Ex Parte Helfman et al

Patent Trial and Appeal Board

Aug 31, 2017

12831641 (P.T.A.B. Aug. 31, 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.
12/831,641 07/07/2010 Jonathan Helfman 88325-802430 (102200US) 2843
51206 7590 09/05/2017
Kilpatrick Townsend & Stockton LLP/Oracle
Mailstop: IP Docketing - 22
1100 Peachtree Street
Suite 2800
Atlanta, GA 30309
EXAMINER
CONYERS, DAWAUNE A
ART UNIT PAPER NUMBER
2152
NOTIFICATION DATE DELIVERY MODE
09/05/2017 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):
ipefiling@kilpatricktownsend.com
oraclepatentmail@kilpatricktownsend.com
KT S Docketing2 @ kilpatrick. foundationip .com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte JONATHAN HELFMAN and JOSEPH H. GOLDBERG
Appeal 2017-004114
Application 12/831,6411
Technology Center 2100
Before HUNG H. BUI, NATHAN A. ENGELS, and
JOSEPH P. LENTIVECH, Administrative Patent Judges.
BUI, Administrative Patent Judge.
DECISION ON APPEAL
Appellants seek our review under 35 U.S.C. § 134(a) from the
Examiner’s Final Rejection of claims 1,3,4, 6—9, 11—15, and 17—20, which
are all the claims pending in the application. Claims 2, 5, and 16 are
canceled. We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.2
1 According to Appellants, the real party in interest is Oracle International
Corporation. Appeal Br. 2.
2 Our Decision refers to Appellants’ Appeal Brief (“Appeal Br.”) filed July
27, 2016; Reply Brief (“Reply Br.”) filed January 17, 2017; Examiner’s
Answer (“Ans.”) mailed November 17, 2016; Final Office Action (“Final
Act.”) mailed November 16, 2015; and original Specification (“Spec.”) filed
July 7, 2010.
Appeal 2017-004114
Application 12/831,641
STATEMENT OF THE CASE
Appellants’ invention relates to “systems and methods for retrieving
sequential information from a dataset [based on a query].” Spec. 12;
Abstract.
Claims 1, 9, and 15 are independent. Representative claim 1 is
reproduced below with disputed limitations in italics:
1. A method of retrieving sequential information from a
dataset including a plurality of existing sequences, the method
comprising:
receiving, by a computer system, a query sequence
comprising a plurality of ordered tokens representing a
sequence against which the plurality of existing sequences in
the dataset is compared;
adding, by the computer system, the tokens of the query
sequence to the existing sequences in the dataset;
creating, by the computer system, a dotplot of the
sequences in the dataset including the added query sequence
and the existing sequences, wherein creating the dotplot of
the sequences comprises representing each of the sequences of
the dataset as a dot on the dotplot by plotting each of the
sequences on a horizontal axis of the dotplot and a vertical axis
of the dotplot;
after the dotplot has been created, determining, by the
computer system, one or more existing sequences comprise a
match or a reverse match of the added query sequence based
on the dotplot by performing a line fitting process on the dots of
the dotplot;
retrieving, by the computer system, the one or more
existing sequences determined to comprise a match or a reverse
match of the query sequence; and
removing, by the computer system, the tokens of the
query sequence from the dataset and leaving the existing
sequences in the dataset.
Appeal Br. 13 (Claims App’x).
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Application 12/831,641
Examiner’s Rejections & References
(1) Claims 1, 3, 4, 6, 9, 11, 12, 15, 17, and 18 stand rejected under
35 U.S.C. § 103(a) as being unpatentable over Mai S. Mabrouk et al.,
“BIOINFTool: Bioinformatics and sequence data analysis in molecular
biology using Matlab,” Proc. Cairo International Biomedical Engineering
Conference 2006; “Mabrouk”) and Surya Saha et al., “Computational
Approaches and Tools Used in Identification of Dispersed Repetitive DNA
Sequences,” Tropical Plant Biology, 2008, 1:85—96; “Saha”). Final Act. 8—
15.
(2) Claims 7, 8, 13, 14, 19, and 20 stand rejected under
35 U.S.C. § 103(a) as being unpatentable over Mabrouk, Saha, and Julia M.
West et al., “eyePattems: Software for Identifying Patterns and Similarities
Across Fixation Sequences,” ETRA 2006; “West”). Final Act. 16—17.
Issue on Appeal
Based on Appellants’ arguments, the dispositive issue on appeal is
whether the combination of Mabrouk and Saha teaches or suggests several
limitations of independent claims 1, 9, and 15. Appeal Br. 7—11; Reply Br.
2-3.
ANALYSIS
In support of the rejection of independent claims 1, 9, and 15, the
Examiner finds Mabrouk teaches Appellants’ claimed “method of retrieving
sequential information from a dataset” comprising: (1) “receiving ... a
query sequence comprising a plurality of ordered tokens representing a
sequence”; (2) “adding ... the tokens of the query sequence to the existing
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Application 12/831,641
sequences in the dataset”; (3) “creating ... a dotplot of the sequences in the
dataset including the added query sequence and the existing sequences” and
(4) “determining . . . one or more existing sequences comprise a match or a
reverse match of the added query sequence based on the dotplot by
performing a line fitting process on the dots of the dotplot.” Final Act. 9—11
(citing Mabrouk pp. 4—5, Figs. 5, 6, and 9).
Mabrouk’s Figure 6 shows matching of pairs of characters between
sequences, as reproduced below:
Fig 6, Pairwise sequence alignment, beginning with
sequences.
As shown in Mabrouk’s Figure 6, a query sequence (i.e., tokens of
query sequences) is added in the left upper entry to be compared with
existing sequences (i.e., “Global Alignment” or “Local Alignment”).
Mabrouk’s Figure 9 shows creating a dotplot of two similar
sequences, as reproduced below:
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Application 12/831,641
As shown in Mabrouk’s Figure 9, a dotplot of two similar matching
sequences (i.e., user’s added “sequence” and existing sequences) is created.
Mabrouk pp. 4—5.
To support the conclusion of obviousness, the Examiner relies on
Saha for teaching the last two steps, including: (5) “retrieving ... the one or
more existing sequences determined to comprise a match or a reverse match
of the query sequence” and (6) “removing ... the tokens of the query
sequence from the dataset and leaving the existing sequences in the dataset.”
Final Act. 11—12 (citing Sahapp. 87, 92).
Appellants dispute the Examiner’s factual findings regarding
Mabrouk and Saha. First, Appellants contend the combination of Mabrouk
and Saha does not teach or suggest “using a dotpot to determine sequences
that match a query sequence that was added to the existing sequences of a
dataset before the dotplot was generated.” Appeal Br. 7—10; Reply Br. 2. In
particular, Appellants argue Mabrouk teaches: (1) a “different approach in
which two sequences are compared and the dotplot is used to present results
of a comparison between the sequences in which alignments have already
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Application 12/831,641
been identified by another method” and (2) the dotplot shown in Figure 9 is
“used to graph two sequences that have already been identified as similar”
and is not used “to determine matching sequences” as recited in claims 1,
9, and 15. Appeal Br. 7—9.
Second, Appellants argue neither Mabrouk nor Saha teaches (1)
“adding a query sequence to a data set before creating the dot plot
representing that dataset” and (2) “adding tokens of the query sequence to
the dataset” and then later “removing [] the tokens of the query sequence
from the dataset and leaving the existing sequences in the dataset” as recited
in claims 1, 9, and 15. Appeal Br. 10—11; Reply Br. 2—3.
We do not find Appellants’ arguments persuasive. Rather, we find the
Examiner has provided a comprehensive response to Appellants’ arguments
supported by a preponderance of evidence. Ans. 2—9. As such, we adopt the
Examiner’s findings and explanations provided therein. Id. For additional
emphasis, we note Mabrouk’s Figures 5—6 show (i) receiving a query
sequence, (ii) adding tokens of query sequences and (iii) adding a query
sequence to a dataset. Ans. 7—9. Contrary to Appellants’ arguments,
Mabrouk’s Figure 9 shows creating a dotplot and a user’s reentry of a
sequence for matching with existing sequences in the database. Ans. 6
(citing Mabrouk’s Figure 9). Lastly, as recognized by the Examiner, Saha
also teaches matching input query sequence (i.e., input dataset) with a set of
reference sequences and then removing tokens of the query sequence from
the dataset. Ans. 9 (citing Saha p. 87).
For the reasons set forth above, Appellants have not persuaded us of
error in the Examiner’s rejection of independent claims 1, 9, and 15.
Accordingly, we sustain the Examiner’s obviousness rejection of
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Application 12/831,641
independent claims 1, 9, and 15 and their dependent claims 3, 4, 6—8, 11—14,
and 17—20.
OTHER ISSUES
In the event of further prosecution of this application, this panel
suggests that the Examiner consider rejecting claims 1,3,4, 6—9, 11—15, and
17—20 under 35 U.S.C. § 101 as being directed to non-statutory subject
matter, i.e., an abstract idea in light of the two-steps framework set out in the
Supreme Court decision in Alice Corp. Pty. Ltd. v. CLS Bank Int 7, 134 S.Ct.
2347 (2014) “for distinguishing patents that claim laws of nature, natural
phenomena, and abstract ideas from those that claim patent-eligible
applications of those concepts.” Alice, 134 S. Ct. at 2355.
According to Alice, the first step in the analysis is to “determine
whether the claims at issue are directed to one of those patent-ineligible
concepts,” such as an abstract idea. Id. If the claims are directed to a patent-
ineligible concept, the second step in the analysis is to consider the elements
of the claims “individually and ‘as an ordered combination’” to determine
whether there are additional elements that “‘transform the nature of the
claim’ into a patent-eligible application.” Id. (citing Mayo, 132 S. Ct. at
1297). In other words, the second step is to “search for an ‘inventive
concept’—i.e., an element or combination of elements that is ‘sufficient to
ensure that the patent in practice amounts to significantly more than a patent
upon the [ineligible concept] itself.’” Id. (citing Mayo, 132 S. Ct. at 1294).
Turning to the first step of the Alice inquiry, we find Appellants’
independent claims 1, 9, and 15 are directed to a patent-ineligible abstract
concept of “retrieving sequential information from a dataset.” All the steps
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recited in Appellants’ claims 1, 9, and 15, including, for example: (i)
“receiving ... a query sequence comprising a plurality of ordered tokens
representing a sequence”; (ii) “adding ... the tokens of the query sequence
to the existing sequences in the dataset”; (iii) “creating ... a dotplot of the
sequences in the dataset including the added query sequence and the existing
sequences”; (iv) “determining . . . one or more existing sequences comprise
a match or a reverse match of the added query sequence based on the dotplot
by performing a line fitting process on the dots of the dotplot”; (v)
“retrieving . . . the one or more existing sequences determined to comprise a
match or a reverse match of the query sequence” and (vi) “removing . . . the
tokens of the query sequence from the dataset and leaving the existing
sequences in the dataset” are abstract processes of collecting, storing, and
analyzing information of a specific content. System claim 9 recites similar
limitations in the context of (i) a memory and (ii) a processor used to
retrieve such information. Nevertheless, information as such is intangible.
See Microsoft Corp. v. AT & T Corp., 550 U.S. 437, 451 n.12 (2007).
Information collection and analysis, including when limited to particular
content, is within the realm of abstract ideas. See, e.g., Internet Patents
Corp. v. Active Network, Inc., 790 F.3d 1343, 1349 (Fed. Cir. 2015);
Digitech Image Techs., LLC v. Elecs. for Imaging, Inc., 758 F.3d 1344, 1351
(Fed. Cir. 2014); and CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d
1366, 1370 (Fed. Cir. 2011).
Turning to the second step of the Alice inquiry, we find nothing in
Appellants’ claims 1, 9, and 15 that adds anything “significantly more” to
transform the abstract concept of collecting, storing, and analyzing
information into a patent-eligible application. Alice, 134 S. Ct. at 2357.
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Application 12/831,641
None of Appellants’ steps recited, whether individually or in an ordered
combination, shows any inventive concept.
Limiting such an abstract concept of “retrieving sequential
information from a dataset” to a general purpose computer having generic
components such as “a memory” and “a processor” recited in Appellants’
claims 1, 9, and 15 does not make the abstract concept patent-eligible under
35 U.S.C. § 101. As recognized by the Supreme Court, “the mere recitation
of a generic computer cannot transform a patent ineligible abstract idea into
a patent-eligible invention.” See Alice, 134 S. Ct. at 2358 (concluding
claims “simply instructing] the practitioner to implement the abstract idea
of intermediated settlement on a generic computer” not patent eligible); see
also Ultramercial, 772 F.3d at 715—16 (claims merely reciting abstract idea
of using advertising as currency as applied to particular technological
environment of the Internet not patent eligible); Accenture Global Servs.,
GmbHv. Guidewire Software, Inc., 728 F.3d 1336, 1344-45 (Fed. Cir.
2013) (claims reciting “generalized software components arranged to
implement an abstract concept [of generating insurance-policy-related tasks
based on rules to be completed upon the occurrence of an event] on a
computer” not patent eligible); Dealertrack, Inc. v. Huber, 674 F.3d 1315,
1333—34 (Fed. Cir. 2012) (“[s]imply adding a ‘computer aided’ limitation to
a claim covering an abstract concept, without more, is insufficient to render
[a] claim patent eligible” (internal citation omitted)).
Because Appellants’ claims 1, 12, and 18 are directed to a patent-
ineligible abstract concept and do not recite something “significantly more”
under the second prong of the Alice analysis, we suggest the Examiner reject
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claims 1, 3, 4, 6—9, 11—15, and 17—20 under 35 U.S.C. § 101 as being
directed to non-statutory subject matter in light of Alice and its progeny.
CONCLUSION
On the record before us, we conclude Appellants have not
demonstrated the Examiner erred in rejecting claims 1,3,4, 6—9, 11—15, and
17-20 under 35 U.S.C. § 103(a).
DECISION
As such, we AFFIRM the Examiner’s final rejection of claims 1,3,4,
6-9, 11-15, and 17-20.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(l)(iv).
AFFIRMED
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