DETAILED ACTION
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 Mar 31 2026 has been entered.
Applicant’s response, filed Mar 31 2026, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. 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 .
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Claim Status
Claims 47-54, 57, and 60-68 are pending.
Claims 1-46, 55-56, and 58-59 are canceled.
Claims 47-53 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, as set forth in the Office Action mailed Apr 17 2025.
Claims 54, 57, and 60-68 are under examination.
Claims 54, 57, and 60-68 are rejected.
Priority
This application is a CON of 15807498 filed Nov 8 2017 (now USP 11,015,154), which claims priority to US provisional applications 62419898, filed Nov 9, 2016, and 62466613, filed Mar 3 2017.
Accordingly, each of claims 54, 57, and 59-68 are afforded the effective filing date of Nov 9, 2016.
Claim Rejections - 35 USC § 112
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 61-68 are 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 rejection is newly stated based upon further consideration of the claims.
Claim 61 recites “wherein the plurality of cultivated dilutions is cultivated from a subset of a plurality of dilutions of a sample in a first cultivation condition”. However, the claim only previously recites “receive taxonomic information of taxa in a plurality of cultivated dilutions”. It is unclear whether the wherein clause is intended to require cultivating the plurality of cultivated dilutions within the metes and bounds of the claimed invention, or if it is only further limiting the type of data used in the invention such that cultivating is not required within the metes and bounds of the invention. As set forth in MPEP 2111.04.I, “wherein” clauses raise the question as to the limiting effect of the language in a claim. As the claims do not recite an active performance of the cultivation, the metes and bounds of the claims are unclear. For compact examination, it is assumed that the determining the abundances is not required to be performed, especially as the limitation is recited as part of the instructions performed by a computer processor. The rejection may be overcome by clarifying what steps are required to be performed. Claims 62-68 are rejected based on their dependency from claim 61.
Claim 67 recites “wherein the abundances of the taxa in the plurality of cultivated dilutions are determined based on a threshold”. However, claim 61 only previously recites “receive taxonomic information… wherein the taxonomic information comprises abundances”. It is unclear whether the wherein clause is intended to require determining the abundances within the metes and bounds of the claimed invention, or if it is only further limiting the type of data used in the invention such that determining the abundances is not required within the metes and bounds of the invention. As set forth in MPEP 2111.04.I, “wherein” clauses raise the question as to the limiting effect of the language in a claim. As the claims do not recite an active performance of the determination, the metes and bounds of the claims are unclear. For compact examination, it is assumed that the determining the abundances is not required to be performed. The rejection may be overcome by clarifying what steps are required to be performed.
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 54, 57, and 60-68 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 portions are necessitated by claim amendment.
MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, the claims are directed to computer systems, i.e., a process, machine, or manufacture within the above 101 categories [Step 1: YES; See MPEP § 2106.03].
Step 2A, Prong One
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
The claims also recite a law of nature or a natural phenomenon. The MPEP at 2106.04(b) further explains that laws of nature and natural phenomena include naturally occurring principles/relations and nature-based products that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature.
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and mathematical concepts (in particular mathematical relationships and formulas) as well as a law of nature or a natural phenomenon are as follows:
Independent claim 54: quantify an abundance of each of the plurality of strings indexed by the first parameter and the second parameter to generate a plurality of string counts, each string count corresponding to an output, wherein the plurality of string counts comprises a string count of strings of the plurality of strings corresponding to the first taxon and indexed by the first dilution, a string count of strings of the plurality of strings corresponding to the second taxon and indexed by the first dilution, and a string count of strings of the plurality of strings corresponding to the first taxon and indexed by the second dilution; and
process the plurality of string counts to generate the plurality of co- occurring outputs in the plurality of strings, wherein the plurality of co-occurring outputs is significantly non-random when processed with respect to the first parameter and the second parameter.
Dependent claim 60 further limits the plurality of co-occurring outputs recited in claim 54.
Independent claim 61: process the taxonomic information of the taxa in the plurality of cultivated dilutions to identify a non-random occurrence of the first taxon in the presence or absence of the second taxon to determine an interaction within the plurality of taxa of microorganisms in the sample in the first cultivation condition.
Dependent claim 66: perform error correction to remove one or more errors in the taxonomic information of the taxa in the plurality of cultivated dilutions.
Dependent claim 67: wherein the abundances of the taxa in the plurality of cultivated dilutions are determined based on a threshold.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation because the method only requires a user to manually process string counts or taxonomic information to generate co-occurring outputs or interactions. Without further detail as to the methodology involved in “quantifying”, “processing” to “generate” or “identify”, “performing error correction”, and “determining”, under the BRI, one may simply, for example, use pen and paper to quantify an abundance of a plurality of strings and generate a plurality of co-occurring outputs of the strings or to process taxonomic information to identify an interaction based on non-random occurrences of taxa. Some of these steps, such as quantifying abundances and identifying non-random occurrences, require mathematical techniques as the only supported embodiments, as is disclosed in the specification at: [0011; 0022; 0055; 0063; 0069; 0071-0073; 0137].
The claims also recite a law of nature/natural phenomenon because the claims recite the natural relationship between the co-occurring output (e.g., taxa, as in claim 60) and the first (e.g., dilution, as in claim 54) and second (e.g., cultivation conditions as in claim 59) parameters in claims 54 and 61. In other words, the claims encompass the identification of the interaction or co-occurrence of taxa in response to exposure to growth conditions and dilution factors. The claims do not preclude these growth conditions and dilution factors to be distinct from those which occur naturally, and therefore the growth of the taxa in response to those conditions and to the competitive effects from other taxa in the culture are natural phenomenon.
Therefore, claims 54 and 61 and those claims dependent therefrom recite an abstract idea and a law of nature/natural phenomenon [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong Two
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d).III).
Additional elements, Step 2A, Prong Two
With respect to the instant recitations, the claims recite the following additional elements:
Independent claim 54: receive a file comprising a plurality of strings, each string (1) indexed by a first parameter and a second parameter and (2) corresponding to an output, wherein the plurality of strings comprises sequence information, and wherein the sequence information corresponds to a plurality of taxa of microorganisms in a sample, wherein the first parameter comprises a degree of dilution for the sample comprising the plurality of taxa of microorganisms, wherein the second parameter corresponds to one or more cultivation conditions, wherein the degree of dilutions comprise a first dilution and a second dilution with an identical inoculum density, wherein the first dilution comprises a first taxon and a second taxon, wherein the second dilution comprises the first taxon and not the second taxon; and
save the plurality of co-occurring outputs to the memory.
Independent claim 61: receive taxonomic information of taxa in a plurality of cultivated dilutions, wherein the taxonomic information comprises abundances of the taxa in the plurality of cultivated dilutions, wherein the plurality of cultivated dilutions is cultivated from a subset of a plurality of dilutions of a sample in a first cultivation condition, wherein the sample comprises a plurality of taxa of microorganisms, wherein the subset of the plurality of dilutions comprises a first dilution and a second dilution with an identical inoculum density, wherein the first dilution comprises a first taxon and a second taxon, wherein the second dilution comprises the first taxon and not the second taxon, and wherein an abundance of the first taxon in a first cultivated dilution of the plurality of cultivated dilutions cultivated from the first dilution is different from an abundance of the first taxon in a second cultivated dilution of the plurality of cultivated dilutions cultivated from the second dilution.
Dependent claims 57, 62-65, and 68 recite steps that further limit the recited additional elements in the claims. For example, claim 57, 59-60, 62-65, and 68 further limit the received plurality of strings/taxonomic information.
The claims also include non-abstract computing elements. For example, independent claims 54 and 61 include a computer system comprising a computer-readable memory storing executable instructions and a computer processor programmed by the executable instructions.
Considerations under Step 2A, Prong Two
With respect to Step 2A, Prong Two, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to data gathering, such as “receive” data, and to data outputting, such as “save” data, perform functions of collecting the data needed to carry out the judicial exceptions. Data gathering and outputting do not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Data gathering and outputting steps are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
Further steps directed to additional non-abstract elements of “a computer system…” do not describe any specific computational steps by which the “computer parts” perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer, such as the computer-readable recording media, are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, and therefore the claim does not integrate that judicial exceptions into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc.… are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (MPEP 2106.05(f)).
The specification does not provide a clear explanation for how the additional elements provide improvements. Therefore, the additional elements do not clearly improve the functioning of a computer, or comprise an improvement to any other technical field. Further, the additional elements do not clearly affect a particular treatment; they do not clearly require or set forth a particular machine; they do not clearly effect a transformation of matter; nor do they clearly provide a nonconventional or unconventional step (MPEP2106.04(d)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exceptions [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B (MPEP 2106.05.A i-vi)
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, the courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a merely generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(II)(i)). As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The data gathering steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
With respect to claims 54 and 61 and those claims dependent therefrom, the computer-related elements or the general purpose computer do not rise to the level of significantly more than the judicial exception. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, which the courts have found to not provide significantly more when recited in a claim with a judicial exception (Alice Corp., 573 U.S. at 225-26, 110 USPQ2d at 1984; see MPEP 2106.05(A)). The specification also notes that computer processors and systems, as example, are commercially available or widely used at [0096-0100]. The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the judicial exceptions (see MPEP 2106.05(b)I-III).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, the instant claims are not drawn to eligible subject matter as they are directed to one or more judicial exceptions without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106.
Response to Applicant Arguments
At p. 6, par. 4 through p. 7, par. 2, Applicant submits that claims 54 and 61 represent an improvement to the technical field. Applicant submits that the step of “processing the plurality of string counts to generate the plurality of co-occurring outputs” cannot be practically performed in the human mind because the sequencing data includes large amounts of sequencing data.
It is respectfully submitted that this is not persuasive. The claims require only “receive a file comprising a plurality of strings” which have already been indexed in claim 54 and “receive taxonomic information of taxa in a plurality of cultivated dilutions, wherein the taxonomic information comprises abundances of the taxa in the plurality of cultivated dilutions” in claim 61. The claims do not require a human to mentally process the raw data to provide these numbers, but rather to act on the already processed steps in a way that recites a mental process. The claims currently recite no features or limitations which would preclude a human to perform the processing step mentally, or with the aid of pen and paper or a computer.
Further, the claims do not limit the plurality of strings in claim 54 or the taxonomic information in claim 61 to comprising the large numbers as submitted by Applicant. Therefore the argument is not commensurate with the scope of the claims. Even if the claims did require such large numbers, Applicant has offered no reasoning that or specific arguments why a human mind cannot perform the “processing” steps as instantly claimed. The courts do not distinguish between mental processes that are performed entirely in the human mind and mental processes that require a human to use a physical aid (e.g., pen and paper or a slide rule) to perform the claim limitation (See MPEP 2104(a)(2), III: e.g., Benson, 409 U.S. at 67, 65, 175 USPQ at 674-75, 674 (noting that the claimed "conversion of [binary-coded decimal] numerals to pure binary numerals can be done mentally," i.e., "as a person would do it by head and hand."); Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1139, 120 USPQ2d 1473, 1474 (Fed. Cir. 2016) (holding that claims to a mental process of "translating a functional description of a logic circuit into a hardware component description of the logic circuit" are directed to an abstract idea, because the claims "read on an individual performing the claimed steps mentally or with pencil and paper")). Nor do the courts distinguish between claims that recite mental processes performed by humans and claims that recite mental processes performed on a computer. As the Federal Circuit has explained, "[c]ourts have examined claims that required the use of a computer and still found that the underlying, patent-ineligible invention could be performed via pen and paper or in a person’s mind." Versata Dev. Group v. SAP Am., Inc., 793 F.3d 1306, 1335, 115 USPQ2d 1681, 1702 (Fed. Cir. 2015). See also Intellectual Ventures I LLC v. Symantec Corp., 838 F.3d 1307, 1318, 120 USPQ2d 1353, 1360 (Fed. Cir. 2016) (‘‘[W]ith the exception of generic computer-implemented steps, there is nothing in the claims themselves that foreclose them from being performed by a human, mentally or with pen and paper.’’); Mortgage Grader, Inc. v. First Choice Loan Servs. Inc., 811 F.3d 1314, 1324, 117 USPQ2d 1693, 1699 (Fed. Cir. 2016) (holding that computer-implemented method for "anonymous loan shopping" was an abstract idea because it could be "performed by humans without a computer").
At p. 7, par. 3, Applicant submits that the claims as a whole do no recite a law of nature or a natural phenomenon because the claims only require a computer system and the serial dilution of a sample, and therefore only describe a law of nature or a natural phenomenon.
It is respectfully submitted that this is not persuasive. At Step 2A, Prong 1, the claims are analyzed to determine whether they recite a judicial exception. The claims are examined limitation by limitation to identify that the claimed concept (the specific claim limitation(s) that recite an exception) aligns with at least one judicial exception (see MPEP 2106.04(I)). It is either during the markedly different characteristic analysis of products of nature at Step 2A, Prong 1, or at Step 2A, Prong 2, that the claims are examined as a whole to determine whether they are directed to the judicial exception. The instant claims are not analyzed with the markedly different characteristic analysis because they do not recite products of nature. At Step 2A, Prong 1, the instant claims are found to encompass the identification of the interaction or co-occurrence of taxa in response to exposure to growth conditions and dilution factors, which is the natural response of the naturally occurring bacteria to such growth conditions. Therefore, the claims rely on characterizing a law of nature or a natural phenomenon.
At p. 7, par. 4 through p. 9, Applicant submits that claims 54 and 61, as a whole, integrate the judicial exception into a practical application under Step 2A, Prong 2 because the claims provide improvement to the field of microbial community analysis and engineering, as supported by the instant specification. Applicant submits that the cultivating step is not an insignificant data gathering or outputting step. Applicant submits that because of these reasons, the claims as a whole integrate the judicial exception into a practical application. At p. 17, par. 4 through p. 18, par. 2, Applicant submits that the claims as a whole are significantly more than the judicial exception under Step 2B because the claims provide an improvement in the field of microbial community analysis and engineering.
It is respectfully submitted that this is not persuasive. As set forth in the above rejection, the steps directed to “processing” the data (i.e., microbial community analysis) received by the computers recite a judicial exception. Judicial exceptions cannot be a practical application of themselves or other judicial exceptions. The courts have made clear that a judicial exception is not eligible subject matter (Bilski, 561 U.S. at 601, 95 USPQ2d at 1005-06 (quoting Chakrabarty, 447 U.S. at 309, 206 USPQ at 197 (1980)) if there are no additional claim elements besides the judicial exception, or if the additional claim elements merely recite another judicial exception that is insufficient to integrate the judicial exception into a practical application. See, e.g., RecogniCorp, LLC v. Nintendo Co., 855 F.3d 1322, 1327, 122 USPQ2d 1377 (Fed. Cir. 2017) ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016) (eligibility "cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself."). For a claim reciting a judicial exception to be eligible, it is the additional elements (if any) in the claim that must "transform the nature of the claim" into a patent-eligible application of the judicial exception, Alice Corp., 573 U.S. at 217, 110 USPQ2d at 1981, either at Prong Two or in Step 2B. If there are no additional elements in the claim, then it cannot be eligible.
Regarding Applicant’s remarks about improving engineering, it is noted that no such limitations are present in the claims. Such arguments are therefore not commensurate with the scope of the claims. As set forth in MPEP 2106.05(a), the full scope of the claim under the BRI should be considered to determine if the claim reflects an improvement in technology. Without the engineering being recited in the claim, such engineering cannot be improved by the method, even though the instant specification discusses such improvements.
Applicant has provided no reasoning for why the cultivating step is not an insignificant data gathering or outputting step. Therefore, there is a lack of factual support in Applicant's arguments because the arguments are not evidentiary. Further, as noted above, the claims do not require an active step of cultivating or diluting, and the argument is not commensurate with the scope of the claims. The cultivation and dilution merely affect the type of data that is received by the systems, which provides no practical application at Step 2A, Prong 2, and does not provide significantly more to the claim at Step 2B.
Regarding Applicant’s remarks about Step 2B, MPEP 2106.05(d) sets forth that, at Step 2B, it is the additional elements which are examined to determine whether they are well-understood, routine, conventional activities previously known to the industry. The analysis at Step 2A, Prong 2, considers the claims as a whole, i.e., the additional elements in combination with the judicial exceptions (see MPEP 2106.05(a)), although the integration or improvement provided in the claim must flow from the additional elements and not the judicial exceptions to be considered persuasive. However, Step 2B requires examining only the additional elements, either alone or in combination with one another, for conventionality. The limitations regarding microbial community analysis pointed to be Applicant are considered to recite a judicial exception as described above and are therefore not considered at Step 2B. Microbial community engineering is not present in the claims, as discussed above, and is also not considered at Step 2B.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 54, 57, and 60-68 are rejected under 35 U.S.C. 103 as being unpatentable over the features of Jimenez et al. (Biotechnology for Biofuels, 2014, 7:1-18; previously cited). Instantly claimed elements which are considered to be equivalent to the prior art teachings are described in bold for all claims. The rejection is newly stated and is necessitated by claim amendment for claims 54, 57, and 60, and based on further consideration of the claims for claims 61-68.
The prior art to Jimenez discloses the diversity, composition and predicted functional profiles of novel bacterial-fungal consortia, on the basis of replicated aerobic wheat straw enrichment cultures (abstract). Jimenez, indicated by the open circles, teaches the instant features, indicated by the closed circles, as follows.
Claim 54 discloses a computer system for identifying a plurality of co-occurring outputs in a plurality of strings, comprising:
a computer-readable memory storing executable instructions; and a computer processor programmed by the executable instructions to:
See below regarding these limitations.
receive a file comprising a plurality of strings, each string (1) indexed by a first parameter and a second parameter and (2) corresponding to an output, wherein the plurality of strings comprises sequence information, and wherein the sequence information corresponds to a plurality of taxa of microorganisms in a sample, wherein the first parameter comprises a degree of dilution for the sample comprising the plurality of taxa of microorganisms, wherein the second parameter corresponds to one or more cultivation conditions, wherein the degree of dilutions comprise a first dilution and a second dilution with an identical inoculum density, wherein the first dilution comprises a first taxon and a second taxon, wherein the second dilution comprises the first taxon and not the second taxon;
This limitation is interpreted as receiving data, where the data is claimed as a product-by-process limitation because the claim requires only a computer processor programmed by the executable instructions to receive taxonomic information of taxa. As set forth in MPEP 2113.I, the patentability of a product does not depend on its method of production but on the structure implied by the process steps. The taxonomic information is interpreted as a product of the method of production (wherein the plurality of cultivated dilutions is cultivated from a subset of a plurality of dilutions of a sample in a first cultivation condition, wherein the sample comprises a plurality of taxa of microorganisms) where the indicated method steps do not provide structure to the taxonomic information. In the instant claim, the structure is implied by the process steps “each string (1) indexed by a first parameter and a second parameter and (2) corresponding to an output, wherein the plurality of strings comprises sequence information, and wherein the sequence information corresponds to a plurality of taxa of microorganisms in a sample, wherein the first parameter comprises a degree of dilution for the sample comprising the plurality of taxa of microorganisms, wherein the second parameter corresponds to one or more cultivation conditions, wherein the degree of dilutions comprise a first dilution and a second dilution with an identical inoculum density, wherein the first dilution comprises a first taxon and a second taxon, wherein the second dilution comprises the first taxon and not the second taxon.”
Jimenez teaches incubating serial dilutions (i.e., first parameter) of microbial communities on treated or untreated straw (i.e., second parameter) and sequencing bacterial 16S rRNA and fungal ITS1 genes (i.e., a plurality of strings which correspond to a plurality of taxa) (abstract; p. 3-5; p. 13, col. 1, par. 3 through p. 14, col. 1, par. 2; Figure 2). Jimenez teaches processing the raw sequencing data (i.e., a file) using various toolkits and algorithms (p. 13, col. 2, par. 3 through p. 14, col. 1, par. 1), which are considered to recite computer algorithms or software (i.e., executable instructions). As Jimenez teaches analyzing the sequencing data based on the culture conditions and dilutions, it is considered that Jimenez fairly teaches data which is indexed by the first and second parameters, as instantly claimed.
Jimenez teaches incubating serial dilutions (i.e., first parameter) of microbial communities on treated or untreated straw and sequencing bacterial 16S rRNA and fungal ITS1 genes (abstract; p. 3-5; p. 13, col. 1, par. 3 through p. 14, col. 1, par. 2; Figure 2).
As Jimenez teaches that in the forest soil inoculum, which served as the base culture for the treated and untreated straw conditions, there 338 operational taxonomic units (OUT’s) detected; at transfer 1, there were already only 109 and 102 OTUs detected in the raw and treated straw conditions; and at transfer 10, there only 100 and 47 OTUs detected in the raw and treated straw conditions, respectively (p. 3, col. 1, par. 1; Figure 1). Therefore, Jiminez is considered to fairly teach a first dilution with a first and a second taxon and a second dilution with only the first taxon as instantly claimed, because there are fewer taxa present in the first transfer of both conditions as compared to the forest soil inoculum, as well as in the sample after ten transfers as compared to the initial transfer sample, indicating that some OTUs (i.e., taxa) have been removed through dilution.
quantify an abundance of each of the plurality of strings indexed by the first parameter and the second parameter to generate a plurality of string counts, each string count corresponding to an output, wherein the plurality of string counts comprises a string count of strings of the plurality of strings corresponding to the first taxon and indexed by the first dilution, a string count of strings of the plurality of strings corresponding to the second taxon and indexed by the first dilution, and a string count of strings of the plurality of strings corresponding to the first taxon and indexed by the second dilution; and process the plurality of string counts to generate the plurality of co-occurring outputs in the plurality of strings, wherein the plurality of co-occurring outputs is significantly non-random when processed with respect to the first parameter and the second parameter; and
Jimenez teaches determining the abundances of the sequences binned into operational taxonomic units (OTUs) at each diluted transfer and condition (i.e., indexed for the taxa and dilution), where the abundance bacteria orders and fungal phylum members are represented with relative error to indicate significant differences at each sequential batch (i.e., significantly non-random co-occurring outputs) (p. 3, col. 1, par. 1; p. 4; Fig. 2-4).
save the plurality of co-occurring outputs to the memory.
Jimenez teaches depositing the sequences in GenBank (p. 14, col. 1, par. 1), which is considered to fairly teach saving the plurality of co-occurring outputs.
Jimenez does not explicitly teach a computer system comprising computer-readable memory storing executable instructions and a computer processor programmed by the executable instructions.
However, it would have been obvious to include a computer system as instantly claimed for performing the method of Jimenez because such a modification represents the automating of a manual activity. The courts have held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art (In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP 2144.04(III)).
Regarding claim 57, the features of Jimenez teach the computer system of claim 54. Claim 57 further adds that the sequence information comprises sequences of 16S rRNA,12S rRNA, 18S rRNA, 28S rRNA, 13S rRNA and 23S rRNA, internal transcribed spacer (ITS), ITS1, ITS2, cytochrome oxidase I (COI), cytochrome b, or any combination thereof.
Jimenez teaches sequencing 16S rRNA and ITS1 sequences (p. 13, col. 2, par. 3 through p. 14, col. 1, par. 1).
Regarding claim 60, the features of Jimenez teach the computer system of claim 54. Claim 60 further the plurality of co-occurring outputs comprises a taxon. Under the BRI, a taxon is interpreted as a taxonomic group of any rank, as is supported by the instant specification at [0010], which discloses that “In some embodiments, each taxon of the taxa corresponds to an operational taxonomic unit (OTU), a species, a genus, or a family”.
Jimenez teaches identifying the abundances of bacterial orders and fungal phylum members (Figure 2) and genus level OTUs (Figures 3-5).
Claim 61 discloses a computer system for determining a microbial interaction, comprising:
a computer-readable memory storing executable instructions; and a computer processor programmed by the executable instructions to:
See below regarding these limitations.
receive taxonomic information of taxa in a plurality of cultivated dilutions, wherein the taxonomic information comprises abundances of the taxa in the plurality of cultivated dilutions, wherein the plurality of cultivated dilutions is cultivated from a subset of a plurality of dilutions of a sample in a first cultivation condition, wherein the sample comprises a plurality of taxa of microorganisms, wherein the subset of the plurality of dilutions comprises a first dilution and a second dilution with an identical inoculum density, wherein the first dilution comprises a first taxon and a second taxon, wherein the second dilution comprises the first taxon and not the second taxon, and wherein an abundance of the first taxon in a first cultivated dilution of the plurality of cultivated dilutions cultivated from the first dilution is different from an abundance of the first taxon in a second cultivated dilution of the plurality of cultivated dilutions cultivated from the second dilution; and
This limitation is interpreted as receiving data, where the data is claimed as a product-by-process limitation because the claim requires only a computer processor programmed by the executable instructions to receive taxonomic information of taxa. As set forth in MPEP 2113.I, the patentability of a product does not depend on its method of production but on the structure implied by the process steps. The taxonomic information is interpreted as a product of the method of production (wherein the plurality of cultivated dilutions is cultivated from a subset of a plurality of dilutions of a sample in a first cultivation condition, wherein the sample comprises a plurality of taxa of microorganisms) where the indicated method steps do not provide structure to the taxonomic information. In the instant claim, the structure is implied by the process steps “wherein the taxonomic information comprises abundances of the taxa in the plurality of cultivated dilutions… wherein the subset of the plurality of dilutions comprises a first dilution and a second dilution with an identical inoculum density, wherein the second dilution comprises the first taxon and not the second taxon, and wherein an abundance of the first taxon in a first cultivated dilution of the plurality of cultivated dilutions cultivated from the first dilution is different from an abundance of the first taxon in a second cultivated dilution of the plurality of cultivated dilutions cultivated from the second dilution”.
Jimenez teaches incubating serial dilutions (i.e., first parameter) of microbial communities on treated or untreated straw (i.e., second parameter) and sequencing bacterial 16S rRNA and fungal ITS1 genes (i.e., a plurality of strings which correspond to a plurality of taxa) (abstract; p. 3-5; p. 13, col. 1, par. 3 through p. 14, col. 1, par. 2; Figure 2). Jimenez teaches processing the raw sequencing data (i.e., a file) using various toolkits and algorithms (p. 13, col. 2, par. 3 through p. 14, col. 1, par. 1), which are considered to recite computer algorithms or software (i.e., executable instructions). As Jimenez teaches analyzing the sequencing data based on the culture conditions and dilutions, it is considered that Jimenez fairly teaches data which is indexed by the first and second parameters, as instantly claimed.
Jimenez teaches incubating serial dilutions (i.e., first parameter) of microbial communities on treated or untreated straw and sequencing bacterial 16S rRNA and fungal ITS1 genes (abstract; p. 3-5; p. 13, col. 1, par. 3 through p. 14, col. 1, par. 2; Figure 2).
As Jimenez teaches that in the forest soil inoculum, which served as the base culture for the treated and untreated straw conditions, there 338 operational taxonomic units (OUT’s) detected; at transfer 1, there were already only 109 and 102 OTUs detected in the raw and treated straw conditions; and at transfer 10, there only 100 and 47 OTUs detected in the raw and treated straw conditions, respectively (p. 3, col. 1, par. 1; Figure 1). Therefore, Jiminez is considered to fairly teach a first dilution with a first and a second taxon and a second dilution with only the first taxon as instantly claimed, because there are fewer taxa present in the first transfer of both conditions as compared to the forest soil inoculum, as well as in the sample after ten transfers as compared to the initial transfer sample, indicating that some OTUs (i.e., taxa) have been removed through dilution.
process the taxonomic information of the taxa in the plurality of cultivated dilutions to identify a non-random occurrence of the first taxon in the presence or absence of the second taxon to determine an interaction within the plurality of taxa of microorganisms in the sample in the first cultivation condition.
Jimenez teaches determining the abundances of the sequences binned into operational taxonomic units (OTUs) at each diluted transfer and condition, where the abundance bacteria orders and fungal phylum members are represented with relative error to indicate significant differences at each sequential batch (p. 3, col. 1, par. 1; p. 4; Fig. 2-4).
Jimenez does not explicitly teach a computer system comprising computer-readable memory storing executable instructions and a computer processor programmed by the executable instructions.
However, it would have been obvious to include a computer system as instantly claimed for performing the method of Jimenez because such a modification represents the automating of a manual activity. The courts have held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art (In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP 2144.04(III)).
Regarding claim 62, the features of Jimenez teach the computer system of claim 61. Claim 62 further adds that the plurality of dilutions of the sample comprises a plurality of serial dilutions of the sample. While this limitation does not limit the structure of the received taxonomic information as described above, it is noted that Jimenez teaches incubating serial dilutions of microbial communities on treated or untreated straw and sequencing bacterial 16S rRNA and fungal ITS1 genes (abstract; p. 3-5; p. 13, col. 1, par. 3 through p. 14, col. 1, par. 2; Figure 2).
Regarding claim 63, the features of Jimenez teach the computer system of claim 61. Claim 63 further adds that the first taxon corresponds to an operational taxonomic unit (OTU), which Bernstein does not teach.
Jimenez teaches determining the abundances of the sequences binned into operational taxonomic units (OTUs), where the abundance bacteria orders and fungal phylum members are represented with relative error to indicate significant differences at each sequential batch (p. 3, col. 1, par. 1; p. 4; Fig. 2).
Regarding claim 64, the features of Jimenez teach the computer system of claim 61. Claim 64 further adds that the first taxon corresponds to a species, a genus, or a family.
Jimenez teaches determining the abundances of the sequences binned into operational taxonomic units (OTUs), where the abundance bacteria orders and fungal phylum members are represented with relative error to indicate significant differences at each sequential batch (p. 3, col. 1, par. 1; p. 4; Fig. 2). Jimenez teaches examining OUTs at the genus level (p. 14, col. 1, par. 1; Figure 3).
Regarding claim 65, the features of Jimenez teach the computer system of claim 61. Claim 65 further adds that the taxonomic information of the taxa in the plurality of cultivated dilutions is based on sequence information of one or more genes selected form the group consisting of 16S rRNA,12S rRNA, 18S rRNA, 28S rRNA, 13S rRNA and 23S rRNA, internal transcribed spacer (ITS), ITS1, ITS2, cytochrome oxidase I (COI), cytochrome b, or any combination thereof.
Jimenez teaches incubating serial dilutions of microbial communities on treated or untreated straw and sequencing bacterial 16S rRNA and fungal ITS1 genes (abstract; p. 3-5; p. 13, col. 1, par. 3 through p. 14, col. 1, par. 2; Figure 2).
Regarding claim 66, the features of Jimenez teach the computer system of claim 61. Claim 66 further adds that the computer processor is further programmed by the executable instructions to perform error correction to remove one or more errors in the taxonomic information of the taxa in the plurality of cultivated dilutions.
Jimenez teaches quality trimming sequences, deleting chimeric sequences, and removing clusters consisting only of singleton sequences (p. 13, col. 2, par. 3 through p. 14, col. 1, par. 1), which is considered to read on error correction.
Regarding claim 67, the features of Jimenez teach the computer system of claim 61. Claim 67 further adds that the abundances of the taxa in the plurality of cultivated dilutions are determined based on a threshold.
Jimenez teaches removing clusters consisting only of singleton sequences (i.e., a threshold) (p. 14, col. 1, par. 1).
Regarding claim 68, the features of Jimenez teach the computer system of claim 61. Claim 68 further adds that the abundances of the taxa in the plurality of cultivated dilutions comprise a relative abundance of the first taxon in the first cultivated dilution of the plurality of cultivated dilutions.
Jimenez teaches characterizing the relative abundances of the identified taxa (abstract; p. 4, col. 1, par. 2 through p. 5, col. 2, par. 2; Figures 2-3 and 5).
Response to Applicant Arguments
Applicant submits at p. 10 through p. 11, par. 2, that Jimenez does not teach incubating serial dilutions because Jimenez teaches sequential transfers, which is different because Jimenez explains that the dilutions were followed by an incubation, which would not result in a serial dilution as described in the instant specification.
It is respectfully submitted that this is not persuasive. In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (the serial dilutions as described in the specification) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). The claims require only that the “the sequence information corresponds to a plurality of taxa of microorganisms in a sample, wherein the first parameter comprises a degree of dilution for a sample comprising a plurality of taxa of microorganisms” (see claim 54 as an example). As submitted by Applicant, Jimenez teaches sequential transfers of 1 to 1,000 dilutions. It is maintained that one of ordinary skill in the art would recognize such teachings as “a degree of dilution” as instantly claimed.
It is noted that claim 62 requires “serial dilutions”. However, as Jimenez teaches that the samples are sequentially diluted from 1 to 1,000 fold over the 10 transfers (abstract), it is considered that such a dilution also reads on serial dilutions as argued by Applicant. It is further noted that
Applicant’s remarks Regarding one of ordinary skill in the art would not know the abundance of a taxon in one transfer in Jimenez is different from another transfer, since the transfers are obtained from the same pre-dilution cell density with the same fold of dilution, are not convincing. Jimenez clearly teaches that the conditions and dilutions the cultures are subjected to throughout the experiment apply a selective processes on the community and result in changes in OUT abundances (p. 2, col. 2, par. 2; Figures 1-4). It is further noted that Applicant’s remarks are not clear in light of the limitation that the “the degree of dilutions comprise a first dilution and a second dilution with an identical inoculum density”. Without performing the method as described by Jimenez, it is not apparent that one of ordinary skill in the art would be able to assess a serially diluted culture, where the dilutions start with an identical inoculum density.
Regarding Applicant’s remarks concerning claims 61-68 over Bernstein at p. 11, the arguments have been fully considered but are moot in view of the new grounds of rejection set forth above as necessitated by claim amendment herein. Jimenez is considered to teach serial dilution as described above.
Conclusion
No claims are allowed.
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/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685
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