DETAILED ACTION
Applicant' s response, filed 07 May 2026, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 07 May 2026 has been entered.
Claim Status
Claims 1-8, 10-17, 19, and 20 are pending and examined herein.
Claims 1-8, 10-17, 19, and 20 are rejected.
Priority
Claims 1-8, 10-17, 19, and 20 do not claim benefit of priority to an earlier filed application. Thus, the effective filling date of claims 1-8, 10-17, 19, and 20 is 01 February 2022.
Claim Objections
The objection of claim 12 for reciting “a biological sequences” in Office action mailed 19 February 2026 is withdrawn in view of the amendment of “the protein domain sequences” received 07 May 2026.
Claim Interpretation
Claims 1 and 12 recite “sparse matrix”. The instant disclosure provides “As used herein, the term “sparse matrix” refers to a matrix in which most of the elements are zero (a matrix where most of the elements have non-zero values is considered to be a dense matrix). In a sparse matrix, the number of non-zero elements is roughly equal to the number of rows or columns and the matrix has few pair-wise interactions” (instant disclosure [0027]).
Claims 1 and 12 recite “clustering, by the processor, the pair-wise distance values”. The instant disclosure provides “As used herein, the terms “cluster” and/or “clustering” refers to hierarchical clustering where similar sequences are closer together than different sequences. Within the context of the present invention, the clustering of sequences forms the initial taxonomic tree (also referred to herein as a “data tree”) for the method of microbiome classification described herein (instant disclosure [0028]).
Claim Rejections - 35 USC § 112
The rejection on the ground of 112/a of claims 1-8, 10-17, 19, and 20 in Office action mailed 19 February is withdrawn in view of the amendment of “each biological sequence in the columns of the matrix is coded with a single unique identifier (UID), a name of the internal nodes is a concatenation of single unique identifiers of each the biological sequence in a cluster” received 07 May 2026.
The rejection on the ground of 112/b of claims 1-8, 10-17, 19, and 20 for reciting “to classify a microbiome comprised of the biological sequences using the taxonomic tree” in Office action mailed 19 February is withdrawn in view of the amendment of “to classify a microbiome comprised of the biological sequences using a closer common ancestor of the final taxonomic tree” received 07 May 2026.
The rejection on the ground of 112/b of claims 1-8, 10-17, 19, and 20 for reciting “a sparse vectorization of a biological sequence” in Office action mailed 19 February is withdrawn in view of the amendment of “a sparse vectorization of the protein domain sequences” received 07 May 2026.
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.
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 1-8, 10-17, 19, and 20 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 below was previously recited.
Claims 1 and 12 recite “the node data” in “an intersection of domain identifiers of the biological sequences become the node data” which renders the metes and bonds of the claim indefinite. The indefiniteness arises because it is unclear if “the node data” is the node data for the internal nodes or if “the node data” is the node data for the leaf nodes. Dependent claims 2-8, 10, 11, 13-17, 19, and 20 are rejected by virtue of their dependency on a rejected claim without alleviating the indefiniteness. For the sake of furthering examination, “the node data” will be interpreted as the data for the internal nodes.
The rejection below is newly recited necessitated by amendment.
Claim 8 recites “the UID” which renders the metes and bonds of the claim indefinite. The indefiniteness arises because it is unclear if “the UID” is referring to the “single unique identifiers” encoded in the columns in independent claim 1 or if “the UID” is referring to the “single unique identifier (UID)” in claim 7. For the sake of furthering examination, this limitation will be interpreted as referring to the “single unique identifier (UID)” in independent claim 1.
112/d
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The rejection below is newly recited necessitated by amendment.
Claims 7 and 16 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. The claims do not further limit the method of claims 1 and 12 from which they depend from because independent claims 1 and 12 already recite each biological sequence/ protein domain sequence in the columns of the matrix is coded with a single unique identifier (UID). Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Examiners comment
It is noted that no argument was presented for the above previously recited rejection. Further, the amendment received 07 May 2026 does not alleviate the issue of indefiniteness as discussed above.
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.
The rejection below has been modified necessitated by amendment.
Claims 1-8, 10-17, 19, and 20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
(Step 1)
Claims 1-8, 10-17, 19, and 20 fall under the statutory category of a process.
(Step 2A Prong 1)
Under the BRI, the instant claims recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mental process”, such as procedures for evaluating, analyzing or organizing information, and forming judgement or an opinion. The instant claims further recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mathematical concept”, such as mathematical relationships and mathematical equations.
Independent claim 1 recites mental processes of “selecting a reference database… wherein each biological sequence is annotated with a code from at least one coding system”, “constructing a matrix comprising rows, columns, and cells… wherein the matrix is a sparse matrix and each row of the matrix is a sparse vectorization of the biological sequences that are related to one or more codes of the at least one coding system”, “computing pair-wise distance… wherein the pair-wise distance computations between all of the rows of the matrix is an NxN matrix, wherein N is a number of codes in the matrix”, “clustering the pair-wise distance values for each code to form a data structure tree comprising clusters, wherein the clusters represent a relationship between a code of the at least one coding system and one or more biological sequences”, “constructing based on the data structure tree comprising clusters, a taxonomic tree… wherein the internal nodes represent clusters of the data structure tree, each biological sequence in the columns of the matrix is coded with a single unique identifier, a name of the internal nodes is a concatenation of single unique identifiers of each biological sequence in a cluster, an intersection of domain identifiers of the biological sequences become the node data, and the internal nodes and the lead nodes represent the biological sequences”, and “applying a classification tool to a final taxonomic tree… using a closer common ancestor of the final taxonomic tree, wherein the classification measures a receiver operating characteristic curve to select a strategy for classifier construction”.
Independent claim 12 recites mental processes of “selecting a reference database… wherein each protein domain sequence is annotated with a code from at least one coding system”, “constructing a matrix comprising rows, columns, and cells… wherein the matrix is a sparse matrix and each row of the matrix is a sparse vectorization of the protein domain sequences that are related to one or more codes of the at least one coding system”, “computing pair-wise distance… wherein the pair-wise distance computations between all of the rows of the matrix is an NxN matrix, wherein N is a number of codes in the matrix”, “clustering the pair-wise distance values for each code to form a data structure tree comprising clusters, wherein the clusters represent a relationship between a code of the at least one coding system and one or more protein domain sequences”, “constructing based on the data structure tree comprising clusters, a taxonomic tree… wherein the internal nodes represent clusters of the data structure tree, each protein domain sequence in the columns of the matrix is coded with a single unique identifier, a name of the internal nodes is a concatenation of single unique identifiers of each protein domain sequences in a cluster, an intersection of domain identifiers of the protein domain sequences become the node data, and the internal nodes and the lead nodes represent the protein domain sequences”, and “applying a classification tool to a final taxonomic tree… using a closer common ancestor of the final taxonomic tree, wherein the classification measures a receiver operating characteristic curve to select a strategy for classifier construction”.
Independent claims 1 and 12 recite a mathematical concept of “constructing a matrix comprising rows, columns, and cells….” and “computing pair-wise distance between the rows of the matrix…”.
The claims recite analyzing/evaluating data and making judgements selecting a reference database, computing pair-wise distance between the rows of the matrix, and applying a classification tool to the final taxonomic tree. The claims recite organizing data of constructing a matrix comprising rows, columns, and cells, clustering the pair-wise distance values for each code to form a data structure tree, and constructing a taxonomic tree comprising internal nodes and leaf nodes. The human mind is capable of analyzing/evaluating data and making judgements such as a selection process of a reference database to use with relevant information, computing pairwise distances using mathematical equations to determine pair-wise distances (see instant disclosure [0022]-[0026]), and performing classifications utilizing a taxonomic tree and organizing data of constructing a sparse matrix with the relevant information, constructing a data structure tree, and constructing a taxonomic tree based on the data structure tree. The claims recite a mathematical concept of computing pair-wise distance between the rows of the matrix which is a mathematical calculation of a pair-wise distance that uses a function to intake numerical values and outputs a numerical value (see instant disclosure [0022]-[0026]) and the claims also recite a mathematical concept of constructing a sparse matrix utilizing numerical data representing the presence, absence, or frequency of a sequence. Dependent claims 2-11 and 13-17, 19, and 20 further limit the mental process/mathematical concept recited in the independent claim but do not change their nature as a mental process/mathematical concept. Thus, claims 1-8, 10-17, 19, and 20 recite abstract ideas.
(Step 2A Prong 2)
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). Integration into a practical application is evaluated by identifying whether there are any additional elements recited in the claim and evaluating those additional elements to determine whether they integrate the exception into a practical application.
The additional element in claims 1 and 12 of using a generic computer to perform judicial exceptions does not integrate the judicial exceptions into a practical application because this is simply applying the judicial exception to a generic computer environment without and improvement to computer technology. This additional element of a generic computer only interacts with the judicial exceptions in a manner by being utilized as tool to perform abstract ideas.
Therefore, the judicial exceptions in the claims are not integrated into a practical application and claims 1-8, 10-17, 19, and 20 are directed to the abstract idea.
(Step 2B)
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 additional element in claims 1 and 12 of using a generic computer to perform judicial exceptions is conventional as shown by MPEP 2106.05(b) and MPEP 2106.05(d)(II).
Therefore, claims do not recite an inventive concept that provides significantly more than the judicial exceptions.
Response to Arguments
Applicant's arguments filed 07 May 2026 have been fully considered but they are not persuasive.
Applicant argues the claims include elements that integrate the judicial exceptions into a practical application by providing a technological improvement in the field of microbiome classification (Reply p. 8-9). Applicant argues the building of the structure of the classifier leads to an increase in computational efficiency (Reply p. 9). Applicant provides that the instant disclosure describes the technological improvement which states that the functional classifier described herein is computationally efficient and therefore, is less expensive and resource intensive than currently used coding systems (Reply p. 9). Applicant further provides that the claims recite limitations in the independent claims which incorporate the improvement described in the instant disclosure (Reply p. 9-10).
This argument has been fully considered but found to not be persuasive. The MPEP states in computer-related technologies, the examiner should determine whether the claim purports to improve computer capabilities or, instead, invokes computers merely as a tool. Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1336, 118 USPQ2d 1684, 1689 (Fed. Cir. 2016) (MPEP 2106.05(a)(I)). In the instant case, the argued improvement of microbiome classification is interpreted as falling under the abstract idea itself. Although the process is computationally efficient and therefore, is less expensive and resource intensive than currently used coding systems, this efficiency is provided by the abstract ideas alone (i.e., the steps of the process reciting judicial exceptions as identified in the above rejection which includes building the structure of the classifier) which are implemented on the computer. The computer is utilized as a tool to perform the judicial exceptions and thus does not improve computer capabilities. Further, the MPEP states “It is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements… In addition, the improvement can be provided by the additional element(s) in combination with the recited judicial exception” (see MPEP 2106.05(a)) which shows that the judicial exception alone cannot provide the improvement. As stated above, the computational efficiency of the process is provided by the judicial exception alone (i.e., the abstract ideas) and thus cannot provide the improvement.
Conclusion
No claims are allowed.
Claims 1-8, 10-17, 19, and 20 are free of the prior art of record. The closest prior art of record is Utro et al. (Science 23: 100988, pp. 1-23 (2020); previously cited) which shows sequence read classification with respect to a functional hierarchy that provides the lowest taxonomic unit of a maximal exact match for a query sequence utilizing a tree-based data structure. However, the prior art of record does not show or render obvious constructing a matrix wherein the matrix is a sparse matrix and each row of the matrix is a sparse vectorization of the biological sequences that are related to one or more codes of the at least one coding system or constructing a taxonomic tree comprising internal nodes and leaf nodes, wherein the internal nodes represent the clusters of the data structure tree, each biological sequence in the columns of the matrix is coded with a single unique identifier (UID), a name of the internal nodes is a concatenation of single unique identifiers of each biological sequence in a cluster, an intersection of domain identifiers of the biological sequences become the node data, and the internal nodes and the leaf nodes represent the biological sequences. Therefore, the claims are free of the prior art of record.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JONATHAN EDWARD HAYES whose telephone number is (571)272-6165. The examiner can normally be reached M-F 9am-5pm.
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/J.E.H./Examiner, Art Unit 1685
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685
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