DETAILED ACTION
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 .
Applicant's response filed 1/8/2026 has been fully considered. The following rejections
and/or objections are either reiterated or newly applied.
Status of Claims
Claims 1-2 and 4-7 pending and examined on the merits.
Claims 3 and 8-9 canceled.
Priority
The instant application filed on 5/20/2022 claims the benefit of foreign priority to Patent Application No. TW111107822 filed on 3/3/2022. Thus, the effective filing date of the claims is 3/3/2022.
The applicant is reminded that amendments to the claims and specification must comply with 35 U.S.C. § 120 and 37 C.F.R. § 1.121 to maintain priority to an earlier-filed application. Claim amendments may impact the effective filing date if new subject matter is introduced that lacks support in the originally filed disclosure. If an amendment adds limitations that were not adequately described in the parent application, the claim may no longer be entitled to the priority date of the earlier filing.
Information Disclosure Statement
The IDS filed on 11/12/2025 has been entered and considered. A signed copy of the corresponding 1449 form has been included with this Office action.
Drawings
The drawings are objected to because Figure 1 is not in English and no translation is provided. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The objection to the specification filed on 10/23/2025 withdrawn in view of Applicant's claim amendments filed on 1/8/2026.
Claim Objections
The objection to claims 2 and 3 filed on 10/23/2025 withdrawn in view of Applicant's claim amendments filed on 1/8/2026. However, amended claims 1 and 6 objected to because of the following informalities:
Amended claim 1 objected to because of the following informalities: line 5 "using an a dynamic time wrapping algorithm" should read "using a dynamic time warping algorithm".
Amended claim 6 objected to because of the following informalities: lines 2-3 "using the dynamic time wrapping algorithm to perform" should read "using the dynamic time warping algorithm to perform".
Appropriate correction is required.
Withdrawn Rejections
35 USC § 112(b)
The rejection filed on 10/23/2025 of claims 1-2 and 4-7 under 35 USC 112(b) withdrawn in view of Applicant's claim amendments filed on 1/8/2026. However, the amendments to the claims also necessitated new grounds for rejection under 35 USC 112(b), see below.
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-2 and 4-7 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.
Claim 1 recites "excluding sequences with insufficient classification information, which are sequences with no information in first five classification hierarchies of species". It is not clear what is meant by "first five classification hierarchies of species", whether this is to be: kingdom [or superkingdom as it is sometimes referred to], phylum, class, order, family; or species, genus, family, order, class; and occasionally there are one or more hierarchical levels below species, so it is also not clear how those might be handled as well. However, the instant specification in para.0029 refers to figure 5 as an example of an "uncultured bacterium" that would be excluded from the database, and the figure clearly shows that the superkingdom (the first classification hierarchy) is not missing, and that "genus" is considered level 1 of the "first five classification hierarchies of species", presumably species being level 0. Therefore, to further prosecution, the limitation is interpreted as "excluding sequences with insufficient classification information, which are sequences with no information in first five classification hierarchies of species, the first five classification hierarchies of species consisting of phylum, class, order, family, and genus".
Claim 1 also recites "the ribosomal RNA database is applied to an analytical process of microbial phase". It is not clear what phases are to be analyzed (lag, exponential, stationary, death, planktonic, biofilm-associated, metabolic, etc phases), or how. The only mentions of microbial "phase" in the disclosure are in the instant specification on para.0003 and para.0030, however these paragraphs do not illuminate the matter beyond their mere mention of the term. Furthermore, there does not appear to be any mention of any particular lifecycle phase of microbes in the disclosure, or any specific analytical process involved in an examination of microbial phase using rRNA. Therefore, to further prosecution the limitation is interpreted as “the ribosomal RNA database is applied to any analytical process of any microbial phase”.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-2 and 4-7 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of a mental process, a mathematical concept, organizing human activity, or a law of nature or natural phenomenon without significantly more. In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claim 1: “selecting a source of a nucleic acid sequence database” and “selecting a kingdom to which a sequence species belongs” both provide an evaluation (selecting involves an evaluation before making the selection) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
“using a dynamic time [warping] algorithm for normalized classification and correction” (or “performing comparison according to the species hierarchy”, as interpreted above) provides a comparison (comparing distance measures involves comparisons) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. The limitation is further interpreted above as “applying a distance algorithm (dynamic time warping (DTW), Manhattan, or similar) to the normalized strings” which provides a mathematical calculation (calculating distance measures involves mathematical calculations) that is considered a mathematical concept, which is an abstract idea.
“filtering out redundant sequences and sequences with inconsistent lengths; setting a threshold for unknown bases other than A, T, C or G, and excluding the unknown bases that exceed the threshold; and excluding sequences with insufficient classification information” provides logical reasoning (filtering or excluding sequences based on rules and thresholds involves drawing conclusions based on premises) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 4: “a seventh-order nomenclature is used for normalization to form a hierarchy relation table, and hierarchies defined in the seventh-order nomenclature comprise kingdom, phylum, class, order, family, genus, and species” provides a way or organizing information (normalizing data to form a hierarchy is a way of structuring data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 5: “finding out information of other hierarchy in the classification hierarchy relation table based on species names in the nucleic acid sequence database, or using a serial number as a search target for comparison with a database that stores the serial numbers based on a serial number of a species in the nucleic acid sequence database” provides a comparison (searching species names or serial numbers to a target involves comparisons) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 6: “performing a comparison according to a species hierarchy, so as to confirm that there is no repetition in sequence classification information” provides a comparison (comparing species involves comparisons) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 7: “selecting sequences belonging to a kingdom of Archaea and a kingdom of Bacteria directed at the 16S rRNA gene database, and excluding other kingdoms or sequences where a kingdom name is mistakenly named as Archaea or Bacteria” provides logical reasoning (selecting or excluding sequences based on rules and thresholds involves drawing conclusions based on premises) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
These recitations are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or are mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. As such, claims 1-2 and 4-7 recite an abstract idea (Step 2A, Prong 1: YES).
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exceptions listed above are not integrated into a practical application because the claims do not recite an additional element or elements that reflects an improvement to technology. Specifically, the claims recite the following additional elements:
Claim 1: “performing normalization and homogenization on species classification rules” provides insignificant extra-solution activities (normalizing strings of data is a pre-solution activity involving data manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
“when a sequence contains the same species sequence with 100% identical conditions, the sequence is a redundant sequence, and sequences with inconsistent lengths are those that are shorter than 1200 bases or longer than 1800 bases in length” provides insignificant extra-solution activities (filtering sequence data is a pre-solution activity involving data manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
The steps for normalizing and filtering data are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application because they are pre-solution activities involving data manipulation steps (see MPEP 2106.04(d)(2)).
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application, or equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment.
The limitations for normalizing and filtering data are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application. Furthermore, no inventive concept is claimed by these limitations as they are well-understood, routine, and conventional.
The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 1-2 and 4-7 are not patent eligible.
Response to Arguments under 35 USC § 101
Applicant’s arguments filed 1/8/2026 are fully considered but they are not persuasive.
Applicant asserts that "performing normalization and homogenization on species classification rules" is a technical feature of claim 1 that "has an inventive concept and reflects an improvement to technology" because it is "clearly demonstrated in the practical application of 'analytical process of microbial phase', which is not well-understood, routine or conventional" (Remarks 1/8/2026 pages 3-4). Examiner notes that the cited amendment to include said microbial phase as a limitation of claim 1 does not particularly point out and distinctly claim the invention, nor does the instant specification provide an adequate written description that explicitly discloses a means to apply the rRNA database "to an analytical process of microbial phase" (see section "Claim Rejections - 35 USC 112" subsections regarding 112(b) and 112(a), above). Therefore, as mentioned in the above sections, this limitation is interpreted as not further limiting claim 1 and is subsequently not considered an additional element of any of the identified judicial exceptions.
Therefore, the rejection of claims 1 under 35 USC 101 is maintained. All other claims depend from this independent claim; therefore, their rejection is likewise maintained.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
Claims 1-2 and 4-7 rejected under 35 U.S.C. 103 as being unpatentable over Robeson et al. (Robeson et al. "RESCRIPt: Reproducible sequence taxonomy reference database management." PLoS computational biology 17.11 (2021): e1009581) in view of Kozlov et al. (Nucleic acids research 44.11 (2016): 5022-5033), Fraley et al (US-20210241857), and Blazewicz et al. (The ISME journal 7.11 (2013): 2061-2068).
Regarding claim 1, Robeson teaches a method for constructing a ribosomal RNA database comprising; selecting a source of a nucleic acid sequence database, and filtering out redundant sequences and sequences with inconsistent lengths (Page 4 last paragraph "These include methods for automated download of sequences and taxonomy from SILVA (selecting marker gene and release version) and NCBI GenBank (selection based on NCBI query or a list of accession numbers). Additional functions allow traceable formatting (e.g., sequence manipulation, taxonomy parsing), filtering (e.g., automatic quality and length filtering), and modification of data (e.g., to merge taxonomies and dereplicate or cluster sequence/taxonomy databases)").
Robeson also teaches performing normalization and homogenization on species classification rules (page 23 paragraph 2 “In this case, a conservative approach is used to remove polyphyletic groups and normalize taxonomic ranks according to their relative evolutionary divergence”, and Page 26 third to last paragraph "The NCBI download method retrieves the requested sequences from the NCBI Nucleotide database, cross-references their taxids with the NCBI Taxonomy database to obtain their taxonomic classifications, then standardizes the taxonomies to adhere to a fixed set of ranks. The set of ranks can be configured by the user but are kingdom (k__), phylum (p_), class (c_), order (o_), family (f_), genus (g_), and species (s__) by default. If a given rank is not present in the NCBI Taxonomy it is propagated down from the nearest higher rank, as described above. Rank propagation can be optionally disabled").
Robeson also teaches selecting a kingdom to which a sequence species belongs (Page 23 paragraph 2 "The GTDB extracts and curates data from both NCBI-RefSeq and NCBI-GenBank to generate a phylogeny of Archaea and Bacteria from roughly 120 ubiquitous single-copy proteins").
Robeson also teaches setting a threshold for unknown bases other than A, T, C or G, and excluding the unknown bases that exceed the threshold; and excluding sequences with insufficient classification information (Page 27 paragraph 2 "SILVA data were filtered to remove sequences containing homopolymer lengths > 8 and/or > 5 ambiguous characters, using the RESCRIPt action cull-seqs with default settings").
Robeson also teaches in the 16S rRNA gene database, when a sequence contains the same species sequence with 100% identical conditions, the sequence is a redundant sequence (Page 11 Figure 6 "DereplicateUniq: Taxonomy and Sequence dereplication using “uniq” mode (i.e. any identical sequences with differing taxonomy will not be merged)" and page 15 "We found that sequence clustering and primer trimming both also contribute to a decrease in taxonomic information, most pronounced at the species rank (Fig 11A). Untrimmed chordate sequences clustered at 97% identity (“Full_97”) contained just 77% as many unique labels as the untrimmed sequences that were only dereplicated (“Full_100”)" indicate this parameter is also adjustable up to 100% for deduplication).
Robeson also teaches in the 16S rRNA gene database, sequences with inconsistent lengths are those that are shorter than 1200 bases or longer than 1800 bases in length (Page 6 last paragraph "Results illustrate varying length distributions across databases, reflecting different proportions of Bacteria and Archaea in each, as well as different methods used to identify start and end sites in each of these databases. Notably, some outliers (as short as 200 nt and as long as 3983 nt) were initially observed in SILVA, NCBI, and GTDB, presumably representing partial and untrimmed 16S rRNA gene sequences. These were removed prior to downstream evaluation to avoid biasing performance metrics", Page 6 Figure 2 (A), and Page 27 paragraph 2 "SILVA, GTDB, and NCBI data were all found to contain unusually long and short 16S rRNA gene sequences (using the RESCRIPt action evaluate-seqs), thus Archaea sequences < 900 nt [50] and Bacteria < 1200 nt [25], as performed for the SILVA releases (e.g. https://www.arbsilva.de/documentation/release-138/) were filtered out using the RESCRIPt action filter-seqslength-by-taxon", these values are editable therefore the filtering parameters would be user-defined based on their preference).
Robeson does not explicitly teach: using a dynamic time warping algorithm for normalized classification and correction; nor the ribosomal RNA database is applied to any analytical process of any microbial phase (as interpreted above).
However, Fraley teaches using a dynamic time warping algorithm for classification of nucleic acid data (Para.0012 "The computer model algorithm can be a machine learning algorithm for automated melt curve identification classification. In some embodiments, the algorithm can identify a target sequence versus junk, identify a novel pathogen, or classify a known sequence. The machine learning algorithm can use a probabilistic model for detection of nucleic acid signatures and for classification into a known pathogen or a novel pathogen unknown to the database. The classification model selected from a generative classifier and a discriminative classifier. The generative classifier can be a Naïve Bayes classifier. The discriminative classifier can be a Support Vector Machine (SVM) or Logistics Regression. In some embodiments, the detection of unknown pathogen can use Dynamic Time Warping").
However, Kozlov teaches applying a distance algorithm (dynamic time warping (DTW), Manhattan, or similar) to the normalized strings in order to determine (or correct for) its appropriate classification (Page 2 col 2 paragraph 4 "Then, we use RAxML (23) to perform a Maximum Likelihood (ML) tree inference using the taxonomic tree as a topological constraint" and page 9 paragraph 4 "Specifically, we decided to merge some OTUs together based on additional evidence such as the phylogenetic tree topology, distances between the sequences (calculated with the arbdist tool) or expert judgement").
However, Blazewicz teaches an analytical process of microbial phase (Page 5 col 2 last paragraph "Recognizing that rRNA concentration reflects past, current and future activities in addition to different life strategies restricts its utility as a metric of real-time activity, but provides the basis for generating and testing important hypotheses. Several studies show that under repeated temporal patterns of changing environmental conditions, microbes may develop an anticipatory life strategy, enduring one phase of the cycle while preparing for a more favorable phase that regularly follows").
Therefore, while Fraley utilizes melt curve data in its models, sequence data is still incorporated for classification of a known sequence, and it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Robeson as taught by Fraley in order to classify a nucleic acid sequence (which includes rRNA) using the database(s) of Robeson (Para.0012 "the algorithm can identify a target sequence versus junk, identify a novel pathogen, or classify a known sequence"). One skilled in the art would have a reasonable expectation of success because both methods are using nucleic acid data as an input into statistical models in order to classify them.
Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Robeson as taught by Kozlov in order to obtain a fully congruent taxonomic tree with corrected inner nodes (Page 2 col 2 paragraph 4 "Thereby, we obtain a strictly bifurcating tree (a reference tree) that is fully congruent with the original taxonomic tree. Further, we label each inner node of the strictly bifurcating reference tree by the lowest common rank of its corresponding child nodes (see Figure 2A). For instance, given annotations (‘Escherichia’, ‘E.coli’) and (‘Escherichia’, ‘E.albertii’) at the child nodes, the parent node will be labeled as (‘Escherichia’)"). One skilled in the art would have a reasonable expectation of success because both approaches are concerned with curating taxonomic data during a database generating process.
Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Robeson as taught by Blazewicz in order to provide meaning insight into microbial community dynamics (page 4 col 2 last paragraph "rRNA-based measurements can provide meaningful insight into microbial community dynamics. rRNA directly relates to a population’s potential to catalyze the specific function of protein synthesis, and can therefore document the relative expression of this function. rRNA-based measurements provide a specific piece of information in the spectrum of molecular approaches (including metagenomics, metatranscriptomics, metaproteomics and community proteogenomics) that are increasingly applied to study microbial communities" and page 6 col 1 paragraph 2 "To utilize rRNA data to characterize microbial assemblages, we need to better our understanding of how these data relate to environmental conditions and community interactions"). One skilled in the art would have a reasonable expectation of success because both methods are concerned with using rRNA as a way for microbial community characterization.
Regarding claim 2, Robeson in view of Kozlov teach the methods of Claim 1 on which this claim depends/these claims depend, respectively. Robeson also teaches: the source of a nucleic acid sequence database comprises a native repository database or a value-added database (Page 20 paragraph 1 "RESCRIPt resolves many of these issues, providing automatic tools for generating and formatting custom sequence and taxonomy databases (from either marker genes or genomes) from NCBI GenBank and from SILVA").
Regarding claims 4 and 5, Robeson in view of Kozlov teach the methods of Claim 1 on which this claim depends/these claims depend, respectively. Robeson also teaches: a seventh-order nomenclature is used for normalization to form a hierarchy relation table, and hierarchies defined in the seventh-order nomenclature comprise kingdom, phylum, class, order, family, genus, and species, and the method for homogenization comprises finding out information of other hierarchy in the classification hierarchy relation table based on species names in the nucleic acid sequence database, or using a serial number as a search target for comparison with a database that stores the serial numbers based on a serial number of a species in the nucleic acid sequence database, after a species name of the serial number is found, the information of other hierarchy is found from the classification hierarchy relation table (Page 26 third to last paragraph "The NCBI download method retrieves the requested sequences from the NCBI Nucleotide database, cross-references their taxids with the NCBI Taxonomy database to obtain their taxonomic classifications, then standardizes the taxonomies to adhere to a fixed set of ranks. The set of ranks can be configured by the user but are kingdom (k__), phylum (p_), class (c_), order (o_), family (f_), genus (g_), and species (s__) by default. If a given rank is not present in the NCBI Taxonomy it is propagated down from the nearest higher rank, as described above. Rank propagation can be optionally disabled").
Regarding claim 6, Robeson in view of Kozlov teach the methods of Claim 5 on which this claim depends/these claims depend, respectively. Kozlov also teaches the step of using the AI technology to perform normalized classification and naming comprises performing a comparison according to a species hierarchy, so as to confirm that there is no repetition in sequence classification information (Page 10 col 1 last paragraph "Interestingly, the overall percentages of identified mislabels in full non-repetitive data sets (GG13_NR99 and SLV123_NR99) and in the corresponding type strain data sets (GG13_T and SLV123_T) are highly similar. However, SILVA_NR99 shows substantially more mislabels at higher taxonomic levels compared to SLV123_T (0.12% versus 0.03% at the phylum level and 0.08% versus 0% at the class level). This finding suggests that in the SILVA database, at least the most obvious misannotations were fixed for type strain sequences" indicates that the SATIVA method is able to identify mislabeled sequences in the input sequence database provided).
Regarding claim 7, Robeson in view of Kozlov teach the methods of Claim 3 on which this claim depends/these claims depend, respectively. Robeson also teaches the step of selecting the kingdom to which the sequence species belongs comprises selecting sequences belonging to a kingdom of Archaea and a kingdom of Bacteria directed at the 16S rRNA gene database, and excluding other kingdoms or sequences where a kingdom name is mistakenly named as Archaea or Bacteria (Page 23 paragraph 2 "The GTDB extracts and curates data from both NCBI-RefSeq and NCBI-GenBank to generate a phylogeny of Archaea and Bacteria from roughly 120 ubiquitous single-copy proteins [24,93]. This phylogeny is used to inform microbial taxonomy, especially in cases where a given taxonomy is observed to be polyphyletic. In this case, a conservative approach is used to remove polyphyletic groups and normalize taxonomic ranks according to their relative evolutionary divergence. Any remaining polyphyletic groups are then flagged as “regions of instability” in the hopes that future in-depth analyses will result in a stable set of classifiable taxa [24,93]. The efforts by NCBI and GTDB enable researchers to not only more accurately classify uncultured microbes, but also place them into ecological and evolutionary context based on their nearest phylogenetic neighbors").
Response to Arguments under 35 USC § 103
Applicant’s arguments filed 1/8/2026 are fully considered but they are not persuasive.
Applicant asserts that "the cited arts do not explicitly teach the technical features of 'performing normalization and homogenization on species classification rules' and 'wherein the ribosomal RNA database is applied to an analytical process of microbial phase' recited in the amended claim 1" (Remarks 1/8/2026 pages 6). Examiner notes that the prior art cited above do in fact teach or fairly suggest the technical features of the amended claim 1.
Therefore, the rejection of claim 1 under 35 USC 103 is maintained. All other claims depend from this independent claim; therefore, their rejection is likewise maintained.
Conclusion
No claims are allowed.
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 TH REE-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 finaI action.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Robert A. Player whose telephone number is (571)272-6350. The examiner can normally be reached Mon-Fri, 8am-5pm.
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/R.A.P./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686
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