluate, select and organize resources relevant to health professionals. Methods: This poster will identify the key technical decisions of the expert committee including the content management system used to manage the data, the use of Dublin Core elements and Medical Subject Headings to describe the resources, and the development and adaptation of taxonomies from MeSH classification to catalog resources. The translation of MeSH terms to French using the CiSMeF portal will also be discussed. Results: In May 2010, the committee launched the CVHL database of free web-based health resources. Content ranged from online articles and reports to videos, interactive databases and clinical practice tools, and included more than 1,600 websites and resources. Discussion: The benefits and challenges of a virtual, pan-Canadian collaboration, and the critical inclusion of a Francophone member to address the bilingual nature of the database, will be presented. In keeping with the nature of the project, the poster will be presented in French and English.

Compositions in life science data

The aim of this talk is to convince the reader that there are a lot of interesting statistical problems in presentday life science data analysis which seem ultimately connected with compositional statistics. Key words: SAGE, cDNA microarrays, (1D-)NMR, virus quasispecies

Information-based data selection for ensemble data assimilation

Ensemble-based data assimilation is rapidly proving itself as a computationally-efficient and skilful assimilation method for numerical weather prediction, which can provide a viable alternative to more established variational assimilation techniques. However, a fundamental shortcoming of ensemble techniques is that the resulting analysis increments can only span a limited subspace of the state space, whose dimension is less than the ensemble size. This limits the amount of observational information that can effectively constrain the analysis. In this paper, a data selection strategy that aims to assimilate only the observational components that matter most and that can be used with both stochastic and deterministic ensemble filters is presented. This avoids unnecessary computations, reduces round-off errors and minimizes the risk of importing observation bias in the analysis. When an ensemble-based assimilation technique is used to assimilate high-density observations, the data-selection procedure allows the use of larger localization domains that may lead to a more balanced analysis. Results from the use of this data selection technique with a two-dimensional linear and a nonlinear advection model using both in situ and remote sounding observations are discussed.

PCA Tomography: how to extract information from data cubes

Astronomy has evolved almost exclusively by the use of spectroscopic and imaging techniques, operated separately. With the development of modern technologies, it is possible to obtain data cubes in which one combines both techniques simultaneously, producing images with spectral resolution. To extract information from them can be quite complex, and hence the development of new methods of data analysis is desirable. We present a method of analysis of data cube (data from single field observations, containing two spatial and one spectral dimension) that uses Principal Component Analysis (PCA) to express the data in the form of reduced dimensionality, facilitating efficient information extraction from very large data sets. PCA transforms the system of correlated coordinates into a system of uncorrelated coordinates ordered by principal components of decreasing variance. The new coordinates are referred to as eigenvectors, and the projections of the data on to these coordinates produce images we will call tomograms. The association of the tomograms (images) to eigenvectors (spectra) is important for the interpretation of both. The eigenvectors are mutually orthogonal, and this information is fundamental for their handling and interpretation. When the data cube shows objects that present uncorrelated physical phenomena, the eigenvector`s orthogonality may be instrumental in separating and identifying them. By handling eigenvectors and tomograms, one can enhance features, extract noise, compress data, extract spectra, etc. We applied the method, for illustration purpose only, to the central region of the low ionization nuclear emission region (LINER) galaxy NGC 4736, and demonstrate that it has a type 1 active nucleus, not known before. Furthermore, we show that it is displaced from the centre of its stellar bulge.

Mobile application as a tool for urban traffic data collection and generation to advanced traveler information systems using Wi-Fi networks available in urban centers

This paper presents an Advanced Traveler Information System (ATIS) developed on Android platform, which is open source and free. The developed application has as its main objective the free use of a Vehicle-to- Infrastructure (V2I) communication through the wireless network access points available in urban centers. In addition to providing the necessary information for an Intelligent Transportation System (ITS) to a central server, the application also receives the traffic data close to the vehicle. Once obtained this traffic information, the application displays them to the driver in a clear and efficient way, allowing the user to make decisions about his route in real time. The application was tested in a real environment and the results are presented in the article. In conclusion we present the benefits of this application. © 2012 IEEE.

DeCS terminology and the new rules on orthography of Portuguese language: guidelines for an update

PURPOSE: To indicate orthographic changes to be used as a basic reference for professionals, researchers, doctors, teachers, students and users, which are directly linked and performing activities in health services in general, aimed at implementing the correct orthography in recovery and production of their scientific studies. METHODS: For data collection, were shown some examples of terminology DeCS (Descriptors in Health Science) analyzed according to the current spelling and compared with the Orthographic Vocabulary of Portuguese Language (VOLP). RESULTS: It was select and listed examples of key words and/or terms related to Health Sciences, which was compared to the respective rules of the Orthographic Agreement of Portuguese Language, and divided into three items: graphical accentuation, the non use of dieresis and exceptions and, the use of hyphen. CONCLUSION: This study show some guidelines for the orthographic alterations of the terms used by scientific community, according the new orthographic rules, contributing for the efficiency in the description of the documents and consequently in their recovery.

Investigation of the effect of using data collection technology on students' attitudes to science instruction

The purpose of this project was to investigate the effect of using of data collection technology on student attitudes towards science instruction. The study was conducted over the course of two years at Madison High School in Adrian, Michigan, primarily in college preparatory physics classes, but also in one college preparatory chemistry class and one environmental science class. A preliminary study was conducted at a Lenawee County Intermediate Schools student summer environmental science day camp. The data collection technology used was a combination of Texas Instruments TI-84 Silver Plus graphing calculators and Vernier LabPro data collection sleds with various probeware attachments, including motion sensors, pH probes and accelerometers. Students were given written procedures for most laboratory activities and were provided with data tables and analysis questions to answer about the activities. The first year of the study included a pretest and posttest measuring student attitudes towards the class they were enrolled in. Pre-test and post-test data were analyzed to determine effect size, which was found to be very small (Coe, 2002). The second year of the study focused only on a physics class and used Keller’s ARCS model for measuring student motivation based on the four aspects of motivation: Attention, Relevance, Confidence and Satisfaction (Keller, 2010). According to this model, it was found that there were two distinct groups in the class, one of which was motivated to learn and the other that was not. The data suggest that the use of data collection technology in science classes should be started early in a student’s career, possibly in early middle school or late elementary. This would build familiarity with the equipment and allow for greater exploration by the student as they progress through high school and into upper level science courses.

CDAPubMed: a browser extension to retrieve EHR-based biomedical literature

Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a huge number of publications. Against this backdrop, novel information retrieval methods are even more necessary. While web search engines are widespread in many areas, facilitating access to all kinds of information, additional tools are required to automatically link information retrieved from these engines to specific biomedical applications. In the case of clinical environments, this also means considering aspects such as patient data security and confidentiality or structured contents, e.g., electronic health records (EHRs). In this scenario, we have developed a new tool to facilitate query building to retrieve scientific literature related to EHRs. Results: We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH), automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii) generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination. Conclusions: CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard PubMed interface. It has been tested on a public dataset of HL7-CDA documents, returning significantly fewer citations since queries are focused on characteristics identified within the EHR. For instance, compared with more than 200,000 citations retrieved by breast neoplasm, fewer than ten citations were retrieved when ten patient features were added using CDAPubMed. This is an open source tool that can be freely used for non-profit purposes and integrated with other existing systems.