We describe a parallel annotation approach for PubMed abstracts. It includes both entity/relation annotation and a treebank containing syntactic structure, with a goal of mapping entities to constituents in the treebank. Crucial to this approach is a modification of the Penn Treebank guidelines and the characterization of entities as relation components, which allows the integration of the entity annotation with the syntactic structure while retaining the capacity to annotate and extract more complex events.