Ex Parte Friedlander et al

Patent Trials and Appeals Board

May 29, 2018

13491884 - (D) (P.T.A.B. May. 29, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/491,884 06/08/2012
80878 7590
Brown & Michaels (END)
c/o Brown & Michaels, PC
118 North Tioga Street
Suite 400
Ithaca, NY 14850
05/31/2018
FIRST NAMED INVENTOR
Robert R. Friedlander
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.
END920120066US2 8378
EXAMINER
ZEMAN, MARY K
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
05/31/2018 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):
docket@bpmlegal.com
lwood@bpmlegal.com
twood@bpmlegal.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte ROBERT R. FRIEDLANDER and JAMES R. KRAEMER
Appeal2017-007534
Application 13/491,884 1
Technology Center 1600
Before DONALD E. ADAMS, JAMES A. WORTH, and
RICHARD J. SMITH, Administrative Patent Judges.
ADAMS, Administrative Patent Judge.
DECISION ON APPEAL
This Appeal2 under 35 U.S.C. § 134(a) involves claims 1, 3, 5-7, and
9 (App. Br. 1; see Final Act. 1; Reply Br. 3 2). Examiner entered a rejection
under 35 U.S.C. § 101. We have jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.
1 Appellants identify "International Business Machines Corporation" as the
real party in interest (App. Br. 1 ).
2 This Appeal is related to Appeal 2017-007533, Application 14/476,234.
3 The Reply Brief is not paginated. Therefore, all reference to page numbers
of the Reply Brief refer to page numbers as if the Reply Brief was number
consecutively beginning with the first page.
Appeal2017-007534
Application 13/491,884
STATEMENT OF THE CASE
Appellants disclose that "with the small amount of differences present
between the genetic sequences from two humans, the 'common' or
'normally expected' sequences of nucleotides can be compressed out or
removed to arrive at 'surprisal data' --differences of nucleotides which are
'unlikely' or 'surprising' relative to the common sequences" (Spec. i-f 12).
Appellants' disclosure "relates to minimizing surprisal data generated when
compared to a reference genome and more specifically to minimizing
surprisal data through application of a hierarchy filter pattern" (Spec. i-f 2).
Claim 1 is representative and reproduced below:
1. A method of minimizing surprisal data representing an entire
genome of an organism for compression and transmission,
comprising a source computer having one or more processors
and one or more computer-readable memories coupled to the
one or more processors performing the steps of:
a) reading and identifying characteristics of the organism's
medical history and background associated with a genetic
sequence of an organism;
b) receiving an input of rank of at least two identified
characteristics associated with the genetic sequence of
the organism;
c) generating a hierarchy of ranked, identified characteristics
based on the rank of the at least two identified
characteristics associated with the genetic sequence of
the organism;
d) comparing the hierarchy of ranked, identified characteristics
to a repository of reference genomes; and
e) if at least one reference genome from the repository matches
the hierarchy of ranked, identified characteristics,
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Appeal2017-007534
Application 13/491,884
i) storing the at least one matched reference genome in a
repository;
ii) breaking the at least one matched reference genome
into pieces comprising nucleotides of the genetic
sequence which comprises at least one gene, at
least some of the pieces being associated with the
identified characteristics;
iii) storing the pieces which are associated with the
identified characteristics in the repository;
iv) combining the stored pieces of the at least one
matched reference genome into a filter pattern;
v) comparing pieces of the nucleotides of the genetic
sequence of the organism which comprises at least
one gene which correspond to the stored pieces of
the at least one matched reference genome to the
nucleotides of the filter pattern of the pieces of the
at least one matched reference genome, to find
differences where nucleotides of the genetic
sequence of the organism which are different from
the nucleotides of the at least one matched
reference genome;
vi) using the differences to create surprisal data
representing an entire genome of the organism and
storing the surprisal data in the repository, the
surprisal data comprising a starting location of the
differences within the reference genome, how the
reference genomes were broken into pieces, a
count of a number of differences at the location
within the at least one matched reference genome
and the nucleotides from the genetic sequence of
the organism which are different from the
nucleotides of the reference genome; and
vii) transmitting to a destination, a compressed,
minimized genome representing an entire genome
by sending the surprisal data, an indication of the
at least one matched reference genome, and how
the reference genome were broken into pieces, and
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Appeal2017-007534
Application 13/491,884
(App. Br. 15-16.)
not sending sequences of nucleotides that are the
same in the genetic sequence of the organism and
the at least one matched reference genome.
Claims 1, 3, 5-7, and 9 stand rejected under 35 U.S.C. § 101
ISSUE
Does the evidence of record support Examiner's finding that
Appellants' claimed invention is directed to patent ineligible subject matter?
ANALYSIS
Examiner finds that Appellants' claimed invention is "directed to a
method of compressing data representing the entire genome of an organism,
wherein genome data is received, certain characteristics of the data are
ranked, the genome is compared to a reference, and utilizing the reference,
certain information is removed, resulting in a compressed genome" and,
therefore, "encompasses a judicial exception: an abstract idea" (Ans. 2; see
also id. at 3 (Examiner identifies the steps in Appellants' independent
claims, which are abstract)). In addition, Examiner asserts that those
elements of Appellants' claimed invention that are not abstract are "routine,
well understood and conventional activit[ies ]" (see Ans. 5---6). Appellants
disagree.
According to Appellants, their claims "recite[] elements/steps in
addition to the judicial exception(s) that are [not] well-understood, purely
conventional or routine in the relevant field" (App. Br. 11 ). In this regard,
Appellants contend that Examiner failed to establish an evidentiary basis on
this record to support a finding that, inter alia, "ranking characteristics in a
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Appeal2017-007534
Application 13/491,884
hierarchy associated with an organism and [the use of] ... this ranking of
characteristics to find a reference genome and generate surprisal data" was
well-understood, routine, and conventional activity in this field prior to
Appellants' claimed invention (see App. Br. 12; see also id. at 12-13).
Appellants further contend that "[t]here are no pending novelty or
obviousness rejections" (App. Br. 11 ). In this regard, Appellants contend
that
the distinguishing limitations [in their claims] are not generally
known, are not routine and conventional, are not found in the
cited references [previously relied upon in prior art rejections
on this record4], and are not found in the alleged abstract idea.
The distinguishing limitations constitute the "significantly
more" than the abstract idea, and constitute the "significantly
more" than the instruction to implement the abstract idea on a
generic computer.
Therefore, the claim[ s] include[] limitations not found in
the alleged abstract idea, and those distinguishing limitations,
which are not generally known, show that the claim is
significantly more than the abstract idea and significantly more
than just implementing the abstract idea on a generic computer.
(App. Br. 13; see also Reply Br. 5---6.)
"Whether something is well-understood, routine, and conventional to
a skilled artisan at the time of the patent is a factual determination."
Berkheimer v. HP Inc., 881F.3d1360, 1369 (Fed. Cir. 2018). On this
record, Examiner failed to establish an evidentiary basis to support a
conclusion that elements of Appellants' claimed invention were well-
understood, routine, and conventional in this field prior to Appellants'
claimed invention.
4 See Office Action mailed January 28, 2014.
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Application 13/491,884
CONCLUSION
The evidence of record fails to support Examiner's finding that
Appellants' claimed invention is directed to patent ineligible subject matter.
The rejection of claims 1, 3, 5-7, and 9 under 35 U.S.C. § 101 is reversed.
REVERSED
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