metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research
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DOI：
10.1093/database/bat060
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发表时间：
2013-08-09
影响因子：
5.8
通讯作者：
Micklem, Gos
中科院分区：
文献类型：
--
作者：
Lyne, Mike;Smith, Richard N.;Micklem, Gos
常见的代谢和内分泌疾病，如糖尿病，影响着全世界数百万人，并对健康产生重大影响，经常导致并发症和死亡。为了寻求更好的预防和治疗，目前正在研究这些复杂的人类疾病的潜在分子和遗传基础，以及与肥胖等风险因素的联系。虽然越来越多的相关基因组和蛋白质组数据集已经成为可用的，数据的数量和多样性，使他们的有效利用具有挑战性。在这里，我们介绍了metabolicMine，一个数据仓库，特别关注常见代谢疾病的基因组学，遗传学和蛋白质组学。metabolicMine是与英国领先的代谢疾病组织合作开发的，它整合了来自一系列实验和模型生物的数据集，以及探索它们的工具。目前的版本汇集了涉及基因、蛋白质、直系同源物、相互作用、基因表达、途径、本体论、疾病、全基因组关联研究和单核苷酸多态性的信息。虽然重点是人类数据，但也包括小鼠和大鼠的关键数据集。与RatMine大鼠基因组数据库的互操作对这些功能进行了补充，小鼠基因组信息学（MGI）小组正在开发相应的小鼠版本。网页界面包含了许多功能，包括关键字搜索，搜索表单库，QueryBuilder和列表分析工具。这为研究人员提供了许多不同的方法来分析，查看和灵活地导出数据。支持多种语言的编程接口和自动代码生成，Web接口的许多功能都可以通过Web服务获得。与分析工具和强大的查询系统相结合的多样化数据集使metabolicMine成为宝贵的研究资源。Web界面使首次使用的用户可以访问，而应用程序编程接口（API）和Web服务为生物信息学家提供了方便的数据访问和工具。metabolicMine可以在http://www.metabolicmine.org上免费获得
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.org