FlyNets and GIF-DB, two internet databases for molecular interactions in Drosophila melanogaster.

GIF-DB and FlyNets are two WWW databases describing molecular (protein-DNA, protein-RNA and protein-protein) interactions occuring in the fly Drosophila melanogaster (http://gifts.univ-mrs.fr/GIFTS_home_page.html ). GIF-DB is a specialised database which focuses on molecular interactions involved in the process of embryonic pattern formation, whereas FlyNets is a new and more general database, the long-term goal of which is to report on any published molecular interaction occuring in the fly. The information content of both databases is distributed in specific lines arranged into an EMBL- (or GenBank-) like format. These databases achieve a high level of integration with other databases such as FlyBase, EMBL, GenBank and SWISS-PROT through numerous hyperlinks. In addition, we also describe SOS-DGDB, a new collection of annotated Drosophila gene sequences, in which binding sites for regulatory proteins are directly visible on the DNA primary sequence and hyperlinked both to GIF-DB and TRANSFAC database entries.     

Harnessing Nutrigenomics: Development of web-based communication, databases, resources, and tools

Nutrient - gene interactions are responsible for maintaining health and preventing or delaying disease. Unbalanced diets for a given genotype lead to chronic diseases such as obesity, diabetes, cardiovascular, and are likely to contribute to increased severity and/or early-onset of many age-related diseases. Many nutrition and many genetic studies still fail to properly include both variables in the design, execution, and analyses of human, laboratory animal, or cell culture experiments. The complexity ofnutrient-gene interactions has led to the realization that strategic international alliances are needed to improve the completeness of nutrigenomic studies - a task beyond the capabilities of a single laboratory team. Eighty-eight researchers from 22 countries recently outlined the issues and challenges for harnessing the nutritional genomics for public and personal health. The next step in the process of forming productive international alliances is the development of a virtual center for organizing collaborations and communications that foster resources sharing, best practices improvements, and creation of databases. We describe here plans and initial efforts of creating the Nutrigenomics Information Portal, a web-based resource for the international nutrigenomics society. This portal aims at becoming the prime source ofinformation and interaction for nutrigenomics scientists through a collaborative effort.     

Parents, ADHD and the internet

The objective of this study is to examine the potential impact of using the internet on medical consultations by analysing the attitudes, attributions, and emotional responses of parents who have been informed by specialists that their child does not have attention-deficit hyperactivity disorder (ADHD) and to examine the nature of the feedback they obtained from members of online internet support groups. Over 40,000 messages from the five most popular international internet forums discussing children with ADHD were analysed. Messages from parents who reported that they had seen at least one specialist (e.g. paediatrician, psychiatrist or psychologist) because of their concerns that their child had ADHD were identified. The children included boys and girls with an age range from 2 to 16?years. Of these, we analysed messages where the parents additionally reported that the specialist had excluded a diagnosis of ADHD. Using these criteria, 91 messages from parents who had consulted over 200 different specialists and 398 replies to these messages were identified for content analysis. The replies to concerned parents were analysed to determine whether they were offered impartial advice. A majority of the parents reported that they did not believe the specialist and were unhappy about their child not being diagnosed with ADHD. They expressed dissatisfaction with the professional's opinions and the implication that their child's conduct was caused by their poor parenting skills. Importantly, 87.6?% of the responses that these parents received, from other members of online forums, reinforced the parent's negative attitude towards the professional's judgement. It was generally suggested that the parents should not believe the expert and should seek a further opinion. The use of the internet may encourage "doctor shopping" and mistrust in health services. Medical professionals and others may need to be aware of this, and parents may need more support than is generally offered to be able to accept alternative explanations for their child's behaviour.     

Biodiversity, genomes, and DNA sequence databases

There are ∼1.4 million organisms on this planet that have been described morphologically but there is no comparable coverage of biodiversity at the molecular level. Little more than 1% of the known species have been subject to any molecular scrutiny and eukaryotic genome projects have focused on a group of closely related model organisms. The past year, however, has seen an ∼80% increase in the number of species represented in sequence databases and the completion of the sequencing of three prokaryotic genomes. Large-scale sequencing projects seem set to begin coverage of a wider range of the eukaryotic diversity, including green plants, microsporidians and diplomonads.     

Consistency,comprehensiveness, and compatibility of pathway databases

Background  

It is necessary to analyze microarray experiments together with biological information to make better biological inferences. We investigate the adequacy of current biological databases to address this need.     

Biotechnology and the internet

This article attempts to bridge the gap between the arena of computers and the ever expanding protocols for individuals interested in accessing available information on biotechnology. A brief overview of the Internet and how to find information is provided. However, the focus of this review is on “what is out there’ for the biotechnologist and how to find it. Internet addresses for some key sites are listed.     

Diabetes and the internet

This paper examines what the World Wide Web has to offer patients, families and professionals in relation to diabetes. The potential pitfalls and dangers are discussed, leading to a wider debate on how the Internet can be expected to impact upon diabetes and other health care provision in the near future, and how health care professionals' practices will have to change. Themes include: the World Wide Web (finding material, assessing authenticity, pitfalls for patients, personalized pages, chat rooms, security); e-mail consultation (benefits, risks, minimizing risk, what to tell patients, legal constraints, security); telemedicine (telemetry, surveillance, security); search engines (journals, etc.); looking ahead (digital television, web-based medical records).     

DNA, diseases and databases: disastrously deficient

Recent progress in disease genetics and genome-related medicine has been substantial, with vast amounts of data being generated. However, this progress has not been matched by adequate database projects that gather and organize these data to enable their useful exploitation. This research area is complex, entailing core databases, locus-specific databases, national mutation databases, genotype-phenotype databases and patient databases--and much work is required to develop and properly integrate these various resources. To promote this, we present a timely overview of the field, emphasize its over-riding importance and discuss the disastrously deficient progress made so far. Many factors contribute to this slow progress (e.g. technological hurdles, publication requirements, the short-sighted and popularist research system). A lack of targeted funding is arguably the most fundamental problem, but one that can be solved.     

Cloud-hosted databases: technologies,challenges and opportunities

One of the main advantages of the cloud computing paradigm is that it simplifies the time-consuming processes of hardware provisioning, hardware purchasing and software deployment. Currently, we are witnessing a proliferation in the number of cloud-hosted applications with a tremendous increase in the scale of the data generated as well as being consumed by such applications. Cloud-hosted database systems powering these applications form a critical component in the software stack of these applications. To better understand the challenges in developing effective cloud-hosted database systems, this article discusses the existing technologies for hosting the database tier of software applications in cloud environments, illustrates their strengths and weaknesses, and presents some opportunities for future work.     

Storing,linking, and mining microarray databases using SRS

Background  

SRS (Sequence Retrieval System) has proven to be a valuable platform for storing, linking, and querying biological databases. Due to the availability of a broad range of different scientific databases in SRS, it has become a useful platform to incorporate and mine microarray data to facilitate the analyses of biological questions and non-hypothesis driven quests. Here we report various solutions and tools for integrating and mining annotated expression data in SRS.     

Science through the internet: Researching, evaluating and citing websites

This article attempts to convey the joys and frustrations of skimming the Internet trying to find relevant information concerning an academic’s work as a scientist, a student or an instructor. A brief overview of the Internet and the “do’s and don’ts” for the neophyte as well for the more seasoned “navigator” are given. Some guidelines of “what works and what does not” and “what is out there” are provided for the scientist with specific emphasis for biologists, as well as for all others having an interest in science but with little interest in spending countless hours “surfing the net”. An extensive but not exhaustive list of related websites is provided.     

Glycoproteomic and glycomic databases

Protein glycosylation serves critical roles in the cellular and biological processes of many organisms. Aberrant glycosylation has been associated with many illnesses such as hereditary and chronic diseases like cancer, cardiovascular diseases, neurological disorders, and immunological disorders. Emerging mass spectrometry (MS) technologies that enable the high-throughput identification of glycoproteins and glycans have accelerated the analysis and made possible the creation of dynamic and expanding databases. Although glycosylation-related databases have been established by many laboratories and institutions, they are not yet widely known in the community. Our study reviews 15 different publicly available databases and identifies their key elements so that users can identify the most applicable platform for their analytical needs. These databases include biological information on the experimentally identified glycans and glycopeptides from various cells and organisms such as human, rat, mouse, fly and zebrafish. The features of these databases - 7 for glycoproteomic data, 6 for glycomic data, and 2 for glycan binding proteins are summarized including the enrichment techniques that are used for glycoproteome and glycan identification. Furthermore databases such as Unipep, GlycoFly, GlycoFish recently established by our group are introduced. The unique features of each database, such as the analytical methods used and bioinformatical tools available are summarized. This information will be a valuable resource for the glycobiology community as it presents the analytical methods and glycosylation related databases together in one compendium. It will also represent a step towards the desired long term goal of integrating the different databases of glycosylation in order to characterize and categorize glycoproteins and glycans better for biomedical research.     

Aminoaciduria databases

Electronic encyclopaedia of human hereditary disorders of amino acid metabolism (aminoacidurias) has been created. The disease inheritance, gene location, gene mutations, biochemistry, and gene therapy of aminoacidurias are described in most detail. The database (DB) is integrated with international DBs available in Internet. The electronic encyclopaedia may serve as an educational system connecting medicine with modern molecular genetics.     

EBI databases and services

The EMBL Outstation-European Bioinformatics Institute (EBI) is a center for research and services in bioinformatics. It serves researchers in molecular biology, genetics, medicine, and agriculture from academia, and the agricultural, biotechnology, chemical, and pharmaceutical industries. The Institute manages and makes available databases of biological data including nucleic acid, protein sequences, and macromolecular structures. It provides to this community bioinformatics services relevant to molecular biology free of charge over the Internet. Some of these databases and services are described in this review. For more information, visit the EBI Web server at http://www.ebi.ac.uk/.