CTNF 17/948,834 CTNF 81817 Notice of Pre-AIA or AIA Status 07-03-aia AIA 15-10-aia The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. Claims 1-19 are the current claims hereby under examination. Claim Rejections - 35 USC § 112 07-30-02 AIA 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. The following is a quotation of 35 U.S.C. 112 (pre-AIA), second paragraph: The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention. Claim 16 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. The limitation “complexity score” appears to be vague and indefinite as it fails to inform a person of ordinary skill in the art of the metes and bounds of the term. The specification at paragraph [0531] describes an example embodiment such as it describes the complexity of a compound and may be computed using the Bertz/1-endrickson/ilhlenfeldt formula. However, this is not limiting as to what encompasses the term or how it is determined. Therefore, the metes and bounds of the term appear indeterminable. As such the limitation has been deemed as vague and indefinite. For examination purposes any parameter describing a molecule will be considered to read on a broad and reasonable interpretation of a “complexity score.” Claim Rejections - 35 USC § 101 07-04-01 AIA 07-04 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 1-19 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claimed invention is directed to a method and system for processing functional assay data to determine a satisfy a significance threshold without significantly more. Analysis of independent claims 1 : Step 1 of the subject matter eligibility test (see MPEP 2106.03). Claims 1 and 19 are directed to a method and instructions executed by the computer, which describes one or more of the four statutory categories of patentable subject matter, i.e., a process/machine. Therefore, further consideration is necessary. Step 2A of the subject matter eligibility test (see MPEP 2106.04). Prong One : Claim 1 recites an abstract idea. In particular, the claim recites the following: a. obtaining functional assay data for a plurality of compounds; b. calculating for each of the one or more functional assays a parameter; and c. determine which of the calculated parameters satisfy a significance threshold. These elements recited in claim 1 are drawn to an abstract idea since they involve a mental process that can be practically performed in the human mind including observation, evaluation, judgment, and opinion and using pen and paper and/or they involve mathematical concepts in the form of mathematical relationships, mathematical formulas or equations, and/or mathematical calculations. Step a involves the mental step of collecting functional assay data. Steps b and c of calculating parameter values and determining which parameters satisfy a significance threshold further involve the mental and/or mathematical steps of generating and comparing data. The identified abstract steps, recited at the high level of generality, do not suggest an undue level of complexity for a person with ordinary skill in the art to be practically performed in the human mind with the aid of pen and paper. Prong Two : Claim 1 does not recite additional elements that integrate the exception into a practical application. Therefore, the claims are “directed to” the abstract idea. There is no practical application because the abstract idea is not applied, relied on, or used in a meaningful way. The processing performed remains in the abstract realm, i.e., the result is not used for a treatment. No improvement to the technology is evident. Therefore, the additional elements, alone or in combination, do not integrate the abstract idea into a practical application. Step 2B of the subject matter eligibility test (see MPEP 2106.05). Claim 1 does not include additional elements. Therefore there are no additional elements that alone or in combination that are sufficient to amount to significantly more than the judicial exception (i.e., an inventive concept) for the same reasons as described above. In view of the above, there is nothing else recited in addition to the recognized JE that integrates the exception into a practical application and/or amounts to significantly more than the above-judicial exception (the abstract idea). Looking at the limitations as an ordered combination (that is, as a whole) adds nothing that is not already present when looking at the elements individually. There is no indication that the combination of elements improves the functioning of a computer, for example, or improves any other technology. There is no indication that the combination of elements permits automation of specific tasks that previously could not be automated. There is no indication that the combination of elements includes a particular solution to a computer-based problem or a particular way to achieve a desired computer-based outcome. Analysis of independent claim 19: Claim 19 has the same analysis as above, but with the addition of the method being carried out using instruction executed on a computer. Patenting abstract ideas cannot be circumvented by attempting to limit the use [the idea] to a particular technological environment. In the instant claims, the computer and/or instructions amount to mere instruction to implement an abstract idea. The hardware recited by the system claims do not offer a meaningful limitation beyond generally linking “the use of the method to a particular technological environment,’ that is, implementation via computers.” see Alice Corp v. CLS Bank Int’l 573 U.S. (2014). Analysis of the dependent claims: Claims 2-18 depend from the independent claims. The dependent claims merely further define the abstract idea by either reciting categories of calculations (e.g. regression analysis), the type of values parameters may have, the type of compounds for which the data is analyzed, or the type of functional assay data that is used in the analysis. Therefore, all the dependent claims appear directed to furthering the abstract idea for similar reasons and are not considered to integrate the JE into a practice application nor add significantly to the JE itself. Claim Rejections - 35 USC § 102 07-07-aia AIA 07-07 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 – 07-08-aia AIA (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. 07-15-aia AIA Claim(s) 1 and 17-18 is/are rejected under 35 U.S.C. 102 (a)(1) as being anticipated by Motulsky and Christopoulos (“Fitting Models to Biological Data using Linear and Nonlinear Regression” Published 2003, pages 1-351) . Motulsky et al. describe at the section “Fitting dose-response curves” starting at page 256 a number of dose response curves including data representing invitro experiments of applying a variety known concentrations of drugs across the same tissues or cell lines wherein a family of dose-response curves may be analyzed, see page 269. This reads on the first step of the method of obtaining a set of functional assay data for a plurality of pharmaceutical compounds. Motulsky et al. further describe throughout choosing and calculating parameter values that are appropriate for the modeling and analysis, e.g. page 16. Motulsky et al. describe at pages 50-57 calculating parameters using linear regression and a p-value threshold, which reads on the last step of determining which of the calculated values satisfy a significance threshold. As such Motulsky et al. teach claim 1. With regards to the method being implemented on a computer, Motulsky et al. describe wherein the steps described above are implemented using a variety of computer programs throughout the text, which reads on the use of a computer program and system as in claims 17-18. Motulsky et al. describe at pages 51-52 wherein linear regression is the right choice in some analysis, which reads on claims 2-3. Motulsky et al. describe wherein a p-value is used along with a p-value of 0.5 as a threshold in regression analysis at pages 55-57, which reads on claims 4-5. Motulsky et al. teach running dose response curve assay experiments using existing compounds at the section “Fitting dose-response curves” which reads on claim 6. Motulsky et al. describe testing radioligands in binding data assays which reads on claim 7 . Claim Rejections - 35 USC § 103 07-06 AIA 15-10-15 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. 07-20-aia AIA 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. 07-23-aia AIA 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. 07-22-aia AIA Claim (s) 10-11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Motulsky et al . as applied to claim 1 above and further in view of Weymouth-Wilson et al. (US P/N 2022/0073557) . Motulsky et al. teach claim 1 as described above. However, Motulsky et al. suggests but do not explicitly teach wherein the one or more functional assays are of a mitochondrial function assay as in claims 10-11. Motulsky et al. suggests this because they lay the basic ground work for what dose response curves are and how they can be analyzed using a variety of modeling. Motulsky et al. are not limited in the kinds of dose response curve data their modeling can be applied, thus suggesting the use of more than the dose response curve data they explicitly describe. Weymouth-Wilson et al. at the background describe drug discovery towards restoring mitochondria function. Weymouth-Wilson et al. at paragraphs [0635]-[0638] describe looking at dose response curves for mitochondrial function and using a similar Prism modeling as taught by Motulsky et al. to analyze the curve data. Therefore it would have been obvious to one of ordinary skill in the art at the time of the instant invention to have performed the analysis taught by Motulsky et al. on the dose response curve data generated by Weymouth-Wilson et al. This is because Weymouth-Wilson et al. using a Prism modeling on dose response curves demonstrates that the known technique was recognized as part of the ordinary capabilities of one of skill in the art. Therefore, using a similar modeling analysis as taught by Motulsky et al. on the mitochondrial function dose response curve data generated by Weymouth-Wilson et al. would be effectively substituting one known technique for another and the results of the substitution would have been predictable . 07-22-aia AIA Claim (s) 12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Motulsky et al . as applied to claim 1 above and further in view of Olszewski et al. (US P/N 2018/0298029) . Motulsky et al. teach claim 1 as described above. However, Motulsky et al. suggests but do not explicitly teach wherein the one or more functional assays are of a glycolysis assay as in claim 12. Motulsky et al. suggests this because they lay the basic ground work for what dose response curves are and how they can be analyzed using a variety of modeling. Motulsky et al. are not limited in the kinds of dose response curve data their modeling can be applied, thus suggesting the use of more than the dose response curve data they explicitly describe. Olszewski et al. describe at the abstract an invention directed towards analyzing drugs that modulate glucose uptake activity or activity related to glycolysis using dose response data . Olszewski et al. at Figs. 8A-8B glycolysis assay data and paragraph [0957] describe looking at dose response curves for glycolysis assay data. Therefore, it would have been obvious to one of ordinary skill in the art at the time of the instant invention to have performed the analysis taught by Motulsky et al. on the dose response curve data generated by Olszewski et al. This is because one of ordinary skill in the art could have applied the known technique as taught by Motulsky et al. to the alternative dose response curve data generated by Olszewski et al. and the results of the substitution would have been predictable. Therefore, using a similar modeling analysis as taught by Motulsky et al. on glycolysis assay dose response curve data generated by Olszewski et al. would be effectively substituting one known technique for another and the results of the substitution would have been predictable . 07-22-aia AIA Claim (s) 13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Motulsky et al . as applied to claim 2 above and further in view of Coy et al. (US P/N 8916517) . Motulsky et al. teach claim 2 as described above. However, Motulsky et al. suggests but do not explicitly teach wherein the one or more compounds are in the range greater than 500 g/mol as in claim 13. Motulsky et al. suggests this because they lay the basic ground work for what dose response curves are and how they can be analyzed using a variety of modeling. Motulsky et al. are not limited in the kinds of dose response curve data their modeling can be applied, thus suggesting the use of more than the dose response curve data they explicitly describe. Coy et al. describe at the background and Fig. 4 using dose response curve data or concentration response curve data from assays to show suitable radionuclides that can be used in treatment. Coy et al. at col. 18 lines 39-45 demonstrate finding compounds with molecular weights greater than 500 g/mol demonstrating molecular weight being useful for finding drugs in the treatment of cancer. Therefore, it would have been obvious to one of ordinary skill in the art at the time of the instant invention to have used data looking at molecular weight where compounds are greater than 500 g/mol as taught by Coy et al., whom demonstrates the usefulness for these compounds for treating cancer, in the analysis taught by Motulsky et al. on dose response curve data. This is because one of ordinary skill in the art would know that molecular weight data can be an important parameter when looking at concentration dose responses or dose response curve data. Additionally, Coy et al. demonstrate that compounds with molecular weights greater than 500 g/mol can be effective in a formulation for treating cancer. As such one of ordinary skill in the art would have been motivated to look at a variety of parameters when evaluating dose response curve data in the analysis for finding effective compounds for treatment. One of ordinary skill in the art could have pursued the known potential solutions with a reasonable expectation of success . 07-22-aia AIA Claim (s) 14 is/are rejected under 35 U.S.C. 103 as being unpatentable over Motulsky et al . as applied to claim 1 above and further in view of Mootha et al. (US P/N 2009/0143279) . Motulsky et al. teach claim 1 as described above. However, Motulsky et al. suggests but do not explicitly teach selecting compounds such that the range of hydrogen bond donor counts is greater than 5 as in claim 14. Motulsky et al. suggests this because they lay the basic ground work for what dose response curves are and how they can be analyzed using a variety of modeling. Motulsky et al. are not limited in the kinds of dose response curve data their modeling can be applied, thus suggesting the use of more than the dose response curve data they explicitly describe. Mootha et al. teach analyzing dose-response curve data for statins and other drugs and identifying structurally related molecules. Mootha et al. teach looking at features such as number of hydrogen bond donors. Mootha et al. is silent with regards to a threshold for the number. However, optimization of parameters is a routine practice that would be obvious for a person of ordinary skill in the art to employ. It would have been customary for an artisan of ordinary skill to determine the optimal donor bond number as a proper parameter in the analysis taught by Motulsky et al. Thus, absent some demonstration of unexpected results from the claimed parameters, the optimization of bond donor counts greater than 5 would have been obvious at the time of Applicant's invention . 07-22-aia AIA Claim (s) 15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Motulsky et al . as applied to claim 1 above and further in view of Errico et al. (US P/N 2011/0301193) . Motulsky et al. teach claim 1 as described above. However, Motulsky et al. suggests but do not explicitly teach selecting compounds such that the range of polar surface area is greater than 200 square angstroms per molecule as in claim 15. Motulsky et al. suggests this because they lay the basic ground work for what dose response curves are and how they can be analyzed using a variety of modeling. Motulsky et al. are not limited in the kinds of dose response curve data their modeling can be applied, thus suggesting the use of more than the dose response curve data they explicitly describe. Errico et al. teach a drug discovery method by analyzing dose-response curve data see paragraphs [0014] and [0026] and Fig. 4. Errico et al. teach looking at parameters such as polar surface area. Errico et al. is silent with regards to a threshold for the number. However, optimization of parameters is a routine practice that would be obvious for a person of ordinary skill in the art to employ. It would have been customary for an artisan of ordinary skill to determine the optimal polar surface area threshold as a proper parameter in the analysis taught by Motulsky et al. Thus, absent some demonstration of unexpected results from the claimed parameters, the optimization of a PSA greater than 200 sq. angstroms would have been obvious at the time of Applicant's invention. Conclusion No claim is allowed Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jason Sims, whose telephone number is (571)-272-7540. If attempts to reach the Examiner by telephone are unsuccessful, the Examiner’s supervisor, Jonathan Moffat can be reached via telephone (571)-272-4390. Papers related to this application may be submitted to Technical Center 1600 by facsimile transmission. Papers should be faxed to Technical Center 1600 via the Central PTO Fax Center. The faxing of such papers must conform with the notices published in the Official Gazette, 1096 OG 30 (November 15, 1988), 1156 OG 61 (November 16, 1993), and 1157 OG 94 (December 28, 1993) (See 37 CFR § 1.6(d)). The Central PTO Fax Center number is (571)-273-8300. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). /JASON M SIMS/Supervisory Patent Examiner, Art Unit 3791 Application/Control Number: 17/948,834 Page 2 Art Unit: 3791 Application/Control Number: 17/948,834 Page 3 Art Unit: 3791 Application/Control Number: 17/948,834 Page 4 Art Unit: 3791 Application/Control Number: 17/948,834 Page 5 Art Unit: 3791 Application/Control Number: 17/948,834 Page 6 Art Unit: 3791 Application/Control Number: 17/948,834 Page 7 Art Unit: 3791 Application/Control Number: 17/948,834 Page 8 Art Unit: 3791 Application/Control Number: 17/948,834 Page 9 Art Unit: 3791 Application/Control Number: 17/948,834 Page 10 Art Unit: 3791 Application/Control Number: 17/948,834 Page 11 Art Unit: 3791 Application/Control Number: 17/948,834 Page 12 Art Unit: 3791 Application/Control Number: 17/948,834 Page 13 Art Unit: 3791 Application/Control Number: 17/948,834 Page 14 Art Unit: 3791