DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
This application filed 08/19/2022 is a National Stage entry of PCT/IL2021/050186, with an International Filing Date of 02/17/2021, and claims priority from Provisional Application 62978840, filed 02/20/2020. The claims are therefore examined as filed on 02/20/2020, the effective filing date. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further review of the priority application(s).
Claim Status
Claims 1-16 are pending.
Claims 1-16 are examined.
Claims 1-16 are rejected.
Information Disclosure Statement
The Information Disclosure Statements are in compliance with the provisions of 37 CFR 1.97. Accordingly, all references have been considered.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of mental processes and mathematical concepts, without significantly more.
The MPEP at MPEP 2106 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of matter?
(2A)(1) Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea?
(2A)(2) Do the claims recite additional elements that integrate the judicial exception into a practical application?
(2B) If the claims recite a judicial exception and do not integrate the judicial exception, do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?
With regard to step (1) (Are the claims directed to a process, machine, manufacture or composition of matter?): Yes. The claims are directed to one of the statutory classes. Claims 1-16 are directed to a process (computer-based method).
With regard to step (2A)(1) (Do the claims recite a judicially recognized exception?): Yes. Claims 1-16 recite the abstract ideas of processing data using mental steps and mathematical concepts. Claims that recite nothing more than abstract ideas, natural phenomena, or laws of nature are not eligible for patent protection (see MPEP 2106.04).
Abstract ideas include mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, evaluating, and organizing information (See MPEP 2106.04(a)(2)). In particular, these abstract ideas include but are not limited to:
Applying an alignment algorithm to generate local alignments by aligning a substring of a sequence to a substring of the target sequence to maximize an alignment score (mental process/mathematical concept; the human mind is capable of aligning sequence strings to find the best/most matching, determining a score based on alignment is equivalent to performing a calculation; claim 1)
Determining unaligned sections of the query sequence to be alignment gaps (mental process, the human mind is capable of determining gaps/nonmatching portions of aligned strings; claim 1)
Removing a number of largest alignment gaps of the query sequence to generate a clean sequence and clean alignment score (mental process/mathematical concept; the human mind is capable of removing gaps/nonmatching portions in an alignment, determining a score based on alignment is equivalent to performing a calculation; claim 1)
Applying a second alignment algorithm to generate a clean alignment and clean alignment score (mental process/mathematical concept; the human mind is capable of applying an algorithm based on alignment, and doing so to compute a score is equivalent to performing a calculation; claim 3)
Reducing the clean alignment score by a gap removal penalty proportional to the number of largest alignment gaps to calculate an adjusted clean alignment score (mental process/mathematical concept; the human mind is capable of applying a gap penalty in an alignment algorithm, and doing so to calculate a score is equivalent to performing a calculation; claim 6)
Further adjusting the alignment score by addition of a probability of successful gap removal (mental process/mathematical concept; the human mind is capable of adjusting a score using a probability, and doing so is equivalent to performing a calculation; claim 7)
Removing different numbers of alignment gaps to generate clean query sequences and reapplying the second alignment algorithm to generate clean alignment scores (mental process/mathematical concept; the human mind is capable of removing gaps and calculating a new score with an algorithm, doing so is equivalent to performing a calculation; claim 11)
Iterating generation of clean alignments and scores (mental process/mathematical concept; the human mind is capable of repeating alignment/calculation of scores, doing so is equivalent to performing a calculation; claim 12)
Dependent claims 2, 4-5, 8-10, 14-16 further limit the abstract ideas recited in the independent claims, and do not change their characterization as abstract ideas.
Therefore, the claims recite elements that constitute one or more judicial exceptions.
With regard to step (2A)(2) (Do the claims recite additional elements that integrate the judicial exception into a practical application?): No. Claim 1 and its dependents recite the additional elements of the method being “computer-based”, and receiving a query sequence for screening against a target database. Claims 3 further recites the additional element of outputting an alignment score indicating homology, with claims 11 provides further detail on the output score.
While the claims recite the additional element of receiving and outputting data, such steps that only amount to necessary data gathering and outputting, without any technical details of how the data is obtained/output that integrate the judicial exception, are insignificant extrasolution activities that do not add a meaningful limitation to the claims (see MPEP 2106.05(g)). As a result, the judicial exception is not integrated into a practical application. In addition, while the claims recite additional elements related to the use of computers, they do not provide any specific details by which the computer performs or carries out the judicial exception listed in step (2A)(1), nor do they provide any details of how specific structures of the computer are used to implement these functions. The judicial exception is therefore not integrated into a practical application because the generically recited computer elements do not add a meaningful limitation to the abstract idea, as they amount to simply implementing the abstract idea on a computer (see MPEP 2106.05(f)). Because the claims do not recite any additional elements that integrate the judicial exception into a practical application, the claims as a whole are directed to an abstract idea.
With regard to step (2B) (Do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?): No. The claims recite an abstract idea with additional elements; however, these additional elements are general computer elements added to abstract ideas, and non-particular instructions to apply the abstract idea by linking it to a field of use or extrasolution activity (see MPEP 2106.05(f-h)). General computer elements used to perform an abstract idea do not provide an inventive concept, and similarly, non-particular instructions to gather or produce data do not provide an inventive concept. Non-particular instructions to gather or output data are also considered well-understood, routine and conventional activities (see MPEP 2106.05(d), which indicates that limitations such as “Receiving or transmitting data over a network” from Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362, and “Storing and retrieving information in memory” from Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, are recognized as conventional activities). The claims therefore do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As a result, the claims as a whole do not provide an inventive concept.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim Rejection
Claims 1, 3-14, and 16 are rejected under 35 U.S.C. 103 as being unpatentable over SEMENYUK 2016 (US 10192026 B2, cited on the IDS filed 8/19/2022) in view of KUBOKOVICH 2019 “Strengthening Security for Gene Synthesis: Recommendations for Governance.”
Claim Interpretation and Scope and Contents of Prior Art
Claim 1 recites a computer-based method for screening DNA sequences to detect obfuscated sequences of concern (SOCs), comprising: receiving a query sequence for screening against a target database of sequences; applying a first alignment algorithm to generate multiple local alignments of the query sequence with a target sequence of the target database, wherein each local alignment aligns a substring of the query sequence to a substring of the target sequence to maximize an alignment score. With respect to this limitation, SEMENYUK teaches a computer based method for screening DNA sequences that can be used to detect a sequence [4-8], with the steps of using a query sequence [5] against variants represented as a reference graph [29] and generating alignments between the query and identified candidate sequence to find the optimal alignment/highest alignment score [6, 11, 130, 156].
Claim 1 further recites determining unaligned sections of the query sequence to be alignment gaps from the aligned substrings of the query sequence, and removing a number of largest alignment gaps of the query sequence to generate a clean query sequence and a respective clean alignment score that is an indicator of a homology of the target sequence and an obfuscated SOC in the query sequence. With respect to this limitation, SEMENYUK teaches determining alignment gaps based on unaligned sections of the query sequence and applying a gap penalty to compute a new alignment score without the gaps [126, 128, Fig 1] that can indicate homology [115, 123].
SEMENYUK teaches that sequences of interest to be detected can be pathogens or genetic diseases [4] but does not specifically teach detecting an obfuscated sequence of concern from a database. However, KOBOKOVICH teaches sequence screening to detect sequences of concern by screening them against one of many databases (pg 420 col 2-421 col 1).
Claim 3 recites the limitation of applying a second alignment algorithm to generate a clean alignment between the clean query sequence and the target sequence and to generate the clean alignment score, and outputting the clean alignment score indicating the homology of the target sequence and the obfuscated SOC in the query sequence. With respect to this limitation, SEMENYUK teaches applying an algorithm with a gap penalty to compute a new alignment score [126, 128, Fig 1, 140-145] that can indicate homology [115, 123].
Claim 4 recites the limitation wherein the first and second alignment algorithms are the same alignment algorithm. With respect to this limitation, SEMENYUK teaches applying the same alignment algorithms to recalculate the score and find an optimal alignment [137-145 ].
Claim 5 recites the limitation wherein the first and second alignment algorithms are BLAST algorithms. With respect to this limitation, SEMENYUK teaches that BLAST can also be used as a scoring scheme [128].
Claim 6 recites the limitation of reducing the clean alignment score by a gap removal penalty proportional to the number of largest alignment gaps removed, to calculate an adjusted clean alignment score indicating the homology of the target sequence and the obfuscated SOC in the query sequence. With respect to this limitation, SEMENYUK teaches that the alignment score can be reduced based on the number of alignment gaps removed and the type of gaps, where the score of the alignment is the sum of all scores for all patched pair, mismatched pairs and gaps [126-128, 132, 140-145].
Claim 7 recites the limitation wherein the adjusted clean alignment score is further adjusted by addition of a probability of biologically successful gap removal to generate a physical SOC. With respect to this limitation, SEMENYUK teaches adjusting the score based on the probabilities of gaps in the form of substitutions and indels [126], or based on if the substitution is more biologically probable [129] and it would be obvious to one of ordinary skill in the art that this probability can extend to biologically successful gap removal (substitute or indel back to match the target database sequence).
Claim 8 recites the limitation wherein the gap removal penalty proportional to the number of largest alignment gaps removed is a per gap removal penalty (prm) multiplied by the number of largest alignment gaps removed. With respect to this limitation, SEMENYUK teaches a linear gap penalty can be applied [132] and that a gap of length r has a negative score g+rs, so the gap penalty can be proportional to the gaps removed [0128].
Claim 9 recites the limitation wherein prm is a function of a number of base pairs removeable by bioengineering tools. With respect to this limitation, SEMENYUK teaches that the gap removal penalty is a function of removable base pairs, or gap length [0128], but does not specify that they are removed by bioengineering tools. However, one of ordinary skill in the art would understand that such base pairs can be removed through bioengineering means (such as CRISPR).
Claim 10 recites the limitation wherein the adjusted clean alignment score further includes a negative increment for each gap opening (pgo) and for each gap extension (pgx), and wherein prm= pgo + pgx*x, where x is the removeable number of base pairs. With respect to this limitation, SEMENYUK teaches an equivalent alignment score calculation g+rs, where g is the gap (gap opening) and r is the number of base pairs (or length) multiplied by an extension score s [0128].
Claim 11 recites the limitation of removing different numbers of alignment gaps from the query sequence to generate different clean query sequences; reapplying the second alignment algorithm to each of the different clean query sequences to generate multiple respective clean alignments and respective adjusted clean alignment scores; and wherein outputting the clean alignment and the adjusted clean alignment score comprises determining a maximum score from among the multiple adjusted clean alignment scores and outputting the maximum score as the adjusted clean alignment score and outputting the respective clean alignment. With respect to this limitation, SEMENYUK teaches removing different insertion/deletion gaps, or limiting the number of gap openings and grouping gaps together to generate multiple alignments and determining the optimal score [138-145].
Claim 12 recites the limitation of iterating generation of clean alignments and respective adjusted clean alignment scores with respect to all of the target database sequences, and claim 13 recites the limitation of ordering the clean alignments and the adjusted clean alignment scores generated with respect to all of the target database sequences according to the adjusted clean alignment score. With respect to these limitations, SEMENYUK does not specify iterating generation of clean alignments and adjusted scores with respect to all target database sequences, however one of ordinary skill in the art would understand that the process can be repeated, or ordered to be repeated for any sequence until a number of matches are found.
Claim 14 recites the limitation wherein the database of target sequences is a database of SOCs. SEMENYUK does not teach that the database is necessarily a database of SOCs, however, KOBOKOVICH teaches screening query sequences against one of many databases that contain sequences of concern (pg 420 col 2-421 col 1, pg 423 par 3).
Claim 16 recites the limitation wherein the first alignment score includes a positive increment for each matching character (rm) and a negative increment for each mismatching character (pmm), for each gap opening (pgo), and for each gap extension (pgx). With respect to this limitation, SEMENYUK teaches that the alignment score involves a positive score for a matched pair, a negative score for a mismatched pair, and a negative score for gaps based on length [128].
Resolving Ordinary Skill in the Art and Obviousness Rationale
A teaching, suggestion, or motivation in the prior art would have led one of ordinary skill in the art to modify or combine the prior art to arrive at the claimed invention. Specifically, a person of ordinary skill in alignment of sequences of interest would have been motivated to combine the teachings of SEMENYUK with the teachings of KOBOKOVICH, in order to achieve the claimed invention, because screening query sequences against sequences of concern is necessary to help control unauthorized access to dangerous pathogens (Abstract). A person of ordinary skill would reasonably expect success from combining these teachings, as they method of SEMENYUK can be applied against any database or target sequence, including the sequences of concern in KOBOKOVICH. Therefore, the claims at issue would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention as there is both a reason to modify or combine the prior art, and a reasonable expectation of success (see MPEP 2143.02 (I)).
Claims Without an Art Rejection
No art rejection is applied to claims 2 and 15. The cited art, while addressing the limitations of applying gap penalties/removing alignment gaps and general calculations for alignment scores, do not teach or render obvious the specific limitations of removing a number of large alignment gaps equal to one less than the number of multiple local alignments, or where the number of alignment gaps removed is set to be all gaps greater than a preset threshold number of base pairs, and wherein the number of alignment gaps removed is subsequently incremented by an iterative process removing the largest alignment gap not previously removed, until the adjusted clean alignment score calculated following the gap removal does not increase. No combinable art before the effective filing date could be found to render the claims as obvious.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY C LEVERETT whose telephone number is (571)272-5494. The examiner can normally be reached 8:00am - 5:00pm M-Th.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R. Skowronek can be reached at (571) 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/MARY C LEVERETT/ Examiner, Art Unit 1687