Plans for HDBase—a research community website for Huntington's Disease
Introduction
Everyone has heard the worn clichés about the growing mountain of biological data, and the difficulties that scientists face in pinpointing data relevant to their research. One solution is to muster a small troop of data experts to hunt for data on behalf of a research community, with the results posted on a website for all to see. This idea, which we call a research community website, was pioneered by the seminal ACeDB project [1] on behalf of the C. elegans research community. Nowadays, such websites are common among model organism communities, including Arabidopsis [2], C. elegans [3], corn [4], Drosophila [5], E. coli and related species [6], frog [7], grains [8], grasses [9], malaria parasites [10], mouse [11], organelles [12], rat [13], rice [14], yeast [15], and zebrafish [16]. This approach has also been adopted by research communities working on particular genetic loci or protein families, including the HLA [17] and cystic fibrosis [18] loci, and the cytochrome P450 [19], [20], GPCR [21], kinesins [22], nuclear receptor [23], and Wnt [24] protein families. This strategy makes just as much sense for disease focused research communities, but has not yet taken hold.
One example of a disease focused research website is Alzforum [25], focused on Alzheimer's Disease (AD) and operated by the Alzheimer Research Forum (ARF). Alzforum is a comprehensive website with information for the general public, patients, caregivers, and scientists. The portion aimed at scientists provides an up-to-date citation database which allows annotation by experts and free-text commentary by registered users in the style of Amazon. com's reader reviews. The site also includes a scientific news section with summaries of important papers and highlights from conferences, and a forum that presents interviews with leading scientists, web delivery of lectures, and mini-reviews accompanied by extensive bibliographies. In addition, the site provides information of community interest: a calendar of coming events, contact information and research profiles of AD scientists, and links to other websites.
The website operated by the amyotrophic lateral sclerosis (ALS) Therapy Development Foundation (ALS-TDF) [26] is also arguably in this class, although they concentrate on research produced by their own organization. The Mad Cow Disease website [27] covered breaking news and science on mad cow and related diseases, including curated lists of prion-like proteins, from 1999 to 2001. Further afield are websites devoted to particular research methods applied to particular diseases, e.g., the Stanford Genomics Breast Cancer Consortium Portal [28] which focuses on microarray studies of breast cancer.
This paper describes a research community website that we are developing for Huntington's Disease (HD). This project, called HDBase [29], is at an early stage. This paper presents an overview of the project, our plans, and some examples of the datasets we are assembling.
Section snippets
Overview of project
The core of HDBase is expert-reviewed scientific content on topics of interest to the HD research community. Scientific direction comes from a steering committee of HD experts who specify the core content to be gathered for the site and review the results to assure its scientific quality.
We work closely with other public databases to improve their HD coverage and to avoid repeating their work. We try not to store data on our site that are readily available elsewhere, and prefer to provide
Method for assembly of high quality bibliographies
Our data collection approach revolves around the assembly of high quality bibliographies on specialized topics. Assembly of bibliographies is something all academics know how to do intuitively—it's part and parcel of our scholarly trade. But, when one sets out to create bibliographies in a systematic fashion, the limits of intuition are quickly reached. How do we define and measure success? How do we do the job more efficiently? How do we balance cost with quality?
In the following subsections,
Example bibliographies and datasets
HDBase is a young project and different aspects are at different stages of completion. Here we describe our progress on the comprehensive bibliography and three focused content areas.
Discussion
HDBase is a research community website for researchers who work on HD. The core of the site is reviewed scientific content on topics of interest to the HD research community. Current topics include information on HD reagents, such as mouse models and antibodies, information on genes and proteins of interest to HD researchers, such as proteins that interact with Htt, and information about specific research topics, such as drug screening studies in mouse and microarray-based gene expression
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Biological Databases for Behavioral Neurobiology
2012, International Review of NeurobiologyCitation Excerpt :As a result, many life science databases in general and behavioral neuroscience databases in particular have grown out of a single research lab to mediate a particular tactical need. For example, neuroscience databases and data management tools include those seeking to manage transcriptional data (Shepherd et al., 1998), complex images such as fMRI scans (Marcus et al., 2007), laboratory information management systems (LIMS) and data management (Baker, Galloway, Jackson, Schmoyer, & Snoddy, 2004), formal collaborations and federated repositories (Gardner et al., 2008), publication data (Ruttenberg, Rees, Samwald, & Marshall, 2009), protein interaction (Colland et al., 2004; Shoemaker et al., 2012) and mass spec data (Horai et al., 2010), behavioral data (Maddatu, Grubb, Bult, & Bogue, 2012), electrophysiological measurements (Günay et al., 2009), and a series of disorder related repositories (Goodman et al., 2003; Matuszek & Talebizadeh, 2009). While not necessarily in conflict with the strategic goals of the greater behavioral neuroscience community, the ad hoc collection of boutique databases, analysis tools and information repositories that exist on the local level are often incompatible with comprehensive data mining.
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