Abstract
Common metabolic and endocrine diseases such as diabetes affect millions of people worldwide and have a major health impact, frequently leading to complications and mortality. In a search for better prevention and treatment, there is ongoing research into the underlying molecular and genetic bases of these complex human diseases, as well as into the links with risk factors such as obesity. Although an increasing number of relevant genomic and proteomic data sets have become available, the quantity and diversity of the data make their efficient exploitation challenging. Here, we present metabolicMine, a data warehouse with a specific focus on the genomics, genetics and proteomics of common metabolic diseases. Developed in collaboration with leading UK metabolic disease groups, metabolicMine integrates data sets from a range of experiments and model organisms alongside tools for exploring them. The current version brings together information covering genes, proteins, orthologues, interactions, gene expression, pathways, ontologies, diseases, genome-wide association studies and single nucleotide polymorphisms. Although the emphasis is on human data, key data sets from mouse and rat are included. These are complemented by interoperation with the RatMine rat genomics database, with a corresponding mouse version under development by the Mouse Genome Informatics (MGI) group. The web interface contains a number of features including keyword search, a library of Search Forms, the QueryBuilder and list analysis tools. This provides researchers with many different ways to analyse, view and flexibly export data. Programming interfaces and automatic code generation in several languages are supported, and many of the features of the web interface are available through web services. The combination of diverse data sets integrated with analysis tools and a powerful query system makes metabolicMine a valuable research resource. The web interface makes it accessible to first-time users, whereas the Application Programming Interface (API) and web services provide convenient data access and tools for bioinformaticians. metabolicMine is freely available online at http://www.metabolicmine.orgDatabase URL: http://www.metabolicmine.org
Highlights
Metabolic disorders, thought to result from the interaction of genetic factors with the environment [1], are seen as a global health concern [2]
Novel genome-wide approaches to the study of disease susceptibility have yielded some interesting results, leading to the discovery of a number of genes implicated in common metabolic diseases [1, 4, 5], including an international effort to find loci associated with type 2 diabetes [6]
Genomics and proteomics methods are perfectly suited to this task in terms of providing a system-wide view necessary for understanding complex diseases, but they come with their own set of interpretation challenges
Summary
Thought to result from the interaction of genetic factors with the environment [1], are seen as a global health concern [2]. MetabolicMine has been built with the InterMine platform because it provides a useful combination of features including fast keyword searches, a flexible querying system, list analysis, visualization tools and a space for researchers to save their own lists and queries.
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