BIOINFORMATICS OF GLYCAN EXPRESSION

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 该技术研究和开发项目涉及其他几个技术项目的整合，这些项目在单独的子项目表中说明。 糖组学是一门新兴学科，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可以访问这些数据，并推断出重要但不明显的数据关系，这些关系可以在人类细胞的发育和病理状态的背景下进行解释。 我们应对这一挑战的方法是开发一个集成的数据系统，该系统包括用于跟踪实验样本和过程的工作流程协议和工具，用于从原始数据中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，以及有助于访问信息并揭示此处收集的数据中的系统关系的本体论工具，以及分布在全世界的数据库中的不同数据之间以及本体本身的领域知识内。 该系统的基本设计已经完成，其组成部分的互操作性是最高优先事项。 为此，我们正在开发三个本体，GlycO，ReactO和EnzyO，其中包含聚糖结构，功能，生物合成和代谢的知识。 因此，这些本体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，允许在生物/生化系统的整体背景下对数据的各个元素进行分类和查看。 这些本体将作为粘合剂，我们的生物信息学系统的组件联系在一起，并作为一个语义基础的软件应用程序，我们将开发，以促进数据访问和揭示数据中的关系。 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性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，与本体中包含的（隐式和显式）知识保持一致。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. 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.