DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
Claims 1-24 are under examination.
Claim Rejections - 35 USC § 101
2. 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 1-24 rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more.
Claims 1-24 are directed to method and system of compressing genetic information in multiple reading frames. As described in Alice Corp. Pty. Ltd. V. CLS Bank Int’l, 573 U.S._, 134 S. Cr. 2347, 110 U.S.P.Q.2d 1976 (2014), a two-step analysis is required in considering the patent eligibility of the claimed subject matter. The first step requires determining if the claimed subject matter is directed to a judicial exception. The instant claims require the steps of encoding a first genetic sequences in computer readable data structures comprising first directed acyclic graphs (DAGs) of first finite automatons (FAs); encoding in a second DAG or second FA, overlapping sequences between the encoded first genetic sequence; calculating for each edge in the second DAG or the second FA a second score; and selecting a sequence represented by a path through the second DAG or second FA. These steps are drawn to either a mathematical algorithm or mental steps. Dependent claims 2-22 recite additional mental steps or mathematical steps. Instant claim 24 also recites the steps of a first routine to generate DAGs or FAs from protein mutation data; a second routine to create overlap DAGs or FAs using as input a series of DAGs or FAs output by the first routine; a third routine to evaluate an overlap DAG or FA to locate the best paths through DAG or FA and to alter edge weights according to specific criteria or stochastically before generate new best paths through the DG or FA; and a fourth routine to score and optimize the best paths. These steps are also drawn to mental steps or mathematical steps. Mental steps are a judicial exception. The courts have found mathematical algorithms to be drawn to the judicial exception of an abstract idea (In re Grams, 888 F.2d 835, 12 U.S.P.Q.2d 1824 (Fed. Cir. 1989)). Thus, the instant claims are drawn to a judicial exception.
This judicial exception is not integrated into a practical application. The instant claims do not recite an element that reflects an improvement in the functioning of a computer or other technology, an element that applies the judicial exception to effect a particular treatment, an element that implements the judicial exception with a particular machine, or an element that effects a transformation of a particular article to a different state or thing. The instant claims recite the elements of a system, a computer processor, and memory. However, the instant claims to not recite structural limitations of these elements. The instant claims do not recite a particular machine. The instant claims do not integrate the judicial exception into a practical application.
The second part of the analysis requires determining if the claims include additional elements that are sufficient to amount to significantly more than the judicial exception. The instant claims recite the additional elements of a system, a computer processor, and memory. However, these elements are well-understood, conventional and routine computer components (Specification, paragraph [0045]). Reciting such well-understood, routine, and conventional components do not transform a judicial exception into patent eligible subject matter. In addition, the recitation of the specific types of data to be used in the judicial exception does not transform the abstract idea into a non-abstract idea. (See buySAFE, Inc. v Google, Inc. 765 F.3d 1350, 112 U.S.P.Q.2d 1093 (Fed.Cir.2014)). Furthermore, the elements taken as a combination are also well-understood, routine, and conventional, since the elements are merely specifying a computer system for implementing the judicial exception. Thus, the instant claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Claim Rejections - 35 USC § 103
3. 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.
Claims 1-6 and 23-24 are rejected under 35 U.S.C. 103 as being unpatentable over Semenyuk (US 2018/0089369 A1) in view of Chin et al. (US 2014/0025312 A1).
Regarding claims 1 and 23, Semenyuk teaches a method and system that includes for a series of first genetic sequence encoding first proteins or nucleic acid sequences, associating a first score with each possible nucleotide or amino acid residue, insertion and deletion at each position (paragraph [0116]-[0120], [0148]-[0151], [0164], [0176]-[0178]); encoding the first genetic sequences in first computer-readable data structures comprising first directed acyclic graphs (DAGs) or a first finite automations (FAs) such that (i) a plurality of potential genetic sequences for the first proteins or nucleic acids sequences are encoded in the first data structures (paragraphs [0120]-[0124], [0140]-[0142]); each edge in the DAGs or first FAs represents a nucleotide residue, insertion, or deletion at that position and the first score associated with the nucleotide residue, insertion or deletion at that position (iii) each path through the first DAGs or accepted sequence in the first FAs represents a potential sequence encoding one of the first proteins or nucleic acid sequences (paragraphs [0090]-[0092] and [0117]-[0120]). In addition Semenyuk teaches that their method is implemented on a computer with a processor and memory (paragraphs [0074]-[0077]).
However, Semenyuk does not teach the step of (iv) for each path through one of the first DAGs or accepted sequence in one of the first FAs, a first aggregate score of the path or accepted sequence is the accumulation of the first score of all edges along the path or accepted sequence.
Chin et al. teach (iv) for each path through one of the first DAGs or accepted sequence in one of the first FAs, a first aggregate score of the path or accepted sequence is the accumulation of the first score of all edges along the path or accepted sequence (paragraph [0131]-[0134], [0149]-[0152]); encoding in the second DAG or second FA, overlapping sequence between the encoded first genetic sequences for the first proteins or nucleic acid sequences (paragraphs [0015], [0092], [0106]-[0109], [0119]-[0122], and [0129]); calculating, for each edge in the second DAG or the second FA, a second score representing a combined total effect of the component edges of the first data structures (paragraphs [0131]-[0133] and [0151]-[0153]); selecting according to the scores of each edge in the second DAG or second FA, a sequence represented by a path through the second DAG or the second FA (paragraphs [0131]-[0133] and [0157]-[0159]).
Regarding claim 2, Semenyuk teaches each score reflects a likelihood of the inclusion of the particular nucleotide residue, a particular insertion, or a particular deletion at the corresponding position (paragraphs [0055]-[0058]. [0117]-[0120], [0158]-[0161] and [0164]).
Regarding claim 3, Semenyuk teaches each score reflects a fitness metric associated with the inclusion of a particular nucleotide residue, or a particular insertion, or a particular deletion at the corresponding position (paragraph [0158]-[0161]).
Regarding claim 4, Semenyuk teaches each score reflects an expression of the probability of the inclusion of a particular nucleotide residue, a particular insertion, or a particular deletion at the corresponding position (paragraph [0055]-[0058], [0117]-[0120], [0158]-[0161], [0164]).
Regarding claim 5, Chin et al. teach each score reflects an expression of the probability of the inclusion of a particular nucleotide residue, a particular insertion, or a particular deletion at the corresponding position (paragraph [0068], [0073], [0131]-[0134]).
Regarding claim 6, Semenyuk teaches encoding, the second DAG or the second FA, overlapping sequence between the encoded genetic sequence for the first proteins or nucleic acid sequences comprises: selecting, in each of the first data structures, a starting position for each data structure, the starting positions each having an edge representing the same nucleotide residue or an insertion or deletion (paragraphs [0095]-[0097], [0110]-[011], and [0117]). Chin et al. teach starting at the starting positions, adding to the second DAG or the second FA an edge each time the transitions between successive nodes in each of the first data structures includes at least one overlapping nucleotide residue or an insertion or deletion, the added edge corresponding to the at least one overlapping nucleotide residue or an insertion or deletion (paragraphs [0054]-[0058], [0094], [0129]).
Regarding claim 24, Semenyuk teaches a system comprising a computer processor and a memory communicatively coupled to the computer processor, the memory storing data and instructions executable by the computer processor, the data and instructions comprising (paragraphs [0014]-[0015], [0074]-[0077]); a first routine operable to cause the computer processor to generate directed acyclic graphs (DAGs) or finite automatons (FAs) from protein mutation data (paragraphs [0120]-[0124], [0140]-[0142]);
However, Semenyuk does not teach a second routine operable to cause the computer processor to create overlap DAGs or FAs using as input a series of DAGs or FAs output by the first routine.
Chin et al. teach a second routine operable to cause the computer processor to create overlap DAGs or FAs using as input a series of DAGs or FAs output by the first routine (paragraphs [0015], [0092], [0106]-[0109], [0119]-[0122], [0129]); a third routine operable to cause the computer to evaluate an overlap DAG or FA to locate best paths through the DAG or FA and to alter edge weights according to specific criteria or stochastically before generating new best paths through DAG or FA (paragraphs [0131]-[0133] and [0157]-[0159]); and a fourth routine operable to cause the computer to score and optimize the best path according to non-local effects or higher-order interactions (paragraphs [0156]-[0158].
It would have been obvious to one of ordinary skill in the art, at the time of filing, to combine the references of Semenyuk and Chin et al. Semenyuk teaches a method of compressing genomic data (abstract). One of ordinary skill in the art would have been motivated to used Semenyuk’s compressed data in the method taught by Chin et al to reduce the amount of linear sequences required to encode a set of genetic elements. Furthermore, one of ordinary skill in the art would have had a reasonable expectation of success since the data of Semenyuk may be readily used in the system of Chin et al.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JERRY LIN whose telephone number is (571)272-2561. The examiner can normally be reached T-F 7am-5pm.
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/JERRY LIN/Primary Examiner, Art Unit 1685
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