DETAILED ACTION
The Applicant’s response, received 14 November 2025, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
Claims 20, 47-53, and 55-59 are pending.
Claims 20, 47-53, and 55-59 are rejected.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
This application is a 371 of PCT/EP2020/053220, filed 07 February 2020.
The effective filing date of claims 20, 47-53, and 55-59 is 07 February 2020.
Claims 20, 47-53, and 55-59 are given the benefit of PCT/EP2020/053220, filed 07 February 2020.
Claims 20, 47-53, and 55-59 are not given the benefit of Foreign Application No. EPO 19156085, filed 07 February 2019, because there is not support for the limitation “generating a directed graph”.
Claims 20, 47-53, and 55-59 are not given the benefit of Foreign Application No. EPO 19190899, filed 08 August 2019, because there is not support for the limitation “generating a directed graph.”
Claims 20, 47-53, and 55-59 are not given the benefit of Foreign Application No. BE 2019/5077, filed 07 February 2019, because there is not support for the limitation “generating a directed graph.”
Information Disclosure Statement
The information disclosure statement (IDS) received 11 July 2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Claim Interpretation
Claims 20, 47-50, 55, and 57 recite the term “biological sequence(s).” This term is interpreted to mean a data sequence of a biopolymer defining at least the biopolymer’s primary structure, and can for example be a deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or a protein (Specification, page 12, ¶ [76]).
Claims 20, 49, 51, 52, 55, 56, and 58 recite the term “characteristic biological subsequence(s).” This term is interpreted to mean a portion of biological sequence data that is smaller than the full biological sequence (Specification, page 12, ¶ [78]), and is one sequence unit shorter than a subsequence that is not found in any biological sequence database (Specification, page 14, ¶¶ [84] - [85]). This term is further interpreted to be synonymous with the term HYFT fingerprint (Specification, page 12, ¶ [79]; & page 14, ¶ [85]).
Claims 20, 48-50, 53, 55, 57, and 59 recite the term “fingerprint data string(s).” This term is interpreted to mean a data string that is representative of one or more characteristic biological subsequences (HYFT fingerprints) (Specification, page 3, ¶ [17]; and page 12, ¶ [79]).
Claim Rejections - 35 USC § 112
The rejection of claims 49-60 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, in the Office action mailed 14 July 2025 is withdrawn in part and maintained in part in view of the amendment received 14 November 2025, as noted below.
The Applicant’s amendment received 14 November 2025 has been fully considered, however after further consideration, new grounds of rejection are raised under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, in view of the amendment.
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 20, 47-53, and 55-59 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.
Independent claims 20, 49, and 55 contain the trademark/trade name “HYFT”. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name.
In the present case, the trademark/trade name is used to identify/describe subsequences of data and, accordingly, the identification/description is indefinite.
Claims 47, 48, 50-53, and 56-59 are indefinite for depending from either of claims 20, 49, or 55 and for failing to remedy the indefiniteness of the claim from which they depend.
Claim 20 is indefinite for reciting “generating a directed graph in order to reconstruct and store the identified characteristic biological subsequence and/or said one or more further characteristic biological subsequences as a HYFT graph comprising said one or more fingerprint data strings, and storing the one or more fingerprint data strings…” at step (b), because it is not clear as to whether “generating a directed graph in order to reconstruct and store…” is an intended use of the directed graph, or if the claim requires an active step of actually reconstructing and storing the sequence data as a directed graph.
Claims 47 and 48 are indefinite for depending from claim 20 and for failing to remedy the indefiniteness of claim 20.
The following rejection is maintained.
Claims 49 and 55 recite the limitation “the characteristic biological sequence” at step (c). There is insufficient antecedent basis for this limitation in the claims, because the claims only provide antecedent basis for the limitation “characteristic biological subsequence” (emphasis added).
Claims 50-53 and 56-59 are indefinite for depending from either claim 49 or 55 and for failing to remedy the indefiniteness of the claim from which they depend.
Response to Arguments
The Applicant’s arguments/remarks received 14 November 2025 have been fully considered, and are not persuasive in part, as noted below.
The Applicant states on page 9/14 of the Remarks that claims 49 and 55 are currently amended to address the indefiniteness concerns raised in the Office action, and at least in view of the amendment to the claims, the rejection is moot.
This argument is not persuasive, because as noted in the above rejection, claims 49 and 55 recite the limitation “the characteristic biological sequence” at step (c). There is insufficient antecedent basis for this limitation in the claims, because the claims only provide antecedent basis for the limitation “characteristic biological subsequence” (emphasis added).
Claim Rejections - 35 USC § 101
The Applicant’s amendment received 14 November 2025 has been fully considered, however after further consideration, the rejection of claims 20 and 47-60 under 35 U.S.C. 101 in the Office action mailed 14 July 2025 is maintained with modification in view of the amendment.
The rejection of claims 54 and 60 under 35 U.S.C. 101 in the Office action mailed 14 July 2025 is withdrawn in view of these claims having been cancelled in the amendment received 14 November 2025.
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 20, 47-53, and 55-59 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mental processes, i.e., concepts performed in the human mind (e.g., observation, evaluation, judgement, opinion); and (b) mathematical concepts (e.g., mathematical relationships, formulas or equations, mathematical calculations).
Subject matter eligibility evaluation in accordance with MPEP 2106.
Eligibility Step 1: Claims 20, 47, and 48 are directed to a method (process) for generating fingerprint data strings; claims 49-53 are directed to a data storage and retrieval system (machine or manufacture); and claims 55-59 are directed to a method (process) for storing and retrieving data.
Therefore, these claims are encompassed by the categories of statutory subject matter, and thus, satisfy the subject matter eligibility requirements under Step 1.
[Step 1: YES]
Eligibility Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2A: Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes whether the claim recites a judicial exception, i.e., whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim.
Independent claim 20 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
at step (a), identifying a characteristic biological subsequence in a biological sequence (i.e., mental processes);
identifying a first subsequence that does not appear in the biological sequence (i.e., mental processes);
removing a terminal sequence unit to form a second subsequence from the first subsequence (i.e., mental processes), and
when the second subsequence does appear in the biological sequence, defining the second subsequence as the characteristic biological subsequence (i.e., mental processes);
at step (b), generating one or more fingerprint data strings representing the identified characteristic biological subsequence and/or one or more further characteristic biological subsequences representing a translation of the identified characteristic biological subsequence (i.e., mental processes);
generating a directed graph in order to reconstruct and store the identified characteristic biological subsequence and/or said one or more further characteristic biological subsequences as a HYFT graph comprising said one or more fingerprint data strings (i.e., mental processes and mathematical concepts);
wherein each fingerprint data string represents a characteristic biological subsequence made up of sequence units, the sequence units comprising amino acids when the characteristic biological subsequence relates to a protein and codons when the characteristic biological subsequence relates to DNA or RNA (i.e., mental processes), and
the characteristic biological subsequences having varying lengths of between 4 and 20 sequence units (i.e., mental processes).
Independent claim 49 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
at step (a), identifying a characteristic biological subsequence in a biological sequence (i.e., mental processes);
identifying a first subsequence that does not appear in the biological sequence (i.e., mental processes);
removing a terminal sequence unit to form a second subsequence from the first subsequence, and when the second subsequence does appear in the biological sequence, defining the second subsequence as the characteristic biological subsequence (i.e., mental processes);
at step (b), generating one or more fingerprint data strings representing the identified characteristic biological subsequence and/or one or more further characteristic biological subsequences representing a translation of the identified characteristic biological subsequence (i.e., mental processes);
at step (c), generating processed biological sequences from the biological sequence by replacing each occurrence of the characteristic biological sequence with a fingerprint marker associated with the one or more fingerprint data strings (i.e., mental processes);
generating a directed graph in order to reconstruct each of the processed biological sequences as a HYFT graph comprising said one or more fingerprint data strings (i.e., mental processes and mathematical concepts);
wherein each fingerprint data string represents a characteristic biological subsequence made up of sequence units, the sequence units comprising amino acids when the characteristic biological subsequence relates to a protein and codons when the characteristic biological subsequence relates to DNA or RNA (i.e., mental processes).
Independent claim 55 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
at step (a), identifying a characteristic biological subsequence in a biological sequence (i.e., mental processes);
identifying a first subsequence that does not appear in the biological sequence (i.e., mental processes);
removing a terminal sequence unit to form a second subsequence from the first subsequence (i.e., mental processes), and
when the second subsequence does appear in the biological sequence, defining the second subsequence as the characteristic biological subsequence (i.e., mental processes);
at step (b), generating one or more fingerprint data strings representing the identified characteristic biological subsequence and/or one or more further characteristic biological subsequences representing a translation of the identified characteristic biological subsequence (i.e., mental processes);
at step (c), generating processed biological sequences from the biological sequence database by replacing each occurrence of the characteristic biological sequence with a fingerprint marker associated with the one or more fingerprint data strings (i.e., mental processes);
generating a directed graph in order to reconstruct each of the processed biological sequences as a HYFT graph comprising said one or more fingerprint data strings (i.e., mental processes and mathematical concepts);
wherein each fingerprint data string represents a characteristic biological subsequence made up of sequence units, the sequence units comprising amino acids when the characteristic biological subsequence relates to a protein and codons when the characteristic biological subsequence relates to DNA or RNA (i.e., mental processes).
Dependent claims 47, 48, 50-53, and 56-59 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 47 further recites:
at least 661 unique sequences with a length of at least 359 sequence units (i.e., mental processes).
Dependent claim 48 further recites:
wherein at least one of the one or more fingerprint data strings is found in each sequence of the biological sequences (i.e., mental processes).
Dependent claim 50 further recites:
wherein at least one of the one or more fingerprint data strings is found in each sequence of the biological sequences (i.e., mental processes).
Dependent claim 51 further recites:
wherein the characteristic biological subsequences have varying lengths of between 4 and 20 sequence units (i.e., mental processes).
Dependent claim 52 further recites:
wherein the replacing each occurrence of the characteristic biological subsequences is performed in order of from longest to shortest characteristic biological subsequences (i.e., mental processes).
Dependent claim 53 further recites:
wherein the one or more fingerprint data strings comprise a direction and positional information (i.e., mental processes).
Dependent claim 56 further recites:
wherein the characteristic biological subsequences have varying lengths of between 4 and 20 sequence units (i.e., mental processes).
Dependent claim 57 further recites:
wherein at least one of the one or more fingerprint data strings is found in each sequence of the biological sequences (i.e., mental processes).
Dependent claim 58 further recites:
wherein the replacing occurrences of the characteristic biological subsequences in step (c) is performed in order of from longest to shortest characteristic biological subsequences (i.e., mental processes).
Dependent claim 59 further recites:
wherein the one or more fingerprint data strings comprise a direction and positional information (i.e., mental processes).
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pen and paper (e.g., identifying a characteristic biological subsequence in a biological sequence), and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas (e.g., generating a directed graph) are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind.
Therefore, claims 20, 47-53, and 55-59 recite an abstract idea.
[Step 2A Prong One: YES]
Eligibility Step 2A Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d) subsection I; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A Prong One are not integrated into a practical application because of the reasons noted below.
Dependent claims 51-53, 56, 58, and 59 do not recite any elements in addition to the judicial exception(s), and thus are part of the judicial exception.
The additional elements in independent claims 20, 49, and 55 include:
a computer (claims 20 and 55);
at least one processor (claims 20, 49, and 55);
a non-transitory computer readable storage medium (claims 20, 49, and 55);
a database (claims 20, 49, and 55); and
storing data (i.e., in a non-transitory computer readable storage medium) (claims 20, 49, and 55).
The additional elements in dependent claims 47, 48, 50, and 57 include:
a database (claims 47, 48, 50, and 57).
The additional elements of a computer (claims 20 and 55); at least one processor (claims 20, 49, and 55); and a non-transitory computer readable storage medium (claims 20, 49, and 55); invoke a computer and/or computer-related components merely as tools for use in the claimed process, and therefore are not an improvement to computer functionality itself, or an improvement to any other technology or technical field, and thus, do not integrate the judicial exceptions into a practical application (MPEP 2106.04(d)(1)).
The additional element of accessing data in a database (claims 20, 47, 48, 49, 50, 55, and 57) is merely a pre-solution activity that is part of the gathering of data for use in the claimed process – a nominal addition to the claims that does not meaningfully limit the claims, and therefore does not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
The additional element of storing data (i.e., in the non-transitory computer readable storage medium) (claims 20, 49, and 55) is merely a post-solution activity used in the claimed process – a nominal addition to the claims that does not meaningfully limit the claims, and therefore does not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
Thus, the additionally recited elements merely invoke a computer and/or computer related components as tools; and/or amount to insignificant extra-solution activity; and as such, when all limitations in claims 20, 47-53, and 55-59 have been considered as a whole, the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 20, 47-53, and 55-59 are directed to an abstract idea (MPEP 2106.04(d)).
[Step 2A Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they amount to significantly more than the judicial exception (MPEP 2106.05A i-vi).
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below.
Dependent claims 51-53, 56, 58, and 59 do not recite any elements in addition to the judicial exception(s).
The additional elements recited in independent claims 20, 49, and 55 and dependent claims 47, 48, 50, and 57 are identified above, and carried over from Step 2A: Prong Two along with their conclusions for analysis at Step 2B. Any additional element or combination of elements that was considered to be insignificant extra-solution activity at Step 2A: Prong Two was re-evaluated at Step 2B, because if such re-evaluation finds that the element is unconventional or otherwise more than what is well-understood, routine, conventional activity in the field, this finding may indicate that the additional element is no longer considered to be insignificant; and all additional elements and combination of elements were evaluated to determine whether any additional elements or combination of elements are other than what is well-understood, routine, conventional activity in the field, or simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, per MPEP 2106.05(d).
The additional elements of a computer (claims 20 and 55); at least one processor (claims 20, 49, and 55); a non-transitory computer readable storage medium (claims 20, 49, and 55); accessing data in a database (claims 20, 47, 48, 49, 50, 55, and 57); and storing data (claims 20, 49, and 55); are conventional (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
Therefore, when taken alone, all additional elements in claims 20, 47-53, and 55-59 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 20, 47-53, and 55-59 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)).
[Step 2B: NO]
Response to Arguments
The Applicant’s arguments/remarks received 14 November 2025 have been fully considered, but are not persuasive.
The Applicant states on page 10/14 (para. 2) of the Remarks that as amended, independent claims 20, 49 and 55 require generating a directed graph in order to reconstruct biological sequences as HYFT graphs comprising one or more fingerprint data strings. The Applicant further states (para. 3) that the amended claims require a level of complexity that cannot practically be performed in the human mind and the claims cannot be directed to an abstract idea of a mental process, and that notably, the claims require sequence units comprising amino acids, of which there are 20 possibilities, and codons, of which there are 64 possibilities, and with these sequence units, the characteristic biological subsequences are defined as having in the biological sequence database a combinatory number which is lower than the total number of different sequence units available thereto, the combinatory number of a biological subsequence being defined as the number of different sequence units that appear in the biological sequence database as a consecutive sequence unit of the biological subsequence. The Applicant points to the MPEP at 2106.04(a)(2)(III)(A) (i.e., a claim to a specific data encryption method for computer communication involving a several-step manipulation of data, Synopsys., 839 F.3d at 1148, 120 USPQ2d at 1481 (distinguishing the claims un TQP Development, LLC v. Intuit Inc., 2014 WL 651935 (E.D. Tex. 2014)”) and further states (para. 4) that the characteristic biological subsequences themselves are required to have varying lengths of between 4 and 20 sequence units, and as such, providing a characteristic biological subsequence according to the amended claims requires a multi-variable transformation of biological sequences in a sequence database that cannot be practically performed in the human mind.
These arguments are not persuasive, because first, the instant claims are analyzed for eligibility in accordance with their broadest reasonable interpretation, and are further analyzed based on the fact patterns set forth by the limitations recited in the claims. Thus, the eligibility analysis of the instant claims in the rejection above results in a different eligibility outcome than in TQP Development, LLC v. Intuit Inc., or Synopsys., as pointed to by the Applicant in the argument above. Second, the fact pattern of the instant claims (i.e., biological sequence information handling, e.g., processing sequences) differs from TQP Development, LLC v. Intuit Inc. (transmitting encrypted data over a communication link by changing encryption keys) and Synopsys (translating a functional description of a logic circuit into a hardware component description of the logic circuit). Third, the amount of data, in and of itself is not a limitation which takes a process out of the realm of the human mind. It is the process performed on that data which is the mental step. Although the amount of data may be considered to be significantly large and take considerable time and effort to process manually, the use of a general-purpose computer to perform the claimed method at a rate and accuracy that can far outstrip the mental performance of a skilled artisan does not change the nature of the activity being performed (i.e., an abstract idea), and therefore does not materially alter the patent eligibility of the claimed subject matter. Fourth, the several-step manipulation of data as recited by the instant claims differs from TQP Development, LLC v. Intuit Inc. not least in that the instantly claimed method involves searching for a subsequence that does not exist within a sequence (e.g., as in para. [84] in the Specification) and identifying the subsequence one sequence unit shorter that does exist within the sequence (e.g., as in para. [85] in the Specification), and using that subsequence for further data analysis (e.g., as in paras. [86] & [87] in the Specification), which differs markedly from claim 1 at issue in TQP Development, LLC v. Intuit Inc. that involves a several-step manipulation of data of (1) inputting a seed value to identical pseudo-random number generators in the transmitter and receiver, (2) using the pseudo-random number generators to generate identical new key values at the transmitter and receiver, and (3) changing the key values at the transmitter and receiver at a time dictated by a predetermined condition of the data being transmitted; specifically, by changing the key value each time a predetermined number of blocks of data are transmitted. Fifth, the steps of generating a directed graph in order to reconstruct biological sequences as HYFT graphs comprising one or more fingerprint data strings comprise the judicial exceptions identified at Step 2A Prong One.
The Applicant points to the specification (Specification, paras. [05-06]) on page 11/14 of the Remarks, and states on page 12/14 (para. 1) that the amended claims address the technical challenges in the art discussed in the specification by configuring a system and method for generating and storing processed biological sequences involving a several-step manipulation. The Applicant points to Smartflash LLC v. Apple Inc. (Fed. Cir. No. 2016-1059), slip op. 8, and Affinity Labs of Texas, LLC v. DIRECTV, LLC, 838 F.3d 1253 (Fed. Cir. 2016), slip op. 6, and further states (para. 2) that the proper test is not merely to determine if an abstract idea can be identified somewhere in the claims, but rather to evaluate the focus of the claimed advance over the prior art to determine the claim’s character as a whole. The Applicant further states (para. 3) that the amended claims, when each is considered as a whole, recite an additional element of a HYFT graph framework according to paras. [31] and [116-120] of the disclosure that applies the alleged judicial exceptions in a manner that imposes a meaningful limit on the judicial exceptions, and therefore integrates the judicial exceptions into a practical application. The Applicant further states (para. 4) that the practical application is an improved sequence graph data structure representing fingerprint data strings at targeted locations, which provides a framework for realigning relevant sequence reads for faster and more accurate characterization of the sequence reads at a lower processing cost. The Applicant further states (para. 5) that the claims are not directed to an abstract idea but recite an improvement in computer technology as in Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1336, 118 USPQ2d 1684, 1689 (Fed. Cir. 2016), and further states that at least paras. [05-9] of the current disclosure describe challenges in accessing, analyzing, or employing sequence information in a meaningful way, and that these challenges are overcome by unconventional additional element of a HYFT graph sequence structure. The Applicant further points to the disclosure and further states on page 13/14 (para. 1) of the Remarks that the focus of the claims is the specifically recited computer-related devices and operations that result in the technical advantages of reducing storage space requirements, reducing computational requirements, providing lossless processing, enabling flexibility and scalability, avoiding accumulation of errors that result from prior art methods, and further resulting in an improved relational database, NoSQL database, or the like, and as such, the claims recite an improvement in computer technology as in Enfish.
These arguments are not persuasive, because first, with regard to the Applicant’s argument “that the proper test not merely to determine if an abstract idea can be identified somewhere in the claims, but rather is to evaluate the focus of the claimed advance over the prior art to determine the claim’s character as a whole” it is noted that this refers to the “abstract idea” step, which is the first part (i.e., Step 2A) of the two-part test used to evaluate the eligibility of claims, and referred to as the Alice/Mayo test. The first part of the Alice/Mayo test is to determine whether the claims are directed to an abstract idea, a law of nature or a natural phenomenon (i.e., a judicial exception). If the claims are directed to a judicial exception, the second part of the Alice/Mayo test is to determine whether the claim recites additional elements that amount to significantly more than the judicial exception, i.e., the "search for an 'inventive concept" (see MPEP 2106 I.). As noted in the rejection above, at Eligibility Step 2A, first it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception, and when all limitations in claims 20, 47-53, and 55-59 have been considered as a whole at Prong Two, the claims are deemed to not recite any additional elements that would integrate any judicial exceptions identified at Prong One into a practical application, and therefore claims 20, 47-53, and 55-59 are directed to an abstract idea (MPEP 2106.04(d)). Second, the step of generating a directed graph is not identified as an additional element, but rather, is identified as a judicial exception (i.e., mental process and mathematical concept) in the above rejection, and therefore the limitation of generating a directed graph does not integrate the judicial exceptions into a practical application at Eligibility Step 2A Prong Two, or provide an inventive concept at Eligibility Step 2B, as discussed in the above rejection. Third, with regard to the Applicant’s attempt to analogize the instant claims to Enfish, it is again noted that the instant claims are analyzed for eligibility in accordance with their broadest reasonable interpretation, and are further analyzed based on the fact patterns set forth by the limitations recited in the claims. Thus, the eligibility analysis of the instant claims in the rejection above results in a different eligibility outcome than in Enfish, as pointed to by the Applicant in the argument above. Fourth, the fact pattern of the instant claims (i.e., biological sequence information handling, e.g., processing sequences) differs from Enfish (a data storage and retrieval system for computer memory). Fifth, the claims at issue in Enfish were found to not be directed to an abstract idea, but rather directed to a specific improvement to the way that computers operate, embodied in a data structure that corresponds to a storage and retrieval structure configured in a computer memory comprising a self-referential table that is designed to improve the way a computer stores and retrieves data in memory, and thus is an improvement to computer functionality itself. Stated a different way, the improvement was found in the structure of the table itself (e.g., relationships between rows and columns), irrespective of any particular data being stored or searched. In contrast, the eligibility analysis of the instant claims has determined, as shown in the rejection above, that the claims are directed to an abstract idea (i.e., sequence data manipulation) at Eligibility Step 2A for which computers are invoked merely as a tool. Sixth, since the eligibility analysis of the instant claims at Step 2A determined that the claims are directed to a judicial exception, the additional elements (which do not include the limitation of a directed graph, which is a judicial exception) recited by the claims are further evaluated at Step 2B to determine whether they amount to an inventive concept, i.e., amount to significantly more than the judicial exceptions. As noted in the rejection above, and in the foregoing responses to arguments, when all instantly claimed additional elements are analyzed at Step 2B, when taken alone, all additional elements in claims 20, 47-53, and 55-59 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 20, 47-53, and 55-59 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)).
The Applicant states on page 13/14 (para. 2) of the Remarks, that finally, taken together, all of these foregoing features are clearly more than limitations that the courts have recognized, or those in the art would recognize, as elements that are well-understood, routine and conventional, and further states that the recited nonconventional and non-generic arrangements of the claim limitations provide improvements to the underlying technology or technical field, as taught in at least the cited portions of the disclosure (Remarks, p. 14, bottom), and points to MPEP 2106.05(a) or, alternatively, MPEP 2106.05(e). The Applicant further states that notably, the claimed limitations move from abstract scientific principle to specific application, and points to MPEP 2106.05(e) citing Classen.
These arguments are not persuasive, because first, with regard to the Applicant pointing to MPEP 2106.05(e) citing Classen, and stating that notably, the claimed limitations move from abstract scientific principle to specific application, it is noted the MPEP 2106.05(e) (Other Meaningful Limitations) shows that the phrase “meaningful limitations” is used to describe additional elements that provide an inventive concept to the claim as a whole. As noted in the rejection above, the additional elements of a computer (claims 20 and 55); at least one processor (claims 20, 49, and 55); a non-transitory computer readable storage medium (claims 20, 49, and 55); accessing data in a database (claims 20, 47, 48, 49, 50, 55, and 57); and storing data (claims 20, 49, and 55); are conventional (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes). Therefore, when taken alone, all additional elements in claims 20, 47-53, and 55-59 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 20, 47-53, and 55-59 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)). Second, the MPEP at 2106.05(e) (Other Meaningful Limitations) shows that there was an additional element (i.e., an immunization step) in Classen that was meaningful because it integrated the results of the analysis (i.e., abstract idea) into a specific and tangible method that resulted in the method “moving from abstract scientific principle to specific application.” In contrast, the instant claims do not recite any additional elements that meaningfully limit the abstract ideas, because the additional elements are conventional at Eligibility Step 2B, as shown in the rejection above.
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 THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/S.W.B./Examiner, Art Unit 1687
/Joseph Woitach/Primary Examiner, Art Unit 1687