Recommendations for locus-specific databases and their curation.

Expert curation and complete collection of mutations in genes that affect human health is essential for proper genetic healthcare and research. Expert curation is given by the curators of gene-specific mutation databases or locus-specific databases (LSDBs). While there are over 700 such databases, they vary in their content, completeness, time available for curation, and the expertise of the curator. Curation and LSDBs have been discussed, written about, and protocols have been provided for over 10 years, but there have been no formal recommendations for the ideal form of these entities. This work initiates a discussion on this topic to assist future efforts in human genetics. Further discussion is welcome.

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.

An Abstract Algebraic Theory of L-Fuzzy Relations for Relational Databases

Classical relational databases lack proper ways to manage certain real-world situations including imprecise or uncertain data. Fuzzy databases overcome this limitation by allowing each entry in the table to be a fuzzy set where each element of the corresponding domain is assigned a membership degree from the real interval [0…1]. But this fuzzy mechanism becomes inappropriate in modelling scenarios where data might be incomparable. Therefore, we become interested in further generalization of fuzzy database into L-fuzzy database. In such a database, the characteristic function for a fuzzy set maps to an arbitrary complete Brouwerian lattice L. From the query language perspectives, the language of fuzzy database, FSQL extends the regular Structured Query Language (SQL) by adding fuzzy specific constructions. In addition to that, L-fuzzy query language LFSQL introduces appropriate linguistic operations to define and manipulate inexact data in an L-fuzzy database. This research mainly focuses on defining the semantics of LFSQL. However, it requires an abstract algebraic theory which can be used to prove all the properties of, and operations on, L-fuzzy relations. In our study, we show that the theory of arrow categories forms a suitable framework for that. Therefore, we define the semantics of LFSQL in the abstract notion of an arrow category. In addition, we implement the operations of L-fuzzy relations in Haskell and develop a parser that translates algebraic expressions into our implementation.

Populational Genetic Databases Is a Specific Ethical and Legal Framework Necessary?

Recent scientific advances and new technological developments, most notably the advent of bio-informatics, have led to the emergence of genetic databases with particular characteristics and structures. Paralleling these developments, there has been a proliferation of ethical and legal texts aimed at the regulation of this new form of genetic database.

Exploring geolocation governance perspectives through the study of appropriation and collective action.

Ce mémoire de maîtrise a été rédigé dans l’objectif d’explorer une inégalité. Une inégalité dans les pratiques liées à la saisie et l’exploitation des données utilisateur dans la sphère des technologies et services Web, plus particulièrement dans la sphère des GIS (Geographic Information Systems). En 2014, de nombreuses entreprises exploitent les données de leurs utilisateurs afin d’améliorer leurs services ou générer du revenu publicitaire. Du côté de la sphère publique et gouvernementale, ce changement n’a pas été effectué. Ainsi, les gouvernements fédéraux et municipaux sont démunis de données qui permettraient d’améliorer les infrastructures et services publics. Des villes à travers le monde essayent d’améliorer leurs services et de devenir « intelligentes » mais sont dépourvues de ressources et de savoir faire pour assurer une transition respectueuse de la vie privée et des souhaits des citadins. Comment une ville peut-elle créer des jeux de données géo-référencés sans enfreindre les droits des citadins ? Dans l’objectif de répondre à ces interrogations, nous avons réalisé une étude comparative entre l’utilisation d’OpenStreetMap (OSM) et de Google Maps (GM). Grâce à une série d’entretiens avec des utilisateurs de GM et d’OSM, nous avons pu comprendre les significations et les valeurs d’usages de ces deux plateformes. Une analyse mobilisant les concepts de l’appropriation, de l’action collective et des perspectives critiques variées nous a permis d’analyser nos données d’entretiens pour comprendre les enjeux et problèmes derrière l’utilisation de technologies de géolocalisation, ainsi que ceux liés à la contribution des utilisateurs à ces GIS. Suite à cette analyse, la compréhension de la contribution et de l’utilisation de ces services a été recontextualisée pour explorer les moyens potentiels que les villes ont d’utiliser les technologies de géolocalisation afin d’améliorer leurs infrastructures publiques en respectant leurs citoyens.

On Implementing Joins, Aggregates and Universal Quantifier in Temporal Databases using SQL Standards

A feasible way of implementing a temporal database is by mapping temporal data model onto a conventional data model followed by a commercial database management system. Even though extensions were proposed to standard SQL for supporting temporal databases, such proposals have not yet come across standardization processes. This paper attempts to implement database operators such as aggregates and universal quantifier for temporal databases, implemented on top of relational database systems, using currently available SQL standards.

Study on period search methods of variable stars: Application to ASAS and CRTS databases

Study on variable stars is an important topic of modern astrophysics. After the invention of powerful telescopes and high resolving powered CCD’s, the variable star data is accumulating in the order of peta-bytes. The huge amount of data need lot of automated methods as well as human experts. This thesis is devoted to the data analysis on variable star’s astronomical time series data and hence belong to the inter-disciplinary topic, Astrostatistics. For an observer on earth, stars that have a change in apparent brightness over time are called variable stars. The variation in brightness may be regular (periodic), quasi periodic (semi-periodic) or irregular manner (aperiodic) and are caused by various reasons. In some cases, the variation is due to some internal thermo-nuclear processes, which are generally known as intrinsic vari- ables and in some other cases, it is due to some external processes, like eclipse or rotation, which are known as extrinsic variables. Intrinsic variables can be further grouped into pulsating variables, eruptive variables and flare stars. Extrinsic variables are grouped into eclipsing binary stars and chromospheri- cal stars. Pulsating variables can again classified into Cepheid, RR Lyrae, RV Tauri, Delta Scuti, Mira etc. The eruptive or cataclysmic variables are novae, supernovae, etc., which rarely occurs and are not periodic phenomena. Most of the other variations are periodic in nature. Variable stars can be observed through many ways such as photometry, spectrophotometry and spectroscopy. The sequence of photometric observa- xiv tions on variable stars produces time series data, which contains time, magni- tude and error. The plot between variable star’s apparent magnitude and time are known as light curve. If the time series data is folded on a period, the plot between apparent magnitude and phase is known as phased light curve. The unique shape of phased light curve is a characteristic of each type of variable star. One way to identify the type of variable star and to classify them is by visually looking at the phased light curve by an expert. For last several years, automated algorithms are used to classify a group of variable stars, with the help of computers. Research on variable stars can be divided into different stages like observa- tion, data reduction, data analysis, modeling and classification. The modeling on variable stars helps to determine the short-term and long-term behaviour and to construct theoretical models (for eg:- Wilson-Devinney model for eclips- ing binaries) and to derive stellar properties like mass, radius, luminosity, tem- perature, internal and external structure, chemical composition and evolution. The classification requires the determination of the basic parameters like pe- riod, amplitude and phase and also some other derived parameters. Out of these, period is the most important parameter since the wrong periods can lead to sparse light curves and misleading information. Time series analysis is a method of applying mathematical and statistical tests to data, to quantify the variation, understand the nature of time-varying phenomena, to gain physical understanding of the system and to predict future behavior of the system. Astronomical time series usually suffer from unevenly spaced time instants, varying error conditions and possibility of big gaps. This is due to daily varying daylight and the weather conditions for ground based observations and observations from space may suffer from the impact of cosmic ray particles. Many large scale astronomical surveys such as MACHO, OGLE, EROS, xv ROTSE, PLANET, Hipparcos, MISAO, NSVS, ASAS, Pan-STARRS, Ke- pler,ESA, Gaia, LSST, CRTS provide variable star’s time series data, even though their primary intention is not variable star observation. Center for Astrostatistics, Pennsylvania State University is established to help the astro- nomical community with the aid of statistical tools for harvesting and analysing archival data. Most of these surveys releases the data to the public for further analysis. There exist many period search algorithms through astronomical time se- ries analysis, which can be classified into parametric (assume some underlying distribution for data) and non-parametric (do not assume any statistical model like Gaussian etc.,) methods. Many of the parametric methods are based on variations of discrete Fourier transforms like Generalised Lomb-Scargle peri- odogram (GLSP) by Zechmeister(2009), Significant Spectrum (SigSpec) by Reegen(2007) etc. Non-parametric methods include Phase Dispersion Minimi- sation (PDM) by Stellingwerf(1978) and Cubic spline method by Akerlof(1994) etc. Even though most of the methods can be brought under automation, any of the method stated above could not fully recover the true periods. The wrong detection of period can be due to several reasons such as power leakage to other frequencies which is due to finite total interval, finite sampling interval and finite amount of data. Another problem is aliasing, which is due to the influence of regular sampling. Also spurious periods appear due to long gaps and power flow to harmonic frequencies is an inherent problem of Fourier methods. Hence obtaining the exact period of variable star from it’s time series data is still a difficult problem, in case of huge databases, when subjected to automation. As Matthew Templeton, AAVSO, states “Variable star data analysis is not always straightforward; large-scale, automated analysis design is non-trivial”. Derekas et al. 2007, Deb et.al. 2010 states “The processing of xvi huge amount of data in these databases is quite challenging, even when looking at seemingly small issues such as period determination and classification”. It will be beneficial for the variable star astronomical community, if basic parameters, such as period, amplitude and phase are obtained more accurately, when huge time series databases are subjected to automation. In the present thesis work, the theories of four popular period search methods are studied, the strength and weakness of these methods are evaluated by applying it on two survey databases and finally a modified form of cubic spline method is intro- duced to confirm the exact period of variable star. For the classification of new variable stars discovered and entering them in the “General Catalogue of Vari- able Stars” or other databases like “Variable Star Index“, the characteristics of the variability has to be quantified in term of variable star parameters.

Exploring Bit-Difference for Approximate KNN Search in High-dimensional Databases

In this paper, we develop a novel index structure to support efficient approximate k-nearest neighbor (KNN) query in high-dimensional databases. In high-dimensional spaces, the computational cost of the distance (e.g., Euclidean distance) between two points contributes a dominant portion of the overall query response time for memory processing. To reduce the distance computation, we first propose a structure (BID) using BIt-Difference to answer approximate KNN query. The BID employs one bit to represent each feature vector of point and the number of bit-difference is used to prune the further points. To facilitate real dataset which is typically skewed, we enhance the BID mechanism with clustering, cluster adapted bitcoder and dimensional weight, named the BID⁺. Extensive experiments are conducted to show that our proposed method yields significant performance advantages over the existing index structures on both real life and synthetic high-dimensional datasets.

Databases and cooperative projects of the IZI documentation centre : promoting media literacy. 'Bases de datos y proyectos cooperativos del centro de documentación IZI : promoviendo la alfabetización de los medios de comunicación'.

El Instituto Internacional Central para la Televisión Juvenil y Educativa (IZI) es un centro de investigación y documentación dedicado a promover la calidad en la televisión y medios de comunicación para niños y jóvenes y educación. El departamento de documentación del IZI cuenta con una base de datos de referencia internacional para educadores, investigadores, padres, estudiantes y especialistas de la información. Además el IZI participa en redes nacionales e internacionales educativas documentales. El objetivo esencial de estos proyectos cooperativos es la promoción de la alfabetización de medios de comunicación, que constituye una habilidad imprescindible en la sociedad del conocimiento.

The PERINE Project : cooperation between European Education Databases

Resumen basado en el del autor. El nombre del proyecto, PERINE, es el acr??nimo de Pedagogical and Educational Research Information Network for Europe, y fue coordinador del proyecto ante el organismo patrocinador, la Comisi??n Europea

Library Guide: Searching Databases - Hints & Tips

Detailed guide to searching bibliographic databases for journal articles. This is a generic guide, useful for any subject.

Data - From Bits to Databases

Slides based on Brookshear, augmented with a lot of simple material to encourage the students to understand binary numbers!