REACTO, AN ONTOLOGY OF THE REACTIONS INVOLVED IN GLYCAN METABOLISM

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 活细胞中多糖的生物合成、重塑和周转是极其复杂的过程。糖链结构是代谢过程的结果，代谢过程包括产生能量丰富的前体，如核苷酸糖，将单个糖残基转移到不断增长的糖链上，以及修剪产生的糖链结构。这些过程中的每一个都对应于由特定酶催化的一系列生化反应。因此，对多糖代谢的了解需要了解相关多糖的结构、将一种结构转化为另一种结构所涉及的细胞机制以及与这些转化相对应的化学反应。我们设计了ReactO本体来体现关于涉及糖代谢的特定生化反应的知识，尽管它的总体设计可以用来描述广泛的酶催化反应。也就是说，ReactO的设计并不是为了体现对糖链或酶结构的明确了解。因此，我们在开发ReactO时面临的一个主要挑战是它与体现这种结构化知识的其他知识库的完全集成。我们正在开发ReactO，不仅是作为一个非常理想的工具来表示和访问关于糖代谢的知识，而且作为一个原型来集成几个相关的但高度集中的本体。

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. The biosynthesis, remodeling and turnover of glycans in living cells are extremely complex processes. Glycan structure is the result of metabolic processes that include generation of energy-rich precursors such as nucleotide sugars, transfer of individual sugar residues to growing glycan chains, and trimming of the resulting glycan structures. Each of these processes corresponds to a collection of biochemical reactions that are catalyzed by specific enzymes. Thus, an understanding of glycan metabolism requires knowledge of the structures of the relevant glycans, the cellular machinery involved in transforming one structure into another, and the chemical reactions corresponding to these transformations. We designed the ReactO ontology to embody knowledge regarding specific biochemical reactions involved in glycan metabolism, although its general design can be used to describe a broad range of enzyme-catalyzed reactions. That is, ReactO is not designed to embody explicit knowledge of glycan or enzyme structure. Thus, a major challenge that we face in developing ReactO is its full integration with other knowledge repositories that embody this structural knowledge. We are developing ReactO not only as a highly desirable tool for representing and accessing knowledge about glycan metabolism, but as a prototype for integrating several related but highly focused ontologies.