Ex Parte Blair et al

Board of Patent Appeals and Interferences

Sep 20, 2006

09881234 (B.P.A.I. Sep. 20, 2006)

The opinion in support of the decision being entered today was not written
for publication and is not binding precedent of the Board.

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte DOUGLAS M. BLAIR, JOHN J. GREFENSTETTE,
H.HADON NASH, DALE I. NEWFIELD, and DUSTIN M. LUCIEN
__________

Appeal No. 2006-2702
Application No. 09/881,234
__________

ON BRIEF
__________

Before SCHEINER, ADAMS, and LEBOVITZ, Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL
This is a decision on the appeal under 35 U.S.C. § 134 from the
examiner’s final rejection of claims 1-23, which are all the claims pending in the
application.
Claim 1 is illustrative of the subject matter on appeal and is reproduced
below:
1. A method of comparing a query dataset N with a subject dataset M,
comprising:

dividing said query dataset N into nN data elements having a size within a
specified range;

dividing said subject dataset M into nM data elements having a size within
said specified range;

determining a number of tasks for an entire comparison of datasets N and
M as nN x nM;

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Application No. 09/881,234

sending all data elements and task definitions to a master central
processing unit (CPU) of a master-slave distributed computing platform,

wherein task definitions comprise at least one comparison
parameter, at least one executable element capable of performing
comparisons, a query data element identification(ID)/descriptor,
and a subject data element ID/descriptor, and

wherein data elements are sent alternately from query and subject
data elements;

sending a task definition for each task from the master CPU to one of a
plurality of slave CPUs when all parts of a task definition and data
elements referenced by said task definition are available at said master
CPU;

sending data elements referenced by said task definition to said slave
CPU;

performing each task on a slave CPU; and

returning task results for each task to said master CPU.

The references relied upon by the examiner are:
Reed et al. (Reed) 5,862,325 Jan. 19, 1999
Smith et al. (Smith), “BCM Search Launcher – An Integrated Interface to
Molecular Biology Data Base Search and Analysis Services Available on the
World Wide Wed,” Genome Methods, Vol. 6, pp. 454-462 (1996)

Altschul et al. (Altschul), “Basic Local Alignment Search Tool,” J. Molec. Biol.,
Vol. 215, No. 3, pp. 403-410 (1990)

GROUNDS OF REJECTION
Claims 1-23 stand rejected under 35 U.S.C. § 112, second paragraph, as
being indefinite in the recitation of the term “task definition.”
Claims 1, 4, 6-13, and 18-23 stand rejected under 35 U.S.C. § 103 as
being unpatentable over the combination of Smith, Altschul, and Reed.

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Application No. 09/881,234
We reverse.
DISCUSSION
Definiteness:
Claims 1-23 stand rejected under 35 U.S.C. § 112, second paragraph, as
being indefinite in the recitation of the term “task definition.” The examiner finds
(Answer, page 3), “[c]laims 1 (line 18) and 13 (lines 22-23) recite the phrase ‘said
task definition’ which is rejected due to the lack of clear antecedent basis.
Several task definitions are mentioned previously in these claims so it is unclear
to which one this phrase is referring.” According to the examiner (id.), “[c]laims
2-12 and 14-23 are also rejected due to their direct or indirect dependency from
claims 1 and [1]3.”
While appellants admit (Brief, page 7), “the claim language is not
necessarily as clear as it could be, appellants assert (Brief, page 8), “the claim
language is sufficiently clear to refer to the immediately preceding form of the
term ‘all parts of a task definition’ as used in the term ‘all parts of a task definition
and data elements referenced by said task definition.’” The examiner is not
persuaded by appellants’ argument finding instead (Answer, page 10) that “‘said
task definition’ is equally applicable to be referring to other ‘task definition’
recitations previously found in the claims, and ‘said task definition’ does not
clearly differentiate the limitation to only include the immediately preceding form
of the phrase that [a]ppellants intend as antecedent basis.”

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Application No. 09/881,234
As set forth in the Manual of Patent Examining Procedure § 2173.05(e),
8th ed. Rev. 3, August 2005, “the failure to provide explicit antecedent basis for
terms does not always render a claim indefinite.” Instead, the legal standard for
indefiniteness under 35 U.S.C § 112, second paragraph, is whether a claim
reasonable apprises those of skill in the art of its scope. See, Amgen Inc. v.
Chugai Pharm. Co., 927 F.2d 1200, 1217, 18 USPQ2d 1016, 1030 (Fed. Cir.
1991).
As we understand the claims “data elements and task definitions” are sent
to a master central processing unit (CPU). When “all parts of a task definition”
and the “data elements referenced by the task definition” are available at the
master CPU the “task definition for each task” as well as the “data elements
referenced by the task definition” are then sent from the master CPU to one of a
plurality of slave CPUs. Therefore, we agree with appellants (Brief, page 8), in
that the phrase “said task definition,” as it appears, e.g., in line 18 of claim 1,
refers “to the immediately preceding form of the term ‘all parts of a task definition’
as used in the term ‘all parts of a task definition and data elements referenced by
said task definition.’”
Accordingly, we reverse the rejection of claims 1-23 under 35 U.S.C.
§ 112, second paragraph, as being indefinite in the recitation of the term “task
definition.”

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Application No. 09/881,234
Obviousness:
Claims 1, 4, 6-13, and 18-23 stand rejected under 35 U.S.C. § 103 as
being unpatentable over the combination of Smith, Altschul and Reed.
The examiner finds (Answer, page 4), Smith teaches “an integrated set of
World Wide Web pages that organize nucleic acid sequence searches and
analyses available by function and provide a single entry for related searches . . .
which represents a ‘system’1 . . . .” According to the examiner (Answer, bridging
paragraph, pages 4-5), “[t]his system provides a method of performing different
searches for a given query sequence (query dataset N) with various sequence
databases (i.e. BLAST database which represents subject dataset M) . . . which
represents a method of comparing datasets. In this regard, the examiner finds
(Answer, page 5), Smith “describe a sequence input field for nucleic acid
searches . . . which is well known in the art to be divided into nucleotides (data
elements).” According to the examiner (id.), “[t]he presence of an input field
suggests that there is a size limitation with a specified range, which is necessarily
more than zero but less than infinity.”
In addition, the examiner finds that Smith teaches “BLAST nucleic
acid sequence searches” of an EST (expressed sequence tag) database.
According to the examiner (id.), “[t]his EST[ ]2 . . . database subset represents a

1 According to the examiner the online version of the Merriam-Webster dictionary
(www.m-w.com/cgi-bin/dictionary?book=Dictionary&va=system), defines the term “system” “as an
integrating group of items forming a unified whole as well as an organization forming a network
especially for distributing something sewing a common purpose.”

2 According to the examiner (Answer, page 5), the online “Genome Glossary”
(www.ornl.gov/sci/techresources/human_Genome/glossary/glossary_e.shtml), defines the term
“EST” “as a short (size) strand of DNA that is part of a cDNA molecule.”

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Application No. 09/881,234
division of the BLAST database (subject dataset) which has a size within a
specified range, as stated in instant claims 1 and 13.”
The examiner also finds (id.), Smith teaches the use of
the Internet allowing for communication between remote sites and
to promote a distributed information space by filling out a HTML
form (user input query) on a web page (at a master CPU (central
processing unit)), launching a search at a remote site (slave CPU),
returning results for further processing by the BCM Search
Launcher server (another slave CPU), and presenting results to the
user (from original master CPU) . . . .

According to the examiner (id.), Webopedia online3 defines the “master-slave”
relationship
as “an architecture in which one device (master) controls one or
more other devices (the slaves), the description provided in the
sentence above represents sending information to a master CPU of
a master-slave distributed computing platform (via query input) by
sending data elements referenced by a task definition to said slave
CPU, performing each task (i.e. comparison search and further
processing) on a slave CPU and returning task results for each task
to said master CPU.[”]

In this regard the examiner finds (Answer, bridging sentence, pages 5-6), Smith
teaches the use of “a plurality of servers (slave CPUs) that can return results to
the user’s system (master CPU) with additional links to auxiliary information that
was initiated from a single entry page . . . .” According to the examiner (Answer,
page 6), Smith teaches that one or more query parameter values may be
specified “which represents more than one data element dataset that can be a
query or subject.”
According to the examiner (Answer, bridging paragraph, pages 8-9), Smith
teaches that “sequence analysis services are extremely useful for molecular

3 www.webopedia.com/TERM/M/master_slave.html.

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biologists to allow access to the ever-expanding sequence data bases without
requiring copious local data base storage, frequent data base updates, the cost
of expensive and sophisticated hardware and software, and the cost and effort of
continuous system maintenance . . . .” The examiner finds, however, that Smith
teaches “that the individual WWW server sites scattered throughout the Web
hinders their efficient use . . . .” Answer, page 9. According to the examiner (id.),
Smith teaches that “the BCM Search Launcher addresses these limitations by
providing an improved interface to simplify access and improve analysis
resources . . . .”
The examiner finds, however, that Smith “does not describe compressing
and uncompressing data, determining a number of tasks as nN x nM, or looping
processes.” Answer, page 7. To make up for this deficiency in Smith, the
examiner relies on Altschul and Reed.
The examiner relies on Altschul to teach that a database can be
compressed “by packing 4 nucleotides into a single byte and using a table to
delimit the boundaries between adjacent sequences . . . .” Id. In this regard, the
examiner finds (id.), Altschul “describe[s] beginning with a matrix of similarity
scores for all possible pairs of residues . . . which represents determining the
number of tasks for an entire comparison of two datasets.” The examiner also
finds (id.), Altschul
Describe[s] performing BLAST with two random sequences (data
sets N and M) of lengths m and n in order to determine the
probability of finding a segment pair with a score greater than S (cut
off score . . .) where y=Kmn e-λS . . . which represents determination
of a number of tasks or points in a matrix in a comparison of two

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Application No. 09/881,234
datasets (i.e. N and M) involving a multiplication of data elements
nN x nM as, stated in instant claims 1 and 13.

According to the examiner (id.), Altschul teaches that “the sequence segments
can be of any length . . . or certain short sequences thus having a specified
range . . . .” The examiner recognizes, however, that like Smith, Altschul does
“not describe uncompressing data or looping processes.”
The examiner relies on Reed to make up for this deficiency in the
combination of Smith and Altschul. According to the examiner (Answer, page 8),
Reed describes “a system and methods that coordinate the transfer of data,
metadata, and instructions between databases to control and process
communications . . . which represents a separation or stripping of metadata from
data.” In this regard, the examiner finds (id.), Reed teaches that “this transfer of
metadata and methods allow for the control by the provider and consumer of the
types and contents of information subsequently transferred . . . which represents
storing minimal information if so desired.” In addition, the examiner finds (id.),
Reed teaches “compressing database, database query, or other file format using
PKZIP . . . that represents packing data into an efficient structure using a
redundancy reduction data compression method.”
In addition, the examiner finds (id.), Reed teaches “corresponding data,
metadata, and instructions in the provider program can control and automate
decryption and decompression of data . . .”; “communication networks that allow
both parties to control, filter, store, index, and process communications from
each other . . . which represents creating an index in an uncompressed manner”;
and “querying a provider database and loops through each communication object

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Application No. 09/881,234
instance (data) which is to be published and which are read . . . which represents
a looping of data (i.e. query sequences) to perform setup, preprocessing, and
table generation.” According to the examiner (id.), Reed “describe[s] the
program begins a second loop through each recipient and using such recipient
attributes and methods to generate and transmit a communications object
instance for all recipients . . . which represents a looping of other data such as
the looping of subject sequences.”
Based on this evidence, the examiner concludes (Answer, page 9),
A skilled artisan at the time of the invention would have been
motivated to make improvements to analysis server sites, such as
that stated by Smith . . . by adding additional features to further
simplify access and improve analysis resources . . . . It would have
been obvious to one having ordinary skill in the art at the time the
invention was made to compress data (as stated by Altschul et al.
and Reed et al.) and to use looping processes (as stated by Reed
et al.) in the method of Smith et al., where the motivation would
have been to offer enhanced, integrated, easy-to-use, and time-
saving techniques to a large number of useful molecular biology
database search and analysis services for organizing and
improving access to these tools for genome researchers worldwide
. . . .

In response, appellants argue (Brief, page 11), there is no suggestion or
motivation to modify “the search launcher interface” of Smith with the combined
teachings of Altschul and Reed. In this regard, appellants assert that Smith “is
merely a WWW gateway to pre-existing search services . . . .” Brief, page 13.
According to appellants (Brief, page 16), Smith “teaches the running of
sequence-to-database searches, but fails to teach or fairly suggest numerous
claim limitations required by all of the claims, including . . .” the requirement of

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Application No. 09/881,234
appellants’ claimed invention “wherein data elements are sent alternately from
query and subject data elements.”
As we understand Smith, the reference teaches that “query” data
elements are sent to a remote processor that already contains the “subject” data
elements, e.g. a sequence database. See e.g., Smith, page 454, wherein Smith
states that Internet “services are extremely useful for molecular biologists, as
they allow access to the ever-expanding sequence data bases without requiring
copious local data base storage. . . .” The examiner fails to identify, and we do
not find, a teaching in Smith to suggest that “data elements are sent alternately
from query and subject data elements.” We remind the examiner that “[a]ll words
in a claim must be considered in judging the patentability of that claim against the
prior art.” In re Wilson, 424 F.2d 1382, 1385, 165 USPQ 494, 496 (CCPA 1970).
In rejecting claims under 35 U.S.C. § 103, the examiner bears the initial
burden of presenting a prima facie case of obviousness. In re Oetiker, 977 F.2d
1443, 1445, 24 USPQ2d 1443, 1444 (Fed. Cir. 1992). For the foregoing
reasons, it is our opinion that the examiner fails to provide the evidence
necessary to establish a prima facie case of obviousness. If the examiner fails to
establish a prima facie case, the rejection is improper and will be overturned. In
re Fine, 837 F.2d 1071, 1074, 5 USPQ2d 1596, 1598 (Fed. Cir. 1988).

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Application No. 09/881,234

Accordingly, we reverse the rejection of claims 1, 4, 6-13, and 18-23 under
35 U.S.C. § 103 as being unpatentable over the combination of Smith, Altschul,
and Reed.

REVERSED

Toni R. Scheiner )
Administrative Patent Judge )
)
) BOARD OF PATENT
)
Donald E. Adams ) APPEALS AND
Administrative Patent Judge )
) INTERFERENCES
)
)
Richard M. Lebovitz )
Administrative Patent Judge )

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DA/dym

Christopher B. Kilner, Esq.
Roberts Abokhair & Mardula, L.L.C.
Suite 1000
11800 Sunrise Valley Drive
Reston, VA 20191-5302