DETAILED ACTION
Status of the Claims
Claims 1-20 are currently pending and are the subject of this Office Action.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
Acknowledgment is made of applicant's claim for priority under 35 U.S.C. 119(e) to U.S. provisional application 63/229,385 filed on 08/04/2021. Receipt is acknowledged of papers submitted under 35 U.S.C. 119(e), which papers have been placed of record in the file.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 09/09/2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
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.
As per MPEP § 2106, the subject matter eligibility analysis begins at Step 1: Is the claim to a process, machine, manufacture, or composition of matter? Here, the claims are drawn to a process, so the answer is yes.
Next, Step 2A asks: Is the claim directed to a law of nature, a natural phenomenon (product of nature) or an abstract idea? Step 2A is a two prong inquiry, wherein Prong One asks does the claim recite an abstract idea, law of nature, or natural phenomenon?
In the present case, independent claim 1 recites a method comprising five steps, specifically, a step of “receiving measured activity from a first assay”, a step of “determining an estimate of activity percentages”, a step of “receiving a first reference”, a step of “receiving a second reference”, and a step of “identifying active compounds of the first assay” and therefore reasonably recites one or more of a mathematical calculation and/or a mental process, which have been identified as abstract idea(s), which are judicial exception(s). See MPEP § 2106.04(a). Independent claim 17 recites the same five steps of claim 1, but prepends a step of “synthesizing a compound of compounds”, wherein the compound is selected by the recites five steps. Independent claim 19 recites the same five steps of claim 1, but prepends a step of “conducting an experiment on a second assay” based on said five steps.
Regarding mathematical calculations, MPEP § 2106.04(a)(2)(I) states:
A claim that recites a mathematical calculation, when the claim is given its broadest reasonable interpretation in light of the specification, will be considered as falling within the "mathematical concepts" grouping. A mathematical calculation is a mathematical operation (such as multiplication) or an act of calculating using mathematical methods to determine a variable or number, e.g., performing an arithmetic operation such as exponentiation. There is no particular word or set of words that indicates a claim recites a mathematical calculation. That is, a claim does not have to recite the word "calculating" in order to be considered a mathematical calculation. For example, a step of "determining" a variable or number using mathematical methods or "performing" a mathematical operation may also be considered mathematical calculations when the broadest reasonable interpretation of the claim in light of the specification encompasses a mathematical calculation.
Regarding mental processes, MPEP § 2106.04(a)(2)(III) states:
The courts consider a mental process (thinking) that "can be performed in the human mind, or by a human using a pen and paper" to be an abstract idea. CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1372, 99 USPQ2d 1690, 1695 (Fed. Cir. 2011). As the Federal Circuit explained, "methods which can be performed mentally, or which are the equivalent of human mental work, are unpatentable abstract ideas the ‘basic tools of scientific and technological work’ that are open to all.’" 654 F.3d at 1371, 99 USPQ2d at 1694 (citing Gottschalk v. Benson, 409 U.S. 63, 175 USPQ 673 (1972)). See also Mayo Collaborative Servs. v. Prometheus Labs. Inc., 566 U.S. 66, 71, 101 USPQ2d 1961, 1965 (2012) ("‘[M]ental processes[] and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work’" (quoting Benson, 409 U.S. at 67, 175 USPQ at 675)); Parker v. Flook, 437 U.S. 584, 589, 198 USPQ 193, 197 (1978) (same).
Claims can recite a mental process even if they are claimed as being performed on a computer. The Supreme Court recognized this in Benson, determining that a mathematical algorithm for converting binary coded decimal to pure binary within a computer’s shift register was an abstract idea. The Court concluded that the algorithm could be performed purely mentally even though the claimed procedures "can be carried out in existing computers long in use, no new machinery being necessary." 409 U.S at 67, 175 USPQ at 675.
For independent claims 1, 17, and 19, the broadest reasonable interpretation of the step “determining an estimate of activity percentages” encompasses embodiments that include a mathematical calculation, namely, the estimation of activity percentages. This is consistent with the specification as well as claim 14 the latter reciting that “the estimate of the activity percentages of the compounds is based on steps comprising loading a set of measured activity percentages and reducing error between the set of measured activity percentages and the estimate of the activity percentages from the first assay”, which is reasonably a mathematical calculation.
Further, for independent claims 1, 17, and 19, the broadest reasonable interpretation of the step “identifying active compounds of the first assay based on the first reference, the second reference, the measured activity, and the estimate of activity percentages” encompasses embodiments that include a mental process, namely, a step of identifying or choosing a subset of compounds based on received information.
The same Guidance requires analysis of Prong Two, which is whether the claim recites additional elements that integrate the exception(s) into a practical application of that exception(s). See MPEP § 2106.04(d), which states that a claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, and MPEP § 2106.05(e), which states that other considerations for Step 2A Prong Two and Step 2B are the presence of “meaningful limitations”, which are limitations when they amount to significantly more than the judicial exception, or when they integrate a judicial exception into a practical application.
In the instant case, for claims 1, 17, and 19, additional steps include three steps of receiving or gathering information or data: a step of “receiving measured activity from a first assay”, a step of “receiving a first reference”, and a step of “receiving a second reference”. The first step of “receiving measured activity from a first assay” encompasses embodiments of simply gathering data previously collected. Similarly, claim 7 states that “the first reference and the second reference are based on a user input”, which is consistent with collecting information. Therefore, these “receiving” steps can reasonably be considered mere data gathering steps, which have been consistently identified by the courts are insignificant extra-solution activities that do not represent integrating the judicial exception(s) into a practical application, as required by prong Two of Step 2A. For detailed discussion of insignificant extra-solution activities and how they relate to subject matter eligibility analysis, please see MPEP § 2106.05(g).
Independent claim 17 recites an additional step of “synthesizing a compound of compounds”, wherein the compound to synthesize is selected based on the recited five steps. Although this is a physical step, effecting a transformation or reduction of a particular article to a different state or thing (see MPEP § 2106.05(c)), it amounts to simply appending well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, which does not integrate the judicial exception into a practical application, nor does it amount to significantly more than the judicial exception. See MPEP § 2106.05(I). Similarly, independent claim 19 recites “conducting an experiment on a second assay based on active compounds identified” in the aforementioned five steps, and fails at Prong Two of the analysis for the same reasons. Note that even when each of the independent claims are analyzed “as a whole”, there is no change in the analysis or conclusion.
Therefore, the claims must further be analyzed to identify additional elements to determine whether the claim as a whole amounts to significantly more than the judicial exception (i.e. Step 2B of the analysis).
Step 2B of the analysis asks: does the claim recite additional elements that amount to “significantly more” than the judicial exception(s)? This is often referred to as a search for an inventive concept and is detailed in MPEP § 2106.05.
In the present case, this analysis closely mirrors that of Prong Two, above, in considering the additional elements of the claims. As outlined above, independent claims 1, 17, and 19 each recite three steps of “receiving”, which were determined to be mere data gathering steps and thus can be considered as insignificant extra-solution activities that do not amount to “significantly more” than the judicial exceptions. Similarly, independent claim 17 recites an additional step of “synthesizing a compound of compounds” and independent claim 19 recites “conducting an experiment on a second assay” based on the aforementioned five steps. As was determined above, these additional elements each amount to simply appending well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, which does not amount to significantly more than the judicial exception(s).
Therefore, the claims are not patent eligible.
In some cases, limitations of dependent claims may result in a claimed invention that is patent eligible, and therefore must be thoroughly considered.
Claims 2-3 recite “preparing a second assay based on the active compounds of the first assay, wherein the second assay comprises second controls” and “conducting an experiment on the second assay”, respectively, however, these steps amount to simply appending well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception so as to essentially represent instructions to merely “apply” the judicial exceptions, which does not integrate the judicial exception into a practical application, nor do they amount to significantly more than the judicial exception(s).
Claim 4 recites “identifying active compounds of the second assay based on the first reference and the second reference, based on the measured activity of the experiment on the second assay”, which itself reasonably can be considered a mental process, being an abstract idea, and is a judicial exception. Therefore, it cannot transform claim 1 into patent eligible subject matter.
Remaining claims 5-16, 18, and 20 merely further define or limit the noise distribution, first and second references, estimation of activity percentages, and therefore cannot be considered as additional elements that integrate the judicial exceptions into practical applications, nor can they amount to “significantly more” than the judicial exceptions, and therefore are similarly patent ineligible.
For further information, please see the latest revision of MPEP § 2104-2106 {Patent Subject Matter Eligibility Under 35 U.S.C. 101}, including MPEP § 2106.04 {Eligibility Step 2A: Whether a Claim is Directed to a Judicial Exception} and 2106.05 {Eligibility Step 2B: Whether a Claim Amounts to Significantly More}, as well as any additional guidance on Subject Matter Eligibility, provided on the USPTO website at
https://www.uspto.gov/patent/laws-and-regulations/examination-policy/subject-matter-eligibility.
Claim Rejections – 35 U.S.C. 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 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.
Mpindi et al.
Claims 1-7 and 17-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Mpindi et al. (Bioinformatics, 2015, 31(23):3815-3821).
Regarding claims 1, 7, Mpindi discloses a method comprising:
receiving measured activity from a first assay, the first assay comprising wells containing compounds and first controls (e.g., positive and negative controls as per Fig. 1), wherein the measured activity is indicative of activation or inhibition by the compounds on a process (e.g., as per the 2.1 Datasets section on pp. 3816-3817);
determining an estimate of activity percentages of the compounds, wherein the estimate of the activity percentages of the compounds is based on a noise distribution and the noise distribution is based on the first controls (e.g., via inter- and intra-plate normalization as per the 2.4 Percent inhibition and 2.5 Within-plate normalization and corrections sections);
receiving a first reference based on a required activity percentage of compounds for the first assay (e.g., hit rates of 5-42% were entered as per the 3.2 Simulation of QC metrics under increasing hit rate section on pp. 3819-3820);
receiving a second reference based on a required accuracy percentage of the compounds identified as active according to the first reference (e.g., flagging single plates with prespecified Z’-factor and SSMD scores as per the right column of p. 3818); and
identifying active compounds of the first assay based on the first reference, the second reference, the measured activity, and the estimate of activity percentages (e.g., as per the 3.3 Application of B-score and Loess methods to real drug testing experimental data section on p. 3820).
Regarding claims 2-4, 17, and 19, Mpindi discloses selecting and repeating assays for resulting hits that fall in certain Z’-factor, B score, and hit rate cutoffs (e.g., as per the 3.3 Application of B-score and Loess methods to real drug testing experimental data section on p. 3820).
Regarding claims 5-6, 18, and 20, Mpindi discloses calculating a Z’-factor, which may be <0.5 (e.g., as per the 2.3 QC control section on p. 3817).
Claim Rejections – 35 U.S.C. 103(a)
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.
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.
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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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.
Mpindi et al. and Kim et al.
Claims 1-9 and 17-20 are rejected under 35 U.S.C. 103 as being unpatentable over Mpindi et al. (Bioinformatics, 2015, 31(23):3815-3821) in view of Kim et al. (RDE, 2015, http://dx.doi.org/10.5395/rde.2015.40.3.249).
Mpindi is relied on as above, however, the reference is silent as to the power relations to Type I and Type II error rate limitations, as set forth in claims 8-9.
Kim discloses use of Type I and Type II error rates in determining statistical power and significance of assay data collected as a means to distinguish from the null hypothesis (e.g., as per the Statistical significance level and the Statistical power section on p. 251).
It would have been prima facie obvious to a person of ordinary skill in the art prior to the effective filing date of the application to apply the analysis and application of Type I and Type II error rates as per Kim in the high-throughput plate assays of Mpindi. One of ordinary skill in the art would have been motivated to do so since this allows one to distinguish from the null hypothesis, as per Kim.
One of ordinary skill in the art would have had a reasonable expectation of success as of the application’s effective filing date in combining the teachings of the prior art references to arrive at the invention as presently claimed since such statistical analysis methods were commonly known, well documented, and easily accessible to the skilled artisan.
Mpindi et al. and Caraus et al.
Claims 1-7 and 10-20 are rejected under 35 U.S.C. 103 as being unpatentable over Mpindi et al. (Bioinformatics, 2015, 31(23):3815-3821) in view of Caraus et al. (Bioinformatics, 2017, 33(20):3258-3267).
Mpindi is relied on as above, however, the reference is silent as to the error assumption limitations, as set forth in claims 10-16.
Caraus discloses adjusting error assumptions associated with the required activity percentage as non-linear errors (e.g., as per the 2.2 Non-linear multiplicative bias elimination (NLMBE) section on p. 3260). Caraus further discloses using NLMBE as an efficient means to preprocess data based on true positive detection rates (e.g., as per the left column of p. 3262). Caraus concludes with a comprehensive bias correction protocol to remove both additive and multiplicative spatial bias, which can be assay- or plate-specific (e.g., as per the 2.5 General data correction protocol on p. 3261).
It would have been prima facie obvious to a person of ordinary skill in the art prior to the effective filing date of the application to apply the error correction and bias elimination methods of Caraus in the high-throughput assay data analysis of Mpindi. One of ordinary skill in the art would have been motivated to do so since Caraus teaches that “we showed that the discussed methods for removing multiplicative spatial bias and the introduced general data correction protocol are effective in detecting and cleaning experimental data generated by screening technologies” (e.g., as per the 4 Discussion section on p. 3266).
One of ordinary skill in the art would have had a reasonable expectation of success as of the application’s effective filing date in combining the teachings of the prior art references to arrive at the invention as presently claimed since Caraus notes that their presented methods and data correction protocol have been implemented in the AssayCorrector package, which is freely available on CRAN (e.g., as per the 4 Discussion section on p. 3266).
Conclusion
No claims are allowed.
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/JEREMY C FLINDERS/
Primary Examiner, Art Unit 1684