BioGPS: Extensible Web 2.0 gene portal for structured and unstructured annotation

描述（申请人提供）：基因门户已成为现代生物学研究的重要资源。高通量实验技术已广泛应用于生物医学研究，科学家们经常面临着对许多他们不熟悉的候选基因进行评估的问题。这些研究人员经常求助于基因门户，从公共数据库中快速总结和整理出他们感兴趣的基因的已知基因注释，使他们能够快速评估基因并为后续测试制定假设。尽管它们目前的用途，也有很多机会来改进基因门户，以更好地服务于科学界。在这里，我们提出了一个新的基因门户网站，称为BioGPS（生物基因门户服务），这是基于网页设计和在线协作的最新概念。这些通常被称为“Web 2.0”的原则，在很大程度上是基于对成功网站（包括Wikipedia、b谷歌和Amazon）的分析而定义的。在BioGPS的上下文中，该提案侧重于Web 2.0的两个关键元素。首先，BioGPS将着重强调可用性的最大化。BioGPS的开发将利用计算机科学中称为人机交互（HCI）的学科的概念和技术。这些努力将包括持续的可用性测试，以及利用技术来最大化用户交互性。其次，BioGPS还将强调可扩展性的概念。我们将设计一个既满足网络用户需求又满足生物信息学科学家需求的网络平台，而不是为一小群网络用户开发一个网站。可扩展性也适用于BioGPS的许多不同领域。BioGPS在数据方面将是可扩展的，允许科学家定制并向基因门户提供他们自己的数据集。BioGPS还将在知识方面进行扩展，使科学家能够通过基因wiki系统协作共享和编辑自由文本基因注释。最后，BioGPS将在应用开发方面具有可扩展性，允许其他生物信息学程序员扩展功能并连接其他生物信息学分析工具。总之，BioGPS基因门户网站将为用户网络提供一个平台，以协同利用社区知识和努力，使跨生物学科的研究人员能够有效地将高通量数据转化为可测试的假设。

DESCRIPTION (provided by applicant): Gene portals have become essential resources for modern biological research. Technologies for high-throughput experimentation are now commonly used in biomedical research, and scientists are often faced with evaluating many candidate genes which are unfamiliar to them. These researchers often turn to gene portals to quickly summarize and curate known gene annotation for their genes of interest from public databases, enabling them to quickly evaluate genes and formulate hypotheses for follow-up testing. Despite their current utility, there are also many opportunities to improve gene portals to better serve the scientific community. Here, we propose the construction of a new gene portal called BioGPS (Biology Gene Portal Services) which is based on recent concepts in web design and online collaboration. These principles, commonly referred to by the moniker "Web 2.0", were largely defined based on an analysis of successful web sites, including Wikipedia, Google, and Amazon. In the context of BioGPS, this proposal focuses on two key elements of Web 2.0. First, BioGPS will place heavy emphasis on maximizing usability. Development of BioGPS will draw on concepts and techniques from the discipline of computer science called Human Computer Interactions (HCI). These efforts will include continual usability testing, and utilizing techniques to maximize user interactivity. Second, BioGPS will also emphasize the concept of extensibility. Rather than develop a web site with a small community of web users, we will design a web platform that serves both the needs of web users and of bioinformatics scientists. Extensibility also applies to many different domain areas with BioGPS. BioGPS will be extensible in terms of data, allowing scientists to customize and contribute their own data sets to the gene portal. BioGPS will also be extensible in terms of knowledge, enabling scientists to collaborative share and edit free-text gene annotation through a gene wiki system. And finally, BioGPS will be extensible in terms of application development, allowing other bioinformatics programmers to extend functionality and link other bioinformatics analysis tools. In summary, the BioGPS gene portal will provide a platform for networks of users to synergistically leverage community knowledge and effort, allowing researchers across biological disciplines to efficiently translate high-throughput data to testable hypotheses. The development of the BioGPS gene portal will allow communities of biological researchers to effectively share knowledge and effort devoted to gene annotation. Generating a detailed and rich view of the function of every gene in the human genome will benefit our understanding of basic biological mechanisms, as well as the role of individual genes in human health.