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

描述(申请人提供)：基因门户网站已成为现代生物学研究必不可少的资源。高通量实验技术现在普遍用于生物医学研究，科学家经常面临评估许多他们不熟悉的候选基因。这些研究人员经常求助于基因门户网站，从公共数据库中快速总结和整理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。尽管它们目前具有实用价值，但也有许多机会来改进基因门户，以更好地为科学界服务。在这里，我们建议构建一个新的基因门户网站，称为BioGPS(生物学基因门户服务)，它基于网页设计和在线协作的最新概念。这些原则通常被称为“Web2.0”，主要是基于对包括维基百科、谷歌和亚马逊在内的成功网站的分析而定义的。在BioGPS的背景下，本提案侧重于Web2.0的两个关键元素。首先，BioGPS将重点放在最大化可用性上。生物GPS的开发将借鉴被称为人机交互(HCI)的计算机科学学科的概念和技术。这些努力将包括持续的可用性测试，以及利用技术来最大限度地提高用户互动性。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，而不是开发一个只有一小部分网络用户的网站。使用BioGPS，可扩展性也适用于许多不同的领域。BioGPS在数据方面将是可扩展的，允许科学家定制自己的数据集并将其贡献给基因门户。BioGPS还将在知识方面具有可扩展性，使科学家能够通过基因维基系统协作共享和编辑自由文本的基因注释。最后，BioGPS在应用程序开发方面将是可扩展的，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。总而言之，BioGPS基因门户将为用户网络提供一个平台，以协同利用社区知识和努力，使生物学学科的研究人员能够有效地将高通量数据转化为可验证的假说。 BioGPS基因门户的开发将使生物研究人员社区能够有效地分享致力于基因注释的知识和努力。对人类基因组中每个基因的功能产生详细而丰富的看法将有助于我们理解基本的生物学机制，以及单个基因在人类健康中的作用。

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.