Ex Parte Abdeen Hussan

Patent Trial and Appeal Board

Jan 13, 2015

10699024 (P.T.A.B. Jan. 13, 2015)

UNITED STATES PATENT AND TRADEMARK OFFICE
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BEFORE THE PATENT TRIAL AND APPEAL BOARD
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Ex parte JAGIR RAZAK JAINUL ABDEEN HUSSAN1
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Appeal 2012-005455
Application 10/699,024
Technology Center 1600
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Before DONALD E. ADAMS, ERIC B. GRIMES, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims relating to a
method for storing and presenting genetic sequence data, which have been
rejected as obvious. We have jurisdiction under 35 U.S.C. § 6(b).
We reverse.

1 According to Appellant, the Real Party in Interest is International Business
Machines Corporation (Appeal Br. 2).
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STATEMENT OF THE CASE
The Specification states that “[t]he techniques described herein
represent genetic sequence data as such data occurs in genome sequences”
and that “[t]echniques are described herein for storing the sequence data and,
at the same time, allowing efficient access/processing on the data” (Spec.
2:19–27).
Claims 3–6, 10, 14–22, and 24–28 are on appeal. Claims 14, 24, and
27 are the independent claims and are directed respectively to a method, a
computer program product, and a system. The critical limitation in each of
the independent claims is
generating . . . entries of a match-set data structure, . . . each
entry comprising a sequence identification to identify a
sequence where a match occurs and offset information to
determine a position within the sequence where the matching
subsequence of the sequence is located, wherein the offset
information comprises a first and second position parameter;
. . .
wherein the first position parameter of each match-set data
structure entry denotes a location in the sequence and the
second position parameter of each match-set data structure
entry denotes an offset from the location.
(Claim 14, steps iii and viii.)
I.
The Examiner has rejected claims 3–6, 10, 14–22, 24, 27, and 282
under 35 U.S.C. § 112, second paragraph, on the basis that the claim
language, in step (viii) of claim 14, requiring generating a sequence

2 The statement of the rejection does not include claims 24, 27, and 28 but
those claims are addressed in the body of the rejection.
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“responsive” to certain data makes the claims indefinite (Ans. 5–6). The
Examiner concludes that “the recitation of the limitation ‘responsive’
renders the claims indefinite for the following reasons. It is unclear in what
way the computer generated sequence is ‘responsive to’ backbone sequence
data and stored match-set data” (id. at 5).
Appellant argues that “the claims provide a definite limitation
regarding how a representation is generated by reciting in the claims that a
computer system generates a representation responsive to a stored backbone
sequence and match-set data” (Appeal Br. 16). Appellant argues that “[t]his
is not a matter of indefiniteness, but rather breadth. Breadth of a claim is not
to be equated with indefiniteness.” (Id.)
We agree with Appellant that the Examiner has not adequately
explained why the claim language makes the scope of the claims unclear.
Claim 14 states that generating and presenting a sequence to a user is
“responsive to the stored backbone sequence and responsive to the at least
one of the stored match-set data entries corresponding to the selected at least
first one of the replets” and that updating the entries in the match-set data
structure is “responsive to the position of the selected at least first one of the
replets” (claim 14, step (viii)).
In the context of the claim language, the disputed limitation simply
requires that the sequence that is generated and presented depends on the
data in the stored backbone sequence and in one of the stored match-set data
entries, and updating the entries in the match-set data depends on the
position of one of the replets. As Appellant points out, the claim language
may be broad, in that the manner in which the stored data are used is not
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spelled out, but the Examiner has not presented an adequate basis for
concluding that a person of ordinary skill in the art would not understand the
meaning of the claim language when viewed in light of the Specification.
II.
The Examiner has rejected claims 4, 5, 14–22, 24, 27, and 28 under
35 U.S.C. § 103(a) based on Rigoutsos,3 Chen,4 Orcutt,5 Zhang,6 and UK
Cropnet7 (Ans. 7). The Examiner has rejected claims 3–6, 10, 14–22, and
24–28 under 35 U.S.C. § 103(a) based on the same references, combined
with Martinez8 (Ans. 16). The same issue is dispositive for both
obviousness rejections.
The Examiner finds that the cited references disclose or suggest all of
the limitations of the independent claims (id. at 9–15). In particular, the
Examiner finds that, although Rigoutsos does not disclose offset information
having first and second position parameters (as recited in claim 14, step
(viii)), this limitation would have been obvious because

3 Isidore Rigoutsos & Aris Floratos, Combinatorial pattern discovery in
biological sequences: the TEIRESIAS algorithm, 14 BIOINFORMATICS 55–67
(1998).
4 Chen et al., DNACompress: fast and effective DNA sequence compression,
18 BIOINFORMATICS 1696–1698 (2002).
5 Orcutt et al., Nucleic acid sequence database computer system, 10
NUCLEIC ACIDS RESEARCH 157–174 (1982).
6 Jnghui Zhang and Thomas L. Madden, PowerBLAST: A New Network
BLAST Application for Interactive or Automated Sequence Analysis and
Annotation, 7 GENOME RESEARCH 649–656 (1997).
7 UK Cropnet, http://ukcrop.net/agr/sequence_display_key (last accessed on
Jan. 28, 2010).
8 Martinez, An efficient method for finding repeats in molecular sequences,
11 NUCLEIC ACIDS RESEARCH 4629–4634 (1983).
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Rigoutsos provides a notation (indicated as LsP) that uses a
sequence ID parameter (i) and an offset position parameter (j)
denoting sequence matches at a specific offset; see p.56, Col. 2,
¶3 to bottom, and Figure 1, which suggests the use of first and
second position parameters, because the sequence IDs taught by
Rigoutsos are associated with positions (in a sequence) and the
offset parameter taught by Rigoutsos denotes the offset position
of the matching sequence.
(Id. at 10.)
Appellant disagrees with this reasoning, arguing that “correctly
understood, the first parameter of Rigoutsos that is cited by Examiner’s
Answer and relied upon for the rejection is an index identifying one of three
enumerate[d] sequences {LFAADCHFFEDTR, LKLALCHESEDR,
AFAGCHADELFT} for which a match is sought. It does not identify a
position within a sequence.” (Reply Br. 4.)
We agree with Appellant that the Examiner has not persuasively
shown that the match-set data structure entries required by the claims on
appeal would have been obvious based on Rigoutsos’ disclosure. Claim 14
requires
generating . . . entries of a match-set data structure, . . . each
entry comprising [1] a sequence identification to identify a
sequence where a match occurs and [2] offset information to
determine a position within the sequence where the matching
subsequence of the sequence is located, wherein the offset
information comprises a first and second position parameter.
(Claim 14, step (iii).) Claim 14 also requires that “the first position
parameter of each match-set data structure entry denotes a location in the
sequence and the second position parameter of each match-set data structure
entry denotes an offset from the location” (id., step (viii).)
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The Specification provides an example in which the TEIRESIAS
algorithm (Spec. 13:27–30) was applied to an input set of sequences (id. at
13:10–24). The results are shown in Table 2 (id. at 13:32 to 14:7). The first
entry in Table 2 shows, for example, “the information concerning the pattern
‘cgcgcgcgcg’, that is the sequence in which [it] occurs (0) and the offset (19)
of the occurrence” (id. at 14:13–15).
The Specification states that “Table 3 . . . presents the information
obtained by transforming the results in Table 2 . . . , generated using the
TEIRESIAS algorithm, such that the information is structured in accordance
with the required Match-Set datastructure” (id. at 14:10–12). The entries of
Table 3 differ from those of Table 2 in that they include a third parameter,
which is either 0 or 1 (id. at 14:20–28). The Specification’s example is
evidence that the “required Match-Set datastructure” (id. at 14:12) differs
from the “Match-Set entries generated by the TEIRESIAS algorithm” (id. at
13:23–33).
Rigoutsos discloses the TEIRESIAS algorithm (Rigoutsos 56, left
col.: “In this discussion we present TEIRESIAS, a novel algorithm for the
discovery of patterns in biological sequences.”). Rigoutsos states that
TEIRESIAS scans sequences for defined patterns, which can include “don’t
care characters” that are indicated by a dot (id. at 56, right col.). Rigoutsos
describes an exemplary pattern “A.CH..E,” which includes the specific
patterns ADCHFFE, ALCHESE, and AGCHADE (id.). Rigoutsos also
provides a set of sequences in which “each sequence . . . matches the pattern
‘A.CH..E’” (id.). The sequences in the set are “{LFAADCHFFEDTR,
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LKLALCHESESDR, AFAGCHADELFT},” where the boldfaced strings
indicate matches (id.).
Rigoutsos states:
Given a pattern P and a set of sequences S = {s1, s2, …, sn}, we
define the offset list of P with respect to S (or simply the offset
list of P, when S is unambiguously implied) to be the following
set:
Ls(P) = {(i, j) | sequence si matches P at offset j}
(id.). Rigoutsos states that for the particular set of sequences given
previously, the offset list for the pattern A.CH..E is “LS(‘A.CH..E’) = {(1,4),
(2,4), (3,3)}” (id.).
Thus, consistent with the Specification’s discussion of the
TEIRESIAS algorithm, Rigoutsos describes the output of the algorithm as a
list of entries that each indicates (a) a sequence in which a match is found
and (b) a position (or offset from the start of the sequence) where the match
begins. Claim 14, however, requires offset information that includes two
parameters: a “first position parameter . . . [that] denotes a location in the
sequence” and a “second position parameter . . . [that] denotes an offset from
the location” (claim 14, step (viii)).
The Examiner reasons that Rigoutsos
suggests the use of first and second position parameters,
because the sequence IDs taught by Rigoutsos are associated
with positions (in a sequence) and the offset parameter taught
by Rigoutsos represents the offset position of the matching
sequence. Therefore, Rigoutsos makes obvious the use of
offset information having a first position parameter and a
second position parameter.
(Answer 19–20.)
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We do not agree that “the sequence IDs taught by Rigoutsos are
associated with positions (in a sequence)” (id.), as found by the Examiner.
Rigoutsos describes its set of sequences as discrete entities. Rigoutsos
states, for example, that “each sequence in the following set matches the
pattern ‘A.CH..E’” (Rigoutsos 56, right col.). Rigoutsos also states that its
offset list indicates that “sequence si matches P at offset j,” (id.); i.e., a
particular sequence has a subsequence that matches pattern P at a particular
offset. Rigoutsos does not support the Examiner’s finding that its sequence
identifiers are associated with a position in a sequence.
Thus, Rigoutsos does not disclose offset information that includes
both a “first position parameter . . . [that] denotes a location in the sequence”
and a “second position parameter . . . [that] denotes an offset from the
location,” as required by claim 14. The Examiner has not persuasively
explained why including both of the required parameters would have been
obvious based on Rigoutsos’ disclosure, or the disclosures of the other cited
references. We therefore reverse the rejection of claim 14 under 35 U.S.C.
§ 103(a).
The other independent claims include the same relevant limitation.
We therefore reverse the rejection under 35 U.S.C. § 103(a) of independent
claims 24 and 27, as well as the rejection of all of the dependent claims.
SUMMARY
We reverse all of the rejections on appeal.

REVERSED
cdc