There are many examples of the use of graphs in Computational Biology. These include Masys et al (2001) and Storch et al (2002). The association of mRNA data with any of the Gene Ontology hierarchies or with the MeSH hierarchies seem to be intimately related. It seems that similar issues will arise when comparing data to known biological pathways or to other graphical data structures. Many of the comparisons and analyses seem to rely on specialized algorithms to assemble and annotate graphs. I will expose some similarities between the approaches and synthesize some common inferential problems. The goal of this research is to determine the tools that are needed for manipulating and analysing the relevant data.