Ex Parte Friedman et al

Patent Trial and Appeal Board

Jun 6, 2016

12498898 (P.T.A.B. Jun. 6, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
12/498,898 0710712009
21003 7590 06/08/2016
BAKER BOTTS L.L.P.
30 ROCKEFELLER PLAZA
44THFLOOR
NEW YORK, NY 10112-4498
FIRST NAMED INVENTOR
Carol Friedman
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.
070050.3791 9251
EXAMINER
HAN, QI
ART UNIT PAPER NUMBER
2659
NOTIFICATION DATE DELIVERY MODE
06/08/2016 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):
DLNYDOCKET@BAKERBOTTS.COM
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte CAROL FRIEDMAN, YVES A. LUSSIER,
and L YUDMILA ENA
Appeal2014-007320
Application 12/498,898
Technology Center 2600
Before JEAN R. HOMERE, JOSEPH P. LENTIVECH, and
KARA L. SZPONDOWSKI, Administrative Patent Judges.
SZPONDOWSKI, Administrative Patent Judge.
DECISION ON APPEAL
Appellants appeal under 35 U.S.C. § 134(a) from the Examiner's final
rejection of claims 1-19 and 21. Claim 20 has been cancelled. (App. Br. 4).
We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.
Appeal2014-007320
Application 12/498,898
STATEMENT OF THE CASE
Appellants' invention is directed to methods and systems for
extracting genotype and phenotypic information from literature, such as
journal articles, via natural language processing. (Spec. 1-2). Claim 1,
reproduced below with the disputed limitations in italics, is illustrative of the
claimed subject matter:
1. A computer implemented method for extracting
genotype-phenotype information from natural language input text,
compnsmg:
receiving natural language input text which includes one or
more genotype-phenotype relationships;
processing, using a processor, said natural language input text
to identify one or more biological terms therein;
associating each of said one or more biological terms within
said natural language input text \'l1ith a lexical definition; and
parsing, using a parser, said one or more associated biological
terms to replace at least one of said one or more of biological terms
with a corresponding associated lexical definition to identify
genotype-phenotype information from said from natural language
input text.
REJECTIONS
Claim 21 stands rejected under 35 U.S.C. § 112(a) or 35 U.S.C. § 112
(pre-AIA), first paragraph, as failing to comply with the written description
requirement.
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Application 12/498,898
Claim 21 stands rejected under 35 U.S.C. § 101 as directed to non-
statutory subject matter.
Claims 1--4, 8, 9, 14--19, and 21 stand rejected under 35 U.S.C.
§ 102(b) as anticipated by Rzhetsky et al. (US 2006/0069512 Al; published
Mar. 30, 2006) or, in the alternative, under 35 U.S.C. § 103(a) as obvious
over the combination ofRzhetsky and Muraca et al. (US 2002/0150966 Al;
published Oct. 17, 2002).
Claims 5-7 stand rejected under 35 U.S.C. § 103(a) as obvious over
the combination of Rzhetsky and Kadashevich et al. (US 5,369,577; issued
Nov. 29, 1994), or in the alternative, Rzhetsky, Muraca, and Kadashevich.
Claims 10-13 stand rejected under 35 U.S.C. § 103(a) as obvious over
the combination of Rzhetsky and Newman (US 5,774,833; issued June 30,
1998), or in the alternative, Rzhetsky, Muraca, and Newman.
ANALYSIS
35 U.S.C. § 112 and 35 U.S. C. § 1 OJ Rejections
Appellants have not presented any rebuttal arguments against the
Examiner's 35 U.S.C. § 112, first paragraph, and 35 U.S.C. § 101 rejections
of claim 21. (See App. Br. 4). Because Appellants have failed to rebut these
rejections on the record before us, we summarily sustain both rejections.
35 U.S.C. § 102 and 35 U.S.C. § 103 Rejections
Issue: Did the Examiner err in finding Rzhetsky discloses, or in the
alternative, the combination of Rzhetsky and Muraca teaches or suggests,
"receiving natural language input text which includes one or more genotype-
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Application 12/498,898
phenotype relationships" and "identify genotype-phenotype information
from said natural language input text" as recited in claim 1?
Appellants contend Rzhetsky does not disclose receiving or
identifying "genotype-phenotype information" as defined in Appellants'
Specification. (App. Br. 10). Specifically, Appellants argue "information
regarding interactions among genes and proteins, alone, is not genotype-
phenotype information as defined in the current application." (Reply Br. 3).
Appellants also provide a dictionary definition of "phenotype information"
as "relat[ing] to the visible properties of an organism caused by the
interaction of the organism's genotype and environment." (App. Br. 10).
We are not persuaded by Appellants' arguments and agree with the
Examiner's findings. (See Final Act. 6-8; Ans. 2-5). Rzhetsky describes a
"natural language processing system that is designed to parse the electronic
versions of articles published in journals that report on structural interactions
among genes and proteins." (Rzhetsky i-f 56). Information is extracted "on
interactions among genes and proteins, their domain/motif structure, and/ or
their sub-cellular and tissue expression/distribution patterns[.]" (Id.; see also
Rzhetsky i-f 57 (describing "recover[ing] structural relationships between the
entities")). Rzhetsky further describes as a result of parsing, terms are
classified "and the relationship between the interactions are established."
(Rzhetsky i-f 61). The Examiner finds, and we agree, Rzhetsky's discloses
gene (genotype) and protein (phenotype) information as recited in claim 1.
(See Ans. 2-3).
In the Specification, Appellants broadly define "genotype-phenotype
information" as "genotype information, phenotype information, a
combination of both and/or information concerning relationships with
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Application 12/498,898
genotype and/or phenotype information." (Spec. 4, 11. 12-14, emphasis
added). The Examiner finds, and we agree, that under the broadest
reasonable interpretation in light of Appellants' Specification, any one of the
aforementioned items could properly be used for the rejection. (Ans. 2-3).
Appellants have not persuasively explained why the Examiner's findings
that Rzhetsky discloses genotype (gene) and phenotype (protein)
information is in error.
Regarding the alternative rejection of claim 1 under 35 U.S.C.
§ 103(a), Appellants argue that Muraca does not cure the noted deficiencies
of Rzhetsky. (See App. Br. 11-13). This argument is not persuasive. As
noted in our discussion of claim 1 above, we find no such deficiencies in
Rzhetsky for Muraca to remedy. Nonetheless, we note Muraca describes the
"phenotype and genotype .. .includes ... the expression and accumulation of
proteins ... ",which is consistent with the Examiner's findings regarding
Rzhetsky. (See Muraca i-f 55).
Accordingly, we sustain the Examiner's prior art rejections of
independent claim 1. For the same reasons, we sustain the Examiner's
rejections of independent claims 14 and 21, which also recite the limitation
"identify genotype-phenotype information from said natural language input
text." For the same reasons, we sustain the Examiner's prior art rejections of
dependent claims 2--4, 8-9, 15-19, which were not argued separately.
With respect to the Examiner's 35 U.S.C. § 103(a) rejection of claims
5-7 and 10-13, Appellants argue neither Kadashevich nor Newman,
respectively, discloses or suggests the disputed "identify genotype-
phenotype information from said natural language input text" limitation.
(App. Br. 13-14). However, as noted above, the Examiner did not rely on
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Application 12/498,898
Kadashevich or Newman to teach or suggest the disputed limitation.
Accordingly, for the same reasons as above, we sustain the Examiner's 35
U.S.C. § 103(a) rejection of claims 5-7 and 10-13.
DECISION
For the above reasons, the Examiner's rejections of claims 1-19 and
21 are affirmed.
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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