Ex Parte Abdeen HussanDownload PDFPatent Trial and Appeal BoardJan 13, 201510699024 (P.T.A.B. Jan. 13, 2015) Copy Citation UNITED STATES PATENT AND TRADEMARK OFFICE __________ BEFORE THE PATENT TRIAL AND APPEAL BOARD __________ Ex parte JAGIR RAZAK JAINUL ABDEEN HUSSAN1 __________ Appeal 2012-005455 Application 10/699,024 Technology Center 1600 __________ 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). Appeal 2012-005455 Application 10/699,024 2 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. Appeal 2012-005455 Application 10/699,024 3 “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 Appeal 2012-005455 Application 10/699,024 4 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). Appeal 2012-005455 Application 10/699,024 5 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).) Appeal 2012-005455 Application 10/699,024 6 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, Appeal 2012-005455 Application 10/699,024 7 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.) Appeal 2012-005455 Application 10/699,024 8 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 Copy with citationCopy as parenthetical citation