Ex Parte Shibuya

Patent Trial and Appeal Board

Apr 15, 2016

13209097 (P.T.A.B. Apr. 15, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
13/209,097 08/12/2011 Tetsuo Shibuya
91031 7590 04/19/2016
CANAANLA W, P,C
PO Box 1860
Los Gatos, CA 95031-1860
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www .uspto.gov
ATTORNEY DOCKET NO. CONFIRMATION NO.
JP920020096US2 9362
EXAMINER
NEGIN, RUSSELL SCOTT
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
04/19/2016 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address( es):
karen@canaanlaw.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Exparte
TETSUO SHIBUY A1
Appeal2014-001592
Application 13/209,097
Technology Center 1600
Before FRANCISCO C. PRATS, JOHN G. NEW, and
RICHARD J. SMITH, Administrative Patent Judges.
SMITH, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a system
for providing information about a cluster of child spliced sequences (e.g.,
nucleotide sequences) obtained from a parent base sequence. We have
jurisdiction under 35 U.S.C. § 6(b).
We reverse.
1 According to Appellant, the real party in interest is International Business
Machines Corporation (IBM). (Appeal Br. 3.)
Appeal2014-001592
Application 13/209,097
STATEMENT OF THE CASE
Claims on Appeal
Claims 1-20 are on appeal. (Claims Appendix, Appeal Br. 9-11.)
Independent claim 1 is illustrative and reads as follows:
1. A system for providing information about a cluster of child spliced
sequences obtained from a parent base sequence comprising a server for
receiving a query sequence and a database containing base sequences,
wherein said server comprises:
a subsystem for recording a plurality of spliced sequences, wherein
each spliced sequence is a query sequence;
a subsystem for comparing a spliced edit distance between each query
sequence and the parent base sequence read from a database with a
predetermined maximum acceptable value;
a subsystem for selecting spliced base sequences of which the spliced
edit distance between each query sequence and the parent base sequence is
not more than said maximum acceptable value to generate a first cluster of
child spliced sequences and recording said first cluster in a storage
subsystem;
a subsystem for generating a second cluster of child spliced sequences
from said first cluster and storing said second cluster; and
a subsystem for sending said second cluster over a network.
(Id. at 9, emphasis added.)
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Appeal2014-001592
Application 13/209,097
Examiner's Rejections
1. Claims 1, 8-15, and 18 stand rejected under 35 U.S.C. § 103(a) as
unpatentable over Tanaka,2 Lewin,3 and Navarro. 4 (Final Act. 2.)5
2. Claim 2 stands rejected under 35 U.S.C. § 103(a) as unpatentable over
Tanaka, Navarro, Lewin, and Mott. 6 (Id. at 8.)
3. Claims 3 and 6 stand rejected under 35 U.S.C. § 103(a) as
unpatentable over Tanaka, Navarro, Lewin, and Zhang.7 (Id. at 10.)
4. Claim 7 stands rejected under 35 U.S.C. § 103(a) as unpatentable over
Tanaka, Navarro, Lewin, and Thudium. 8 (Id. at 13.)
5. Claims 4, 5, 16, 17, and 20 stand rejected under 35 U.S.C. § 103(a) as
unpatentable over Tanaka, Navarro, Lewin, and Koleszar. 9 (Id. at 14.)
6. Claim 19 stands rejected under 35 U.S.C. § 103(a) as unpatentable
over Tanaka, Navarro, Lewin, and Mitsuhashi. 10 (Id. at 16.)
Appellant indicates that all claims stand or fall with claim 1, the only
independent claim. (Appeal Br. 4.)
2 Tanaka et al., Autonomous Distributed Genome Database and Its
Application to Mouse cDNA and Human Genome Sequence Matching, 11
Genome Informatics 378-79 (2000) ("Tanaka").
3 Lewin, GENES V, 164, 150 (1994).
4 Navarro et al., A New Indexing Method for Approximate String Matching,
LNCS 1645, pp. 163-185 (1999) ("Navarro").
5 Office Action dated Mar. 13, 2013.
6 Mott, EST_GENOME: a program to align spliced DNA sequences to
unspliced genomic DNA, 13 CABIOS APPLICATIONS NOTE 477-78 (1997).
7 Zhang et al., Fission yeast gene structure and recognition, 22 Nucleic
Acids Research 1750-59 (1994).
8 Thudium et al., US 6,893,840 B2, issued May 17, 2005, filed Oct. 12,
2001.
9 Koleszar et al., US 6,519,583 Bl, issued Feb. 11, 2003.
10 Mitsuhashi et al., US 5,556,749, issued Sept. 17, 1996.
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Appeal2014-001592
Application 13/209,097
ISSUE
Whether a preponderance of evidence of record supports the
Examiner's conclusion of obviousness with respect to claim 1.
ANALYSIS
Tanaka discloses a computer system that is used to match similarities
between mouse cDNA and human genome sequences. (Final Act. 3.)
Tanaka describes testing the feasibility of that system by using a computer
program to compare the nucleotides of mouse full-length cDNA with the
sequence for human chromosome 22. (Appeal Br. 5.)
The record on appeal reflects a dispute regarding the following
sentence in Tanaka relating to the testing of the system:
But we nevertheless found some interesting matching patterns in
[the program search results], such as: (1) many cDNA regions
match contiguous human chromosome regions, (2) a part of
cDNA matches many specific regions of human chromosome 22,
and (3) most of cDNA regions match human chromosome
regions that are separate but occur in the same order.
(Tanaka 379, emphasis added.)
The Examiner concluded that it would have been obvious to one of
ordinary skill in the art "to modify the mouse cDNA to human genomic
DNA matching of [Tanaka] by use of the maximum edit distances derived in
[Navarro] because it is obvious to combine known elements in the prior art
to yield a predictable result." (Final Act. 5.) In support of that conclusion,
the Examiner interpreted Tanaka's reference to "many cDNA regions" in the
above sentence as corresponding to the first cluster of spliced regions. (Id.
at 4.) The Examiner also interpreted Tanaka's reference to "part of the
cDNA" [sic, "part of cDNA"] in the above sentence as corresponding to the
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Appeal2014-001592
Application 13/209,097
"second cluster of child spliced sequences" derived from the first cluster.
(Id.)
Appellant makes several arguments in support of the contention that
Tanaka "only teach[ es] a single cluster." (Appeal Br. 4.) For example,
Appellant addresses the above sentence of Tanaka by stating that "[ w ]ith
respect to items (1) and (2) of Tanaka [] there is no indication whatsoever in
[Tanaka] that the results of item (2) are generated from the results of item
(1)." (Reply Br. 6.) Furthermore, Appellant argues that the description of
item (2) in the above sentence "does not support the Examiner's position
that item (2) is derived from item (1)." (Id. at 6-7.)
We find on this record that Appellant has the better argument.
Moreover, the Examiner bears the initial burden of establishing a prima facie
case of obviousness and has not done so. See In re Oetiker, 977 F.2d 1443,
1445 (Fed. Cir. 1992).
Claim 1 recites "a subsystem for generating a second cluster of child
spliced sequences from said first cluster." (Appeal Br. 9.) The Examiner
interpreted Tanaka's reference to "part of cDNA" as corresponding to the
"second cluster of child spliced sequences." (Final Act. 4.) But the
Examiner never explains why a person of ordinary skill in the art would
interpret that phrase from Tanaka in that way. Moreover, the Examiner does
not explain why or how that phrase from Tanaka would correspond to "a
subsystem for generating a second cluster of child spliced sequences from
said first cluster" as recited in claim 1.
"[R]ejections on obviousness grounds cannot be sustained by mere
conclusory statements; instead, there must be some articulated reasoning
with some rational underpinning to support the legal conclusion of
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Appeal2014-001592
Application 13/209,097
obviousness." KSR Int'! Co. v. Teleflex Inc., 550 U.S. 398, 418 (2007)
(quoting In re Kahn, 441F.3d977, 988 (Fed. Cir. 2006)). In our view, the
Examiner's interpretation of Tanaka and its applicability to claim 1 does not
meet that standard.
CONCLUSION OF LAW
A preponderance of evidence of record fails to support the Examiner's
conclusion that claim 1 is obvious under 35 U.S.C. § 103(a).
SUMMARY
We reverse all the rejections on appeal.
REVERSED
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