DETAILED ACTION
Applicant’s response, filed 12 May 2026 has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 12 May 2026 has been entered.
Status of Claims
Claims 1, 7, and 16 are cancelled.
Claims 22-23 are newly added.
Claims 2-6, 8-15, and 17-23 are pending.
Claims 2-6, 8-15, and 17-23 are rejected.
Priority
Applicant’s claim for the benefit of a prior-filed application, U.S. Non-Provisional App. No. 16/799,823 and U.S. Provisional App. No. 62/810,338 under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Accordingly, the effective filing date of the claimed invention is 25 Feb. 2019.
Claim Rejections - 35 USC § 112(a)
The rejection of claims 2-6, 8-15, and 17-21 under 35 U.S.C. 112(a) in the Office action mailed 12 Dec. 2025 has been withdrawn in view of claim amendments received 12 May 2026.
Claim Rejections - 35 USC § 112(b)
The rejection of claim 21 under 35 U.S.C. 112(b) in the Office action mailed 12 Dec. 2025 has been withdrawn in view of claim amendments received 12 May 2026.
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.
Claim 23 is 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. This rejection is newly recited and necessitated by claim amendment.
Claim 23 recites “The method of claim 11…”. There is insufficient antecedent basis for “The method of claim 11”, because claim 11 recites “A system…” and not a method. For purpose of examination, claim 23 is interpreted to mean “The system of claim 11, wherein the…”.
Response to Arguments
Applicant's arguments filed 12 May 2026 regarding 35 U.S.C. 112(b) have been fully considered but they are not persuasive because they do not pertain to the new grounds of rejection set forth above.
Claim Rejections - 35 USC § 101
The rejection of claims 6 and 17 under 35 U.S.C. 101 in the Office action mailed 12 Dec. 2025 has been withdrawn in view of the cancellation of these claims received 12 May 2026.
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 2-6, 8-15, and 17-23 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. Any newly recited portion is necessitated by claim amendment.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claims 2 and 11 being representative) is directed to a method and system for determining oxygen availability in soil. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claims 2 and 11 recite the following steps which fall under the mathematical concepts and/or mental processes groupings of abstract ideas:
identifying/identify alignments between reference genes and the nucleic acid sequence reads;
determining/determine a set of measures of a plurality of metabolic pathways of microorganisms present in the soil sample by processing the alignments between the reference genes and the nucleic acid sequence reads;
determining/determine a plurality of soil health indicators using the set of measures of the plurality of metabolic pathways of microorganisms present in the soil sample, wherein each of the plurality of soil health indicators is associated with a different level of soil drainage at the geographic location;
determining/determine oxygen availability at the geographical location as a function of the plurality of soil health indicators; and
determining/determine an agricultural intervention for soil at the geographical location based on the oxygen availability.
The identified claim limitations falls into one of the groups of abstract ideas of mental processes for the following reasons. In this case, the step of identifying alignments between reference genes and reads can be practically performed in the mind by simply comparing sequences between reference genes and reads, similar to the claims to "comparing BRCA sequences and determining the existence of alterations," where the claims cover any way of comparing BRCA sequences such that the comparison steps can practically be performed in the human mind, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 763, 113 USPQ2d 1241, 1246 (Fed. Cir. 2014). The step of determining a set of measures using the aligned sequence reads amounts to a mere analysis of aligned read data, such as counting a number of reads aligned to particular genes to determine gene abundances, as described in Applicant’s specification at para. [0016] and [0021]. Furthermore, determining soil health indicators using the set of measures of metabolic pathways can be practically performed in the mind by analyzing the functions of the metabolic pathways. Similarly, determining oxygen available using the soil health indicators amounts to a mere analysis of data (e.g. analyzing soil health indicator groups to infer oxygen content), which can be practically performed in the mind. Last, determining an agricultural intervention using the oxygen availability involves determining if the soil needs more or less oxygen, and choosing an appropriate intervention that provides or reduces oxygen, respectively. That is, other than reciting these limitations are carried out by a processor in claim 11, nothing precludes the steps from being practically performed in the mind. Therefore, these limitations recite a mental process. See MPEP 2106.04(a)(2) III.
Furthermore, the limitation of determining oxygen availability as a function of the plurality of soil health indicators further recites a mathematical concept. The limitation amounts to a textual equivalent to performing mathematical calculations in light of Applicant’s specification at para. [0079]-[0081] which discloses the oxygen availability is calculated using weighted sums, averages, or ratio, and therefore, the limitation encompasses a mathematical calculation. See MPEP 2106.04(a)(2) I. C.
Claims 2 and 11 further recite a law of nature of a natural correlation between the expression of metabolic pathways in microorganisms of soil and oxygen availability in the soil. See MPEP 2106.04(b).
Dependent claims 3-6, 8-10, 12-15, 17-19, and 22-23 further recite an abstract idea and/or are part of the abstract idea of independent claims 2 and 11. Dependent claims 3-4 and 12-13 further limit the mental process of determining the set of measures for metabolic pathways to determine a first measure of aerobic respiration and a second measure of anaerobic respiration. Dependent claims 5 and 14 further limit the mental process of determining the plurality of soil health indicators to comprise determining a ratio, which additionally recites a mathematical concept. Dependent claims 6 and 15 further recite a mental process and mathematical concept of determining a weighted sum of gene counts. Dependent claims 7 and 16 further limit the mental process of determining soil health indicators to determine indicators associated with a different level of soil drainage at the geographical location. Dependent claims 8 and 17 further recite the mental process and mathematical concept of determining that oxygen availability is inversely related to soil clay content of the soil. Dependent claims 9 and 18 further limit the mental process of determining measures for metabolic pathways to be for metabolic pathways with a plurality of different electron acceptors. Dependent claims 10 and 19 further recite the mental process of determining the agricultural intervention to be one of the recited interventions. Dependent claims 22-23 further limit the abstract idea in claims 1 and 11 of determining a set of measures of metabolic pathways to be of aerobic respiration and anaerobic respiration. Therefore, claims 2-6, 8-15, and 17-23 recite an abstract idea and law of nature. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
Dependent claims 2-6, 8-10, 12-15, 17-19, and 22-23 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements of claims 1 and 11 include:
a sampling container for obtaining a soil sample from a geographical location (claim 11 only);
a sequencer for determining nucleic acid sequence reads… (claim 11 only);
one or more processors and a memory (i.e. a computer) (claim 11 only);
determining using a sequencer nucleic acid sequence reads of genetic material in a soil sample from a geographical location (claim 2 only);
receive the nucleic acid sequence reads of genetic material in the soil sample from the geographical location from the sequencer (claim 11 only);
providing/provide the agricultural intervention for presentation to a user (i.e. outputting data).
The additional elements of claims 20-21 include:
implementing the agricultural intervention, wherein the agricultural intervention includes one or more of: altered tillage, addition of mineral or organic materials, drainage ditches, tile drainage, and altered irrigation (claim 20); and
cause the one or more processors to cause the determined agricultural intervention to be implemented by providing a command to a device to treat the soil at the geographical location with a treatment loaded onto the device, wherein the agricultural intervention includes one or more of: addition of mineral or organic materials and altered irrigation (i.e. transmitting data) (claim 21).
The additional elements of a sampling container for obtaining soil, a sequencer for determining reads, and determining nucleic acid sequence reads of genetic material in a soil sample only serve to collect the data necessary for the abstract idea. Similarly, the additional element of providing the agricultural intervention for presentation only serves to output data generated by the abstract idea. Therefore, these additional elements amount to insignificant extra-solution activity that does not integrate the recited judicial exception into a practical application. See MPEP 2106.05(g).
Furthermore, regarding the additional elements of a processor, memory, and outputting/transmitting data, these are generic computer components and/or processes. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application. See MPEP 2106.05(f).
Last, the additional element of implementing the agricultural intervention including one or more of altered tillage, addition of mineral or organic materials, drainage ditches, tile drainage, and altered irrigation is not sufficient to integrate the recited judicial exception into a practical application because the limitation amounts to mere instructions to apply the judicial exception. MPEP 2106.05(f) explains the recitation of claim limitations that attempt to cover any solution to an identified problem with no restriction on how the result is accomplished and no description of the mechanism for accomplishing the result, does not integrate a judicial exception into a practical application or provide significantly more because this type of recitation is equivalent to the words "apply it". See Electric Power Group, LLC v. Alstom, S.A., 830 F.3d 1350, 1356, 119 USPQ2d 1739, 1743-44 (Fed. Cir. 2016); Intellectual Ventures I v. Symantec, 838 F.3d 1307, 1327, 120 USPQ2d 1353, 1366 (Fed. Cir. 2016); Internet Patents Corp. v. Active Network, Inc., 790 F.3d 1343, 1348, 115 USPQ2d 1414, 1417 (Fed. Cir. 2015). In the instant case, claim 1 broadly recites “…determining an agricultural intervention for soil…based on the oxygen availability”. However, the claims provide no details regarding how a particular agricultural intervention is determined based on particular oxygen availability, and instead encompasses applying agricultural interventions that, for example, increase oxygen availability even if the determined oxygen availability is higher than desired.
Therefore, the additionally recited elements amount to insignificant extra-solution activity, merely use a computer as a tool, and/or amount to mere instructions to apply an exception, and as such, the claims as a whole do no integrate the abstract idea into practical application. Thus, claims 2-6, 8-15, and 17-23 are directed to an abstract idea and law of nature. [Step 2A, Prong 2: NO]
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. See MPEP § 2106.05.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception for the following reasons.
First, dependent claims 2-6, 8-10, 12-15, 17-19, and 22-23 do not recite any elements in addition to the judicial exception, and thus cannot provide significantly more.
Regarding claims 2 and 11, the additional elements of a sequencer and sequencing genetic material to determine sequencing reads are well-understood, routine, and conventional. This position is supported by Applicant’s own specification, which at para. [0089] discloses a plurality of commercially available sequencing platforms that produce sequence reads.
Furthermore, the additional elements of a sampling container, one or more processors ,and sequencing genetic material of a soil sample are well-understood, routine, and conventional. This position is supported by Vestergaard et al. (Make big data smart- how to use metagenomics to understand soil quality, 2017, Biol Fertil Soils, 53, pg. 479 to 484; cited in IDS filed 25 Oct. 2022; previously cited). Vestergaard overviews guidelines for the experimental design of metagenomics surveys to characterize community function of soil microbiomes (pg. 479, col. 2, para. 2), including that the analysis of metagenomic datasets involves soil sampling, sequencing, and bioinformatics data analysis (Table 1). Vestergaard further discloses collecting soil samples into tubes (Figure 1), various sequencing technologies for sequencing the samples to obtain sequence reads (pg. 481, col. 1, para. 2 to pg. 482, col. 1, para. 2), and uploading the raw sequencing data to a server (Table 1), which requires the use of a computer containing a processor and memory.
Regarding claim 20, as discussed above, the additional element of implementing the agricultural intervention including one or more of altered tillage, addition of mineral or organic materials, drainage ditches, tile drainage, and altered irrigation is well-understood, routine, and conventional, as supported by Vestergaard. Vestergaard reviews guidelines for characterizing soil microbiomes as discussed above, and further explains that soil microbiomes change strongly in response to land management, like fertilization or tillage (pg. 480, col. 1, para. 1) and management-related properties like fertilization regiments, tillage, cropping sequence, plant protection measures, and plant biomass should be provided (pg. 480, col. 2, para. 1), demonstrating the conventionality of these agricultural interventions. Furthermore, the limitation amounts to mere instructions to apply the judicial exception, as discussed above. MPEP 2106.05(f) explains the recitation of claim limitations that attempt to cover any solution to an identified problem with no restriction on how the result is accomplished and no description of the mechanism for accomplishing the result, does not provide significantly more because this type of recitation is equivalent to the words "apply it". See Electric Power Group, LLC v. Alstom, S.A., 830 F.3d 1350, 1356, 119 USPQ2d 1739, 1743-44 (Fed. Cir. 2016); Intellectual Ventures I v. Symantec, 838 F.3d 1307, 1327, 120 USPQ2d 1353, 1366 (Fed. Cir. 2016); Internet Patents Corp. v. Active Network, Inc., 790 F.3d 1343, 1348, 115 USPQ2d 1414, 1417 (Fed. Cir. 2015).
Last, regarding the additional elements of a processor, memory, and outputting data, these are conventional computer components and/or processes. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit).
Therefore, 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]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea and natural correlation without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
Response to Arguments
Applicant's arguments filed 12 May 2026 regarding 35 U.S.C. 101 have been fully considered but they are not persuasive.
Applicant remarks the claims are directed to a technical real-world improvement in the field of determining oxygen availability in soil, and provides an improved method of determining oxygen availability as compared to previous methods because conventional approaches are focused on understanding what genes and organisms are present in soils using sequencing data, and in contrast, present claims 2 and 11 determine oxygen availability based on functional gene data that reflects the presence of genes for various respiration pathways, which provides a sophisticated and quantitative assessment of the balance between aerobic and anaerobic processes in soil (Applicant’s remarks at pg. 7, para. 4 to pg. 9, para. 1). Applicant further remarks limitations of previous methods is that soil analysis is based on abundance of specific, known and named genes and organisms, while claims 2 and 11 recite improvements by not relying on information that is currently known about the genes associated with specific organisms in soil and instead relying on the entire microbiome’s functional genetic potential for respiration (Applicant’s remarks at pg. 9, para. 2-3).
This argument is not persuasive. First, the argument is not commensurate with the claims because independent claims 2 and 11 do not require that the metabolic pathways for which a set of measures is determined are for aerobic and anaerobic respiration.
Regardless, it is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements, or by the additional element(s) in combination with the recited judicial exception. Furthermore, it is important to keep in mind that an improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology. See MPEP 2106.05(a).
In the instant case, the alleged improvement described by Applicant is solely provided by an improved analysis of genetic/sequencing information that analyzes genes of metabolic pathways (i.e. an improved abstract idea), which is not an improvement to technology. Furthermore, Applicant has not provided an explanation regarding how an additional element of the claims, either alone or in combination with the abstract idea, provide an improvement.
Applicant further remarks claims 2 and 11 provide direct, actionable agricultural interventions to a user utilizing the improved determination of oxygen availability, and thus the claims are directed to patent eligible subject matter (Applicant’s remarks at pg. 9, para. 4 to pg. 10, para. 2).
This argument is not persuasive. The additional element of providing an agricultural intervention (i.e. outputting data) (claim 2) and transmitting a command to a device to treat the soil (i.e. transmitting data) are not sufficient to provide integration because the limitation only uses computers in a conventional way to output data generated by the abstract idea. Furthermore, the additional element of implementing the agricultural intervention in claim 20 is not sufficient to integrate the recited judicial exception into a practical application because the limitation amounts to mere instructions to apply the judicial exception. The claims provide no details regarding how a particular agricultural intervention is determined based on particular oxygen availability, and instead encompasses applying agricultural interventions that, for example, increase oxygen availability even if the determined oxygen availability is higher than desired. See MPEP 2106.05(f).
Conclusion
No claims are allowed.
Claims 2-6, 8-15, and 17-23 are free of the prior art for the reasons discussed in the Office action mailed 21 May 2025.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAITLYN L MINCHELLA whose telephone number is (571)272-6485. The examiner can normally be reached 7:00 - 4:00 M-Th.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685
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