The paper introduces a dependency annotation effort which aims to fully annotate an Uyghur corpus. It is the first attempt of its kind to develop a large scale tree-bank for Uyghur. In this paper, we provide the motivation for following the dependency theory as the annotation scheme and argue that the dependency grammar is better suited to model the various linguistic phenomena in Uyghur. In our solution, the syntactic relations are encoded as labeled dependency relations among segments of lexical items and sequence of inflectional groups separated by derivational boundaries. We present the basic annotation scheme including morphological and syntactically dependency relation. We also show how the scheme handles some phenomenon such as omissions in copula sentences, punctuations and coordinations, etc.