DETAILED ACTION
Applicant’s response, filed 21 Nov. 2025 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 .
Status of Claims
Claim 1 is cancelled.
Claims 20-21 are newly added.
Claims 2-21 are pending.
Claims 2-21 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 following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
Claims 2-6, 8-15, and 17-21 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, at the time the application was filed, had possession of the claimed invention. Any newly recited portion is necessitated by claim amendment.
Claims 2 and 11, and dependent claims 3-6, 8-10, 12-15, and 17-21, recite “…determining/determine a plurality of soil health indicators using the set of measures of the plurality of metabolic pathways of microorganisms; determining/determine oxygen availability at the geographical location as a function of the plurality of soil health indicators”, and encompasses determining oxygen availability using any set of soil health indicators determined from any measures of metabolic pathways. Under certain circumstances, omission of a limitation can raise an issue regarding whether the inventor had possession of a broader, more generic invention. See, e.g., PIN/NIP, Inc. v. Platte Chem. Co., 304 F.3d 1235, 1248, 64 USPQ2d 1344, 1353 (Fed. Cir. 2002). Furthermore, the Federal Circuit has explained that a specification cannot always support expansive claim language and satisfy the requirements of 35 U.S.C. 112 "merely by clearly describing one embodiment of the thing claimed." LizardTech v. Earth Resource Mapping, Inc., 424 F.3d 1336, 1346, 76 USPQ2d 1731, 1733 (Fed. Cir. 2005). See MPEP 2163 I. B.
In the instant case, Applicant’s specification at para. [0012], [0078]-[0082],[0128], and FIG. 6 disclose the embodiment relating to determining an oxygen availability in the soil sample. Applicant’s specification at para. [0079] discloses the presence of oxygen in the soil are determined from pathways of aerobic respiration and anaerobic metabolism including denitrification, iron reduction, sulfate reduction, and methanogenesis, and provides a list of aerobic or anaerobic pathways in Tables 4 and 8 that can be used to determine specific soil health indicators that are then used to determine oxygen availability. Therefore, the only embodiment described in the specification utilizes metabolic pathways of aerobic respiration and anaerobic metabolism to determine particular soil health indicators associated with soil drainage, aerobic respiration, and anaerobic respiration, which are then used to determine oxygen availability.
Similarly, the originally filed claim, requires that the soil health indicators are selected from soil health indicators associated with different levels of soil drainage (as depicted in Table 4), but does not provide support for the broader invention of using any soil health indicators to determine oxygen availability. Therefore, overall, Applicant’s specification, including the originally filed claim, does not provide support for the broader invention that determines oxygen availability from any set of soil health indicators determined from any set of metabolic pathways, as claimed. Furthermore, after a search of the prior art, such soil health indicators determined from metabolic pathways that are then used to predict oxygen availability are not generally known to one of ordinary skill in the art.
For the reasons discussed above, the specification does not provide a sufficient disclosure of the limitations of claims 2 and 11, and dependent claims 3-6, 8-15, and 17-21, noted above to demonstrate to one of ordinary skill in the art that the inventor possessed the invention at the time the application was filed. This is a new matter rejection and aa written description rejection. For more information regarding the written description requirement, see MPEP §2161.01- §2163.07(b). It is noted claims 7 and 16 are not rejected because they require the set of measures of metabolic pathways include a first and second measure of aerobic respiration and anaerobic respiration, respectively, and that the soil health indicators relate to soil drainage.
Response to Arguments
Applicant's arguments filed 21 Nov. 2025 regarding 35 U.S.C. 112(a) have been fully considered but they are not persuasive.
Applicant remarks the example of soil drainage referred to in [0078] is only exemplary and not restrictive, and para. [0078] also explicitly refers to improving soil structure as an intervention that can impact oxygen availability, and further remarks that one of ordinary skill in the art would understand that different factors can impact oxygen availability in the soil, including soil texture, soil structure, soil compaction, and water content (Applicant’s remarks at pg. 7, para. 2 to pg. 8, para. 1).
This argument is not persuasive. First, para. [0078] mention of “improving soil structure as an intervention” is referring to “potential agricultural interventions including altered tillage, addition of mineral or organic materials to improve soil structure and drainage, or engineering solutions like drainage ditches…”, which merely describes agricultural interventions of the soil for the treatment of “soils [that] are poorly drained” (see para. [0079]). This does not provide support for other soil health indicators specifically being used in a function to determine oxygen availability in the soil.
Regarding, Applicant’s argument that one of ordinary skill in the art would understand that different factors can impact oxygen availability, the specification must describe the claimed invention in a manner understandable to a person of ordinary skill in the art in a way that shows that the inventor actually invented the claimed invention at the time of filing. Id.; Ariad, 598 F.3d at 1351, 94 USPQ2d at 1172. generic claim language in the original disclosure does not satisfy the written description requirement if it fails to support the scope of the genus claimed. Ariad, 598 F.3d at 1349-50, 94 USPQ2d at 1171 ("[A]n adequate written description of a claimed genus requires more than a generic statement of an invention’s boundaries.") (citing Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1405-06). Simply because one of ordinary skill in the art might understood that certain factors impact oxygen availability, this does not explain how these soil health indicators are determined using measures of metabolic pathways of microorganisms and furthermore how essentially any soil health indicator can be combined in a function to determine oxygen availability as claimed.
Applicant remarks that the specification at para. [0079] discloses oxygen availability soil health indicators “may represent the prevalence of oxygen in the soil, as reflected by the presence of genetic elements involved various microbial respiration pathways”, and thus the specification discloses assessment of the level of oxygen present in the soil directly by examination of such soil health indicators without the need to consider soil drainage specifically (Applicant’s remarks at pg. 8, para. 2).
This argument is not persuasive. Applicant’s specification at para. [0079] does broadly discloses that oxygen soil health indicators may represent oxygen prevalence in soil, and are determined from genetic elements in microbial respiration pathways. However, as explained in the above and previous rejection, the Federal Circuit has explained that a specification cannot always support expansive claim language and satisfy the requirements of 35 U.S.C. 112 "merely by clearly describing one embodiment of the thing claimed." LizardTech v. Earth Resource Mapping, Inc., 424 F.3d 1336, 1346, 76 USPQ2d 1731, 1733 (Fed. Cir. 2005). See MPEP 2163 I. B. MPEP 2163 further explains the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice (see i)(A) above), reduction to drawings (see i)(B) above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the inventor was in possession of the claimed genus (see i)(C) above).
In the instant case, Applicant’s specification at para. [0080] provides a specific list of aerobic or anaerobic pathways in Tables 4 and 8 that can be used to determine specific soil health indicators that are then used to determine oxygen availability. This does not provide support for the broader genus of determining any soil health indicators using any measures of metabolic pathways, and then using any soil health indicators in some combination to determine oxygen availability.
Applicant remarks that Table 4 at para. [0082] of the specification lists example categories used in soil health indicators for agricultural oxygen availability, and while SHI level 3 relates to soil drainage, SHI levels 1 and 2 directly relate to the presence of aerobic (indicative of high oxygen levels) or anaerobic indicators (indicative of low oxygen levels), and additional Table 8 lists genes, gene identifiers, and metabolic pathways and classes used for soil health indicators for agricultural oxygen cycling, and none of these genes indicate a dependence on soil drainage (Applicant’s remarks at pg. 8, para. 3-4).
This argument is not persuasive. As discussed above, the claims involve determining any soil health indicators based on any measures of metabolic pathways, which are then used to determine oxygen availability. Regardless of whether all soil health indicators relate to soil drainage specifically, Applicant’s specification still only discloses a particular set of soil health indicators that can be used in predicting oxygen availability, as discussed above. Furthermore, after a search of the prior art, such soil health indicators determined from metabolic pathways that are then used to predict oxygen availability are not generally known to one of ordinary skill in the art.
Last, while Applicant mentions Table 8, this table describes metabolic pathways that can be used for determining the soil health indicators for oxygen availability. However, this does not describe how these metabolic pathways are combined to determine soil health indicators outside of what is presented in Table 4 of Applicant’s specification, which only relate to aerobic respiration, anaerobic respiration, and soil drainage.
Applicant remarks the use of categories and genes and pathways listed in Tables 4 and 8 Is not restricted to a determination of drainage related soil health indicators specifically, and the person skilled in the art would understand that the determination of soil health indicators is directly reflective of the level of oxygen in the soil, and there could be a number of different potential factors that impact oxygen level, and the person skilled in the art would have understood from the specification that the inventor was in possession of the invention defined by the claims (Applicant’s remarks at pg. 8, para. 5).
This argument is not persuasive. What is conventional or well known to one of ordinary skill in the art need not be disclosed in detail. See Hybritech Inc. v. Monoclonal Antibodies, Inc., 802 F.2d at 1384, 231 USPQ at 94. See also Capon v. Eshhar, 418 F.3d 1349, 1357, 76 USPQ2d 1078, 1085 (Fed. Cir. 2005). However, while there may be various different factors that impact oxygen level, as discussed previously and above, after a search of the prior art, such soil health indicators determined from metabolic pathways that are then used to predict oxygen availability are not generally known to one of ordinary skill in the art. The only description of metabolic pathways used in determining soil health indicators are those presented in Tables 4 and 8 as discussed in the above rejection. Applicant’s specification provides zero guidance on how one of ordinary skill in the art could determine any soil health indicator used in determining oxygen availability based on any measure of a metabolic pathway as presently claimed.
Claim Rejections - 35 USC § 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.
Claim 21 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 21 recites “…wherein the computer program instructions…cause the one or more processors to cause the determined agricultural intervention to be implemented, wherein the agricultural intervention includes one or more of: addition of mineral or organic materials and altered irrigation”. It is unclear in what way the processor is intended to cause addition of physical materials or to alter irrigation. For example, it is unclear if the instructions are required to only instruct a processor to transmit instructions for causing the agricultural intervention to be implemented or if the claim actually intends for instructions to cause the processor to physically implement the agricultural intervention. Given, Applicant’s specification does not appear to provide support for the latter, the limitation is interpreted to mean the processor transmits information for causing the agricultural intervention to be implemented (i.e. outputting instructions to implement the intervention).
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 2-21 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 1 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;
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 3-10 and 12-19 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. Therefore, claims 2-21 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 2-10 and 12-19 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, wherein the agricultural intervention includes one or more of: addition of mineral or organic materials and altered irrigation (i.e. transmitting data- see 112(b) interpretation above) (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 2-21 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 2-10 and 12-19 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 21 Nov. 2025 regarding 35 U.S.C. 101 have been fully considered but they are not persuasive.
Applicant remarks claim 2 has been amended to clarify that the sequence reads are carried out by a sequencer which cannot be performed in the mind, and claim 11 also recites a sequencer (Applicant’s remarks at pg. 8, para. 6 to pg. 9, para. 1).
Applicant’s remark is acknowledged. However, it is noted that the step of determining sequence reads of genetic material in a soil sample and a sequencer, as recited in claims 2 and 11 were already treated as additional elements (not part of the judicial exception) and the previous rejection and again above.
Applicant remarks the human mind is not practically capable of identifying alignments between genes and reads because gene information is contained in extensive databases such as KEGG, UniProt, etc. (Applicant’s remarks at pg. 9, para. 2).
This argument is not persuasive. As discussed in the above rejection, 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 instant claims cover any way of aligning, such as simply by comparing two sequences, and do not required using any particular databases, which encompass a mental process.
Applicant remarks that the claims are to be considered in Step 2A, Prong 2 as a whole, and the claims do not merely recite the abstract determining of an agricultural intervention by any means, but instead, when properly considered as a whole, the claims require a specific apparatus (a sequencer) be used to determine reads and that alignments are used to obtain the set of measures, and further remarks there are other means to process information from soil, but the claims are drafted with specific technical details involving analysis of functional genes to provide a practical agricultural intervention such that they are integrate into a practical application (Applicant’s remarks at pg. 9, para. 4 to pg. 10, para. 2).
This argument is not persuasive. While the claims are considered as a whole under Step 2A, prong 2, Prong Two asks does the claim recite additional elements that integrate the judicial exception into a practical application. See MPEP 2106.04 II. As discussed in the above rejection, the additional elements relating to determining sequence reads by sequencing only serve to collect data for use by the abstract idea, which does not integrate the recited judicial exception into a practical application. See MPEP 2106.05(g). Furthermore, simply because there might be other ways to assay genetic information in soil other than by sequencing, does not mean the limitation cannot amount to necessary data gathering. For example, See MPEP 2106.05(h), explaining that a data gathering step that is limited to a particular data source (such as the Internet) or a particular type of data (such as power grid data or XML tags) could be considered to be both insignificant extra-solution activity and a field of use limitation. See, e.g., Ultramercial, 772 F.3d at 716, 112 USPQ2d at 1755.
Last, regarding the additional element of providing an agricultural intervention (i.e. outputting data) or implementing the agricultural intervention (claim 2) are not sufficient to provide integration because the limitation only uses computers in a conventional way to output data generated by the abstract idea and amounts to mere instructions to apply the judicial exception for the reasons explained in the above rejection. See MPEP 2106.05(f). Therefore, when considering the claims as a whole, the claim does not recite additional elements that integrate the judicial exception into a practical application.
Applicant remarks the ordered combination of steps cannot be dismissed as conventional activity when properly considering the claims as a whole because the claims use a computer in a novel way to determine a measure of metabolic pathways and ultimately determine oxygen availability, and further remarks that because the Office notes the claims are free of the prior art, this affirms the claimed approach is novel and inventive, and thus is eligible (Applicant’s remarks at pg. 10, para. 3).
This argument is not persuasive. Lack of novelty under 35 U.S.C. 102 or obviousness under 35 U.S.C. 103 of a claimed invention does not necessarily indicate that additional elements are well-understood, routine, conventional elements. Because they are separate and distinct requirements from eligibility, patentability of the claimed invention under 35 U.S.C. 102 and 103 with respect to the prior art is neither required for, nor a guarantee of, patent eligibility under 35 U.S.C. 101. See MPEP 2106.05 I.
Under Step 2B, the conventionality of additional elements are evaluated. However, whether the abstract idea is conventional is not considered. Therefore, while the claims are free of the prior art due to a novel abstract idea (i.e. the analysis of the sequence reads to determine oxygen availability), the additional elements in the claim are well-understood, routine, and conventional, as discussed in the above rejection.
Applicant further remarks the claimed subject matter amounts to significantly more because the claimed invention provides an improvement in the technical field of metagenomics by providing a novel framework for determining soil health indicators derived using measures of metabolic pathways, and thus the claims as a whole amount to significantly more than the judicial exception and the claims provide a novel way to evaluate genetic material from a soil sample to provide an agricultural intervention that can be applied (Applicant’s remarks at pg. 10, para. 4 to pg. 11, para. 1).
This argument is not persuasive. MPEP 2106.05(a) states the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements. See the discussion of Diamond v. Diehr, 450 U.S. 175, 187 and 191-92, 209 USPQ 1, 10 (1981)) in subsection II, below. In addition, the improvement can be provided 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. In the instant case, the alleged improvement in determining soil health indicators using measures of pathways is part of the abstract idea, and thus reflects an improved abstract idea rather than an improvement to technology.
Then under Step 2B, examiners Carry over their identification of the additional element(s) in the claim from Step 2A Prong Two; and Carry over their conclusions from Step 2A Prong Two on the considerations discussed in MPEP §§ 2106.05(a) - (c), (e) (f) and (h). Therefore, the above conclusion under Step 2A, Prong 2 regarding improvements in MPEP 2106.05(a) carries over to Step 2B.
Applicant remarks the claimed method and system begin with a physical soil sample and transforms the content of the physical sample into a structured sequence read data set, which are further transformed by a multi-step process into a new and useful form, specifically an agricultural intervention that represents a concrete recommendation, which is a clear path of a transformation of a physical sample that represents an important technological advance in determining the impact of the microbiome in soil on crop yield (Applicant’s remarks at pg. 11, para. 3 to pg. 12, para. 1).
This argument is not persuasive. Regarding Applicant’s argument regarding the transformation of the physical sample into a read data set and then to an agricultural intervention, MPEP 2106.05(c) states changing to a different state or thing usually means more than simply using an article or changing the location of an article, and further explains purely mental processes in which thoughts or human based actions are "changed" are not considered an eligible transformation. For data, mere "manipulation of basic mathematical constructs [i.e.,] the paradigmatic ‘abstract idea,’" has not been deemed a transformation. CyberSource v. Retail Decisions, 654 F.3d 1366, 1372 n.2, 99 USPQ2d 1690, 1695 n.2 (Fed. Cir. 2011) (quoting In re Warmerdam, 33 F.3d 1354, 1355, 1360, 31 USPQ2d 1754, 1755, 1759 (Fed. Cir. 1994)). Here, the sequencing step only serves to collect data for use by the abstract idea to generate sequencing reads, and then the “transformation” of a sequence read data set to an identified agricultural intervention is merely a transformation/analysis of data, which is not a transformation of an “article” including a physical object to a different state or thing.
Regarding Applicant’s argument of a “technological advance” in determining the impact of the microbiome in soil on crop yield, the claims do not recite additional elements that integrate the judicial exception into the practical application of an improvement to technology for the reasons already discussed above.
Applicant remarks that claims 20 and 21 are eligible for the same reasons as claims 2 and 11, and furthermore because they recite the identification of alignments between reference genes and reads and thus are also independently eligible (Applicant’s remarks at pg. 12, para. 2).
This argument is not persuasive for the same reasons discussed above for claims 2 and 11. It is further noted claims 20-21 did not add a limitation regarding the alignment, which was instead added to the independent claims. However, this limitation is part of the abstract idea as discussed above, and therefore cannot provide integration of itself into a practical application, or provide significantly more.
Conclusion
No claims are allowed.
Claims 2-21 are free of the prior art for the reasons discussed in the Office action mailed 21 May 2025.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685