Dataset Information

T1DBase, a community web-based resource for type 1 diabetes research.

ABSTRACT: T1DBase (http://T1DBase.org) is a public website and database that supports the type 1 diabetes (T1D) research community. The site is currently focused on the molecular genetics and biology of T1D susceptibility and pathogenesis. It includes the following datasets: annotated genome sequence for human, rat and mouse; information on genetically identified T1D susceptibility regions in human, rat and mouse, and genetic linkage and association studies pertaining to T1D; descriptions of NOD mouse congenic strains; the Beta Cell Gene Expression Bank, which reports expression levels of genes in beta cells under various conditions, and annotations of gene function in beta cells; data on gene expression in a variety of tissues and organs; and biological pathways from KEGG and BioCarta. Tools on the site include the GBrowse genome browser, site-wide context dependent search, Connect-the-Dots for connecting gene and other identifiers from multiple data sources, Cytoscape for visualizing and analyzing biological networks, and the GESTALT workbench for genome annotation. All data are open access and all software is open source.

SUBMITTER: Smink LJ

PROVIDER: S-EPMC540049 | biostudies-literature | 2005 Jan

REPOSITORIES: biostudies-literature

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T1DBase, a community web-based resource for type 1 diabetes research.

Smink Luc J LJ Helton Erin M EM Healy Barry C BC Cavnor Christopher C CC Lam Alex C AC Flamez Daisy D Burren Oliver S OS Wang Yang Y Dolman Geoffrey E GE Burdick David B DB Everett Vincent H VH Glusman Gustavo G Laneri Davide D Rowen Lee L Schuilenburg Helen H Walker Neil M NM Mychaleckyj Josyf J Wicker Linda S LS Eizirik Decio L DL Todd John A JA Goodman Nathan N

Nucleic acids research 20050101 Database issue

T1DBase (http://T1DBase.org) is a public website and database that supports the type 1 diabetes (T1D) research community. The site is currently focused on the molecular genetics and biology of T1D susceptibility and pathogenesis. It includes the following datasets: annotated genome sequence for human, rat and mouse; information on genetically identified T1D susceptibility regions in human, rat and mouse, and genetic linkage and association studies pertaining to T1D; descriptions of NOD mouse con ...[more]

PMID: 15608258

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Project description:BackgroundGeneral Practitioners and community nurses rely on easily accessible, evidence-based online information to guide practice. To date, the methods that underpin the scoping of user-identified online information needs in palliative care have remained under-explored. This paper describes the benefits and challenges of a collaborative approach involving users and experts that informed the first stage of the development of a palliative care website 1.MethodThe action research-inspired methodology included a panel assessment of an existing palliative care website based in Victoria, Australia; a pre-development survey (n = 197) scoping potential audiences and palliative care information needs; working parties conducting a needs analysis about necessary information content for a redeveloped website targeting health professionals and caregivers/patients; an iterative evaluation process involving users and experts; as well as a final evaluation survey (n = 166).ResultsInvolving users in the identification of content and links for a palliative care website is time-consuming and requires initial resources, strong networking skills and commitment. However, user participation provided crucial information that led to the widened the scope of the website audience and guided the development and testing of the website. The needs analysis underpinning the project suggests that palliative care peak bodies need to address three distinct audiences (clinicians, allied health professionals as well as patients and their caregivers).ConclusionWeb developers should pay close attention to the content, language, and accessibility needs of these groups. Given the substantial cost associated with the maintenance of authoritative health information sites, the paper proposes a more collaborative development in which users can be engaged in the definition of content to ensure relevance and responsiveness, and to eliminate unnecessary detail. Access to volunteer networks forms an integral part of such an approach.

Project description:Functional characterization of bacterial proteins lags far behind the identification of new protein families. This is especially true for bacterial species that are more difficult to grow and genetically manipulate than model systems such as Escherichia coli and Bacillus subtilis To facilitate functional characterization of mycobacterial proteins, we have established a Mycobacterial Systems Resource (MSR) using the model organism Mycobacterium smegmatis This resource focuses specifically on 1,153 highly conserved core genes that are common to many mycobacterial species, including Mycobacterium tuberculosis, in order to provide the most relevant information and resources for the mycobacterial research community. The MSR includes both biological and bioinformatic resources. The biological resource includes (i) an expression plasmid library of 1,116 genes fused to a fluorescent protein for determining protein localization; (ii) a library of 569 precise deletions of nonessential genes; and (iii) a set of 843 CRISPR-interference (CRISPRi) plasmids specifically targeted to silence expression of essential core genes and genes for which a precise deletion was not obtained. The bioinformatic resource includes information about individual genes and a detailed assessment of protein localization. We anticipate that integration of these initial functional analyses and the availability of the biological resource will facilitate studies of these core proteins in many Mycobacterium species, including the less experimentally tractable pathogens M. abscessus, M. avium, M. kansasii, M. leprae, M. marinum, M. tuberculosis, and M. ulceransIMPORTANCE Diseases caused by mycobacterial species result in millions of deaths per year globally, and present a substantial health and economic burden, especially in immunocompromised patients. Difficulties inherent in working with mycobacterial pathogens have hampered the development and application of high-throughput genetics that can inform genome annotations and subsequent functional assays. To facilitate mycobacterial research, we have created a biological and bioinformatic resource (https://msrdb.org/) using Mycobacterium smegmatis as a model organism. The resource focuses specifically on 1,153 proteins that are highly conserved across the mycobacterial genus and, therefore, likely perform conserved mycobacterial core functions. Thus, functional insights from the MSR will apply to all mycobacterial species. We believe that the availability of this mycobacterial systems resource will accelerate research throughout the mycobacterial research community.

Dataset Information

T1DBase, a community web-based resource for type 1 diabetes research.

Publications

T1DBase, a community web-based resource for type 1 diabetes research.

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