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 .
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 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.
Claim Status
Claims 1-20 are pending.
Claims 1-3, 5-6, 8-11, 13, 16-18, and 20 are objected to.
Claims 1-20 are rejected.
Priority
Applicant's claim for the benefit of a prior-filed application, PCT/CN2020/134810, filed Dec 9 2020, is acknowledged.
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d) to App. No. CN202010084107.4, filed Feb 10 2020. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55. Should the applicant desire to obtain the benefit of foreign priority under 35 USC 119(a)-(d), a certified English translation of the foreign priority application must be submitted. Failure to provide a certified translation may result in no benefit being accorded for the non-English application.
Accordingly, each of claims 1-20 are afforded the effective filing date of Feb 10 2020.
Information Disclosure Statement
The information disclosure statements (IDS) filed on Jul 15 2022 and Feb 10 2023 are in compliance with the provisions of 37 CFR 1.97 and have therefore been considered. Signed copies of the IDS documents are included with this Office Action.
Drawings
The drawings are objected to for the following informalities: in Fig. 3, the portion of the graph indicating “Area variance” and “Area difference before and after fitting” are represented with indistinguishable shadings. The figure should be corrected so that the different areas are able to be distinguished based on their shading.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The amendments to the specification submitted Apr 22 2022 are accepted.
Claim Objections
The claims are objected to for the following informalities:
The claims recite multiple limitations which include a plurality of steps. As set forth in 37 CFR 1.75, where a claim sets forth a plurality of steps, each step of the claim should be separated by a line indentation (see MPEP 608.01(i)). Such limitations include:
Claim 1: “step S4: extracting…, performing peak fitting…, and obtaining…”;
Claim 2: “step S12, positioning…, and applying…, decomposing…, identifying…, and identifying…”;
Claim 2: “step S14: finally selecting…, finding…, matching…, and only selecting…”;
Claim 2: “step S15: performing…, calculating…”; and
Claims 6, 11, 13, and 17: “step S136, determining… and in a case of no overlapping peaks, fitting…”.
In claim 2, the comma after S12 should be changed to a colon to maintain consistent claim formatting.
In claim 2, the “and” before “applying” on the first line of step S12 should be removed, and a comma and “and” should after the formula in step S12.
In claim 2, step S12, the colon after “where in the weight matrix convolution filter is” should be removed.
There should be a comma after the formula and equations recited in claims 2 and 8-9.
In claim 3, the comma at the end of the 1st limitation should be changed to a semicolon to maintain consistent claim formatting. Claim 10 is similarly objected to.
In claims 5, 16, 18, and 20, “step S42: recording following features” is not grammatically correct.
In claims 5, 16, 18, and 20, an “and” should be added at the end of limitation step S42, 6.
In claim 6, “steps of fitting a peak comprises” in lines 2-3 should be amended to recite “steps of fitting a peak comprise[[s]]”. Claims 11, 13, and 17 are similarly objected to.
In claim 6, step S133, the claim should be amended to recite “[[a]] the masked region” because the claim already recites “masking a region” in step S132.
In claim 6, the comma after “step S136” should be changed to a semicolon to maintain consistent claim formatting. Claims 11, 13, and 17 are similarly objected to.
Claim Interpretation
Contingent Claiming
In the interest of compact prosecution, the instant claims are examined to consider all claim limitations. However, the claims contain recitations of intended use and contingent claim language that affect the scope of the claims, as listed below. The courts have stated that claims must be given their broadest reasonable interpretation (BRI) consistent with the specification (see MPEP § 2111).
The instant claims include a recitation of contingent claim language.
With respect to contingent claiming, said contingencies as claimed require that the claims are interpreted as provided for in the MPEP at 2111.04 (II), wherein: “the broadest reasonable interpretation of a method (or process) claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met). For example, assume a method claim requires step A, if a first condition happens and step B if a second condition happens. If the claimed invention may be practiced without either the first or second condition happening, then neither step A or B is required by the broadest reasonable interpretation of the claim. If the claimed invention requires the first condition to occur, then the broadest reasonable interpretation of the claim requires step A. If the claimed invention requires both the first and second conditions to occur, then the broadest reasonable interpretation of the claim requires both steps A and B”.
In the instant claims, the following is a “contingent” recitation:
Claim 3 and 10: “selecting an optimal mass spectrum with the most anchor peaks from the plurality of mass spectra in a case where the plurality of mass spectra have different calibration coefficients”; and “summing an absolute intensity or a square intensity of a mass spectrum with an absolute intensity or a square intensity of another mass spectrum only in a case where a calibration coefficient of the mass spectrum and a calibration coefficient of the optimal spectrum meet a condition”. As these limitations are interpreted to be substeps of the step of “synthesizing the plurality of mass spectra by using a self-weighted average method” (see the below 35 USC 112(b) rejection), the entirety of claims 3 and 10 are interpreted to be contingent.
Claims 6, 11, 13, and 17: “step S136… in a case of no overlapping peaks, fitting a single Gaussian peak by Levenberg- Marquardt algorithm to find specified parameters to minimize a tuning function”.
With respect to the interpretations above, it is suggested that the claims be amended to recite alternative language so as to avoid interpretation of contingent claiming.
Claim Rejections - 35 USC § 112
35 U.S.C. 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1-20 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 1, step S1, recites “recalibrating a single mass spectrum, for each detection point of a sample, obtaining a plurality of mass spectra corresponding to different positions of the detection point, wherein each mass spectrum of the plurality of mass spectra is recalibrated by using a group of anchor peaks with an expected mass-to-charge ratio”. It is not clear whether the claim intends to recite the multiple steps of “recalibrating” and “obtaining” which are not related or which are intended to be related. Therefore, the relationship of the “single mass spectrum” which is being recalibrated with “each mass spectrum of the plurality of mass spectra” being recalibrated by using a group of anchor peaks is not clear. For compact examination, it is assumed that the claim intends that the single mass spectrum is referenced by “each mass spectrum of the plurality of mass spectra” and that the claim should be amended accordingly, perhaps such that recalibrating a single mass spectrum is performed by obtaining a plurality of mass spectra corresponding to different positions of the detection point. Claims 2-20 are rejected based on their dependence from claim 1.
Claim 2 recites the formula
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and the Bruker function
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. However, the claim does not describe what the various parameters of the formula and the function indicate. Therefore, the metes and bounds of the formula and the function are unclear. The rejection may be overcome by clarifying the descriptions of the parameters in the formula and function. Claims 6, 8-13 and 16-17 are rejected based on their dependency. It is further noted that the recited “Bruker function” is interpreted as requiring the recited form
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as it is not clear that a “Bruker function” is a well known term in the art that PHOSITA would recognize to imply any additional structure beyond the recited form.
Claim 2, step S14, recites “finally selecting an anchor peak, for a detected peak list, finding a cut-off signal-noise ratio, matching a peak in the detected peak list with a list of the reference peaks, and only selecting a peak whose mass is within a specific range of the candidate reference peak and whose signal-noise ratio is higher than the cut-off signal-noise ratio”. It is not clear whether the claim intends to recite the multiple steps of “recalibrating” and “obtaining” which are not related or which are intended to be related. For compact examination, it assumed that the steps of “finding a cut-off signal-noise ratio”, “matching a peak”, and “only selecting a peak” are intended to be substeps of “finally selecting an anchor peak”, which could be conveyed by adding a “by” after “finally selecting an anchor peak, for a detected peak list,” or similar. Claims 6, 8-13 and 16-17 are rejected based on their dependency.
Claim 2, step S15, recites “performing a recalibration operation”. However, the claim previously recites “wherein in the step S1, recalibrating the single mass spectrum comprises”. It is therefore not clear if the recalibration operation intends to refer to the same action of recalibrating the single mass spectrum comprises or if it requires the performance of a separate recalibration operation which is a substep of the recalibrating. For compact examination, it is assumed that the recalibration operation is intended to refer to the recalibrating recited earlier in the claim. The rejection may be overcome by clarifying the relationship between these limitations. Claims 6, 8-13 and 16-17 are rejected based on their dependency.
Claim 2, step S15, recites “performing a recalibration operation, calculating a calibration coefficient…”. It is not clear whether the claim intends to recite the multiple steps of “performing” and “calculating” which are not related or which are intended to be related. For compact examination, it assumed that the step of “calculating a calibration coefficient” is intended to be a substep of “performing a recalibration operation”, which could be conveyed by adding a “by” after “performing a recalibration operation”. Claims 6, 8-13 and 16-17 are rejected based on their dependency.
Claim 2, step S15, recites “wherein a mapping function between a mass spectrometer and mass-to-charge ratio is a Bruker function…”. First, the claims do not previously recite a mapping function. It is therefore not clear what action or limitation the wherein clause intends to further limit. For compact examination, it is assumed that the mapping function is a part of the nonlinear fitting method recited earlier in step S15. Second, it is not clear whether the claim intended to recite “a mass spectrometer” or “a mass spectrum” or similar, because a mass spectrometer is the instrument which generates the mass spectra data and it is not clear what is meant by mapping mass-to-charge ratio to such an instrument. For compact examination, it is assumed that the claim intended to recite a mass spectrum or similar. The rejection may be overcome by clarifying what the wherein clause intends to limit. Claims 6, 8-13 and 16-17 are rejected based on their dependency.
Claim 3 recites “synthesizing the plurality of mass spectra by using a self-weighted average method, selecting an optimal mass spectrum with the most anchor peaks from the plurality of mass spectra in a case where the plurality of mass spectra have different calibration coefficients; initializing a mass spectrum synthesized by performing the self-weighted average method on the plurality of mass spectra with the optimal mass spectrum; summing an absolute intensity or a square intensity of a mass spectrum with an absolute intensity or a square intensity of another mass spectrum only in a case where a calibration coefficient of the mass spectrum and a calibration coefficient of the optimal spectrum meet a condition”. It is not clear if the steps of “selecting an optimal mass spectrum”, “initializing a mass spectrum synthesized by performing the self-weighted average method” and “summing an absolute intensity or a square intensity” are substeps of performing the step of “synthesizing the plurality of mass spectra by using a self-weighted average method”, as one of the steps actually recites “initializing a mass spectrum synthesized by performing the self-weighted average method”, or if the steps are intended to be separate from “synthesizing the plurality of mass spectra by using a self-weighted average method”. For compact examination, it is assumed that the steps are intended to be substeps of “synthesizing the plurality of mass spectra by using a self-weighted average method”. The rejection may be overcome by clarifying the relationship between the limitations. Claim 10 is similarly rejected. Claims 7-19 are rejected based on their dependence from claims 3 and 10.
Claim 6, step S135, recites “masking a point, and further masking a point, having a signal-noise ratio… greater than a ratio given value and a noise greater than a noise given value”. It is not clear whether the claim requires two separate points to be masked, and if so, which point is being further limited by “having a signal-noise ratio… greater than a ratio given value and a noise greater than a noise given value”. For compact examination, it is assumed that just one point is required to be masked, and that the limitation regarding the signal-noise ratio and the noise further limits that one point. The rejection may be overcome by clarifying the relationship between the different terms in the limitation. Claims 11, 13, and 17 are similarly rejected. Claims 8-9 are rejected based on their dependency from claim 6.
Claim 9 recites “Hf is a fitting height above the baseline corresponding to a point Mf; a parameter Mf represents a fitting mass”. It is not clear that Mf is meant to represent two different types of data as there is only one occurrence of Mf in the equation of claim 9. For compact examination, it is assumed that Mf represents a fitting mass, as set forth in the specification at [0030]. The rejection may be overcome by clarifying the descriptions of the parameters in the equation.
Claim 9 recites the parameter mi in the equation but does not describe the parameter in the text. Therefore, the metes and bounds of the parameter and the equation are unclear. The rejection may be overcome by clarifying the scope of the parameter.
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more.
MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, the claims are directed to a method, i.e., a process, machine, or manufacture within the above 101 categories [Step 1: YES; See MPEP § 2106.03].
Step 2A, Prong One
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and mathematical concepts (in particular mathematical relationships and formulas) are as follows:
Independent claim 1: step S1, recalibrating a single mass spectrum, for each detection point of a sample, wherein each mass spectrum of the plurality of mass spectra is recalibrated by using a group of anchor peaks; with an expected mass-to-charge ratio;
step S2, synthesizing the plurality of mass spectra, wherein on a basis of the step S1, the plurality of mass spectra corresponding to the different positions of the detection point are synthesized into a unitary mass spectrum of the detection point;
step S3: performing wavelet filtering on the unitary mass spectrum of the detection point, on a basis of the step S2, to eliminate high-frequency noise and a baseline through a wavelet- based digital filter; and
step S4: extracting a peak feature value, performing peak fitting to obtain a fitted curve of the unitary mass spectrum of the detection point on a basis of the step S3, and obtaining a peak height, a peak width, a peak area, a mass offset, and a signal-noise ratio based on a-the fitted curve of the unitary mass spectrum of the detection point.
Dependent claims 2-20 recite further steps that limit the judicial exceptions in independent claim 1 and, as such, also are directed to those abstract ideas. For example, claim 2 further limits recalibrating the single mass spectrum to selecting reference peaks, positioning and fitting peaks, applying a weight matrix convolution filter, selecting an anchor peak, and performing the recalibration by calculating a calibration coefficient; claims 3 and 10 further limit synthesizing the plurality of mass spectra to being performed using a self-weighted average method; claims 4, 12, and 14 further limit performing wavelet filtering to obtain a filtered mass spectrum and then performing another round of recalibration; claims 5, 16, 18, and 20 further limit step S4 to fitting a peak and recording features of the peak; claims 6, 11, 13, and 17 further limit step S13 of claim 2 for fitting a peak; claims 7, 15, and 19 further limit the self-weighted average method of claim 3; claim 8 further limits step S131 of claim 6 for determining the expected line width to being determined by an equation; and claim 9 further limits the tuning function of step S136 of claim 6 to being determined by an equation.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation because the method only requires a user to manually obtain descriptions of a mass spectrum peak based on a fitted curve of a unitary mass spectrum. Without further detail as to the methodology involved in “recalibrating”, “synthesizing”, “performing wavelet filtering”, “extracting a peak feature value”, “performing peak fitting to obtain a fitted curve”, and “obtaining” different parameters of the fitted curve, under the BRI, one may simply, for example, use pen and paper to recalibrate the single mass spectrum using a group of anchor peaks, synthesize mass spectra into a unitary mass spectrum, perform wavelet filtering on the unitary mass spectrum, extract a peak feature value, perform peak fitting to obtain a fitted curve of the unitary mass spectrum, and obtain peak parameters from the fitted curve. These steps as described in the independent and dependent claims explicitly recite mathematical techniques and require mathematical techniques as the only supported embodiments, as is disclosed in the specification at: [0017-0039].
Therefore, claim 1 and those claims dependent therefrom recite an abstract idea [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong Two
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d).III).
Additional elements, Step 2A, Prong Two
With respect to the instant recitations, the claims recite the following additional elements:
Independent claim 1: obtaining a plurality of mass spectra corresponding to different positions of the detection point.
Considerations under Step 2A, Prong Two
With respect to Step 2A, Prong Two, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to data gathering, such as “obtaining” data as in claim 1, perform functions of collecting the data needed to carry out the judicial exceptions. Data gathering and outputting do not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Data gathering and outputting steps are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
The specification discloses advantages of the method at [0011], including extracting reliable feature values, ameliorating the limitation of the prior art and improving the accuracy of nucleotide detection, and improving the credibility of nucleic acid mass spectrum data acquisition, but does not provide a clear explanation for how the additional elements provide these improvements. Therefore, the additional elements do not clearly improve the functioning of a computer, or comprise an improvement to any other technical field. Further, the additional elements do not clearly affect a particular treatment; they do not clearly require or set forth a particular machine; they do not clearly effect a transformation of matter; nor do they clearly provide a nonconventional or unconventional step (MPEP2106.04(d)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exceptions [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B (MPEP 2106.05.A i-vi)
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, the courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer or a person when claimed in a merely generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(II)(i)). As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The data gathering steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, the instant claims are not drawn to eligible subject matter as they are directed to one or more judicial exceptions without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
(g)(1) during the course of an interference conducted under section 135 or section 291, another inventor involved therein establishes, to the extent permitted in section 104, that before such person’s invention thereof the invention was made by such other inventor and not abandoned, suppressed, or concealed, or (2) before such person’s invention thereof, the invention was made in this country by another inventor who had not abandoned, suppressed, or concealed it. In determining priority of invention under this subsection, there shall be considered not only the respective dates of conception and reduction to practice of the invention, but also the reasonable diligence of one who was first to conceive and last to reduce to practice, from a time prior to conception by the other.
A rejection on this statutory basis (35 U.S.C. 102(g) as in force on March 15, 2013) is appropriate in an application or patent that is examined under the first to file provisions of the AIA if it also contains or contained at any time (1) a claim to an invention having an effective filing date as defined in 35 U.S.C. 100(i) that is before March 16, 2013 or (2) a specific reference under 35 U.S.C. 120, 121, or 365(c) to any patent or application that contains or contained at any time such a claim.
Claims 1, 3, 7, 14-15, and 18-19 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by over Yang et al. (BMC Bioinformatics, 2009, 10(1):1-13; newly cited).
The prior art to Yang discloses a comparison of peak detection algorithms for mass spectrometry data analysis (title). Yang, indicated by the open circles, teaches the instant features, indicated by the closed circles, as follows. Instantly claimed elements which are considered to be equivalent to the prior art teachings are described in bold for all claims.
Claim 1 discloses a numerical processing method for a nucleic acid mass spectrum, comprising:
step S1, recalibrating a single mass spectrum, for each detection point of a sample, obtaining a plurality of mass spectra corresponding to different positions of the detection point, wherein each mass spectrum of the plurality of mass spectra is recalibrated by using a group of anchor peaks with an expected mass-to-charge ratio;
Yang teaches that a spectrum first undergoes a smoothing procedure (Figure 1), where the input spectrum is represented as m/z (i.e., mass to charge ratio) and an intensity vector (p. 4, col. 1, par. 1), and the moving smoothing filters are applied on a small set of consecutive data points around a central point, which is the output (p. 4, col. 1, par. 2 through p. 6, col. 2, par. 6). The surrounding points are considered to read on anchor peaks as instantly claimed because they are used to output, or recalibrate, the center point. As the data is comprised of mass spectrometry signals which have a mass-to-charge ratio, it is considered that the points in the examined subset of the array would have an expected mass-to-charge ratio as instantly claimed.
step S2, synthesizing the plurality of mass spectra, wherein on a basis of the step S1, the plurality of mass spectra corresponding to the different positions of the detection point are synthesized into a unitary mass spectrum of the detection point;
Yang teaches expressions for a spectrum after smoothing (p. 4, col. 1, par. 1), and representing the spectra graphically (Figure 3), where the expression and the representations are considered to read on a synthesized unitary mass spectrum of the detection point as instantly claimed.
step S3: performing wavelet filtering on the unitary mass spectrum of the detection point, on a basis of the step S2, to eliminate high-frequency noise and a baseline through a wavelet-based digital filter; and
Yang teaches that after smoothing, the data undergoes baseline correction to subtract the baseline from the signal (Figure 1; p. 6, col. 2, par. 7), which can include different continuous wavelet transform (CWT) (i.e., wavelet filtering) (p. 7, section B4). It is considered that such an operation of baseline correction would eliminate high-frequency noise and the baseline as instantly claimed as Yang teaches that CWT provided the best performance (p. 12, col. 1, par. 2).
step S4: extracting a peak feature value, performing peak fitting to obtain a fitted curve of the unitary mass spectrum of the detection point on a basis of the step S3, and obtaining a peak height, a peak width, a peak area, a mass offset, and a signal-noise ratio based on a-the fitted curve of the unitary mass spectrum of the detection point.
Yang teaches after baseline correction, peak picking is performed (Figure 1). Yang teaches peak finding criteria (p. 7, col. 2 through p. 8, col. 2, par. 5), where a model function to fit peaks is performed (p. 8, col. 2, par. 2-3), which reads on obtained a fitted curve of the unitary mass spectrum as instantly recited. Yang teaches that the criteria for finding peaks include a local maximum (i.e., peak height) (P4), a peak width (P8), a peak area (P5), a mass difference (i.e., mass difference) (P8), and a signal to noise ratio (P1).
Regarding claims 3, 7, 14-15, and 18-19, Yang teaches the method of claim 1 as described above. Claim 3 further adds contingent limitations to claim 1, as described in the above claim interpretation section. Because the limitations of claim 3, and all of the claims that depend therefrom, are contingent and are therefore not required to be performed, Yang is considered to teach claims 3, 7, 14-15, and 18-19.
Claim Rejections - 35 USC § 103
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Yang, as applied to claim 1 in the above 35 USC 102 rejection, and in view of the features of Yang.
Regarding claim 4, Yang teaches the method of claim 1 as described above. Claim 4 further adds performing wavelet filtering on the unitary mass spectrum of the detection point to eliminate the high-frequency noise and the baseline to obtain a filtered mass spectrum, and then performing another round of recalibration on the filtered mass spectrum and adjusting a mass-to-charge ratio value accordingly. Yang teaches does not teach performing another round of recalibration on the filtered mass spectrum and adjusting a mass-to-charge ratio value accordingly.
However, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to duplicate, in the course of routine experimentation and with a reasonable expectation of success, the performance of the recalibration after performing wavelet filtering because the duplication of a part of an invention has no patentable significance unless a new and unexpected result from the duplication is provided. It is considered that one of ordinary skill in the art would have found it obvious to perform the recalibration again for the predicted result of further smoothing the mass spectrum, as taught by Yang (Figure 1).
Conclusion
No claims are allowed.
Claims 2, 5-6, 8-13, 16-17, and 20 appear to be free of the prior art. Neither the closest prior art to Yang et al. (BMC Bioinformatics, 2009, 10(1):1-13; newly cited) nor any art identified in the indicated prior art searches appear to teach selecting a group of reference peaks with recited criteria and performing a weight matrix convolution filter with the filter in claim 2 or all of the recorded features of claims 5 and 20 as claimed.
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/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685