Appeal No. 2005-2663 Page 12
Application No. 10/140,323
graph theory mathematics . . . to determine an adjacency list characterizing all direct
and indirect genetic interactions in said genetic network.”
We have reviewed Küffner but do not find a disclosure therein of a method
meeting the limitations of claim 1. As we understand Küffner, it discloses a method of
analyzing data pertaining to a metabolic pathway; i.e., a series of chemical reactions
catalyzed by enzymes that convert a starting material into a final product. See, e.g.,
Figures 11 and 12. Thus, as we understand them, the nodes in the graph shown in
Küffner’s Figure 12 represent different chemical compounds and the edges represent
chemical reactions (or the enzymes that catalyze them).
Küffner states that a “metabolic display (MD) (e.g. Figure 12) is a PETRI net,
which exhibits in a compact (though redundant) way the space of all pathways between
given source and sink in a network compatible with a set of constraints.” In other words,
the PETRI net disclosed by Küffner is designed to show all the possible paths that a
molecule could travel as it was converted from a starting material (source) into a final
product (sink), and thereby present a more realistic view of what actually happens in
biological systems than is given by the simplified metabolic pathways usually presented
in textbooks (and in Küffner’s Figure 11). Therefore, the method disclosed by Küffner
does not appear to be one that would act on data in the way defined by claim 1 on
appeal, nor does it appear to generate “an adjacency list characterizing all direct and
indirect genetic interactions in [a] genetic network.”
The examiner has not adequately explained how the cited reference discloses all
the limitations of the claimed method and the limitations are not apparent to us. We
therefore reverse the rejection under 35 U.S.C. § 102(a).
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