trome, trEST and trGEN: databases of predicted protein sequences.

We previously introduced two new protein databases (trEST and trGEN) of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Here, we present the updates made on these two databases plus a new database (trome), which uses alignments of EST data to HTG or full genomes to generate virtual transcripts and coding sequences. This new database is of higher quality and since it contains the information in a much denser format it is of much smaller size. These new databases are in a Swiss-Prot-like format and are updated on a weekly basis (trEST and trGEN) or every 3 months (trome). They can be downloaded by anonymous ftp from ftp://ftp.isrec.isb-sib.ch/pub/databases.

Intelligence-led crime scene processing. Part I : Forensic intelligence.

Forensic science is generally defined as the application of science to address questions related to the law. Too often, this view restricts the contribution of science to one single process which eventually aims at bringing individuals to court while minimising risk of miscarriage of justice. In order to go beyond this paradigm, we propose to refocus the attention towards traces themselves, as remnants of a criminal activity, and their information content. We postulate that traces contribute effectively to a wide variety of other informational processes that support decision making inmany situations. In particular, they inform actors of new policing strategies who place the treatment of information and intelligence at the centre of their systems. This contribution of forensic science to these security oriented models is still not well identified and captured. In order to create the best condition for the development of forensic intelligence, we suggest a framework that connects forensic science to intelligence-led policing (part I). Crime scene attendance and processing can be envisaged within this view. This approach gives indications abouthowto structure knowledge used by crime scene examiners in their effective practice (part II).

Les registres publics à l'ère du numérique

Les registres publics contiennent des informations très riches sur les administrés. Étant de plus en plus souvent informatisés et capables d'échanger des données, ces registres pourraient constituer une ressource inestimable à l'heure de mettre en place l'administration numérique. Cela ne va par contre pas sans poser des problèmes de protection des données et implique dans tous les cas la mise en place de processus de décision quant au partage de ces données, en fonction d'objectifs précis et dans un contexte donné. Dans cet article, nous proposons un cadre d'analyse qui permet d'évaluer les besoins en information pour une prestation administrative donnée, ainsi que les possibilités de partage ou les restrictions en matière de protection de la sphère privée. Public registers contain highly rich information about citizens. As these registers are, to a steadily increasing extent, digitized and designed for data-sharing purposes, they represent an invaluable resource when implementing e-government. At the same time, they raise a number of serious data protection issues that entail, at all events, establishing a decision-making process to frame the sharing of these data on the basis of specific objectives and in accordance with a particular context. In this article, I propose an analytical framework serving to assess both the informational requirements associated with a given administrative service as well as the opportunities for sharing data, coupled with privacy restrictions.

The Gene Ontology in 2010: extensions and refinements.

The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.

How do the different components of episodic memory develop? Role of executive functions and short-term feature-binding abilities.

This study investigated the development of all 3 components of episodic memory (EM), as defined by Tulving, namely, core factual content, spatial context, and temporal context. To this end, a novel, ecologically valid test was administered to 109 participants aged 4-16 years. Results showed that each EM component develops at a different rate. Ability to memorize factual content emerges early, whereas context retrieval abilities continue to improve until adolescence, due to persistent encoding difficulties (isolated by comparing results on free recall and recognition tasks). Exploration of links with other cognitive functions revealed that short-term feature-binding abilities contribute to all EM components, and executive functions to temporal and spatial context, although ability to memorize temporal context is predicted mainly by age.

Proposta i implementació d'un motor de recuperació d'informació especialitzat en dret d'estrangeria (Codex)

CODEX SEARCH és un motor de recuperació d'informació especialitzat en dret d'estrangeria que està basat en eines i coneixement lingüístics. Per a desenvolupar un SRI (sistema de recuperació d'informació) eficient en el domini indicat no n'hi ha prou amb emprar un model tradicional de RI (recuperació d'informació), és a dir, comparar els termes de la pregunta amb els de la resposta, bàsicament perquè no expressen implicacions. En aquest sentit, la solució lingüística proposada es basa a incorporar el coneixement dels especialistes mitjançant la integració en el sistema d'una llibreria de casos. Els casos són exemples de procediments aplicats per experts/ertes en la solució de problemes que han ocorregut en la realitat i que han acabat en èxit o fracàs. Els resultats obtinguts en aquesta primera fase són molt encoratjadors, però és necessari continuar la investigació en aquest camp per millorar el rendiment del prototip.

EuroPhenome: a repository for high-throughput mouse phenotyping data.

The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated high-throughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies.

The Biblioteca de Catalunya: working for the present and the future

The Biblioteca de Catalunya (BC) was created in 1907 by the Institut d’Estudis Catalans (IEC). In 1914 the Mancomunitat de Catalunya gave the library its condition of cultural and public service, open to researchers and scholars. The library underwent several changes as a consequence of political events, along the most of 20th century. In 1981 it was recognized by law as national library and it recovered its foundational aim of gathering, preserving and disseminating the bibliographical output of Catalonia and the production related with the Catalan linguistic field. As the proud host of ANADP2, the BC wants to show the attendees to the conference how, since 2004, has positioned itself to face the challenge of the new informational and technological paradigm. The library strategy for oncoming years includes giving open and free access online to the digitization of many of his collections through the portals MDC (Digital Memory of Catalonia), ARCA (Old Catalan Serials Archive) and Google Books project; the creation of the Web Archive of Catalonia and, as the last step in the consolidation of its policy, a high-security preserving repository named COFRE, based on the international guidelines and initiatives and the experience of the BC itself.

Uncertainty, electoral incentives and political myopia

We study the determinants of political myopia in a rational model of electoral accountability where the key elements are informational frictions and uncertainty. We build aframework where political ability is ex-ante unknown and policy choices are not perfectlyobservable. On the one hand, elections improve accountability and allow to keep well-performing incumbents. On the other, politicians invest too little in costly policies withfuture returns in an attempt to signal high ability and increase their reelection probability.Contrary to the conventional wisdom, uncertainty reduces political myopia and may, undersome conditions, increase social welfare. We use the model to study how political rewardscan be set so as to maximise social welfare and the desirability of imposing a one-term limitto governments. The predictions of our theory are consistent with a number of stylised factsand with a new empirical observation documented in this paper: aggregate uncertainty, measured by economic volatility, is associated to better fiscal discipline in a panel of 20 OECDcountries.

Application of text-mining for updating protein post-translational modification annotation in UniProtKB.

BACKGROUND: The annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles are being published on this topic. To help curators cope with this growing body of information we have developed a system which extracts information from the scientific literature for the most frequently annotated PTMs in UniProtKB. RESULTS: The procedure uses a pattern-matching and rule-based approach to extract sentences with information on the type and site of modification. A ranked list of protein candidates for the modification is also provided. For PTM extraction, precision varies from 57% to 94%, and recall from 75% to 95%, according to the type of modification. The procedure was used to track new publications on PTMs and to recover potential supporting evidence for phosphorylation sites annotated based on the results of large scale proteomics experiments. CONCLUSIONS: The information retrieval and extraction method we have developed in this study forms the basis of a simple tool for the manual curation of protein post-translational modifications in UniProtKB/Swiss-Prot. Our work demonstrates that even simple text-mining tools can be effectively adapted for database curation tasks, providing that a thorough understanding of the working process and requirements are first obtained. This system can be accessed at http://eagl.unige.ch/PTM/.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters

Information about the genomic coordinates and the sequence of experimentally identified transcription factor binding sites is found scattered under a variety of diverse formats. The availability of standard collections of such high-quality data is important to design, evaluate and improve novel computational approaches to identify binding motifs on promoter sequences from related genes. ABS (http://genome.imim.es/datasets/abs2005/index.html) is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. A simple and easy-to-use web interface facilitates data retrieval allowing different views of the information. In addition, the release 1.0 of ABS includes a customizable generator of artificial datasets based on the known sites contained in the collection and an evaluation tool to aid during the training and the assessment of motif-finding programs.

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

In past years, comprehensive representations of cell signalling pathways have been developed by manual curation from literature, which requires huge effort and would benefit from information stored in databases and from automatic retrieval and integration methods. Once a reconstruction of the network of interactions is achieved, analysis of its structural features and its dynamic behaviour can take place. Mathematical modelling techniques are used to simulate the complex behaviour of cell signalling networks, which ultimately sheds light on the mechanisms leading to complex diseases or helps in the identification of drug targets. A variety of databases containing information on cell signalling pathways have been developed in conjunction with methodologies to access and analyse the data. In principle, the scenario is prepared to make the most of this information for the analysis of the dynamics of signalling pathways. However, are the knowledge repositories of signalling pathways ready to realize the systems biology promise? In this article we aim to initiate this discussion and to provide some insights on this issue.