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

项目摘要 基因门户已成为现代生物学研究的重要资源。技术 用于高通量实验现在通常用于生物医学研究， 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来快速总结和策划已知的基因 从公共数据库中注释他们感兴趣的基因，使他们能够快速评估 基因，并制定后续测试的假设。尽管它们目前的效用， 许多机会来改善基因门户网站，以更好地为科学界服务。这里我们 建议建立一个新的基因门户网站，称为BioGPS（生物基因门户网站服务） 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Web 2.0的绰号，主要是基于对 成功的网站，包括维基百科，谷歌和亚马逊。在BioGPS中， 该提案重点关注Web 2.0的两个关键要素。首先，BioGPS将重点放在 最大化可用性。BioGPS的开发将借鉴 人机交互（Human Computer Interactions，HCI）。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。而不是开发一个网络 网站与网络用户的小社区，我们将设计一个网络平台，既服务于 网络用户和生物信息科学家的需求。可扩展性也适用于许多不同的 在BioGPS领域。BioGPS在数据方面将是可扩展的，允许科学家 定制并向基因门户网站提供自己的数据集。BioGPS也将是可扩展的 在知识方面，使科学家能够协作共享和编辑自由文本基因 通过基因维基系统进行注释。最后，BioGPS将在以下方面进行扩展： 应用程序开发，允许其他生物信息学程序员扩展功能， 链接其他生物信息学分析工具。总之，BioGPS基因门户网站将提供一个 为用户网络提供平台，以协同方式利用社区知识和努力， 使生物学科的研究人员能够高效地翻译高通量的 数据到可检验的假设。项目叙述 BioGPS基因门户网站的开发将使生物学研究人员社区能够 有效地共享基因注释知识和努力。生成详细的 对人类基因组中每个基因功能的丰富了解将有助于我们理解 基本的生物学机制，以及个体基因在人类健康中的作用。

PROJECT SUMMARY 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. PROJECT NARRATIVE 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.