CAREER:Life Science Databases: Integration and Beyond

下一个十年的一个中心信息技术问题将是创造一种手段，通过这种手段，通常通过互联网查询一组不同种类的生命科学数据库。生命科学网络数据库保存着对研究人员至关重要的信息。尽管在上述数据库中收集了数据并提供了数据处理的自动程序，但由于缺乏可比较的数据表示、数据库之间数据交换的统一界面以及满足科学家个人需要的可定制基础设施（即支持视图），用户对这些数据库的访问往往仍然不够。本职业计划的研究目标是通过开发支持视图的生命科学数据库信息集成系统（BACIIS+生物和化学信息集成系统Plus -视图）来解决这些问题。BACIIS+将允许生命科学数据库之间更好的通信，将提供持续和快速的扩展和适应不断发展的生物领域，并将通过动态视图提供更好和更可定制的数据访问和数据分析方法。BACIIS+开发中涉及的开放性研究问题包括：1）大型数据集的管理，2）地理上分布的自治数据库的互操作性，3）这些数据库的无缝语义集成，对用户完全透明，以及4）支持分布式多数据库视图。语义集成旨在以有意义的方式集成数据，而语法集成则包括从不同数据库收集和粘贴数据。静态视图由范围中预定义的一组有限的视图组成。而动态视图是按需创建的，其范围完全由用户定义。计划开设两门新的研究生课程：生命科学信息系统和计算生物学算法。第一门课程将涵盖生命科学数据背景下信息提取和管理的复杂性。第二门课程将涵盖序列相似性分析的顺序和并行算法的基础。 来自礼来公司和陶氏益农公司的合作者参与了课程，提供了行业观点。拟议的课程建立在PI目前的课程基础上，该课程涵盖高级分子生物学，包括三个主要部分：生物信息学，计算建模和分子机械。 该计划通过高级设计项目积极寻求本科生和少数民族学生的参与。 一个全校范围的生物信息学计划包括一个新成立的信息学院和印第安纳州基因组学中心。 正在筹备一个关于生命科学数据库互操作性的国际讲习班。

One central information technology problem of the next decade will be the creation of a means through which to query a heterogeneous set of life science databases, generally via the Internet. Life science web databases hold information that is critical to researchers. Even though, in the above databases, data have been collected and automated procedures for data manipulation have been provided, user accessibility to such databases is very often still inadequate due to the lack of a comparable data representation, a unified interface for data exchange among the databases, and a customizable infrastructure (i.e. support for views) that addresses the individual needs of scientists. The research objective of this career plan is to address these issues by developing an information integration system for life science databases that supports views (BACIIS+ Biological and Chemical Information Integration System Plus -- views). BACIIS+ will allow for better communication between life science databases, will provide for continuous and rapid expansion and adaptation to the evolving biological field, and will provide better and more customizable approaches for data access and data analysis through dynamic views. The open research issues involved in the development of BACIIS+ include : 1) the management of large data sets, 2) the interoperability of geographically distributed autonomous databases, 3) the seamless semantic-based integration of these databases with total transparency to the user, and 4) the support for distributed multi-database views. Semantic integration aims at integrating data in a meaningful way while syntactic integration consists of just collecting and pasting together data from different databases. Static views consist of a limited set of views predefined in scope. Whereas dynamic views are created on-demand and their scope is completely defined by the user. Two new graduate courses are planned: Life science information systems, and Computational biology algorithms. The first course will cover the complexity of information extraction and management in the context of life science data. The second course will cover the foundation of sequential and parallel algorithms for sequence similarity analysis. Collaborators from Eli Lilly & Company and Dow AgroSciences are involved in the courses, providing industry perspectives. The proposed courses build on a current course by the PI that covers advanced molecular biology and includes three major sections: bioinformatics, computational modeling, and molecular machinery. The plan actively seeks the participation of undergraduate and minority students through senior design projects. A campus-wide bioinformatics initiative includes a newly established School of Informatics and the Indiana Genomics Center. An international workshop on the interoperability of life science databases is in development.