Appeal No. 2005-2663 Page 5
Application No. 10/140,323
Thus, claim 1 is directed to a method for determining the adjacency list of a
graph representation of a genetic network by starting with an accessibility list derived
from genetic perturbation data, applying graph theory mathematics to determine a
condensation of the genetic network graph,2 and applying graph theory mathematics to
the condensation’s accessibility list.
Claim 2 adds the limitation that a recursive algorithm is applied. Claim 3 adds
the further limitation that the algorithm determines the adjacency list of the “most
parsimonious graph,” i.e., the simplest set of regulatory interactions that will fully explain
the accessibility list. See the specification, page 14 and Figure 7.
Claim 4 depends from claim 2 and adds the limitation that the algorithm
determines the longest path of the graph. “Paths are sequences of edges connecting
adjacent nodes.” Specification, page 6. Thus, the longest path in the graph would
represent the longest series of regulatory interactions between genes in the network;
“[a] by-product of the algorithm [that calculates the maximum path] is the adjacency list
of each node.” Page 41.
2. Definiteness
The examiner rejected claims 6 and 7 under 35 U.S.C. § 112, second paragraph,
as being indefinite. Claim 6 depends from claim 4 and recites a series of steps in
pseudocode that are implemented in the recursive algorithm. The examiner reasoned
that “the last line of claim 6 recites a list of G which causes the claim to be vague and
2 A “condensation” of a graph is derived by “collaps[ing] all nodes that are part of a cycle.” Specification,
page 13. A cycle in a genetic network is a set of genes that all influence each other (directly or indirectly).
Thus, perturbing any one gene in the cycle affects all of them: “Single gene perturbations cannot resolve
gene orders in a cycle.” Page 12. Therefore, all the genes in a cycle must be condensed to a single
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