The present paper outlines an ongoing project of annotation of the extended nominal coreference and the bridging anaphora in the Prague Dependency Treebank. We describe the annotation scheme with respect to the linguistic classification of coreferential and bridging relations and focus also on details of the annotation process from the technical point of view. We present methods of helping the annotators -- by a pre-annotation and by several useful features implemented in the annotation tool. Our method of the inter-annotator agreement is focused on the improvement of the annotation guidelines; we present results of three subsequent measurements of the agreement.