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).

Creating local bibliographic databases: new tools for evidence-based health care*

The Internet has created new opportunities for librarians to present literature search results to clinicians. In order to take full advantage of these opportunities, libraries need to create locally maintained bibliographic databases. A simple method of creating a local bibliographic database and publishing it on the Web is described. The method uses off-the-shelf software and requires minimal programming. A hedge search strategy for outcome studies of clinical process interventions is created, and Ovid is used to search MEDLINE. The search results are saved and imported into EndNote libraries. The citations are modified, exported to a Microsoft Access database, and published on the Web. Clinicians can use a Web browser to search the database. The bibliographic database contains 13,803 MEDLINE citations of outcome studies. Most searches take between four and ten seconds and retrieve between ten and 100 citations. The entire cost of the software is under $900. Locally maintained bibliographic databases can be created easily and inexpensively. They significantly extend the evidence-based health care services that libraries can offer to clinicians.

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.

Health-Sector Responses to Intimate Partner Violence Fitting the Response Into the Biomedical Health System or Adapting the System to Meet the Response?

This study aims to analyze how middle-level health systems’ managers understand the integration of a health care response to intimate partner violence (IPV) within the Spanish health system. Data were obtained through 26 individual interviews with professionals in charge of coordinating the health care response to IPV within the 17 regional health systems in Spain. The transcripts were analyzed following grounded theory in accordance with the constructivist approach described by Charmaz. Three categories emerged, showing the efforts and challenges to integrate a health care response to IPV within the Spanish health system: “IPV is a complex issue that generates activism and/or resistance,” “The mandate to integrate a health sector response to IPV: a priority not always prioritized,” and “The Spanish health system: respectful with professionals’ autonomy and firmly biomedical.” The core category, “Developing diverse responses to IPV integration,” crosscut the three categories and encompassed the range of different responses that emerge when a strong mandate to integrate a health care response to IPV is enacted. Such responses ranged from refraining to deal with the issue to offering a women-centered response. Attempting to integrate a response to nonbiomedical health problems as IPV into health systems that remain strongly biomedicalized is challenging and strongly dependent both on the motivation of professionals and on organizational factors. Implementing and sustaining changes in the structure and culture of the health care system are needed if a health care response to IPV that fulfills the World Health Organization guidelines is to be ensured.

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.

Online literature searching and databases at the U.S. Environmental Protection Agency, Environmental Research Center, Library, Cincinnati, Ohio /

Mode of access: Internet.

Research and development in progress : biomedical and environmental research program /

"Issuance Date: December 1972."

NCI/MARC summer training supplement : Comprehensive Minority Biomedical Program, Division of Extramural Activities, National Cancer Institute in conjunction with Minority Access to Research Careers, National Institute of General Medical Sciences.

Mode of access: Internet.