BIOINFORMATICS OF GLYCAN EXPRESSION

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 这一技术研究和开发项目涉及几个其他技术项目的整合，这些技术项目在单独的子项目表格中描述。Glycomics是一门新兴学科，在生物信息学工具的开发方面仍然落后于蛋白质组学，这些工具需要跟踪和处理大量原始数据，使具有不同背景的科学家能够访问这些数据，并推断可以在人类细胞发育和病理状态背景下解释的重要但不明显的数据关系。我们应对这一挑战的方法是开发一个集成的数据系统，其中包括用于跟踪实验样本和过程的工作流协议和工具，用于从原始数据提取相关信息的数据处理工具，用于保存结果数据的数据库模式，以及将促进访问信息并揭示此处收集的数据内部以及分布在世界各地的数据库中和本体本身的领域知识内的不同数据之间的系统关系的本体工具。已经制定了该系统的基本设计，将其组成部分的互操作性放在最优先的位置。为此，我们正在开发三个本体论，Glyco，ReactO和Enzyo，它们结合了关于多糖结构、功能、生物合成和代谢的知识。因此，这些本体论描述了糖组学概念之间的基本关系及其与实验数据的关联，从而允许在生物/生化系统的整体背景下对数据的个别元素进行分类和查看。这些本体论将作为粘合剂，将我们的生物信息学系统的组成部分联系在一起，并作为我们将开发的软件应用程序的语义基础，以促进数据访问并揭示数据中的关系。我们系统的一个关键组件是我们正在开发的图形浏览和查询界面。我们的糖组学生物信息学系统的高度集成是其最佳功能的先决条件，每个组件都以模块化的方式设计，保持与本体中包含的(隐含和显式)知识的一致性。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This technological research and development project involves integration of several other technological projects which are described in separate subproject forms. Glycomics is an emerging discipline, which still lags behind proteomics in terms of the development of bioinformatic tools that are required to track and process vast amounts of raw data, make it accessible to scientists with diverse backgrounds, and deduce important but non-obvious data relationships that can be interpreted in the context of developmental and pathological states of human cells. Our approach to this challenge is the development of an integrated data system that includes workflow protocols and tools for keeping track of experimental samples and processes, data processing tools to extract relevant information from the raw data, database schema to save the resulting data, and ontological tools that will facilitate access to the information and reveal systematic relationships within the data collected here, as well as among diverse data that is distributed in databases throughout the world and within the domain knowledge of the ontology itself. The basic design of this system has been developed, placing highest priority on the interoperability of its component parts. To this end we are developing three ontologies, GlycO, ReactO, and Enzyo, which incorporate knowledge of glycan structure, function, biosynthesis, and metabolism. These ontologies thus describe fundamental relationships between glycomics concepts and their association to experimental data, allowing individual elements of the data to be classified and viewed in the overall context of the biological/biochemical system. These ontologies will serve as the glue that ties the components of our bioinformatics system together and as a semantic basis for software applications that we will develop to facilitate data access and to reveal relationships within the data. A key component of our system is a graphical browsing and querying interface that we are developing. The highly integrated nature of our bioinformatics system for glycomics is a prerequisite for its optimal functionality, with each component being designed in a modular fashion that maintains consistency with the (implicit and explicit) knowledge contained in the ontologies.