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 .
Status of the Claims
Claims 1-11 and 13-22 are pending. Claim 12 is canceled.
Claims 13-18 were withdrawn following a restriction required filed 22 August 2025 and elected without traverse in the reply filed 20 October 2025. Following authorization by Jordan Garner on 12 November 2025, claims 19-20 are also treated as claims 13-18 as being directed to chemical identifiers rather than biological identifiers.
Claims 1-11 and 21-22 are examined herein.
Priority
As detailed on the date filing receipt, the application claims priority as early as 08 January 2021. At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825 because it does not contain a "Sequence Listing" as a separate part of the disclosure or a CRF of the “Sequence Listing.”.
Required response - Applicant must provide:
A "Sequence Listing" part of the disclosure; together with
An amendment specifically directing its entry into the application in accordance with 37 CFR 1.825(a)(2);
A statement that the "Sequence Listing" includes no new matter as required by 37 CFR 1.821(a)(4); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(a)(3).
If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
If the "Sequence Listing" part of the disclosure is submitted according to item 1) c) or d) above, applicant must also provide:
A CRF in accordance with 37 CFR 1.821(e)(1) or 1.821(e)(2) as required by 1.825(a)(5); and
A statement according to item 2) a) or b) above.
Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825 because the application does not contain a statement that the CRF is identical to the "Sequence Listing" part of the disclosure, as described above in item 1), as required by 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii).
Required response - Applicant must provide such statement.
Specific deficiency - This application contains a “Sequence Listing as a PDF file (37 CFR 1.821(c)(2)) or as physical sheets of paper (37 CFR 1.821(c)(3)), but fails to comply with the requirements of 37 CFR 1.821 - 1.825 because a copy of the "Sequence Listing" in computer readable form (CRF) has not been submitted as required by 37 CFR 1.821(e)(1)(i) or 1.821(e)(2)(i) as indicated in item 2) above.
Required response - Applicant must provide:
A new CRF of the “Sequence Listing” in accordance with 37 CFR 1.821(e)(1)(i) or 1.821(e)(2)(i) and
A statement that the content of the CRF is identical of the “Sequence Listing” part of the disclosure, submitted as a PDF file (37 CFR 1.821(c)(2)) or on physical sheets of paper (37 CFR 1.821(c)(3)), as required by 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii).
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
In summary, there are sequences in Fig. 5D but no sequence identifiers or the required documents that accompany disclosed sequences.
Response to remarks regarding the objection about sequences
Applicant remarks state the disclosure of sequences in Figure 5D are exemplary and the invention does not claim the sequences, and thus a sequence listing is not required (pg. 12). This is not consistent with CFR 1.821, which recites the requirement applies to applications containing the sequences, not specifically claiming the sequences. Therefore, sequence identifiers and appropriate disclosure of the sequences is required.
Specification
The objection to the disclosure is withdrawn in view of amendment correcting the typographical error.
Claim Objections
Objections previously applied to claim 1-3, 6, and 11 are withdrawn except for the objection to claim 2 regarding periods, which is maintained. According to MPEP 608.01(m), “Each claim begins with a capital letter and ends with a period. Periods may not be used elsewhere in the claims except for abbreviations. See Fressola v. Manbeck, 36 USPQ2d 1211 (D.D.C. 1995)”. The applicant may consider an amendment to replace “a.” and “b.” with “(a)” and “(b)” respectively.
Claim 11 is objected to because the spacing is not consistent with the rest of the application.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
The rejection under 35 USC 112(b) is withdrawn following amendment regarding the “patent documents.”
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 1-11 are rejected under 35 USC § 101 because the claimed inventions are directed to an abstract idea without significantly more. "Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 § I). Abstract ideas include mathematical concepts, and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)). The claims as a whole, considering all claim elements individually and in combination, are directed to a judicial exception at Step 2A, Prong 2, and the additional elements of the claims, considered individually and in combination, do not provide significantly more at Step 2B than the abstract idea of generating an artificial data environment in a computer memory.
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of
nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The claims are directed to a method (claims 1-11), which falls within one of the categories of statutory subject matter. [Step 1: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
Mathematical concepts recited in claim 1 include: extrapolating data to a first array, transforming data into numbers, generating a second array, and placing data within the second array using an algorithm. These steps are interpreted as mathematical steps of data conversion and populating arrays, where arrays are common mathematical concepts. Claim 1 recites calculating a distance metric, where calculating a metric is a verbal description of a mathematical concept.
Mental steps recited in claim 1 include assigning a curated form to a map, where assignment of data is a data evaluation or organization step; filtering based on a condition, where filtering is interpreted as data comparison and thus a mental process; and ranking according to a criterion, where ranking is data evaluation and organization.
Dependent claim 2 recites sequence alignment, which is a mental process as the segments, which appear to be approximately 10 bases long (Fig. 5D), are not too complicated for the human mind. Dependent claim 2 recites converting into a numerical form, which is a mathematical concept for the same reasons as discussed above.
Dependent claim 3 recites comparing features in an array, where the features are adjacent numbers, and so such a comparison is interpreted as a mathematical concept. Dependent claim 3 recites identifying common and non-common features, which is interpreted as a data analysis step and so a mental process of identifying differences, or a mathematical concept of a numerical comparison. Dependent claim 3 recites recombining the biologic features and placing them into the array, where these steps are interpreted as data manipulation of the numerical representations and placing the new numerical representations in an array, which are mathematical concepts. Claim 3 recites outputting a biological identifier, interpreted as a nucleic acid or amino acid sequence, which is interpreted as a mental process of converting the numbers into non-numerical form.
Claims 4-5 recite similar steps as claim 3, including selecting data, comparing features, identifying features, generated new forms, and generating a new data form to accommodate new data.
Claim 6 recites extrapolating identifier changes, generating a new combination placed in an array, and outputting a formula – interpreted as similar to an identifier – of a chemical structure based on the numerical value in the area, which are interpreted as abstract ideas for the reasons stated above.
Claim 7 recites generating a synthesis strategy, interpreted as planning and thus a mental process.
Claims 9-11 recite additional information about the biologic identifier.
Claims 21-22 recite the metrics for comparison including a computed similarity and number of forms within a given distance, which are interpreted as the criteria for performing the mental step of data comparison.
Hence, the claims explicitly recite numerous elements that, individually and in combination,
constitute abstract ideas. The claims must therefore be examined further to determine whether they
integrate that abstract idea into a practical application (MPEP 2106.04(d)). [Step 2A Prong One: Yes]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Claim 1 recites additional elements that are not abstract ideas: submitting a search to a database, obtaining a curated set of identifiers not enumerated in the previously returned documents, a computer with memory, and outputting a visual representation of an array. Claim 6 recites generating a visual display indicating numerical forms and generating a time series plot. Claim 8 recites synthesizing a biopharmaceutical based on the biologic identifier.
The claims comprising searching on a database in memory are interpreted as using a general computer to perform the functions that constitute the abstract idea. Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; and MPEP 2106.05(f)).
Obtaining identifiers is a data gathering step required for perform the abstract steps. Therefore, it is considered to be an insignificant extra-solution activity, which does not integrate the abstract ideas into a practical application (MPEP 2106.05(g)).
The claim elements comprising visual display are interpreted as data outputting, which is insignificant extra-solution activity (MPEP 2106.05(g)).
The claim elements comprising storing reads and computer modules storing code are mere instructions to apply an exception using a computer (MPEP 2106.05(f)) and insignificant extra solution activity (MPEP 2106.05(g)).
The synthesizing step is interpreted as generically claimed instructions to apply the abstract idea (MPEP 2106.05(f)). The synthesizing step does not meaningfully limit the claim because any structure could be synthesized as determined by the combinations of features in the array.
Thus, the claims recite elements in addition to the abstract ideas which do not integrate the abstract ideas into a practical application, and must be examined further to determine whether elements in addition to the abstract ideas provide significantly more (MPEP 2106.05). [Step 2A Prong Two: Yes]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
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 of 101 analysis determines whether the claims contain additional elements that amount to an inventive concept, and an inventive concept cannot be furnished by an abstract idea itself (MPEP 2106.05).
Claim 1 recites additional elements that are not abstract ideas: submitting a search to a database, obtaining a curated set of identifiers not enumerated in the previously returned documents, a computer with memory, and outputting a visual representation of an array. Claim 6 recites generating a visual display indicating numerical forms and generating a time series plot. Claim 8 recites synthesizing a biopharmaceutical based on the biologic identifier.
Searching a database and obtaining documents are a database are interpreted as transmitting data, which is a conventional computer activity (buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014); MPEP 2106.05(d)).
Display steps are interpreted as insignificant extra-solution activity (MPEP 2106.05(g)) which do not impose meaningful limits on the claim, here displaying an output of the analysis (Ameranth, 842 F.3d at 1241-42, 120 USPQ2d at 1854-55; MPEP 2106.05(g)).
A review by Sanchez-Lengeling (Science 361(6400): 360-365, 2018; previously cited) teaches molecular design as vectors and tensors, and thus within arrays (pg. 362, col. 1, last paragraph), where molecules of interest are ultimately potentially synthesized (pg. 362, col. 2, first paragraph).
Therefore, the recited additional elements, alone or in combination with the judicial exceptions, do not appear to provide an inventive concept. [Step 2B: No]
Conclusion: Claims are Directed to Non-statutory Subject Matter
For these reasons, the claims, when the limitations are considered individually and as a whole,
are directed to an abstract idea and lack an inventive concept. Hence, the claimed invention does not
constitute significantly more than the abstract idea, so the claims are rejected under 35 USC § 101 as
being directed to non-statutory subject matter.
Response to the 29 June 2026 Applicant Remarks
Applicant remarks state a particular data structure designed to improve computer functioning (pg. 13, last paragraph), analogous to McRO and Enfish. This argument is not persuasive because the disclosed steps are abstract. The steps include using an array of nodes populated by values, where the values are at least partially informed by descriptor-vector distance – interpreted as a calculated metric – which produces an output indicating a likelihood, also interpreted as a mathematical concept (pg. 13, sixth paragraph). Enfish describes an improvement to a computer but the instant claims recite largely mathematical steps of populating arrays, calculating distance metrics, and weighting to output a rank, and thus the improvement appears to be using the abstract steps for an alleged improvement to the abstract idea of determining data similarity.
Applicant remarks further assert analogy to McRO, wherein the instant claims’ steps produce an outcome that was previously subjective or manual to realize an improvement (pg. 14, third and fourth paragraph). However, this situation does not appear to be the state of the prior art, as the specification discloses using machine learning and statistics to convert chemical structures to symbolic representation (pg. 2, paragraph [4]) and low dimensionality visualization (pg. 2, paragraph [8]). The disclosed specific way are also abstract steps, specifically assigning distance-to-weight vectors, filtering, and ranking by similarity.
Generating and populating an array using an algorithm by computing distances and applying thresholds are considered to be a mathematical processes, while ranking is a mental step of data comparison.
Applicant remarks state it is improper to ask whether the claims involve a patent-ineligible concept when determining an improvement at Step 2A (pg. 14, last paragraph to pg. 15, first paragraph). However, each step in the previous office action is analyzed to determine if an abstract idea or additional element is present, and the latter are further examined at Step 2B for whether they amount to significantly more than the abstract idea(s). Applicant remarks further state: “The amended claim does not simply cause the processor to display a ranked list; it configures the processor to generate an output reflecting the ranked likelihood that curated biologic identifiers interact with a defined biological target of interest” (g. 15, second paragraph). It is unclear what the distinction is between causing a computer to display a result and configuring the computer to do so. The computer components appear to be general purpose computer elements. Further, using the ranked output to make a selection is not claimed. Making a selection based on the outputted ranked data is not required and would be considered a mental step. Downstream investigation is not claimed and thus a particular, useful application is not claimed.
Therefore, the rejection under 35 USC 101 is maintained.
Claim Rejections - 35 USC § 103 and Non-Statutory Double Patenting
The rejections under 35 USC 103 and regarding non-statutory double patenting with respect to Brogle (US 10,013,467 B1; previously cited on the 01 August 2022 IDS form) are withdrawn in view of argument and amendment regarding a second, separately-sourced set of biologic identifiers not found in the searched documents, coding them in the same form, assigning each to its closest node by distance to that node's weight vector, comparing the survivors to the document-derived coded forms resident in their assigned nodes by descriptor vector distance, filtering, and ranking the remainder to produce an output indicating the likelihood that each curated identifier interacts with the subject matter (pg. 16, second and third paragraphs). Brogle does not teach such a list and the claims are considered to be free of the prior art.
Conclusion
THIS ACTION IS MADE FINAL. 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Robert J Kallal whose telephone number is (571)272-6252. The examiner can normally be reached Monday through Friday 8 AM - 4 PM EST.
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/R.J.K./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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