Ex parte BAKER et al.

Board of Patent Appeals and Interferences

Sep 28, 1998

07853459 (B.P.A.I. Sep. 28, 1998)

Application for patent filed March 18, 1992.1
1
THIS OPINION WAS NOT WRITTEN FOR PUBLICATION
The opinion in support of the decision being entered today
(1) was not written for publication in a law journal and
(2) is not binding precedent of the Board.
Paper No. 34
UNITED STATES PATENT AND TRADEMARK OFFICE
_____________
BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
_____________
Ex parte BRENDA S. BAKER,
KENNETH W. CHURCH, JONATHAN I. HELFMAN
and
BRIAN W. KERNIGHAN
_____________
Appeal No. 95-1682
Application 07/853,4591
______________
ON BRIEF
_______________
Before JERRY SMITH, BARRETT and FLEMING, Administrative Patent
Judges.
Appeal No. 95-1682
Application 07/853,459
Supplemental Examiner's answer, paper 26, mailed 2
October 23, 1995, page 2.
2
FLEMING, Administrative Patent Judge.
DECISION ON APPEAL
This is a decision on appeal from the final rejec-
tion of claims 4, 6, 8, 9, 13, 16 and 18 through 22. Claims 1
through 3, 7 and 17 have been canceled. Claims 5, 10, 11, 12,
14, 15 and 23 through 27 have been allowed. 2
Appellants’ invention relates to apparatus and
methods for interactively studying similarities of values in
very large bodies of data.
Independent claims 4 and 8 are reproduced as fol-
lows:
4. Apparatus for displaying similarities between
lines of text in a sequence of n lines of text, the apparatus
comprising:
means for representing a n x n matrix whether there
is a first mark in element (i,j) of the matrix if a comparison
of line (i) with line (j) indicates that line (i) and line (j)
have similar values; and
means for mapping the n x n matrix onto a display
matrix, the mapping being done such that second marks indicat-
ing significant first marks are displayed in the display
matrix.
Appeal No. 95-1682
Application 07/853,459
3
8. Apparatus for displaying similarities between
sequences of tokens on a display device comprising:
means (702) for producing the tokens in the se-
quences from data; and
means (704) for receiving the tokens and making a
dotplot (405) representing a comparison of each of the tokens
in one of the sequences with all of the tokens in another of
the sequences and providing the dotplot to the display device,
the apparatus being characterized in that:
the means for making the dotplot is able to make a
dotplot wherein each sequence of tokens being compared con-
tains at least n tokens, where n >> 10,000; and
the means for making the dotplot makes the dotplot
of a size such that the dotplot fits in its entirety on the
display device.
The references relied on by the Examiner are as
follows:
James Pustell et al. (Pustell), "A high speed, high capacity
homology matrix: zooming through SV40 and polyoma," 10 Nucleic
Acids Research, no. 15, 4765-4782 (1982)
Jacob V. Maizel, Jr. et al. (Maizel), "Enhanced graphic matrix
analysis of nucleic acid and protein sequences," 78 Proc.
Natl. Acad. Sci. USA, no. 12, 7665-7669 (December 1981)
Alfred V. Aho et al. (Aho), "Compilers - Principles, Tech-
niques, and Tools," 83-88 (Addison-Wesley Publishing Co.,
1986)
Appeal No. 95-1682
Application 07/853,459
4
Gerard Salton, Automatic Text Processing - The Transformation,
Analysis, and Retrieval of Information by Computer, 238-240,
284-289 (Addison-Wesley Publishing Co., 1989)
Edward M. McCreight, "A Space-Economical Suffix Tree Construc-
tion Algorithm," 23 Journal of the Assoc. for Computing Ma-
chinery, no. 2, 262-272 (April 1976)
Claims 4, 8, 13 and 16 stand rejected under 35
U.S.C. § 103 as being unpatentable over Pustell and Maizel.
Claims 6 and 9 stand rejected under 35 U.S.C. § 103 as being
unpatentable over Pustell, Maizel and Aho. Claims 18 through
20 stand rejected under 35 U.S.C. § 103 as being unpatentable
over Pustell, Maizel, Aho and Salton. Claims 21 and 22 stand
rejected under 35 U.S.C. § 103 as being unpatentable over
Pustell, Maizel, Aho, Salton and McCreight.
Appeal No. 95-1682
Application 07/853,459
Appellants filed an appeal brief on April 8, 1994. We3
will refer to this appeal brief as simply the brief. Appel-
lants filed a reply appeal brief on September 12, 1994. We
will refer to this reply appeal brief as the reply brief. The
Examiner responded to the reply brief in the supplemental
Examiner's answer and thereby entered and considered the reply
brief. Appellants filed a supplemental reply appeal brief on
December 26, 1995. We will refer to this reply appeal brief
as the supplemental reply brief. The Examiner stated in the
Examiner’s letter, mailed March 14, 1996, that the supplemen-
tal reply brief has been entered and considered and a response
by the Examiner is not deemed necessary.
The Examiner responded to the brief with an Examiner's4
answer, mailed July 12, 1994. We will refer to the Examiner's
answer as simply the answer. The Examiner responded to the
reply brief with a supplemental Examiner's answer dated Octo-
ber 23, 1995. We will refer to the Supplemental Examiner's
answer as simply the supplemental answer.
5
Rather than repeat the arguments of Appellants or
the Examiner, we make reference to the briefs and the 3
answers for the details thereof.4
OPINION
After a careful review of the evidence before us, we
agree with the Examiner that claims 4, 8, 13 and 16 are prop-
erly rejected under 35 U.S.C. § 103. Thus, we will sustain
the rejection of these claims but we will reverse the rejec-
tion of the remaining claims on appeal for the reasons set
forth infra.
Appeal No. 95-1682
Application 07/853,459
6
On pages 8-10 of the brief, pages 3-4 of the reply
brief and pages 2 and 3 of the supplemental reply brief,
Appellants argue that the Examiner’s rejection of claim 8 as
being unpatentable is improper because Maizel and Pustell
cannot handle many more than 10,000 bases. We note that
Appellants' claim 8 recites "the means for making the dotplot
is able to make a dotplot wherein each sequence of tokens
being compared contains at least n tokens, where n >> 10,000."
On page 2 of the supplemental reply brief, Appel-
lants state that they do not doubt that the Maizel program can
handle sequences of more than 10,000 bases. However, the
Appellants argue that Maizel and Pustell cannot in fact handle
many more than 10,000 bases as recited in Appellants' claim 8.
We find that the Examiner has established a prima
facie case. Maizel teaches on page 7665 that these programs
enable the approach to be used with sequences of more than
10,000 bases. Appellants have not shown how the claim lan-
guage of "n >> 10,000" distinguishes over the teachings of
Maizel. Furthermore, Appellants have not shown that the
Maizel programs are not enabled to be used with sequences of
Appeal No. 95-1682
Application 07/853,459
7
many more that 10,000 bases. We note that Appellants
state on page 4 of the reply brief that claims 13 and 16 stand
or fall with claim 8. There- fore, we will sustain the
Examiner's rejection of Appellants' claims 8, 13 and 16.
In regard to claim 4, Appellants argue on pages 4-6
of the reply brief and pages 3-4 of the supplemental reply
brief that claim 4 distinguishes the teachings of Maizel and
Pustell by claiming "[a]pparatus for displaying similarities
between lines of text in a sequence of n lines of text."
Appellants argue that Pustell and Maizel compare elements that
are single characters (G,C,T,A) while Appellants’ claim 4
requires the elements to be lines of text.
However, the Examiner points out in the answer that
Pustell and Maizel teach the comparison of bases (G,C,T,A)
which are nucleotides. The Examiner argues that these nucleo-
tides are a sequence of characters that are a line of text.
We note that a claimed "line of text" does not
require that the line be made of words. Furthermore, Appel-
lants' claim language does not preclude the Examiner's inter-
pretation that a base (G,C,T or A) is a token repesenting a
Appeal No. 95-1682
Application 07/853,459
8
line of text and thereby, Pustell and Maizel teach an appara-
tus for displaying similarities between "lines of text in a
sequence of n lines of text" as recited in Appellants' claim
4. Thus, we find that the Examiner's interpretation of Appel-
lants' claim 4 language is reasonable. Therefore, we will
sustain the Examiner's rejection of Appellants' claim 4.
Claims 6 and 9 stand rejected under 35 U.S.C. § 103
as being unpatentable over Pustell, Maizel and Aho. Appel-
lants argue on pages 6 and 7 of the reply brief that Pustell,
Maizel and Aho fail to teach means for modifying the data to
produce tokens which are more easily comparable than the
tokens of the data as recited in Appellants' claims 6 and 9.
It is the burden of the Examiner to establish why
one having ordinary skill in the art would have been led to
the claimed invention by the reasonable teachings or sugges-
tions found in the prior art, or by a reasonable inference to
the
artisan contained in such teachings or suggestions. In re
Sernaker, 702 F.2d 989, 995, 217 USPQ 1, 6 (Fed. Cir. 1983).
Appeal No. 95-1682
Application 07/853,459
9
In addition, the Federal Circuit states that "[t]he mere fact
that the prior art may be modified in the manner suggested by
the Examiner does not make the modification obvious unless the
prior art suggested the desirability of the modification." In
re Fritch, 972 F.2d 1260, 1266 n.14, 23 USPQ2d 1780, 1783-84
n.14 (Fed. Cir. 1992), citing In re Gordon, 733 F.2d 900, 902,
221 USPQ 1125, 1127 (Fed. Cir. 1984). "Additionally, when
deter-mining obviousness, the claimed invention should be
considered as a whole; there is no legally recognizable
'heart' of the invention." Para-Ordnance Mfg., Inc. v. SGS
Importers Int’l,
Inc., 73 F.3d 1085, 1087, 37 USPQ2d 1237, 1239 (Fed. Cir.
1995), cert. denied, 117 S.Ct. 80 (1996), citing W. L. Gore &
Assocs., Inc. v. Garlock, Inc., 721 F.2d 1540, 1548, 220 USPQ
303, 309 (Fed. Cir. 1983), cert. denied, 469 U.S. 851 (1984).
After a careful review of Pustell, Maizel and Aho,
we fail to find any teachings or suggestions of a means for
modifying the data to produce tokens which are more easily
Appeal No. 95-1682
Application 07/853,459
10
comparable than the tokens of the data. Maizel shows tokens
but does not show the process of modifying the original data
to produce the tokens or aggregating the bases into other
tokens. Therefore, we will not sustain the Examiner’s rejec-
tion of claims 6 and 9.
Claims 18 through 20 stand rejected under 35 U.S.C.
§ 103 as being unpatentable over Pustell, Maizel, Aho and
Salton. Appellants argue on page 9 of the reply brief that
Pustell, Maizel, Aho and Salton fail to teach or suggest that
the tokens of claim 8 are "values of an attribute of records
in a sequence thereof" as recited in claim 18, that the tokens
of claim 8 are "words in a text" as recited in claim 19 and
that the tokens of claim 20 are "lines in a text."
After a careful review of Pustell, Maizel, Aho and
Salton, we fail to find that these references teach modifying
the Pustell homology matrix program for scoring sequences of
DNA bases to provide tokens that are values of an attribute of
records in a sequence or words of a text. However, we do find
as we have pointed out for claim 4, Pustell and Maizel teach
Appeal No. 95-1682
Application 07/853,459
11
that the tokens are bases and that these tokens are lines in a
text.
Therefore, we will sustain the Examiner's rejection of claim
20 but will not sustain the Examiner's rejection of claims 18
and 19.
Claims 21 and 22 stand rejected under 35 U.S.C. §
103 as being unpatentable over Pustell, Maizel, Aho, Salton
and McCreight. Appellants's only argument is found on page 10
of the reply brief. There, Appellants argue that since there
is nothing in claims 21 and 22 that has anything to do with
the term weighting, Salton adds nothing to the rejection. The
Appellants then state that because claim 8 is patentable over
Pustell and Maizel and claim 20 is patentable over Pustell,
Maizel and Aho, then claims 21 and 22 are patentable as well.
As we have sustained the Examiner's rejection of
claims 8 and 20, we will sustain the Examiner's rejection of
claims 21 and 22 for the same reason. Appellants have chosen
not to argue any of the specific limitations of claims 21 and
22 as a basis for patentability. We are not required to raise
Appeal No. 95-1682
Application 07/853,459
12
and/or consider such issues. As stated by our reviewing court
in In re Baxter Travenol Labs., 952 F.2d 388, 391, 21 USPQ2d
1281, 1285 (Fed. Cir. 1991), "[i]t is not the function of this
court to
examine the claims in greater detail than argued by an appel-
lant, looking for nonobvious distinctions over the prior art."
37 CFR § 1.192(a) as amended at 58 Fed. Reg. 54510, Oct. 22,
1993, which
was controlling at the time of Appellants filing the brief,
states as follows:
The brief . . . must set forth the authori-
ties and arguments on which the appellant
will rely to maintain the appeal. Any
arguments or authorities not included in
the brief may be refused consideration by
the Board of Patent Appeals and Interfer-
ences.
Also, 37 CFR § 1.192(c)(6)(iv) states:
For each rejection under 35 U.S.C. 103, the
argument shall specify the errors in the
rejection and, if appropriate, the specific
limitations in the rejected claims which
are not described in the prior art relied
on in the rejection, and shall explain how
such limitations render the claimed subject
matter unobvious over the prior art. If
Appeal No. 95-1682
Application 07/853,459
13
the rejection is based upon a combination
of references, the argument shall explain
why the references, taken as a whole, do
not suggest the claimed subject matter, and
shall include, as may be appropriate, an
explanation of why features disclosed in
one reference may not properly be combined
with features disclosed in another refer-
ence. A general argument that all the
limitations are not described in a single
reference does not satisfy the requirements
of this paragraph.
Thus, 37 CFR § 1.192 provides that this board is not under any
greater burden than the court which is not under any burden to
raise and/or consider such issues.
In view of the foregoing, the decision of the Exam-
iner rejecting claims 4, 8, 13, 16 and 20 through 22 under 35
U.S.C. § 103 is affirmed; however, the decision of the Exam-
iner rejecting claims 6, 9, 18 and 19 under 35 U.S.C. § 103 is
reversed.
No time period for taking any subsequent action in
con- nection with this appeal may be extended under 37 CFR
§ 1.136(a). AFFIRMED-IN-PART
Appeal No. 95-1682
Application 07/853,459
14
JERRY SMITH )
Administrative Patent Judge )
)
)
) BOARD OF
PATENT
LEE E. BARRETT ) APPEALS AND
Administrative Patent Judge ) INTERFER-
ENCES
)
)
)
MICHAEL R. FLEMING )
Administrative Patent Judge )
psb
Appeal No. 95-1682
Application 07/853,459
15
P.V.D. Wilde
AT&T Bell Laboratories
600 Mountain Avenue
P.O. Box 636
Murray Hill, NJ 07974-0636