In this paper we describe on-going work aimed at creating a dependency-based annotated treebank for the BioMedical domain. Our starting point is the GENIA corpus, which is a corpus of 2000 MEDLINE abstracts, which has been manually
annotated for various biological entities, according to the GENIA Ontology. There is an exponential growth of published research in this sector, which makes it difficult even for the experts to follow the recent developments. This creates the need for tools that can automatically process the research literature and extract only relevant information, such as interactions between genes and proteins. In order for these tools to be developed, annotated resources, such as corpora and Treebanks are of fundamental importance. Such resources will support the development of practical domain-specific information extraction tools.