The ARKdb: genome databases for farmed and other animals

The ARKdb genome databases provide comprehensive public repositories for genome mapping data from farmed species and other animals (http://www.thearkdb.org) providing a resource similar in function to that offered by GDB or MGD for human or mouse genome mapping data, respectively. Because we have attempted to build a generic mapping database, the system has wide utility, particularly for those species for which development of a specific resource would be prohibitive. The ARKdb genome database model has been implemented for 10 species to date. These are pig, chicken, sheep, cattle, horse, deer, tilapia, cat, turkey and salmon. Access to the ARKdb databases is effected via the World Wide Web using the ARKdb browser and Anubis map viewer. The information stored includes details of loci, maps, experimental methods and the source references. Links to other information sources such as PubMed and EMBL/GenBank are provided. Responsibility for data entry and curation is shared amongst scientists active in genome research in the species of interest. Mirror sites in the United States are maintained in addition to the central genome server at Roslin.

Mendel-GFDb and Mendel-ESTS: databases of plant gene families and ESTs annotated with gene family numbers and gene family names

There is no control over the information provided with sequences when they are deposited in the sequence databases. Consequently mistakes can seed the incorrect annotation of other sequences. Grouping genes into families and applying controlled annotation overcomes the problems of incorrect annotation associated with individual sequences. Two databases (http://www.mendel.ac.uk) were created to apply controlled annotation to plant genes and plant ESTs: Mendel-GFDb is a database of plant protein (gene) families based on gapped-BLAST analysis of all sequences in the SWISS-PROT family of databases. Sequences are aligned (ClustalW) and identical and similar residues shaded. The families are visually curated to ensure that one or more criteria, for example overall relatedness and/or domain similarity relate all sequences within a family. Sequence families are assigned a ‘Gene Family Number’ and a unified description is developed which best describes the family and its members. If authority exists the gene family is assigned a ‘Gene Family Name’. This information is placed in Mendel-GFDb. Mendel-ESTS is primarily a database of plant ESTs, which have been compared to Mendel-GFDb, completely sequenced genomes and domain databases. This approach associated ESTs with individual sequences and the controlled annotation of gene families and protein domains; the information being placed in Mendel-ESTS. The controlled annotation applied to genes and ESTs provides a basis from which a plant transcription database can be developed.

trEST, trGEN and Hits: access to databases of predicted protein sequences

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent efficient and effective searches of HTG and EST data for protein sequence homologies by standard search methods. Here, we briefly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especially to biologists not having access to a powerful local bioinformatics environment. trEST and trGEN are regularly regenerated databases of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Hits is a web-based data retrieval and analysis system providing access to precomputed matches between protein sequences (including sequences from trEST and trGEN) and patterns and profiles from Prosite and Pfam. The three resources can be accessed via the Hits home page (http://hits.isb-sib.ch).

Quality of pharmaceutical advertising and gender bias in medical journals (1998-2008): a review of the scientific literature

Objective: To review the scientific literature on pharmaceutical advertising aimed at health professionals in order to determine whether gender bias has decreased and the quality of information in pharmaceutical advertising has improved over time. Methods: We performed a content analysis of original articles dealing with medical drug promotion (1998-2008), according to quality criteria such as (a) the number, validity and accessibility of bibliographic references provided in pharmaceutical advertising and (b) the extent to which gender representations were consistent with the prevalence of the diseases. Databases: PUBMED, Medline, Scopus, Sociological Abstract, Eric and LILACS. Results: We reviewed 31 articles that analyzed advertising in medical journals from 1975-2005 and were published between 1998 and 2008. We found that the number of references used to support pharmaceutical advertising claims increased from 1975 but that 50% of these references were not valid. There was a tendency to depict men in paid productive roles, while women appeared inside the home or in non-occupational social contexts. Advertisements for psychotropic and cardiovascular drugs overrepresented women and men respectively. Conclusions: The use of bibliographic references increased between 1998 and 2008. However, representation of traditional male-female roles was similar in 1975 and 2005. Pharmaceutical advertisements may contribute to reinforcing the perception that certain diseases are associated with the most frequently portrayed sex.

Evaluation of quality of life related to nutritional status

The way in which the quality of life related to health (HRQoL) is affected by the nutritional status of the patient is a subject of constant interest and permanent debate. The purpose of the present paper is to review those studies that relate HRQoL to nutritional status and examine the tools (questionnaires) that they use to investigate this relationship. A critical review of published studies was carried out via an investigation of the following databases: MEDLINE (via PubMed); EMBASE; The Cochrane Library; Cumulative Index to Nursing and Allied Health Literature (CINAHL); Institute for Scientific Information (ISI) Web of Science; Latin American and Caribbean Health Sciences Literature (LILACS); Spanish Health Sciences Bibliographic Index (IBECS). The search was carried out from the earliest date possible until July 2007.The medical subject heading terms used were ‘quality of life’, ‘nutritional status’ and ‘questionnaires’. The articles had to contain at least one questionnaire that evaluated quality of life. Twenty-eight documents fulfilling the inclusion criteria were accepted, although none of them used a specific questionnaire to evaluate HRQoL related to nutritional status. However, some of them used a combination of generic questionnaires with the intention of evaluating the same. Only three studies selectively addressed the relationship between nutritional status and quality of life, this evaluation being performed not by means of specific questionnaires but by statistical analysis of data obtained via validated questionnaires.

Los usuarios ante los alimentos genéticamente modificados y su información en el etiquetado

OBJETIVO: Analizar la opinión que los usuarios tienen sobre alimentos genéticamente modificados y su información en el etiquetado. MÉTODOS: Realizada revisión sistemática de la literatura científica sobre los alimentos transgénicos y el etiquetado a partir de la consulta de las bases de datos bibliográficas: Medline (vía PubMed), EMBASE, ISIWeb of Knowledge, Cochrane Library Plus, FSTA, LILACS, CINAHL y AGRICOLA. Los descriptores seleccionados fueron: «organisms, genetically modified» y «food labeling». La búsqueda se realizó desde la primera fecha disponible hasta junio de 2012, seleccionando los artículos pertinentes escritos en inglés, portugués y castellano. RESULTADOS: Se seleccionaron 40 artículos. En todos ellos, se debía haber realizado una intervención poblacional enfocada al conocimiento de los consumidores sobre los alimentos genéticamente modificados y su necesidad, o no, de incluir información en el etiquetado. El consumidor expresa su preferencia por el producto no-genéticamente modificado, y apunta que está dispuesto a pagar algo más por él, pero, en definitiva compra el artículo que está a mejor precio en un mercado que acoge las nuevas tecnologías. En 18 artículos la población se mostraba favorable a su etiquetado obligatorio y seis al etiquetado voluntario; siete trabajos demostraban el poco conocimiento de la población sobre los transgénicos y, en tres, la población subestimó la cantidad que consumía. En todo caso, se observó la influencia del precio del producto genéticamente modificado. CONCLUSIONES: La etiqueta debe ser homogénea y aclarar el grado de tolerancia en humanos de alimentos genéticamente modificados en comparación con los no modificados. Asimismo, debe dejar claro su composición, o no, de alimento genéticamente modificado y la forma de producción de estos artículos de consumo. La etiqueta también debe ir acompañada de un sello de certificación de una agencia del estado y datos para contacto. El consumidor expresa su preferencia por el producto no-genéticamente modificado pero señaló que acaba comprando el artículo que está a mejor precio en un mercado que acoge las nuevas tecnologías.

How to make a natural language interface to query databases accessible to everyone: An example

Natural Language Interfaces to Query Databases (NLIDBs) have been an active research field since the 1960s. However, they have not been widely adopted. This article explores some of the biggest challenges and approaches for building NLIDBs and proposes techniques to reduce implementation and adoption costs. The article describes {AskMe*}, a new system that leverages some of these approaches and adds an innovative feature: query-authoring services, which lower the entry barrier for end users. Advantages of these approaches are proven with experimentation. Results confirm that, even when {AskMe*} is automatically reconfigurable against multiple domains, its accuracy is comparable to domain-specific NLIDBs.

Bibliographic index of North American archaeocyathids / [by] Matthew H. Nitecki --

v.17:no.2(1967)

Reducing task’s redundancy – the strategy of Faculty of Pharmacy Library to centralize all scientific research

Introduction – Based on a previous project of University of Lisbon (UL) – a Bibliometric Benchmarking Analysis of University of Lisbon, for the period of 2000-2009 – a database was created to support research information (ULSR). However this system was not integrated with other existing systems at University, as the UL Libraries Integrated System (SIBUL) and the Repository of University of Lisbon (Repositório.UL). Since libraries were called to be part of the process, the Faculty of Pharmacy Library’ team felt that it was very important to get all systems connected or, at least, to use that data in the library systems. Objectives – The main goals were to centralize all the scientific research produced at Faculty of Pharmacy, made it available to the entire Faculty, involve researchers and library team, capitalize and reinforce team work with the integration of several distinct projects and reducing tasks’ redundancy. Methods – Our basis was the imported data collection from the ISI Web of Science (WoS), for the period of 2000-2009, into ULSR. All the researchers and indexed publications at WoS, were identified. A first validation to identify all the researchers and their affiliation (university, faculty, department and unit) was done. The final validation was done by each researcher. In a second round, concerning the same period, all Pharmacy Faculty researchers identified their published scientific work in other databases/resources (NOT WoS). To our strategy, it was important to get all the references and essential/critical to relate them with the correspondent digital objects. To each researcher previously identified, was requested to register all their references of the ‘NOT WoS’ published works, at ULSR. At the same time, they should submit all PDF files (for both WoS and NOT WoS works) in a personal area of the Web server. This effort enabled us to do a more reliable validation and prepare the data and metadata to be imported to Repository and to Library Catalogue. Results – 558 documents related with 122 researchers, were added into ULSR. 1378 bibliographic records (WoS + NOT WoS) were converted into UNIMARC and Dublin Core formats. All records were integrated in the catalogue and repository. Conclusions – Although different strategies could be adopted, according to each library team, we intend to share this experience and give some tips of what could be done and how Faculty of Pharmacy created and implemented her strategy.

Europe on the Internet. A selection of useful websites, databases and documents for information on the European Union and the wider Europe. July 2016

No abstract.

Selected bibliographic references on methodologies for community health status assessment /

Includes index.