The Andalusian Public Health System Virtual Library. Four years on

The Andalusian Public Health System Virtual Library (Biblioteca Virtual del Sistema Sanitario Público de Andalucía, BV-SSPA) set up in June 2006 was determined by the II Quality Plan 2005-2008. It consists of a regional government action with the aim of democratizing the health professional access to quality scientific information, regardless of the professional workplace. Andalusia is a region with more than 8 million inhabitants, with 92,000 health professionals for 41 hospitals, 1,500 primary healthcare centres, and 10 centres for non-medical attention purposes. • To obtain documentary resources for health professionals. • To help citizens to find health information. • To coordinate the Andalusian Health Documentary centres. • To establish strategic agreements with organizations. • To contribute to the Knowledge Management Development • The BV-SSPA acquires in a centralised way, all of the information resources for the whole system. • It offers services for all professionals: o Document Supply Service o Online Learning o User service • Remote access to these resources and services. • Communication and marketing plan to promote the knowledge and use of the BV-SSPA. Presently the BV-SSPA has reached: • The subscription of 2,431 electronic reviews, 8 data bases and other scientific information resources. • The establishment of the Document Supply Service, which focuses all the article orders from and for the Andalusian Public Health System. • The starting up for the online learning platform. • The introduction of the user service and virtual reference service in beta mode. • The use of appropriate tools, as the meta-researcher and the link resolver, which allow the presentation of resources and services in a tidy, easily findable way, through a Web 2.0 page where the user can take part with his contributions and where his offers and suggestion are gathered. • Access to the resources, for the Andalusian Health Professionals worldwide requiring only an internet connection. Andalusian Health Professionals have access to the greatest Health Science Electronic Resources Collection in Spain. The BV-SSPA has become the undisputed medium for the Health Research and Clinical Healthcare in our region, being consolidated as the Knowledge Manager into the Andalusian Public Health System. In 2010, it faces new projects such as the institutional repository creation, HypatiaSalud; the analysis of our research activity; and the drafting of a normalised licence model for the contracting of electronic resources.

Digital inmigrants and digital natives expectation collection in the Andalusian Public Health System Virtual Library: communication with our users

The Andalusian Public Health System Virtual Library (Biblioteca Virtual del Sistema Sanitario Público de Andalucía, BV-SSPA) provides access to health information resources and services to healthcare professionals through its Website. This virtual environment demands higher users’ knowledge in order to satisfy of the need of information of our users, as digital natives as digital immigrants, improving at the same time the communication with all of them. 1. To collect clients' views and expectations according to their nature of digital natives and immigrants. 2. To know our online reputation. A Collecting User Expectation Questionnaire will be built, taking into account the segmentation of the BV-SSPA users’ professional groups of the Andalusian Public Health System. A pilot test will be run to check the survey dimensions and items about practices, attitudes and knowledge of our users. Two Quality Function Deployment (QFD) matrices will enable the BV-SSPA services to be targeted to our digital natives or digital immigrants, according to their nature, finding the best way to satisfy their information needs. We provide feedback on BV-SSPA: users can have the opportunity to post feedback about the site via the 'Contact us' section and comment about their experience. And Web 2.0 is a shop window, providing the opportunity to show the comments; and through time, our online reputation will be built, but the BV-SSPA must manage its own personal branding. Web 2.0 tools are a driver of improvement, because they provide a key source of insight into people's attitudes. Besides, the BV-SSPA digital identity will be analyzed through indicators like major search engine referrals breakdown, top referring sites (non search engines), or top search engine referral phrases, among others. Definition of digital native and digital immigrant profiles of the BV-SSPA, and their difference, will be explained by their expectations. The design of the two QFD matrices will illustrate in just one graph the requirements of both groups for tackling digital abilities and inequalities. The BV-SSPA could deliver information and services through alternative channels. On the other hand, we are developing a strategy to identify, to measure and to manage a digital identity through communication with the user and to find out our online reputation. With the use of different tools from quantitative and qualitative methodology, and the opportunities offered by Web 2.0 tools, the BV-SSPA will know the expectations of their users as a first step to satisfy their necessities. Personalization is pivotal to the success of the Site, delivering tailored content to individuals based on their recorded preferences. The valuable user research can be used during new product development and redesign. Besides positive interaction let us build trust, show authenticity, and foster loyalty: we improve with effort, communication and show.

El Papel del Bibliotecario Integrado en las Comisiones Clínicas, Docencia Postgraduada e Investigación en el Área Sanitaria Este de Málaga-Axarquía (ASEMA)

The concept of Library of the Health Sciences has noticeably changed during the last decade. The embedded librarian is a recently emerged figure, who works as a member of multidisciplinary groups with the mission of providing them with relevant literature as well as media for acquisition, exchange and dissemination of information. This figure has been gradually implanted in some committees of the ASEMA. The objective of the present work is to describe the functions of the embedded librarian and its results in our area.

A Formal Framework for Specifying, Reusing and Implementing Educational Settings. Third level

Aquest fitxer conté la ontologia que descriu un metamodel de l'especificació Open Service Interface Design v.2.0 proposada per OKI. Ha estat creada en OWL i estesa amb un conjunt de regles SWRL. S'adjunta també el conjunt de regles.

El blog y otras herramientas comunicativas de la biblioteca del Área de Gestión Sanitaria Este de Málaga - Axarquía

In 2006 the Library of the Andalusian Public Health System (BVSSPA) is constituted as a Virtual Library which provides Resources and Services that are accessed through inter-hospital local area network (corporate intranet) and Internet. On the other hand, the Hospital de la Axarquia still did not have any institutional or self-presence on the Internet and the librarian ask the need to create a space for communication with the "digital users" of the Library of the area through a website. MATERIALS AND METHODS. The reasons why we opted for a blog were: -It was necessary to make no financial outlay for its establishment. It allowed for great versatility, both in its administration and in its management by users. -The ability to compile on the same platform different Web 2.0 communication tools. Between different options available we chose Blogger Google Inc. The blog allowed entry to the 2.0 services or Social Web in the library. The benefits offered were many, especially the visibility of the service and communication with the user. 2.0 tools that have been incorporated into the library are: content syndication (RSS) which allowed users to stay informed about updates to the blog. Share documents and other multimedia as presentations through SlideShare, images through Flickr or Picasa, or videos (YouTube). And the presence on social network like Facebook and Twitter. RESULTS. The analysis of the activity we has been traking by Google Analytics tool, helping to determine the number of blog visits. Since its stablishment, on November 17th 2006, until November 29th 2010 the blog has received 15,787 visitors, 38,422 page views were consulted, at each visit on average 2.4 pages were consulted and each visit has an average stay at the site of 4'31''. DISCUSSION. The blog has served as a communication and information tool with the user. Since the creation of the blog we have incorporated technologies and tools to interact with the user. With all the tools used we have applied the concept of "open source" and the contents were generated from the activities organized in the Knowledge Management Unit from the anatomo-clinical sessions, the training activities, dissemination events, etc. The result has been the customization of library services, contextualized in the Knowledge Management Unit - Axarquia. In social networks we have shared information and files with the professionals and the community. CONCLUSIONS. The blog has allowed us to explore technologies that allow us to communicate with the user and the community, disseminate information and documents with the participation of users and become the "Interactive Library" we aspire to be.

Affymetrix Whole-Transcript Human Gene 1.0 ST array is highly concordant with standard 3' expression arrays.

The recently released Affymetrix Human Gene 1.0 ST array has two major differences compared with standard 3' based arrays: (i) it interrogates the entire mRNA transcript, and (ii) it uses DNA targets. To assess the impact of these differences on array performance, we performed a series of comparative hybridizations between the Human Gene 1.0 ST and the Affymetrix HG-U133 Plus 2.0 and the Illumina HumanRef-8 BeadChip arrays. Additionally, both RNA and DNA targets were hybridized on HG-U133 Plus 2.0 arrays. The results show that the overall reproducibility of the Gene 1.0 ST array is best. When looking only at the high intensity probes, the reproducibility of the Gene 1.0 ST array and the Illumina BeadChip array is equally good. Concordance of array results was assessed using different inter-platform mappings. Agreements are best between the two labeling protocols using HG-U133 Plus 2.0 array. The Gene 1.0 ST array is most concordant with the HG-U133 array hybridized with cDNA targets. This may reflect the impact of the target type. Overall, the high degree of correspondence provides strong evidence for the reliability of the Gene 1.0 ST array.

Intrauterine exposure to carbamazepine and specific congenital malformations: systematic review and case-control study.

OBJECTIVE: To identify specific major congenital malformations associated with use of carbamazepine in the first trimester of pregnancy. DESIGN: A review of all published cohort studies to identify key indications and a population based case-control study to test these indications. SETTING: Review of PubMed, Web of Science, and Embase for papers about carbamazepine exposure in the first trimester of pregnancy and specific malformations, and the EUROCAT Antiepileptic Study Database, including data from 19 European population based congenital anomaly registries, 1995-2005. PARTICIPANTS: The literature review covered eight cohort studies of 2680 pregnancies with carbamazepine monotherapy exposure, and the EUROCAT dataset included 98 075 registrations of malformations covering over 3.8 million births. MAIN OUTCOME MEASURES: Overall prevalence for a major congenital malformation after exposure to carbamazepine monotherapy in the first trimester. Odds ratios for malformations with exposure to carbamazepine among cases (five types of malformation identified in the literature review) compared with two groups of controls: other non-chromosomal registrations of malformations and chromosomal syndromes. RESULTS: The literature review yielded an overall prevalence for a major congenital malformation of 3.3% (95% confidence interval 2.7 to 4.2) after exposure to carbamazepine monotherapy in the first trimester. In 131 registrations of malformations, the fetus had been exposed to carbamazepine monotherapy. Spina bifida was the only specific major congenital malformation significantly associated with exposure to carbamazepine monotherapy (odds ratio 2.6 (95% confidence interval 1.2 to 5.3) compared with no antiepileptic drug), but the risk was smaller for carbamazepine than for valproic acid (0.2, 0.1 to 0.6). There was no evidence for an association with total anomalous pulmonary venous return (no cases with carbamazepine exposure), cleft lip (with or without palate) (0.2, 0.0 to 1.3), diaphragmatic hernia (0.9, 0.1 to 6.6), or hypospadias (0.7, 0.3 to 1.6) compared with no exposure to antiepileptic drugs. Further exploratory analysis suggested a higher risk of single ventricle and atrioventricular septal defect. CONCLUSION: Carbamazepine teratogenicity is relatively specific to spina bifida, though the risk is less than with valproic acid. Despite the large dataset, there was not enough power to detect moderate risks for some rare major congenital malformations.

SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements

Selenoproteins are a diverse group of proteinsusually misidentified and misannotated in sequencedatabases. The presence of an in-frame UGA (stop)codon in the coding sequence of selenoproteingenes precludes their identification and correctannotation. The in-frame UGA codons are recodedto cotranslationally incorporate selenocysteine,a rare selenium-containing amino acid. The developmentof ad hoc experimental and, more recently,computational approaches have allowed the efficientidentification and characterization of theselenoproteomes of a growing number of species.Today, dozens of selenoprotein families have beendescribed and more are being discovered in recentlysequenced species, but the correct genomic annotationis not available for the majority of thesegenes. SelenoDB is a long-term project that aims toprovide, through the collaborative effort of experimentaland computational researchers, automaticand manually curated annotations of selenoproteingenes, proteins and SECIS elements. Version 1.0 ofthe database includes an initial set of eukaryoticgenomic annotations, with special emphasis on thehuman selenoproteome, for immediate inspectionby selenium researchers or incorporation into moregeneral databases. SelenoDB is freely available athttp://www.selenodb.org.

A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins

Selenoproteins contain the amino acid selenocysteine which is encoded by a UGA Sec codon. Recoding UGA Sec requires a complex mechanism, comprising the cis-acting SECIS RNA hairpin in the 3′UTR of selenoprotein mRNAs, and trans-acting factors. Among these, the SECIS Binding Protein 2 (SBP2) is central to the mechanism. SBP2 has been so far functionally characterized only in rats and humans. In this work, we report the characterization of the Drosophila melanogaster SBP2 (dSBP2). Despite its shorter length, it retained the same selenoprotein synthesis-promoting capabilities as the mammalian counterpart. However, a major difference resides in the SECIS recognition pattern: while human SBP2 (hSBP2) binds the distinct form 1 and 2 SECIS RNAs with similar affinities, dSBP2 exhibits high affinity toward form 2 only. In addition, we report the identification of a K (lysine)-rich domain in all SBP2s, essential for SECIS and 60S ribosomal subunit binding, differing from the well-characterized L7Ae RNA-binding domain. Swapping only five amino acids between dSBP2 and hSBP2 in the K-rich domain conferred reversed SECIS-binding properties to the proteins, thus unveiling an important sequence for form 1 binding.

FGF signaling controls caudal hindbrain specification through Ras-ERK1/2 pathway

Background: During early steps of embryonic development the hindbrain undergoes a regionalization process along the anterior-posterior (AP) axis that leads to a metameric organization in a series of rhombomeres (r). Refinement of the AP identities within the hindbrain requires the establishment of local signaling centers, which emit signals that pattern territories in their vicinity. Previous results demonstrated that the transcription factor vHnf1 confers caudal identity to the hindbrain inducing Krox20 in r5 and MafB/Kreisler in r5 and r6, through FGF signaling [1].Results: We show that in the chick hindbrain, Fgf3 is transcriptionally activated as early as 30 min after mvHnf1 electroporation, suggesting that it is a direct target of this transcription factor. We also analyzed the expression profiles of FGF activity readouts, such as MKP3 and Pea3, and showed that both are expressed within the hindbrain at early stages of embryonic development. In addition, MKP3 is induced upon overexpression of mFgf3 or mvHnf1 in the hindbrain, confirming vHnf1 is upstream FGF signaling. Finally, we addressed the question of which of the FGF-responding intracellular pathways were active and involved in the regulation of Krox20 and MafB in the hindbrain. While Ras-ERK1/2 activity is necessary for MKP3, Krox20 and MafB induction, PI3K-Akt is not involved in that process.Conclusion: Based on these observations we propose that vHnf1 acts directly through FGF3, and promotes caudal hindbrain identity by activating MafB and Krox20 via the Ras-ERK1/2 intracellular pathway.

OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature

Background: Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required. Results: Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes http://ibi.imim.es/osirisform.html. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, http://ibi.imim.es/OSIRISv1.2.html webcite) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented. Conclusion: OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.

Internet como fuente generadora de contenidos especializados

La plena vigencia de la Web 2.0, así como los tímidos inicios de la Web semántica, propician una excelente oportunidad para el Periodismo especializado. En una sociedad intercomunicada en la que todo aquel que disponga de las herramientas básicas puede convertirse en emisor de contenidos digitales, el papel mediador del periodista debe ser reforzado con el de selector y guía del mapa informativo que ofrece Internet. Con este ánimo se publica el presente texto que recoge las aportaciones de docentes e investigadores del ámbito científico del Periodismo especializado. A sus reflexiones, análisis y críticas han añadido gran cantidad de cuadros y tablas cuya finalidad didáctica no es otra que la de poner un poco de orden en el caos informativo de la red.

Paljon puhuttu AJAX

Web 2.0 viittaa toisen polven rikkaisiin verkkosovelluksiin, jotka lähestyvät käytettävyydeltään työpöydän ohjelmia. AJAX (Asyncrhonous JavaScript and XML) on ryhmä tekniikoita, joilla rakennetaan rikkaita verkkosovelluksia. AJAX on saanut valtavasti huomiota mullistavien ominaisuuksiensa ansiosta ja se on syrjäyttämässä tuttuja malleja verkkoympäristössä. Kaikki puhuvat AJAXista, mutta harva todella tietää mistä on kyse. Tämän opinnäytteen tavoitteena on selvittää mistä AJAXissa oikein on kyse, miten se on mullistanut verkkosovelluksia ja mihin suuntaan se on menossa tulevaisuudessa. Tutkimuksen kohteena olivat myös AJAXin kilpailijat, joita verrattiin tähän teoreettisella tasolla. Alan kirjallisuuteen nojautuvassa teknisessä selvityksessä esiteltiin AJAX-tekniikat ja niiden toimintatavat AJAX-sovelluksissa. Median esille tuomien AJAXin uraauurtavien hyvien ominaisuuksien lisäksi käytiin tutkimuksessa läpi kriittisesti myös sen heikkoja puolia. SWOT-analyysissä selvisi, että AJAXin vahvuuksia ovat nopeus ja asynkronisuus ja heikkouksista suurimpia olivat tietoturva-aukot ja navigointimallin muutoksen mukanaan tuomat ongelmat. Analyysin tuloksena AJAXin mahdollisuuksiksi nähtiin laajempi levinneisyys ja kehittyminen sekä näiden mukanaan tuomat hyödyt. Uhkina nähtiin kilpailijat ja AJAXin suosion lasku. Tuloksissa selvisi myös, että kilpailijat esiintyvät kuitenkin AJAXin kanssa yhteiskäytössä, minkä vuoksi niiden vertailu kilpailijoina on hankalaa. Kilpailu on tärkeää, sillä se lisää tekniikoiden kehittymistä ja standardien muodostumista ja johtaa entistä parempiin rikkaisiin verkkosovelluksiin. Heikkouksistaan huolimatta AJAX on käyttöominaisuuksiltaan varteenotettava malli ja säilyttää varmasti paikkansa muiden WWW-sovellustekniikoiden joukossa.

Biana: a software framework for compiling biological interactions and analyzing networks

Background: The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.Results: We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php.Conclusions: BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

La Utilización de la plataforma Weibo por periodistas chinos en los asuntos públicos en China

Esta investigación se concentra en la plataforma Weibo, que está introduciendo nuevas formas de redacción de noticias y distribución de informaciones en China. Se trata de un servicio de microblogging chino, parecido al Twitter pero adaptado a los usuarios chinos. Siendo una herramienta de web 2.0, Weibo ha cambiado el trabajo cotidiano de los periodistas chinos. En el presente estudio se elabora análisis de contenido cuantitativo y cualitativo con fin de explorar la forma de utilización por los periodistas chinos en los asuntos públicos.