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International audience; In the present work, we examine and describe the representation of students’ mental health, as reflected in information resources available on PubMed and on LibraryThing, and as evidenced by Medical Knowledge Organization Systems (MKOS) used to index documents on this topic.

International audience; Libraries, as information mediators for responsible fishing, can make an effort to balance the limitations of self-archiving practice of those profiteering from open access, but not maintaining e-repositories. In other words, it will allow librarians to change the nature of this system using to do so the capabilities of technology to provide the information quickly, to forget the world of the subscriptions, to switch to the free market of information in science and technology, through the direct supply of documents. In a world standardized by permanent change and innovation, that is essential for capitalism's survival, the perpetual technological development is into the hands of the reactionaries, who fear it as a subject of political discussion. This initiative must be driven by the division of labour, getting ahead people who seek a managerial position, within the framework of cooperative collection development,or inside consortia, or determining the use of information technology.; Las bibliotecas, como mediadores en la información para la pesca responsable, pueden hacer un esfuerzo que contrarreste las limitaciones en la voluntad de autoarchivo de quienes se benefician del acceso abierto, pero colaboran poco al mantenimiento de repositorios. Es decir, los bibliotecarios podrán cambiar la naturaleza de este sistema utilizando las capacidades de la tecnología para facilitar rápidamente información, con el objetivo de olvidar el mundo de las suscripciones para cambiar al mercado libre en la información en ciencia y tecnología, por medio del suministro directo de documentos. En un mundo en el que la innovación y el cambio permanente se han convertido en la norma y en la condición misma de la supervivencia del capitalismo, el desarrollo tecnológico perpetuo se encuentra en manos de los reaccionarios, quienes temen que pueda ser objeto de discusión política. Es la división del trabajo la que debe llevar la iniciativa, por delante del mundo de la gestión, sea en el marco del desarrollo cooperativo de colecciones, bien en el de los consorcios e incluso en el de la tecnología.; Les bibliothèques comme des médiateurs d'information pour une pêche responsable, peuvent faire un effort pour équilibrer les limitations de la pratique d'autoarchivage à l'encontre de ceux qui profitent de l'accès libre, bien qu'ils n'entretiennent pas des référentiels numériques. Autrement dit, ceci permettrait aux bibliothècaires de changer la nature de ce système, utilisant pour ce faire les possibilités de la technologie comme moyen de fournir rapidement des informations, oubliant le monde des abonnements, au passage sur le marché libre de l'information en sciences et technologies, par le biais de la fourniture directe de documents. Dans un monde à l'esprit d'innovation et de standardisation, qui est indispensable à la survie du capitalisme, le développement technologique perpétuel est aux mains des réactionnaires, qui le craignent en tant que sujet de discussion politique. Cette initiative doit être impulsée par la division du travail, en prenant le pas de ceux qui cherchent une position managériale, dans le cadre du développement coopératif des collections, ou à l'intérieur des consortiums, ou afin de déterminer l'utilisation des technologies.

Motivation: Contigs-Assembly and Annotation Tool-Box (CAAT-Box) is a software package developed for the computational part of a genome project where the sequence is obtained by a shotgun strategy. CAAT-Box contains new tools to predict links between contigs by using similarity searches with other whole genome sequences. Most importantly, it allows annotation of a genome to commence during the finishing phase using a gene-oriented strategy. For this purpose, CAAT-Box creates an Individual Protein file (IPF) for each ORF of an assembly. The nucleotide sequence reported in an IPF corresponds to the sequence of the ORF with 500 additional bases before the ORF and 200 bases after. For annotation, additional information like Blast results can be added or linked to the IPFs as well as automatic and/or manual annotations. When a new assembly is performed, CAAT-Box creates new IPFs according to the old IPF panel. CAAT-Box recognizes the modified IPFs which are the only ones used for a new automatic analysis after each assembly. Using this strategy, the user works with a group of IPFs independently of the closure phase progression. The IPFs are accessible by a web server and can therefore be modified and commented by different groups. Result: CAAT-Box was used to obtain and to annotate several complete genomes like Listeria monocytogenes or Strepcoccus agalactiae. Availability: The program may be obtained from the authors and is freely available to non-profit organisations.

Summary: With the establishment of high-throughput (HT) screening methods there is an increasing need for automatic analysis methods. Here we present RReportGenerator, a user-friendly portal for automatic routine analysis using the statistical platform R and Bioconductor. RReportGenerator is designed to analyze data using predefined analysis scenarios via a graphical user interface (GUI). A report in pdf format combining text, figures and tables is automatically generated and results may be exported. To demonstrate suitable analysis tasks we provide direct web access to a collection of analysis scenarios for summarizing data from transfected cell arrays (TCA), segmentation of CGH data, and microarray quality control and normalization. Availability: RReportGenerator, a user manual and a collection of analysis scenarios are available under a GNU public license on http://www-bio3d-igbmc.u-strasbg.fr/~wraff Contact: wolfgang.raffelsberger@igbmc.u-strasbg.fr

As computational neuroscience matures, many simulation environments are available that are useful for neuronal network modeling. However, methods for successfully documenting models for publication and for exchanging models and model components among these projects are still under development. Here we briefly review existing software and applications for network model creation, documentation and exchange. Then we discuss a few of the larger issues facing the field of computational neuroscience regarding network modeling and suggest solutions to some of these problems, concentrating in particular on standardized network model terminology, notation, and descriptions and explicit documentation of model scaling. We hope this will enable and encourage computational neuroscientists to share their models more systematically in the future.Read More: http://informahealthcare.com/doi/abs/10.3109/0954898X.2012.722743

International audience; Les incitations à la recherche et à l’évaluation se multiplient en soins palliatifs. Pourtant, faute de formation initiale, le manque d’une certaine culture méthodologique des professionnels est un frein à leur développement. L’introduction en 2009 d’une épreuve de lecture critique d’un article médical (LCA) à l’examen classant national témoigne du fait que savoir lire un article scientifique est désormais reconnu comme l’une des compétences indispensables à transmettre aux étudiants en médecine. Cet article décrit tout d’abord en quoi consiste un enseignement de LCA, son intérêt et les limites de sa mise en oeuvre, pour ensuite ouvrir une réflexion sur l’adaptation de la LCA à l’apprentissage et à l’exercice de la médecine palliative. L’enseignement de la LCA vise la maîtrise des outils de recherche documentaire, la méthode de lecture rapide et les bases méthodologiques nécessaires pour la compréhension des informations scientifiques et l’analyse de leur validité. Cet enseignement est utile et nécessaire, en soins palliatifs comme dans tout autres spécialités médicochirurgicales. Néanmoins, il est fondé sur un paradigme (la médecine fondée sur le niveau de preuve) qui a montré ses limites et ses dérives : l’utilisation des concepts qui lui sont sous-jacents doit donc être réfléchie et adaptée aux contraintes et aux principes fondateurs des soins palliatifs. Cela ne peut s’envisager qu’avec une motivation forte et une ouverture franche des praticiens de soins palliatifs et des méthodologistes, conditions nécessaires à une réelle collaboration.; The incentives for research and evaluation are increasing in palliative care. However, lack of methodological skills among professionals is an obstacle to their development. In 2009, a test for critical appraisal of literature (CAL) was introduced as a part of the national residency examination for medical students. Reading a scientific article is now recognized as one of the skills necessary to convey to future doctors. This paper first describes what CAL is and what it means to teach it. Second, it addresses the question whether or not CAL should be integrated as a part of a training program in palliative medicine and how this is feasible. CAL skills concern information retrieval and basic methodological knowledge necessary for the understanding of scientific information and analysis of its validity. Such skills are useful and necessary in palliative care as they are in all other medical or surgical specialties. However,CAL is based on a paradigm (evidence-based medicine), which has proved to be as powerful as potentially dangerous. Its underlying concepts must be used with caution and adapted to the constraints and founding principles of palliative care. This supposes strong motivation and open-minded collaboration between palliative care practitioners and methodologists.

[ES] La reconfiguración de la revista y el artículo científico en el nuevo modelo de precios en transición pone el énfasis en el cambio hacia el entorno en acceso abierto. Abriendo así nuevas cronologías gestionarias. En el espacio de la autoridad editores, bibliotecarios y autores explican, dispares, la responsabilidad y los modelos de las fuentes de información. Una industria sostenible y productora de beneficios persigue la clase de interacción que le es necesaria para comprender por completo el problema. La relación no fácil entre los problemas oceanográficos y los pesqueros, su insularidad, es un caso de variación de grado en la integración que en el acceso a las publicaciones ejemplifica bien la >solicitud> entre las publicaciones electrónicas gratuitas y los costes de las publicaciones en papel., [EN] The scientific journal and scientific paper reconfiguration inside the new prices model transition emphasize a change that opens up the open access environment. With the opening of new managerial chronologies. In the open space authority editors, librarians and authors explain, in the disparity, the responsibility and the models of the information sources. A sustainable and profitable industry search for the kind of interaction that is necessary to the full understanding of the problem. The uneasy relationship between the oceanographic and fisheries problems, its insularity, is a case of variation of the degree of integration that is well exemplified by the >closeness> between the free of charge electronic publications and the costs of the paper publications., Éste artículo está elaborado a partir del texto de la conferencia virtual organizada por Oceanógrafos sin Fronteras (Kiel, Al emania) y Aqua Center (Nuevo Chimbo- te, Perú), el día 13 de diciembre del 2007 a las 16:00 h (hora europea).

International audience; OBJECTIVES: To assess and understand adverse drug reactions (ADRs), a systematic review of reference databases like Pubmed is a necessary and mandatory step in Pharmacovigilance. In order to assist pharmacovigilance team with a computerized tool, we performed a comparative study of 4 different approaches to query Pubmed through ADR-drug terms. The aim of this study is to assess how an ontology of adverse effects, used to normalize and extend queries, could improve this search. MATERIAL AND METHOD: The ontological resource OntoEIM contains 58,000 classes and integrates MedDRA terminology. The entry point is a ADR-Drug term and the four methods are (i) a direct search on Pubmed (ii) a search with a normalized query enhanced with domain-specific Mesh Heading criteria, (iii) a search with the same elaborated query extended to the MeSH sub-hierarchy of the adverse effect entry and (iv) a search with a set of MedDRA terms grouped by subsomption in the OntoEIM ontology. For each of the 16 queries performed and analysed, relevant publications are selected "manually" by two pharmacovigilant experts. RESULTS: The recall is respectively of 63%, 50%, 67% and 74%, the precision of 13%, 26%, 29% and 4%. The best recall is provided by the ontology-based method, for 4 cases out of 16 this method returns relevant publications when the others return no results. CONCLUSION: Results show that an ontology-based search tool improves the recall performance, but other tools and methods are needed to raise the precision.

PURPOSES: The main purpose of this survey was to know both the performance and the limitations associated with the scientific information systems, in the context of coordination and continuity between clinical and primary health care research, namely enabling the implementation of research results into primary care practice. To help with this process, the second purpose is the assessment of the trends in the publications along the period between 2002 and 2007.METHODS: A combined review process was conducted using clinical essays and guidelines with a strategy based on free text search. Web of Knowledge (WOK) and Scopus databases have been used.RESULTS: 6433 articles were selected from WOK, involving 26756 authors, who have written for 1233 journals. These include, 45% coming out of the European Union (in the first instance, United Kingdom, the Netherlands, Germany, Spain, Italy and France), 44.6% from the United States and 17.1% from Canada. On how research results are transferred to clinical practice, as measured by the annual rate of articles published on clinical practice guides, the core years were 2004 (15%) and 2007 (17.6%).CONCLUSION: Few people are tasked with studying the potential of the knowledge-based clinical essays and guidelines transferred into ordinary medical practice, with the target set in the field of primary health care. This finding may be the fact that the more frequently occurred illnesses are being studied but with a minor emphasis., OBJETIVOS: El propósito principal de esta investigación es conocer tanto la eficacia como los límites que presentan los sistemas deinformación científica, respecto a la coordinación y continuidad entre la investigación clínica y la atención primaria, es decir, la aplicación delos resultados de la investigación a la práctica asistencial. Para conseguirlo, el segundo propósito es evaluar las tendencias en laspublicaciones durante el período comprendido desde 2002 a 2007.MÉTODOS: Se realizó una búsqueda documental combinada de ensayos clínicos y guías de práctica clínica con una estrategia basada entexto libre. Se utilizaron las bases de datos Web of Knowledge (WOK) y Scopus.RESULTADOS: Se seleccionaron 6433 artículos en WOK, en los que participaron 26756 autores, escribiendo en 1233 revistas. 45 % de laspublicaciones procedieron de la Unión Europea (Reino Unido, Holanda, Alemania, España, Italia y Francia en cabeza), el 44.6 % de los USA yel 17.1 % de Canadá. En la evolución de la transferencia de la investigación a la práctica clínica, medida por el número anual de artículossobre guías publicados, destacan los años 2004 (15%) y 2007 (17.6%).CONCLUSIONES: La tarea de inventariar el potencial de conocimiento aportado por los ensayos y guías a la práctica de la atención primaria espoco frecuente. Este resultado puede ser debido a que las enfermedades más comunes sean las menos estudiadas., OBJECTIFS: Le but principal de cette enquête est de bien connaître tant l'efficacité comme les limites découlant des systèmes d'informationscientifique, dans le cadre de la coordination et la continuité entre la recherche clinique et en matière de santé primaire, c'est-à-dire,dans la mise en oeuvre des résultats de la recherche à la pratique des soins. Pour ce faire, le deuxième but est l'évaluation de tendancesen matière de publications au cours de la période comprise entre 2002 et 2007.MÉTHODES: On a procédé a un examen documentaire combiné des essais et des directives cliniques avec une stratégie reposant sur le textelibre. Il a été fait appel aux bases de données Web of Knowledge (WOK) et Scopus.RÉSULTATS: 6433 articles ont été choisis sur WOK, impliquant 26756 auteurs, qui ont écrit dans 1233 revues. Notamment, 45% de publicationsprovenant de l'Union Éuropéenne (retrouvant sa place de première instance le Royaume Uni, Hollande, Allemagne, Espagne, Italie et France),44.6% des États-Unis et 17.1% du Canada. Sur l'évolution du transfert des résultats de la recherche dans la pratique clinique,mesurée par rapport au nombre annuel d'articles sur les directives publiées, on soulignera les années 2004 (15%) et 2007 (17.6%).CONCLUSIONS: La tâche d'étudier le potentiel de connaissance qu'apportent les essais et les directives cliniques à la pratique médicale en vue des soins de santé primaire, reste assez peu fréquente. Ce résultat pourrait être la conséquence du fait que les maladies les plus repanduessoient les moins étudiées.

International audience; OBJECTIVE: The aim of this study was to evaluate antibiotic prescription in a French university hospital. DESIGN: Our hospital participated in an international European Surveillance of Antimicrobial Consumption (ESAC) project study, including a longitudinal survey of monthly antibiotic use between 1998 and 2005, and a point prevalence study in 2006. All patients in the hospital on the day of survey were included in the study. Antibiotic treatments were assessed according to local antibiotic guidelines. RESULTS: Between 1998 and 2005, antibiotic use increased from 551.9 to 628.5 defined daily doses per 1000 patient-days. This increase was linked to the increase of penicillin and fluoroquinolone consumption. In the point prevalence survey, 251 (27.0%) of the 930 included patients received one or several antibiotics for a total of 395 antibiotic prescriptions. Community-acquired infections were the first indication of treatment (41.8% of prescriptions), hospital-acquired infections accounted for 34.9% of prescriptions, surgical and medical antibiotic prophylaxis for 22.4%. The assessment of antibiotic prescriptions showed that 73.7% of them were in conformity with local recommendations. CONCLUSIONS: This type of study is relevant to identify critical points of inadequate antibiotic use so as to suggest corrective measures to prescribers.

International audience; The mobility of the Spanish biochemists from Europe to the United States over the past 80 years (1927-2006) is approached from a historical perspective. The academic community on human genetics has awarded this emigrated Spanish community with the Nobel Prize as well as other awards from European foundations. The vertical/horizontal integration methodology offers an opportunity to understand the extremely satisfactory history of a small European community overseas. To piece the puzzle together, continuous reference is made to the theory of systems. To test and use this holistic history, the circulation of knowledge produced on cancer has been studied as intrinsically related to time by using algorithmic historiography. Francisco Duran Reynals and Severo Ochoa have been selected as examples of the vertical integration. The former one because he was the director of an important collaborator, his own wife; the latter, as the founder of a Spanish specific research school in America based in his own work. The simultaneous stay of several young Spanish scientists at the Columbia University (Mariano Barbacid, Manuel Perucho and Ángel Pellicer) serves to design the horizontal integration, to create a holon hierarchy to reflect the criteria of subsidiarity and acceptability, and to focus on the Spanish discoveries and contributions to cancer research. The transatlantic flows of knowledge generated by the Spanish elite of biochemists in the USA from 1927 on define a network of geographical displacements. As a result, the social structure thus visualizes the identity of the international mobility of scientists who leave for Europe/USA, and their return to Spain. A model of the brain drain of professionals to the USA, that retain 80% of the Spanish cancer researchers, is developed.; La movilidad de los bioquímicos españoles desde Europa a los Estados Unidos, durante los últimos 80 años (1927-2006), se aproxima desde una perspectiva histórica. La comunidad de investigadores que trabaja en genética humana ha galardonado con el premio Nobel a este grupo de españoles emigrados, así como con otras distinciones procedentes de fundaciones europeas. La metodología de integración vertical/horizontal ofrece una oportunidad para entender esta historia extremadamente satisfactoria acerca de un pequeño grupo de europeos de ultramar. Para armar el rompecabezas, se menciona continuamente la teoría de sistemas. Al objeto de experimentar y hacer uso de ésta concepción holística, se estudia por medio de la historiografía algorítmica la circulación del conocimiento producido sobre el cáncer. Como ejemplos de ésta integración vertical se han seleccionado a Francisco Duran Reynals y a Severo Ochoa. El primero porque fue el director de una importante colaboradora, su propia esposa; el segundo, en tanto que fundador de una escuela de investigación específicamente española en América sobre la base de su propia obra. El desplazamiento simultaneo de un grupo de jóvenes científicos españoles a la Columbia University (Mariano Barbacid, Manuel Perucho y Ángel Pellicer) sirve de base para diseñar la integración horizontal, recrear una jerarquía de holones donde se reflejan los criterios de subsidiariedad y de aceptabilidad, y para concentrarse sobre los descubrimientos y contribuciones españolas en lo que concierne a la investigación sobre el cáncer. Los flujos transatlánticos de conocimiento generados por la élite española de los bioquímicos, en los EE.UU. y a partir de 1927, definen una red de desplazamientos geográficos. De este modo la estructura social que resulta, visualiza la identidad de la movilidad internacional de los científicos que parten hacia Europa/Estados Unidos y su retorno a España. Apareciendo un modelo de fuga de cerebros de profesionales hacia los EE.UU., donde se quedan el 80% de los investigadores españoles sobre el cáncer.; La mobilité des biochimistes espagnols dès l'Europe aux États Unis, au cours de 80 années (1927-2006), est approchée d'une perspective historique. La communauté académique a fait octroi à cette communauté espagnole emigrée du prix Nobel et de distinctions en provenance de fondations européennes. La méthodologie d'integration verticale/horizontale offre une opportunité pour comprendre l'histoire extrémement satisfaisante d'une petite communauté européenne d'outre-mer. Pour réunir l'information la théorie de systèmes peut servir. Et pour éprouver et faire usage de cette démarche holistique, la circulation de la connaissance produite sur le cancer, a été étudiée par le moyen de l'historiographie algorithmique. Francisco Duran Reynals et Severo Ochoa ont été sélectionnés en tant qu'exemples de l'integration verticale. Le premier parce qu'il a été le directeur d'une collaboratrice importante, sa propre épouse; le second, en tant que fondateur d'une école de recherche spécifiquement espagnole en Amérique. L'engagement simultané d'un groupe de jeunes scientifiques espagnols en Columbia University (Mariano Barbacid, Manuel Perucho, Ángel Pellicer) permet d'élaborer l'intégration horizontale, de récréer une hiérarchie d'holons où les critères de subsidiarité et d'acceptabilité sont reflétés, et de se concentrer sur les découvertes et contributions espagnoles à l'égard de la recherche sur le cancer. Les flux transatlantiques de connaissances découlant de l'élite espagnole des biochimistes aux États Unis à partir de 1927 définissent un réseau de déplacements géographiques. Dans ce cadre, la structure sociale visualise l'identité de la mobilité internationale des scientifiques qui partent pour aller en Europe/États Unis, et leur retour en Espagne. Un modèle de l'évasion de matière grise vers les États Unis en résulte, capable de retenir 80% des chercheurs espagnols s'intéressant au cancer.

20 pages., [ES] El concepto de Acceso Abierto a las publicaciones juega un papel clave en la economía de la información. La conciencia de muchos de sus beneficios se realiza a expensas del precio y del número de las fuentes de información. A través de un análisis de los diferentes casos de estudio, se presentan las “lecciones aprendidas” y se deducen diversas conclusiones acerca de las características fundamentales de la política de apoyo y del marco legislativo en que se basan diferentes ideas tributarias de la imagen de mejor práctica que tiene el acceso abierto en ciencias marinas., [EN] The concept of Open access to publications shows a key role in the information economy. The conscience of much of its profits is attained in spite of its price and the number of information sources. Throughout the analysis of different cases of study, the "learned lessons" are presented and diverse conclusions are deduced on the fundamental characteristics of the support policies and law frames which base the tributary ideas of the best practice image that open access offers in marine sciences., [PT] O conceito de Acesso Livre às publicações desempenha um papel chave na economia da informação. A consciência de muitos dos seus benefícios é alcançada apesar do preço e do número das fontes de informação. Através de uma análise de diversos estudos de caso, apresentam-se as “lições aprendidas” e deduzem-se conclusões a respeito das características fundamentais de uma política de apoio e do marco legislativo em que se baseiam diferentes idéias tributárias da imagem de melhores práticas que tem o acesso aberto em ciências marinhas.

Background The high-density oligonucleotide microarray (GeneChip) is an important tool for molecular biological research aiming at large-scale detection of small nucleotide polymorphisms in DNA and genome-wide analysis of mRNA concentrations. Local array data management solutions are instrumental for efficient processing of the results and for subsequent uploading of data and annotations to a global certified data repository at the EBI (ArrayExpress) or the NCBI (GeneOmnibus). Description To facilitate and accelerate annotation of high-throughput expression profiling experiments, the Microarray Information Management and Annotation System (MIMAS) was developed. The system is fully compliant with the Minimal Information About a Microarray Experiment (MIAME) convention. MIMAS provides life scientists with a highly flexible and focused GeneChip data storage and annotation platform essential for subsequent analysis and interpretation of experimental results with clustering and mining tools. The system software can be downloaded for academic use upon request. Conclusion MIMAS implements a novel concept for nation-wide GeneChip data management whereby a network of facilities is centered on one data node directly connected to the European certified public microarray data repository located at the EBI. The solution proposed may serve as a prototype approach to array data management between research institutes organized in a consortium.

BackgroundLarge-scale genomic studies based on transcriptome technologies provide clusters of genes that need to be functionally annotated. The Gene Ontology (GO) implements a controlled vocabulary organised into three hierarchies: cellular components, molecular functions and biological processes. This terminology allows a coherent and consistent description of the knowledge about gene functions. The GO terms related to genes come primarily from semi-automatic annotations made by trained biologists (annotation based on evidence) or text-mining of the published scientific literature (literature profiling).ResultsWe report an original functional annotation method based on a combination of evidence and literature that overcomes the weaknesses and the limitations of each approach. It relies on the Gene Ontology Annotation database (GOA Human) and the PubGene biomedical literature index. We support these annotations with statistically associated GO terms and retrieve associative relations across the three GO hierarchies to emphasise the major pathways involved by a gene cluster. Both annotation methods and associative relations were quantitatively evaluated with a reference set of 7397 genes and a multi-cluster study of 14 clusters. We also validated the biological appropriateness of our hybrid method with the annotation of a single gene (cdc2) and that of a down-regulated cluster of 37 genes identified by a transcriptome study of anin vitroenterocyte differentiation model (CaCo-2 cells).ConclusionThe combination of both approaches is more informative than either separate approach: literature mining can enrich an annotation based only on evidence. Text-mining of the literature can also find valuable associated MEDLINE references that confirm the relevance of the annotation. Eventually, GO terms networks can be built with associative relations in order to highlight cooperative and competitive pathways and their connected molecular functions.

Motivation: Microarray technology makes it possible to measure thousands of variables and to compare their values under hundreds of conditions. Once microarray data are quantified, normalized and classified, the analysis phase is essentially a manual and subjective task based on visual inspection of classes in the light of the vast amount of information available. Currently, data interpretation clearly constitutes the bottleneck of such analyses and there is an obvious need for tools able to fill the gap between data processed with mathematical methods and existing biological knowledge. Results: THEA (Tools for High-throughput Experiments Analysis) is an integrated information processing system allowing convenient handling of data. It allows to automatically annotate data issued from classification systems with selected biological information coming from a knowledge base and to either manually search and browse through these annotations or automatically generate meaningful generalizations according to statistical criteria (data mining). Availability: The software is available on the website http://thea.unice.fr/ Supplementary information: Supplementary tables as well as files containing the biological data used in this publication can be downloaded from our website http://bioinfo.unice.fr/publications/thea_article/

OBJECTIVE: The aim of this study was to analyze the functioning of the French committees for the protection of people in biomedical research (CCPPRB). DESIGN: An independent evaluator visited all of the committees and analyzed their functioning by assessing the annual activity reports, filling data grids and observing the committees in session. RESULTS: We observed that the representation of a range of professions, which is required by law, was not always respected. This was partly because the administrative authority had accumulated delays in nominating members. Another explanation could be the absence of remuneration for the work and attendance of the members. There was considerable inter-committee variation concerning the way documents were distributed to the members during sessions and the extent of investigator and promoter involvement. Finally, large differences in the number of dossiers handled between committees led us to investigate the fairness of dossier distribution, as the number of dossiers dealt with has consequences, particularly for the finality of the opinions of the committees. CONCLUSIONS: This evaluation of the committees playing a crucial role in protecting participants in research trials provides new information that could be helpful for improving the way in which these committees function in the context of the European Directive.

Spanish scientific community has grown on marine sciences-related research concerns for the years 1999 and 2000 in Spain. Many solutions to sea-related problems have been interesting in the context of marine biology and chemistry, big science areas like oceanology, aquaculture, fishery and ecology. A number of studies have been conducted : the Spanish aquaculture directory (ed. 1999), the report from the Ministry of Education "Marine science research in Spain (1981-1998)" (ed. 1999), the report from the Ministry of Agriculture "Evaluation of the activities of research and technological development in aquaculture on the (1982/1997)" (ed. 1999), the "White book on Aquaculture in Spain" (ed. 1999); outside of the follow-up surveys contrasting topics shown to be of concern to marine sciences in Spain., En la comunidad científica española ha crecido el interés por la investigación en ciencias marinas durante los años 1999 y 2000. Muchas soluciones a problemas relacionados con el mar han resultado de interés en el contexto de la biología y de la química marina, y en grandes áreas de la ciencia como la oceanología, la acuicultura, la pesca y la ecología. Numerosos estudios se han realizado : el directorio español de acuicultura (ed. 1999), el informe del ministerio de agricultura "Evaluación de las actividades de investigación y desarrollo tecnológico en acuicultura en el período 1982/1997" (ed. 1999), el "Borrador del libro blanco de la acuicultura en España" (ed. 1999); además de las encuestas de seguimiento que contrastan diferentes temáticas y demuestran ser útiles para las ciencias marinas en España., En Espagne l'intérêt de la communauté scientifique pour la recherche en sciences marines a crû pour les années 1999 et 2000. Bien des solutions à des problèmes en rapport avec la mer ont été intéressants dans le cadre de la biologie et a chimie marine, et dans les grands domaines scientifiques de l'océanographie, l'aquaculture, la pêche et l'écologie. Plusieurs études ont été menées : le répertoire espagnol de l'aquaculture (ed. 1999), le rapport du ministère de l'éducation "Recherche en sciences marines en Espagne (1981-1989)" (ed. 1999), le rapport du ministère de l'agriculture "Évaluation des activités de recherche et dévelopment technologique sur l'exercice 1982/1997" (ed. 1999), le "Livre blanc sur l'Aquaculture en Espagne" (ed. 1999); en outre, des études de suivi sur des sujets contrastés qui ont démontrées être utiles pour les sciences marines en Espagne.

This article displays the very essence of what e-content is about. A complete, varied, and very important collection in its field, held in a variety of formats and media, and the need to make it all available electronically., Éste artículo expone el e-contenido en su auténtica esencia. Una colección, completa, variada, y muy importante, expuesta en diversos formatos y soportes, con la necesidad de hacerla totalmente accesible de modo electrónico., Cet article affiche l'essence même du contenu numérique. Une collection très complète, variée et importante dans son champ, disponible sous une diversité de formats et dans divers médias, et le besoin de la rendre toute offerte par voie électronique.

Spanish scientific community has grown on marine sciences-related research concerns for the years 1999 and 2000 in Spain. Many solutions to sea-related problems have been interesting in the context of marine biology and chemistry, big science areas like oceanology, aquaculture, fishery and ecology. A number of studies have been conducted : the Spanish aquaculture directory (ed. 1999), the report from the Ministry of Education "Marine science research in Spain (1981-1998)" (ed. 1999), the report from the Ministry of Agriculture "Evaluation of the activities of research and technological development in aquaculture on the (1982/1997)" (ed. 1999), the "White book on Aquaculture in Spain" (ed. 1999); outside of the follow-up surveys contrasting topics shown to be of concern to marine sciences in Spain., En la comunidad científica española ha crecido el interés por la investigación en ciencias marinas durante los años 1999 y 2000. Muchas soluciones a problemas relacionados con el mar han resultado de interés en el contexto de la biología y de la química marina, y en grandes áreas de la ciencia como la oceanología, la acuicultura, la pesca y la ecología. Numerosos estudios se han realizado : el directorio español de acuicultura (ed. 1999), el informe del ministerio de agricultura "Evaluación de las actividades de investigación y desarrollo tecnológico en acuicultura en el período 1982/1997" (ed. 1999), el "Borrador del libro blanco de la acuicultura en España" (ed. 1999); además de las encuestas de seguimiento que contrastan diferentes temáticas y demuestran ser útiles para las ciencias marinas en España., En Espagne l'intérêt de la communauté scientifique pour la recherche en sciences marines a crû pour les années 1999 et 2000. Bien des solutions à des problèmes en rapport avec la mer ont été intéressants dans le cadre de la biologie et a chimie marine, et dans les grands domaines scientifiques de l'océanographie, l'aquaculture, la pêche et l'écologie. Plusieurs études ont été menées : le répertoire espagnol de l'aquaculture (ed. 1999), le rapport du ministère de l'éducation "Recherche en sciences marines en Espagne (1981-1989)" (ed. 1999), le rapport du ministère de l'agriculture "Évaluation des activités de recherche et dévelopment technologique sur l'exercice 1982/1997" (ed. 1999), le "Livre blanc sur l'Aquaculture en Espagne" (ed. 1999); en outre, des études de suivi sur des sujets contrastés qui ont démontrées être utiles pour les sciences marines en Espagne.

Summary: GOAnno is a web tool that automatically annotates proteins according to the Gene Ontology (GO) using evolutionary information available in hierarchized multiple alignments. GO terms present in the aligned functional subfamily can be cross-validated and propagated to obtain highly reliable predicted GO annotation based on the GOAnno algorithm. Availability: The web tool and a reduced version for local installation are freely available at http://igbmc.u-strasbg.fr/GOAnno/GOAnno.html Contact: chalmel@igbmc.u-strasbg.fr Supplementary information: The website supplies a detailed explanation and illustration of the algorithm at http://igbmc.u-strasbg.fr/GOAnno/GOAnnoHelp.html

International audience; In recent history of science a controversy has been developed on the origins of the research on oncogenes, as a new discipline, due to the concession of the Dr. Josef Steiner Cancer Research Foundation Award, in 1988, to Dr. Barbacid, in view of the winners of the 1989 Nobel Prize in Medicine or Physiology. The history of this case is approached through a sociological view, namely the professional anticipationism. The documentary method, always present in cancer research (as it was the case when the Li-Fraumeni syndrome was determined), is able to recognize the new ideas and its degree of elaboration, from a historical perspective.We supply a periodization of the discovery of the scientific fact that initiates tumor formation. And we afford the phases of the elementary discoveries encapsulated in the history of the scientific program, using a historiographical tipology own to citation analysis. We understand thenatural history of the case studying theoretically the demographic structure of the population of the Spanish scientific authors participating inthis scientific research.; Con la concesión del premio 1988 del Instituto de Fisiología de la Universidad de Berna, Suiza, al Dr. Barbacid, y el resultado del premio Nobel 1989de Medicina o FGisiología, se abre para la historia de la ciencia una polémica discusión acerca del orígen de la nueva disciplina de investigación sobre oncogenes. Los ganadores del premio Nobel se habrían beneficiado de una decisión precipitada por parte del comité que concede el galardón. El premio recayó en un equipo norteamericano que trabajaba en el mismo área que Mariano Barbacid. El método documental, siempre presente en la investigación sobre cáncer (p.e. en la determinación del síndrome de Li-Fraumeni), es apto para reconocer las nuevas ideas y su grado de elaboración, con una perspectiva histórica.Enmarcamos en un período de tiempo, 1981-1985, el descubrimiento del hecho científico que inicia la formación del tumor. Y abordamos, con ayuda de una tipología historiográfica propia del análisis de citas, las fases de los descubrimientos elementales de que consta la historia del programa de investigación. Entendemos la historia natural del caso elaborando la pirámide de población de los autores españoles que en él participan.; Significative en l'histoire de la science des dernières années a été la discussion sur les origines de la recherche à propos de l'oncogène (en tantque nouvelle discipline) à l'intention de l'attribution au Dr. Barbacid du prix de la Dr. Josef Steiner Cancer Research Foundation, en 1988lorsqu'on prend en considération les gagnants du prix Nobel 1989 en Médécine et Physiologie. L'analyse sociologique permet d'approcher l'histoire de ce cas du point de vue de l'anticipationisme professionnel. La méthode documentaire, toujours prérsente dans la recherche sur le cancer (comme lorsque le syndrome de Li-Fraumeni a été déterminé), est en mesure de reconnaître des idées nouvelles et ses divers dégrés d'élaboration, dans une perspective historique.Une périodisation a été désignée pour la découverte du fait scientifique qui entraîne la formation d'une tumeur. Et les étapes des découvertes élémentaires imbriquées dans l'histoire du programme scientifique sont fournies, en faisant usage de la tipologie historiographique propre à l'analyse des citations. L'histoire naturelle du cas est comprise par l'étude en fonction de principes théoriques de la structure démographique de la population des auteurs scientifiques espagnols participants à cette recherche scientifique.

The aim of this paper is to perform an analysis of the bibliography included in the works published on medical records and clinical archives. This is achieved by analyzing 776 bibliographic references retrieved from the 94 journal articles in the IME (Spanish Medical Index) database throughout the period 1981-1990. The results obtained have been organized by more cited spanish and non-spanish journals, years, document types, and countries. Among the notable achievements is that #Atención Primaria# is the most cited spanish journal with 33 citations; the total number of cited journals is 146. Journal articles (52'96%) and books (31'83%) are the most cited document types. As for the countries, used information comes mainly from Spain, United States and Great Britain. The most cited authors have been R. Peris, L. Weed, C. Margolis and M.L. Terrada. The findings of the study have highlighted the high proportion of articles on this subject area that contains no references (25%), and that there is a high rate of spanish publications and books consumption when compared against other medical matters., El objetivo del artículo es realizar un análisis de la bibliografía citada en los trabajos publicados sobre la historia clínica y sobre los archivos de historias clínicas. Para ello se han analizado 776 citas bibliográficas recogidas en los 94 artículos de revista obtenidos a partir de la base de datos IME (#Indice Médico Español#) durante el período 1981-1990. La bibliografía obtenida se ha distribuido por revistas españolas y extranjeras más citadas, años, tipos documentales, y países. En los resultados se destaca que la revista española más citada ha sido #Atención Primaria# con 33 citas; el número total de revistas citadas es de 146. Los tipos documentales más citados han sido los artículos de revistas, con el 52'96% y los libros, con el 31'83%. Con relación a los países, la información utilizada proviene mayoritariamente de España, Estados Unidos y Gran Bretaña. Entre los autores más citados destacan R. Peris, L. Weed, C. Margolis y M.L. Terrada. En las conclusiones se destaca el elevado porcentaje de artículos sobre estas materias sin bibliografía, el 25%, y la elevada proporción en el consumo de bibliografía española y de libros en relación a otras materias médicas., Cette étude a pour objectif d'effectuer une analyse de la bibliographie aux items publiés sur les dossiers médicaux et les archives cliniques. Pour y parvenir on analyse 776 références bibliographiques dans 94 articles de revues accesibles sur la base de données IME (Index médical espagnol) pour la période 1981-1990. Les résultats obtenus ont été classés par les journaux espagnols et non espagnols le plus souvent cités dans le monde, années, typologie documentaire, et pays. Ce qui est notable, c'est que, #Atención Primaria# est le journal espagnol le plus cité (33 citations); le nombre total de journaux cités s'élève à 146. Les types documentaires les plus cités sont les articles de revue (52'96%) et les livres (31'83%). En ce qui concerne les pays d'origine, cela permet de distinguer l'Espagne, les États Unis et la Grande Bretagne. Les auteurs les plus cités sont R. Peris, L. Weed, C. Margolis et M.L. Terrada. Les conclusions de l'étude ont souligné la proportion des articles sur ce sujet n'incluant aucune référence bibliographique (25%), et le fait qu'il y a un nombre élevé de publications espagnoles et de livres lorsqu'on compare avec d'autres sujets médicaux.

International audience; Introduction: The objective of this study is the descriptive study of the production of Spanish articles related to medical documentation, in 1994.Methods: The set of articles was obtained by reviewing the summaries of over 250 Spanish medical and documentation journals, and confirming their appropriateness for inclusion by the examination of the text. A database was created by using DBase IV, which enabled the statistical overview of the information. Results: 280 Spanish articles on medical documentation subjects were obtained. 63 per cent of all articles are original works and 18 per cent abstracts of the communications submitted to congresses and published in journals. The works were published in 63 different journals and the ones that have carried more articles were: Medicina Clínica (10 %), Atención Primaria (9 %), Revista de Calidad Asistencial (9 %) and Todo Hospital (8,5 %). 15 per cent of the published articles come from Documentation, Archive, Admission or Health Information Units and Services; with the other works disseminated to other units, the most prominent of which are those of Epidemiology and Public Health, Family medicine and Pharmacy. More than one thousand authors contributed and average collaborating authors for each article was estimated at 4.Conclusions: Medical Documentation is a young discipline, that is in full development and consolidation, as indicated by the recent increase of research in this field, the distribution of publications in multiple journals and their provenance from various centres and services.; Introducción: El objetivo de este trabajo es el estudio descriptivo de la producción de artículos españoles sobre Documentación Médica en 1994.Métodos: La población de artículos se obtuvo revisando los sumarios de más de 250 revistas españolas de medicina y documentación, y confirmando su pertenencia mediante el examen del texto. Se creó una base de datos en dBASE IV que permitió la descripción estadística de la información.Resultados: Se han obtenido 280 artículos españoles sobre temas relacionados con la documentación médica. El 63 % de los artículos son trabajos originales y el 18 % resúmenes de comunicaciones a congresos publicados en revistas. Los trabajos se publicaron en 63 revistas distintas y las que más artículos han aportado son: Medicina Clínica (10 %), Atención Primaria (9 %), Revista de Calidad Asistencial (9 %) y Todo Hospital (8,5 %). El 15 % de los artículos procede de Unidades o Servicios de Documentación, Archivo, Admisión o Información Sanitaria; el resto de trabajos se dispersan en otras unidades, entre las que destacan las de Epidemiología y Salud Pública, Medicina Familiar y Comunitaria y Farmacia. Colaboraron más de mil autores y el número medio de autores por trabajo fue de cuatro.Conclusiones: La Documentación Médica es una disciplina joven, en pleno desarrollo y consolidación, como indica el reciente aumento de la investigación en este campo, la dispersión de las publicaciones en múltiples revistas y su procedencia desde diversos centros y servicios.; Introduction: L'objectif de ce travail est l'étude descriptif des articles espagnols sur la documentation médicale en 1994. Méthodes: La population des articles a été obtenue en étudiant les sommaires de plus de 250 journaux espagnols medicaux et de documentation, attestant leur appartenance au moyen de l'examination du texte. Une base de données au format dBASEIV pour permettre la description statistique de l'information.Résultats: 280 articles espagnols ont été obtenus sur les questions relatives à la documentation médicale. 63% des articles sont des travaux originaux et 18% des résumés de communication dans des congrès publiés dans des revues. Les travaux ont été publiés par 63 revues différentes, dont celles au plus gros volume de contributions ont été: Medicina Clínica (10 %), Atención Primaria (9 %), Revista de Calidad Asistencial (9 %) and Todo Hospital (8,5 %). 15% des articles émane des Unités ou Services de Documentation, Archives, Admission ou Information Sanitaire; le reste des travaux se dispersent dans d'autres unités, parmi lesquelles sont à relever celles d'Épidémiologie et Santé Publique, Médécine Familiale et Communitaire et Pharmacie. Ayant coopéré plus de mille auteurs et le nombre moyen d'auteurs par article était de quatre.Conclusions: La Documentation Médicale est une discipline jeune, en plein essor et consolidation, comme cela est indiqué d'après la récente augmentation de la recherche sur ce champ, la dissemination des publications sur des multiples revues et sa provenance de divers centres et services.

An algorithmic method for interpreting medical literature through quality criteria is presented. The resulting set of bibliographic references is compared with the references cited in a doctoral dissertation, a procedures manual, and a number of statistical yearbooks. An approach based on mechanical and repetitive measures proved to be pertinent when checked against independent criteria based on experts' subjective evaluations.The methodology is based on criteria already proven in the world of scientific publishing. Its content is versatile, computer manageable, verifiable and applicable at different levels., Se presenta un algoritmo para la interpretación en términos de calidad de la literatura médica. El conjunto de referencias bibliográficas resultante se compara con la literatura incorporada en una tesis de doctorado, un manual de procedimientos y una serie de anuarios estadísticos. Un procedimiento basado en criterios mecánicos y repetitivos demuestra su pertinencia al cotejarlo con los criterios independientes basados en las estimaciones subjetivas de los expertos.El método se fundamenta en ajustes de evaluación ya contrastados en el ámbito de la publicación científica; resulta versátil, automatizable, verificable y capaz de aplicación a diferentes escalas., Ce document présente un algorithme pour l'interprétation en termes de qualité de la littérature médicale. L'ensemble des références bibliographiques qui résulte est comparé avec la littérature intégrée dans une thèse doctorale, un manuel des procédures et une série d'annuaires statistiques. Une procédure fondée sur des critères de sélection mécaniques et répétitifs se révèle pertinente par rapport aux critères subjectifs des experts. La méthode utilisée repose sur des ajustements d'évaluation déjà vérifiés dans le domaine de la publication scientifique; elle est polyvalente, automatisable, vérificable et en mesure d'être applicable à différents niveaux.