Zhang Wuxue, Zhang Yong, Zheng Hui, Zhang Chen, Xiong Wei, Olyarchuk John G, Walker Michael, Xu Weifeng, Zhao Min, Zhao Shuqi, Zhou Zhuan, Wei Liping
Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering College of Life Sciences, Peking University, Beijing 100871, P.R. China.
Nucleic Acids Res. 2007 Jan;35(Database issue):D737-41. doi: 10.1093/nar/gkl876. Epub 2006 Nov 10.
A synapse is the junction across which a nerve impulse passes from an axon terminal to a neuron, muscle cell or gland cell. The functions and building molecules of the synapse are essential to almost all neurobiological processes. To describe synaptic structures and functions, we have developed Synapse Ontology (SynO), a hierarchical representation that includes 177 terms with hundreds of synonyms and branches up to eight levels deep. associated 125 additional protein keywords and 109 InterPro domains with these SynO terms. Using a combination of automated keyword searches, domain searches and manual curation, we collected 14,000 non-redundant synapse-related proteins, including 3000 in human. We extensively annotated the proteins with information about sequence, structure, function, expression, pathways, interactions and disease associations and with hyperlinks to external databases. The data are stored and presented in the Synapse protein DataBase (SynDB, http://syndb.cbi.pku.edu.cn). SynDB can be interactively browsed by SynO, Gene Ontology (GO), domain families, species, chromosomal locations or Tribe-MCL clusters. It can also be searched by text (including Boolean operators) or by sequence similarity. SynDB is the most comprehensive database to date for synaptic proteins.
突触是神经冲动从轴突末端传递到神经元、肌肉细胞或腺细胞所经过的连接部位。突触的功能和构成分子几乎对所有神经生物学过程都至关重要。为了描述突触的结构和功能，我们开发了突触本体论（SynO），这是一种层次化表示，包含177个术语，有数百个同义词，分支多达八级深度。将125个额外的蛋白质关键词和109个InterPro结构域与这些SynO术语相关联。通过自动关键词搜索、结构域搜索和人工整理相结合的方式，我们收集了14000个非冗余的突触相关蛋白质，其中包括3000个人类蛋白质。我们用有关序列、结构、功能、表达、途径、相互作用和疾病关联的信息以及指向外部数据库的超链接对这些蛋白质进行了广泛注释。数据存储在突触蛋白质数据库（SynDB，http://syndb.cbi.pku.edu.cn）中并呈现出来。SynDB可以通过SynO、基因本体论（GO）、结构域家族、物种、染色体位置或Tribe-MCL聚类进行交互式浏览。它也可以通过文本（包括布尔运算符）或序列相似性进行搜索。SynDB是迄今为止关于突触蛋白质最全面的数据库。
