Ex Parte Emler et al

Patent Trial and Appeal Board

Apr 11, 2017

12744573 (P.T.A.B. Apr. 11, 2017)

United States Patent and Trademark Office
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
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
12/744,573 05/25/2010 Stefan Emler 14-358-WO-US 3571
20306 7590 04/11/2017
MCDONNELL BOEHNEN HULBERT & BERGHOFF LLP
300 S. WACKER DRIVE
3 2ND FLOOR
CHICAGO, IL 60606
EXAMINER
WHALEY, PABLO S
ART UNIT PAPER NUMBER
1631
MAIL DATE DELIVERY MODE
04/11/2017 PAPER
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.
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte STEFAN EMLER and PIERRE-ANDRE MICHEL
Appeal 2016-007991
Application 12/744,5731
Technology Center 1600
Before DONALD E. ADAMS, ELIZABETH A. LaVIER, and
RACHEL H. TOWNSEND, Administrative Patent Judges.
LaVIER, Administrative Patent Judge.
DECISION ON APPEAL
Pursuant to 35 U.S.C. § 134(a), Appellants seek review of the
Examiner’s rejection of claims 1—7 and 17—20. We have jurisdiction under
35 U.S.C. § 6(b). For the reasons set forth below, we AFFIRM.
BACKGROUND
The Specification describes “a computer-implemented method and a
computer system for assessing classification annotations assigned to DNA
sequences stored in a database.” Spec. 1:6—8. Claim 1 is illustrative:
1. A method, comprising:
1 Appellants state the real party in interest is SmartGene GmbH. Appeal Br.
1.
Appeal 2016-007991
Application 12/744,573
accessing a database storing a plurality of deoxyribonucleic
acid (DNA) sequences using a computer, wherein each DNA
sequence is annotated with a predetermined classification
annotation for one or more taxonomies, systems, and functions
related to the DNA sequence;
grouping the plurality of DNA sequences into a plurality of
groups based on the predetermined classification annotations
using the computer, wherein each group of the plurality of
groups is associated with a different predetermined
classification annotation; and
for a designated group of the plurality of groups, the computer:
aligning the DNA sequences of the designated group
using an alignment algorithm;
after aligning the DNA sequences in the designated
group, determining a measure of distance for each pair of
DNA sequences in the designated group based on
similarity between the DNA sequences in the pair;
determining a centroid sequence for the designated
group, wherein the centroid sequence has a shortest
aggregate measure of distance over all the DNA
sequences in the designated group; and
assigning a quantitative confidence level for each DNA
sequence in the designated group regarding the
predetermined classification annotation assigned to said
each DNA sequence and based on the measure of
distance between the DNA sequence and the centroid
sequence.
Appeal Br. 31 (Claims Appendix).
REJECTIONS MAINTAINED ON APPEAL
1. Claims 1—7 and 17—20 stand rejected under 35 U.S.C. § 101 as
directed to patent-ineligible subject matter. Ans. 2.
2
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Application 12/744,573
2. Claims 1—7 and 17—20 stand rejected under 35 U.S.C. § 112,
second paragraph, as indefinite. Ans. 6.
3. Claims 1—7 and 17—20 stand rejected under 35 U.S.C. § 103 as
unpatentable over Donati2 and Xu.3 Ans. 7.
DISCUSSION
A. Rejection 1: §101
Section 101, which provides that a patent may be obtained for the
invention of “any new and useful process, machine, manufacture, or
composition of matter, or any new and useful improvement thereof,” is
limited implicitly insofar as “[ljaws of nature, natural phenomena, and
abstract ideas are not patentable.” Alice Corp. Pty. Ltd. v. CLS Banklnt’l,
134 S. Ct. 2347, 2354 (2014) (quoting Assn for Molecular Pathology v.
Myriad Genetics, Inc., 133 S. Ct. 2107, 2116 (2013)). The Supreme Court
has established a two-step framework for this analysis, wherein a claim does
not satisfy § 101 if
(1) it is “directed to” a patent-ineligible concept, i.e., a law of
nature, natural phenomenon, or abstract idea, and (2), if so, the
particular elements of the claim, considered “both individually
and ‘as an ordered combination,” do not add enough to
“transform the nature of the claim into a patent-eligible
application.”
Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016)
(quoting Alice, 134 S. Ct. at 2355).
2 Donati et al., WO 2007/072214 A2, published June 28, 2007.
3 Xu & Wunsch, Survey of Clustering Algorithms, 16 IEEE Transactions
Neural Networks 645 (2005).
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Application 12/744,573
The Examiner finds that claim 1 is directed to an abstract idea,
without significantly more. See Final Action 2. Specifically, the Examiner
finds:
In this case, under the [broadest reasonable interpretation], steps
for grouping DNA sequences, aligning sequences, determining
measures of distance, determining a centroid sequence, and
assigning a quantitative confidence levels all require
algorithmic/mathematical procedures for converting one form
of numerical representation to another, and/or mathematical
concepts for organizing and relating data, i.e. an idea “of itself’.
Id. at 2—3. Further, the Examiner finds that the other limitations of claim 1
fail to include additional elements sufficient to amount to significantly more
than the abstract idea, as the database-accessing step constitutes “routine and
conventional data gathering,” and the recited computing elements are
“generic” and “perform[] their routine and conventional functions.” Id. at 3.
Appellants’ arguments to the contrary are not persuasive. First,
Appellants posit that claim 1 is not directed to any judicial exception to
§101, reasoning that the concepts embodied therein are distinct from those
provided as examples of ineligible subject matter in the USPTO’s “2014
Interim Guidelines on Patent Subject Matter Eligibility,” 79 Fed. Reg. 74618
(Dec. 16, 2014), as updated. See Appeal Br. 3—6. However, the Guidelines’
examples are just that—examples, not a limiting set. See also Enfish, LLC v.
Microsoft Corp., 822 F.3d 1327, 1334 (Fed. Cir. 2016) (“The Supreme
Court has not established a definitive rule to determine what constitutes an
‘abstract idea’ sufficient to satisfy the first step of the Mayo/Alice inquiry.”)
(citing Alice, 134 S. Ct. at 2357).
Second, Appellants argue that claim 1 is not directed to an abstract
idea because the Examiner conclusorily “minimized the importance and
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Application 12/744,573
detail recited in several features of claim 1.” Appeal Br. 7; see also Reply
Br. 2—3. We disagree. As the Examiner’s analysis (summarized above; see
generally Final Action 2—5; Ans. 2—6) demonstrates, the Examiner
considered claim 1 by its elements and in its entirety (