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PubMed2002

Using the internet to assess and teach medical students in dermatology.

BACKGROUND AND OBJECTIVES: We wish to develop and evaluate a user-friendly online interactive teaching and examination model as an adjunct to traditional bedside teaching of medical students during a clinical rotation in dermatology. METHODS: Following completion of an online examination, senior medical students at the University of British Columbia (n = 178) were asked to complete an online survey to evaluate their acceptance of this new method. The online examination model was evaluated through students' responses to the questionnaire-based evaluation they were asked to complete following their examination. Responses were evaluated on a standardized 5-point scale. RESULTS: A high response rate was achieved (98.9%). Overall, 93% of senior medical students felt that the Internet was a useful and effective way to administer a dermatology examination. Most (90%) preferred the online examination to a traditional paper-and-pencil examination and the majority (88%) felt that the quality of digital images presented was sufficient to make an accurate diagnosis. In addition, students strongly supported the further development of teaching resources on the web and would use these resources in learning dermatology (93%). CONCLUSIONS: The development of an online interactive examination tool for dermatology is technically feasible with current technology. Senior medical students are not only accepting of this new technology but also prefer it to more traditional formats and indicate enthusiasm for the development of further online teaching resources in dermatology.

British Columbia↗
PubMed2006

BBP: Brucella genome annotation with literature mining and curation.

BACKGROUND: Brucella species are Gram-negative, facultative intracellular bacteria that cause brucellosis in humans and animals. Sequences of four Brucella genomes have been published, and various Brucella gene and genome data and analysis resources exist. A web gateway to integrate these resources will greatly facilitate Brucella research. Brucella genome data in current databases is largely derived from computational analysis without experimental validation typically found in peer-reviewed publications. It is partially due to the lack of a literature mining and curation system able to efficiently incorporate the large amount of literature data into genome annotation. It is further hypothesized that literature-based Brucella gene annotation would increase understanding of complicated Brucella pathogenesis mechanisms. RESULTS: The Brucella Bioinformatics Portal (BBP) is developed to integrate existing Brucella genome data and analysis tools with literature mining and curation. The BBP InterBru database and Brucella Genome Browser allow users to search and analyze genes of 4 currently available Brucella genomes and link to more than 20 existing databases and analysis programs. Brucella literature publications in PubMed are extracted and can be searched by a TextPresso-powered natural language processing method, a MeSH browser, a keywords search, and an automatic literature update service. To efficiently annotate Brucella genes using the large amount of literature publications, a literature mining and curation system coined Limix is developed to integrate computational literature mining methods with a PubSearch-powered manual curation and management system. The Limix system is used to quickly find and confirm 107 Brucella gene mutations including 75 genes shown to be essential for Brucella virulence. The 75 genes are further clustered using COG. In addition, 62 Brucella genetic interactions are extracted from literature publications. These results make possible more comprehensive investigation of Brucella pathogenesis. Other BBP features include publication email alert service, Brucella researchers' contact database, and discussion forum. CONCLUSION: BBP is a gateway for Brucella researchers to search, analyze, and curate Brucella genome data originated from public databases and literature. Brucella gene mutations and genetic interactions are annotated using Limix leading to better understanding of Brucella pathogenesis.

Algorithms↗
PubMed2006

Maternity care in the bush: using the Internet to provide educational resources to isolated practitioners.

INTRODUCTION: Telecommunication infrastructure is being rolled out across Australia with little knowledge about the uptake by health professionals in remote areas. Computer mediated communication has the potential to offer educational support to remote practitioners; however, the viability of this is uncertain. The aim of this research was to establish and evaluate an internet-based resource library targeting the needs of remote area maternity service providers. METHODS: A participatory action research (PAR) approach was used to involve remote area maternity service providers in the Northern Territory of Australia. The evaluation of the resource library included its performance on reach, agency affiliation and richness, factors identified to affect the sustainability and utility of such a resource. An additional component of the evaluation framework documented the facilitators of and barriers to using an information technology strategy to reduce the isolation of remote area maternity service providers. RESULTS: Overall, the evaluation of the resource library was very positive. Feedback from the PAR team described the resource as contemporary, useful and relevant. Practitioners in leadership and education positions identified the resource library as a valuable tool that enabled them to access professional knowledge, which could then be distributed to any remote-based practitioners, who experienced difficulties with access themselves. The evaluation found that logistical issues were a major problem for potential users. Hardware inadequacies, access difficulties, unfamiliarity with computers, and a lack of management support for nursing and midwifery staff to utilise the resource, were all identified barriers. Remote-area practitioners highlighted education, training and 24 hour support as key priorities. CONCLUSIONS: Results from this research clearly showed the potential of web-based resources to offer educational support through access to clinical guidelines, reports and research, thus reducing the isolation of the remote practitioner. However, it highlighted the need for clear strategic direction at policy level, whereby all stakeholders unite to synchronise the rollout of information technology infrastructure with the necessary education, training and support as an integral component.

Attitude of Health Personnel↗
PubMed2006

An object-oriented programming system for the integration of internet-based bioinformatics resources.

The Internet consists of a vast inhomogeneous reservoir of data. Developing software that can integrate a wide variety of different data sources is a major challenge that must be addressed for the realisation of the full potential of the Internet as a scientific research tool. This article presents a semi-automated object-oriented programming system for integrating web-based resources. We demonstrate that the current Internet standards (HTML, CGI [common gateway interface], Java, etc.) can be exploited to develop a data retrieval system that scans existing web interfaces and then uses a set of rules to generate new Java code that can automatically retrieve data from the Web. The validity of the software has been demonstrated by testing it on several biological databases. We also examine the current limitations of the Internet and discuss the need for the development of universal standards for web-based data.

Computational Biology↗
PubMed1999

Effective poultry programming in the next century. Innovative applications of distance education: getting into the knowledge marketplace.

The number of internet-based resources for use in poultry science distance education is growing. These new resources present opportunities as well as challenges to land grant university programs and traditions. This article includes an explanation of the emerging field of distance education and offers a rich assortment of web-based resources for poultry scientists.

Agriculture↗
PubMed1996

Immunology resources on the World Wide Web.

The power of the World Wide Web (WWW) lies in its ability to disseminate up-to-date information that may not be available by other means. Increasing exposure of research scientists and clinicians, amongst others, to the Internet has, in turn, stimulated the available resources to multiply and become more accessible and useful. Here, we review WWW sites of particular interest to immunologists.

Academic Medical Centers↗
PubMed2026

A full review of online education resources available on antifungal stewardship.

BACKGROUND AND OBJECTIVES: Antifungal resistance represents an increasing global threat, driven by the rising burden of fungal disease. Antifungal stewardship (AFS) is a critical component of broader antimicrobial resistance (AMR) efforts, but education in this area remains less established than antibacterial stewardship initiatives. The scope and characteristics of the current landscape of online AFS resources have not yet been systematically described. To identify and evaluate online educational resources focused on fungal disease management and AFS, and assess their accessibility, format, educational design and implementation focus. METHODS: A structured search of internet search engines, distribution platforms and organizational websites was conducted to identify English-language web-based resources related to fungal disease management and stewardship. Resources were evaluated using predefined criteria including access model, format, length, educational design, interactivity and AFS content. An overall educational value score (1-10) was assigned. RESULTS: Twenty-three educational resources were identified. Most were delivered as online unfacilitated courses (11, 48%) and were short (<4&#x2005;h) (12, 52%). Most focused on guidelines and syndromic management (18, 78%) and targeted doctors and/or nurses/midwives (22, 96%). Limited interactivity was reported in nine (39%) courses. Five courses (22%) had either a substantial or comprehensive focus on AFS. CONCLUSIONS: Online AFS educational resources are available and support awareness and knowledge development. However, they remain relatively few in number. Greater emphasis on implementation-focused learning, behaviour change components and broader global representation may enhance their impact.

Journal Article↗
PubMed2006

A systematic approach to infer biological relevance and biases of gene network structures.

The development of high-throughput technologies has generated the need for bioinformatics approaches to assess the biological relevance of gene networks. Although several tools have been proposed for analysing the enrichment of functional categories in a set of genes, none of them is suitable for evaluating the biological relevance of the gene network. We propose a procedure and develop a web-based resource (BIOREL) to estimate the functional bias (biological relevance) of any given genetic network by integrating different sources of biological information. The weights of the edges in the network may be either binary or continuous. These essential features make our web tool unique among many similar services. BIOREL provides standardized estimations of the network biases extracted from independent data. By the analyses of real data we demonstrate that the potential application of BIOREL ranges from various benchmarking purposes to systematic analysis of the network biology.

Computational Biology↗
PubMed2003

Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities.

Culture-independent DNA fingerprints are commonly used to assess the diversity of a microbial community. However, relating species composition to community profiles produced by community fingerprint methods is not straightforward. Terminal restriction fragment length polymorphism (T-RFLP) is a community fingerprint method in which phylogenetic assignments may be inferred from the terminal restriction fragment (T-RF) sizes through the use of web-based resources that predict T-RF sizes for known bacteria. The process quickly becomes computationally intensive due to the need to analyze profiles produced by multiple restriction digests and the complexity of profiles generated by natural microbial communities. A web-based tool is described here that rapidly generates phylogenetic assignments from submitted community T-RFLP profiles based on a database of fragments produced by known 16S rRNA gene sequences. Users have the option of submitting a customized database generated from unpublished sequences or from a gene other than the 16S rRNA gene. This phylogenetic assignment tool allows users to employ T-RFLP to simultaneously analyze microbial community diversity and species composition. An analysis of the variability of bacterial species composition throughout the water column in a humic lake was carried out to demonstrate the functionality of the phylogenetic assignment tool. This method was validated by comparing the results generated by this program with results from a 16S rRNA gene clone library.

Bacteria↗
PubMed2005

Bio-Health Information: a Preliminary Review of On-line Cystic Fibrosis Resources.

The aims of this study are to determine, and to better understand, elements that are common across a range of bio-health information resources; and to characterize those resources in terms of search and display functionality. Our ultimate goal is to better define the role of bio-health information in clinical practice and in biological research. This paper reports our first step, which is to compare different web-based resources that describe cystic fibrosis. The resources came from PubMed, Nucleotide, EMBL-EBI, DDBJ, OMIM, MeSH, ICD-10, and the Cystic Fibrosis Mutation Database. We found obvious differences in terms of scope and purpose. However, while there were obvious similarities between related resources in terms of content, we also found differences among these resources in terms of display form, specificity of qualifiers, file format and the potential for computer processing. While our work is in its early stages, this study has clarified the nature of bio-health information resources and has allowed us to begin to characterize these resources in terms of their suitability in clinical practice and in biological research.

Cystic Fibrosis↗
PubMed2000

Mouse tumor biology database (MTB): enhancements and current status.

The Mouse Tumor Biology Database (MTB) is a Web-based resource that provides access to information on tumor frequency and latency, genetics and pathology in genetically defined mice (transgenics, targeted mutations and inbred strains). MTB is designed to serve as an information resource for cancer genetics researchers who use the laboratory mouse as a model system for understanding human disease processes. Data in MTB are obtained from the primary scientific literature and direct submissions by the research community. MTB is accessible from the Mouse Genome Informatics Web site (http://www. informatics.jax.org). User support is available for MTB via Email at mgi-help@informatics.jax.org

Animals↗
PubMed2006

Clinical Digital Libraries Project: design approach and exploratory assessment of timely use in clinical environments.

OBJECTIVE: The paper describes and evaluates the use of Clinical Digital Libraries Project (CDLP) digital library collections in terms of their facilitation of timely clinical information seeking. DESIGN: A convenience sample of CDLP Web server log activity over a twelve-month period (7/2002 to 6/2003) was analyzed for evidence of timely information seeking after users were referred to digital library clinical topic pages from Web search engines. Sample searches were limited to those originating from medical schools (26% North American and 19% non-North American) and from hospitals or clinics (51% North American and 4% non-North American). MEASUREMENT: Timeliness was determined based on a calculation of the difference between the timestamps of the first and last Web server log "hit" during each search in the sample. The calculated differences were mapped into one of three ranges: less than one minute, one to three minutes, and three to five minutes. RESULTS: Of the 864 searches analyzed, 48% were less than 1 minute, 41% were 1 to 3 minutes, and 11% were 3 to 5 minutes. These results were further analyzed by environment (medical schools versus hospitals or clinics) and by geographic location (North America versus non-North American). Searches reflected a consistent pattern of less than 1 minute in these environments. Though the results were not consistent on a month-by-month basis over the entire time period, data for 8 of 12 months showed that searches shorter than 1 minute predominated and data for 1 month showed an equal number of less than 1 minute and 1 to 3 minute searches. CONCLUSIONS: The CDLP digital library collections provided timely access to high-quality Web clinical resources when used for information seeking in medical education and hospital or clinic environments from North American and non-North American locations and consistently provided access to the sought information within the documented two-minute standard. The limitations of the use of Web server data warrant an exploratory assessment. This research also suggests the need for further investigation in the area of timely digital library collection services to clinical environments.

Geography↗
PubMed2002

Where to find a mate? Resource-based sexual communication of webbing clothes moth.

Mate location in moths typically entails long-range attraction of males to female-produced pheromone. Here, we show that male and female webbing clothes moths, Tineola bisselliella, seek larval habitats (dry carrion, animal lairs, etc) to encounter mates. With males seeking, and arriving at, larval habitat earlier at night than females, male-produced pheromonal and sonic signals enhance the habitat's attractiveness to females. This resource-based mating strategy of T bisselliella differs from that known for most other moths. It may have evolved in response to larval habitats that are patchy and temporary, but that disseminate attractive semiochemicals so abundantly that T bisselliella encounter them more readily than their own pheromones.

Animal Communication↗
PubMed2003

ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database.

The automated sequence annotation pipeline (ASAP) is designed to ease routine investigation of new functional annotations on unknown sequences, such as expressed sequence tags (ESTs), through querying of web-accessible resources and maintenance of a local database. The system allows easy use of the output from one search as the input for a new search, as well as the filtering of results. The database is used to store formats and parameters and information for parsing data from web sites. The database permits easy updating of format information should a site modify the format of a query or of a returned web page.

Database Management Systems↗
PubMed2004

GeneDB: a resource for prokaryotic and eukaryotic organisms.

GeneDB (http://www.genedb.org/) is a genome database for prokaryotic and eukaryotic organisms. The resource provides a portal through which data generated by the Pathogen Sequencing Unit at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be made publicly available. It combines data from finished and ongoing genome and expressed sequence tag (EST) projects with curated annotation, that can be searched, sorted and downloaded, using a single web based resource. The current release stores 11 datasets of which six are curated and maintained by biologists, who review and incorporate information from the scientific literature, public databases and the respective research communities.

Animals↗
PubMed2005

The GATO gene annotation tool for research laboratories.

Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.

Biomedical Research↗
PubMed2005

Proteomic resources: integrating biomedical information in humans.

Recent improvements in high-throughput proteomic technologies have unleashed the potential for generating vast amounts of data. Managing and sharing proteomic data is not an easy task. In this article, we will discuss some of the high-throughput proteomic techniques that are commonly used today. We will also review the major issues in sharing and dissemination of proteomic data and the recent community initiatives to standardize data formats and ontologies. An overview of the web-based resources and databases for analysis of proteomic data is also provided. Integration of disparate proteomic data sources with genomic and transcriptomic data should make systems biology type of approaches feasible in the near future.

Amino Acid Sequence↗
PubMed2003

Use of emergency observation and assessment wards: a systematic literature review.

INTRODUCTION: Observation and assessment wards allow patients to be observed on a short-term basis and permit patient monitoring and/or treatment for an initial 24-48 hour period. They should permit concentration of emergency activity and resources in one area, and so improve efficiency and minimise disruption to other hospital services. These types of ward go under a variety of names, including observation, assessment, and admission wards. This review aims to evaluate the current literature and discuss assessment/admission ward functionality in terms of organisation, admission criteria, special patient care, and cost effectiveness. METHODS: Search of the literature using the Medline and BIDS databases, combined with searches of web based resources. Critical assessment of the literature and the data therein is presented. RESULTS: The advantages and disadvantages of the use of assessment/admission wards were assessed from the current literature. Most articles suggest that these wards improve patient satisfaction, are safe, decrease the length of stay, provide earlier senior involvement, reduce unnecessary admissions, and may be particularly useful in certain diagnostic groups. A number of studies summarise their organisational structure and have shown that strong management, staffing, organisation, size, and location are important factors for efficient running. There is wide variation in the recommended size of these wards. Observation wards may produce cost savings largely relating to the length of stay in such a unit. CONCLUSION: All types of assessment/admission wards seem to have advantages over traditional admission to a general hospital ward. A successful ward needs proactive management and organisation, senior staff involvement, and access to diagnostics and is dependent on a clear set of policies in terms of admission and care. Many diagnostic groups benefit from this type of unit, excluding those who will inevitably need longer admission. Vigorous financial studies have yet to be undertaken in the UK. Definitions of observation, assessment, and admission ward are suggested.

Cost-Benefit Analysis↗