Ex Parte Schwartz et al

Patent Trial and Appeal Board

Sep 8, 2016

12698224 (P.T.A.B. Sep. 8, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
12/698,224 02/02/2010
27114 7590 09/12/2016
W ARF/MKE/QUARLES & BRADY LLP
Attn: IP Docket
411 E. WISCONSIN A VENUE
SUITE 2350
MILWAUKEE, WI 53202-4426
FIRST NAMED INVENTOR
David Charles Schwartz
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.
960296.00991 3551
EXAMINER
NEGIN, RUSSELL SCOTT
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
09/12/2016 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):
pat-dept@quarles.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte DAVID CHARLES SCHWARTZ and JESSICA SEVERIN
Appeal2015-003813
Application 12/698,224
Technology Center 1600
Before ERIC B. GRIMES, TIMOTHY G. MAJORS and DAVID COTTA,
Administrative Patent Judges.
COTT A, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a
computer system for validating single molecule assemblies. The Examiner
rejected the claims on appeal as obvious under 35 U.S.C. § 103(a).
We reverse.
STATEMENT OF THE CASE
Claims 1, 3-5, 7-9, 11-19, and 21 are on appeal. Claim 1, the only
independent claim, is illustrative and reads as follows (emphasis added):
1. A computer system for validating single molecule
assemblies, the computer system comprising:
(a) a first database comprising single molecule data,
the single molecule data derived from optical
mapping of a single molecule assembly, wherein:
Appeal2015-003813
Application 12/698,224
said single molecule assembly comprises
a first single molecule fragment and a
second molecule fragment; and
said first database comprises information
to associate said single molecule data of the
first single molecule fragment with said
single molecule data of the second molecule
fragment;
(b) a second database comprising biomedical data
associated with the single molecule assembly;
( c) a first database connector communicatively linked
to the first database, and a second database
connector communicatively linked to the second
database;
( d) a user interface pro grammatically linked to the
first database connector and the second database
connector, the user interface displaying the single
molecule data from the first database and the
biomedical data from the second database, the user
interface programmed to:
display the single molecule data alongside
the biomedical data;
provide horizontal and vertical scaling of the
single molecule data,
receive user commands for interacting with
the single molecule data and the biomedical
data;
delete a whole map from the single molecule
data upon receipt of a first command from the
user input device;
delete a restriction cut from the single
molecule data upon receipt of a second
command from the user input device; and
merge said first single molecule fragment
and said second molecule fragment upon
receipt of a third command from the user input
device; and
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Application 12/698,224
( e) a user input device communicatively linked to the
user interface, the user input device transmitting at
least one user input command for interacting with
the single molecule data.
The claims stand rejected as follows:
Claims 1, 3-5, 7-9, 11-12, 14--19, and 21under35 U.S.C. § 103(a) as
unpatentable over the combination of Iwabuchi, 1 Haefliger,2 Harris, 3
Schwartz, 4 and Schwartz II. 5
Claim 13 under 35 U.S.C. § 103(a) as unpatentable over Iwabuchi,
Haefliger, Harris, Schwartz, Schwartz II, and Otero. 6
The Examiner found that Figures 1and2 oflwabuchi, which show
images of human chromosomes, met the "first database" requirement of
claim 1. Non-Final Act. 6.7 The Examiner further found (as we understand
it) that the chromosomal map disclosed in Figure 6 of Haefliger met the
1 Iwabuchi et al., Simultaneous Detection of Near-Field Topographic and
Fluorescence Images of Human Chromosomes via Scanning Near-Field
Optical/Atomic-Force Microscopy (SNOAM), Vol. 25, No. 8 NUCLEIC Acrns
RESEARCH 1662-1663 (1997) ("Iwabuchi").
2 Haefliger et al., Four Novel Members of the Connexin Family of Gap
Junction Proteins, Vol. 267, No. 3 J. BIO. CHEM. 2057-2064 (1992)
("Haefliger").
3 Harris, Genotator: A Workbench for Sequence Automation, GENOME
RESEARCH 7:754--762 (1997) ("Harris").
4 Schwartz et al., U.S. Patent No. 6,340,567 Bl, issued Jan. 22, 2002
("Schwartz").
5 Schwartz, U.S. Patent No. 6,150,089, issued Nov. 21, 2000 ("Schwartz
II").
6 Otero et al., U.S. Patent Publication No. 2002/0046151 Al, published Apr.
18, 2002 ("Otero").
7 Office Action mailed Oct. 13, 2013.
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Appeal2015-003813
Application 12/698,224
"second database" requirement of claim 1. Id. at 7 ("Figure 6 of Haefliger et
al. illustrates schematics of chromosomal maps wherein to the left each map,
chromosomal loci are linked to biomedical data."). The Examiner then
found that Harris taught the "user interface" and "user input" requirements
of claim 1. Id. Finally, the Examiner found that Schwartz taught optical
mapping with restriction cuts as required by claim 1. Id. at 8.
While the Examiner found that no single reference disclosed all of the
elements of claim 1, the Examiner found that it would have been obvious in
view of the combined disclosures of the cited art. The Examiner explained:
It would have been obvious to someone of ordinary skill in the
art at the time of the instant invention to modify the chromosomal
imaging study if [sic] Iwabuchi et al. by associating biomedical
data with chromosomal loci as in Haefliger et al. wherein the
motivation would have been that Figure 6 ofHaefliger et al. maps
chromosomal sequence loci to relevant medical data pertaining
to each locus such that the chromosomal schematic has a more
physiological purpose. There \vould have been a reasonable
expectation of success in combining the human chromosomal
images of I wabuchi et al. with the mouse chromosomal maps of
Haefliger et al. because the mapping techniques regarding loci
on chromosomal images and diagrams is a general algorithm
independent of the species of animal [or] plant associated with
the chromosome.
It would have been further obvious to someone of ordinary skill
in the art at the time of the instant invention to modify the
chromosomal imaging study if [sic] I wabuchi et al. and the
association of biomedical data with chromosomal loci as in
Haefliger et al. by use of the graphical user interfaces of Harris
wherein the motivation would have been that allowing a user to
view and annotate the DNA sequence data increases the
accessibility and ability for the DNA sequence data to be
analyzed ....
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Appeal2015-003813
Application 12/698,224
It would have been further obvious to someone of ordinary skill
in the art at the time of the instant invention to modify the
restriction mapping of a single molecule schematics of Schwartz
et al. and Haefliger et al. [sic, with] the graphical user interfaces
of Harris by use of the restriction fragment schematic of
Schwartz et al. because it is obvious to combine known elements
in the prior art to yield a predictable result. In this instance,
restriction fragments are an alternative to fragments of
chromosomes. There would have been a reasonable expectation
of success in combining Schwartz et al. and Iwabuchi et al.
because both studies are analogously applicable to analyzing the
structure and mapping of single biological molecules and
molecule fragments. It is noted that the DNA of Schwartz et al.
is derived from chromosomes .... It is also noted that the
chromosomes of Figure 1 of Iwabuchi et al. contain DNA.
There would have been further reasonable expectation of success
in combining the schematic restriction fragment diagrams of
Schwartz et al. as being depicted [sic, as] the pixelating imagery
of Iwabuchi et al. because the document of Schwartz teaches (in
Example 13) that restriction fragments are displayable as
pixelated images as an alternative to schematic diagrams ....
Non-Final Act. 10-12.
Appellants argue, among other things, that the cited art does not
include first and second databases, Br. 17-20.
REJECTION OF CLAIMS 1, 3-5, 7-9, 11-12, 14--19, AND 21
OVER THE COMBINATION OF IWABUCHI, HAEFLIGER, HARRIS,
SCHWARTZ, AND SCHWARTZ II
Claim 1 and the claims depending therefrom require a "first database
comprising single molecule data ... derived from optical mapping."
Appellants argue the Examiner's combination of Iwabuchi, Haefliger,
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Appeal2015-003813
Application 12/698,224
Harris, Schwartz and Schwartz II does not teach this element. App. Br. 17-
20.
The Examiner found that Figures 1 and 2 of Iwabuchi disclosed a
"first database" as set forth in claim 1. Final Act. 6. Figures 1 and 2 are
reproduced below.
t'l1-,'1N'l:". ! . 't)~·(:%!:i::·;: n~..}.~ .·\~":\.~ (~~rM; i.m~>.'. :..ti::f):ii~·l~~ ~~- K"'J..,.-::O.~f-ti...~:i .:;f iht:r:~~ n1':--~•t~\:l'>·::- ·~.~~::.1~-r~:~1;~.ff~~ <:·:~ ~ .f-1.!~-...'" ;,,'.•X·i.'t~h:) ~~~ :oj:. -\~~·;- ii:i..1~ ~~-"' l" liJ~ ;.i:_1 ft.:~• 'f~~
tl.3~-:. -:~)· .... -~! ~i:Mt«.!} ~:1· ~\·~·~R :-t~;"!li!- -:.f ~l>r: L1~>\lo~~·::- {..; st: ~H·- TN-: ~~Ji::. infr•:}!'•.ll;i'.i,t~f.I. :ti :;}'(i:.: ~~'X'1!.:-t~::. })~·:<_t~ l.:: .::.J1b.l>;.{ll:';if .~ ... l!>-l ~ :11-:ir t:X- .fb:-:s,il~ !Rfo:i:"! .. ;loi:.\::~ ~ti. in~:
•X·~-:~·~.J--:~!~}i1:<.1 C1Xi~~~-~ :;(!~x>:;, ~1)' tr.~ -..~1:\A~~-~ :{}l~~:k-.i ~-"' :fo: fox.HxK ~ ~H1l:1:)fa: \).) ;;:i p)t-:,.x1tko.:.:i:rk' :<>N•:·:N b) f~:;i-::;:· t~:; ~x-..11.x:ion :s1:::·1~~ -nffi~lM"ll:
figur!t :?.. Nefil-·fk:l4 fil.Jf.:re:)c.e:r.:ce im~ge of the hunw .. '1 metapbn$e chromoso~ne
cnrr1:sµond:i:ng 10 fb) in F!j..'Ut"t' ~ obtai .. ncd. with Ar laser be.au~ <:'.XCitaLlon (A~
4H8 nm: emisJioo >520 nm). The im;;ge area is 7 x 2 µm. Maxrmum im~nsity
oi fluorc~r:cncc from r:hromo>omc was 7-folj higher ti1an backg.1\ltl..'"td k«t!
(0.5 x 103 mV)
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Appeal2015-003813
Application 12/698,224
Iwabuchi 1663. "Figure 1 shows a typical topographic image of human
metaphase chromosomes which are recognized as three different types of
chromosomes." Id. at 1662. "Figure 2 shows the round shape of the
fluorescent chromosome corresponding to (b) in Figure 1." Id.
The Examiner contends that "absent a definition of 'database' in the
specification; since the images of Iwabuchi et al. are collections of data,
these images are interpreted to be databases of image data." Non-Final Act.
at 12. The Examiner explained: "Figures 1 and 2 of Iwabuchi et al. are
interpreted to be an illustration of a pixelated table of data (i.e. wherein the
table of data is interpreted to be a database)." Ans. 3.
Appellants argue that "the Examiner's interpretation of the word
'database' is not only unreasonably broad, but it is also inconsistent with the
'plain meaning' of the word as used by those of ordinary skill in the art."
Br. 18. Appellants further argue that "under the Examiner's logic, any
collection of data could be equivalent to and anticipate a 'database.' Such
treatment would effectively render the limitation 'database' in the claims
meaningless." Id. at 19.
We agree with the Appellants that Figures 1 and 2 of Iwabuchi are not
"databases." Appellants' Specification states that
"database" ... as used herein, [is] to be understood consistently
with [its] commonly accepted meanings in the relevant art, i.e.,
the art of computer sciences and information management.
Specifically, a database in various embodiments of this
disclosure may be flat data files and/or structured database
management systems such as relational databases and object
databases. Such a database thus may comprise simple textual,
tabular data included in flat files as well as complex data
structures stored in comprehensive database systems. Single
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Appeal2015-003813
Application 12/698,224
molecule data may be represented both in flat data files and as
complex data structures.
Spec. ,-r 28.
Iwabuchi's Figures 1 and 2 are simultaneously-provided images from
a scanning near-field optical/atomic force microscope. Iwabuchi 1662
("Scanning near-field optical/atomic microscopy (SNOAM) provided us
with simultaneous topographical and optical images of human
chromosomes ... "). The Examiner assumes that the images in I wabuchi were
formed from a table of pixelated data, but, even if true, there is nothing in
Iwabuchi to suggest that the table of pixels was organized for searching or
even capable of being searched. Moreover, there is nothing in Iwabuchi to
suggest that the data represented in the images in Figures 1 and 2 were
stored or retrieved from storage. In short, while the images in I wabuchi may
be comprised of data, they are not "databases," even giving that term its
broadest reasonable interpretation in light of the Specification.
"[O]bviousness requires a suggestion of all limitations in a claim."
CFMT, Inc. v. Yieldup Intern. Corp., 349 F.3d 1333, 1342 (Fed. Cir. 2003)
(citing In re Royka, 490 F.2d 981, 985 (CCPA 1974)). Because the
Examiner has not sufficiently established a teaching or suggestion of the
"first database ... " limitation of claim 1 in the applied art, we reverse the
Examiner's rejection of claims 1, 3-5, 7-9, 11-12, 14--19, and 21 over the
combination of Iwabuchi, Haefliger, Harris, Schwartz, and Schwartz II.
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Appeal2015-003813
Application 12/698,224
REJECTION OF CLAIM 13 OVER THE COMBINATION
OF IWABUCHI, HAEFLIGER, HARRIS, SCHWARTZ, SCHWARTZ II
AND OTERO
The Examiner's obviousness rejection of claim 13 over Iwabuchi,
Haefliger, Harris, Schwartz, Schwartz II, and Otero also relied upon the
finding that Figures 1 and 2 of I wabuchi constitute a "first database."
Accordingly, we reverse the Examiner's rejection of claim 13 for the same
reasons we reverse the Examiner's rejection of claims 1, 3-5, 7-9, 11-12,
14--19, and 21.
SUMMARY
For the set forth herein, the Examiner's final decision to reject claims 1,
3-5, 7-9, 11-19, and 21 is reversed.
REVERSED
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