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 13-20 are pending. Claim 12 is canceled.
Claims 13-18 are withdrawn following a restriction required filed 22 August 2025 and elected without traverse in the reply filed 20 October 2025.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 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.
Information Disclosure Statement
Information disclosure statements (IDS) were filed on 01 August 2022 and 20 October 2025. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the references are being considered by the examiner.
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.
Specification
The disclosure is objected to because of the following informality: “protein” is misspelled as “protien” (pg. 23, paragraph 80).
Appropriate correction is required.
Claim Objections
Claims 1 is objected to because the “submitting” element of claim 1 is not indented as the following elements are.
Claim 2 is objected to because the steps of claim 2 should be in the present participle (e.g., “aligning” and “converting”) to be in the same format as the other method steps. The steps of claim 2 should be joined by the conjunction “and” if both the “aligning” and “converting” steps are required. Furthermore, claim 2 is objected to for reciting “a.”, “b.”, and “c.” to delineate components of the claimed kit. 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 3 is objected to because “Original” has a period rather than a close parenthesis.
Claim 6 is objected to because, in the second limitation, “the publication” should recite “a rate of publication.” Additionally, claim 6 also recites “a development path for an inventor or assignee; common to the patent documents returned from the search.” It is assumed the semicolon should be a comma.
Claim 11 is objected to because “the biologic target is protein” should recite “the biologic target is a protein.”
Appropriate correction is required.
Claim Rejections - 35 USC § 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.
Claims 6-8 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.
Claim 6 recites the limitation "the patent documents” but patent documents are not previously instantiated in the claim or its parents. There is insufficient antecedent basis for this limitation in the claim. Claims 7-8 are rejected on similar grounds because they depend on claim 6 and do not resolve the antecedence issue.
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 both individually and in combination, do not amount to significantly more 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, adding data into the first array, generating a second array, and placing data within the second array. These steps are interpreted as mathematical steps of data conversion and populating arrays, where arrays are common mathematical concepts.
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.
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: 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, 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)).
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.
[Step 2A Prong Two: No]
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 1recites additional elements that are not abstract ideas: submitting a search to a database, 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 is 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; newly 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.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-13 are rejected under 35 U.S.C. 103 as being unpatentable over the features of Brogle (US 10,013,467 B1; previously cited on the 01 August 2022 IDS form).
Claim 1 recites submitting, in electronic form, a search to at least one document database for documents describing the subject matter using a defined search strategy.
Brogle teaches “submitting, in electronic form, a search to at least one document database for documents describing the subject matter using a defined search strategy” (pg. 31, lines 47-48).
Claim 1 recites extrapolating, to a first array within the memory of the computer, at least one
biologic identifier described in at least one document returned from the search, the extrapolating step using an extraction module comprising code executing in a processor.
Brogle teaches “extrapolating, to a first array within the memory of the computer, at least one chemical identifier described in at least one document returned from the search, the extrapolating step using an extraction module comprising code executing in a processor” (col. 31, lines 50-54) and biologic identifiers (col. 5, line 53).
Claim 1 recites transforming each biologic identifier in the first array into a respective coded form having a range of values using a conversion module comprising code executing in the processor.
Brogle teaches “transforming each chemical identifier in the first array into a respective coded form having a range of values using a conversion module comprising code executing in the processor” (col. 31, lines 55-58) and biologic identifiers (col. 5, line 53).
Claim 1 recites populating the respective coded forms into a second array within the memory of the computer.
Brogle teaches “populating the respective coded vector forms into a second array within the memory of the computer” (col. 31, line 59-60).
Claim 1 recites generating a virtual n-dimensional array of nodes configured to encompass the
range of values in the second array using a node array generator module comprising code executing in the processor, each node of the virtual n-dimensional array having an associated weight vector value based on the range of values in the second array.
Brogle teaches “generating a virtual n-dimensional array of nodes configured to encompass the range of values in the second array using a node array generator module comprising code executing in the processor, each node of the virtual n-dimensional array having an associated weight vector value based on the range of values in the second array” (col. 31, lines 61-66).
Claim 1 recites placing each coded form in the second array into a node of the virtual n-dimensional array according to an unsupervised learning algorithm using a placement module
comprising code executing in the processor to effect a placement.
Brogle teaches “placing each coded form in the second array into a node of the virtual n-dimensional array according to an unsupervised learning algorithm using a placement module comprising code executing in the processor to effect a placement” (col. 32, lines 1-5).
Claim 1 recites outputting a visual representation of the virtual n-dimensional array.
Brogle teaches outputting a visual representation of the n-dimensional array (col. 32, lines 6-7).
Claim 2 recites transforming each biologic identifier in the first array into a respective coded form includes aligning each biologic identifier in the first array using a multiple sequence alignment algorithm implemented by the computer and converting the aligned biologic identifiers using a conversion array into respective coded forms, where the conversion array is a dimensionally reduced substitution matrix.
Brogle teaches using the processor to align the sequences for optimal comparison purposes (col. 20, line 1) and conversion using a substitution matrix for generating a numerical sequence (col. 13, lines 5-10).
Claim 3 recites selecting a target node among the nodes within the virtual n-dimensional array.
Brogle teaches selecting a target node among the nodes within the virtual n-dimensional array (col. 32, lines 8-9).
Claim 3 recites comparing, using a biologic feature (“BF”) module which comprises code executing in the processor, at least one BF corresponding to the coded form contained within a first node adjacent to the target node to at least one BF corresponding to the coded form contained in at least a second node adjacent to the target node, the first and second nodes sharing a border with the target node in the virtual n-dimensional array.
Brogle teaches comparing, using a chemical feature ("CF") module which comprises code executing in the processor, at least one CF corresponding to the coded form contained within a first node adjacent to the target node to at least one CF corresponding to the coded form contained in at least a second node adjacent to the target node, the first and second nodes sharing a border with the target node in the virtual n-dimensional array (col. 32, lines 11-19) and biologic identifiers (col. 5, line 53).
Claim 3 recites identifying common and non-common BFs between the target and second nodes using a commonality module which comprises code executing in the processor.
Brogle teaches identifying common CFs between the target and second nodes using a commonality module which comprises code executing in the processor (col. 32, lines 20-22) and biologic identifiers (col. 5, line 53).
Claim 3 recites generating at least one new coded form based on combinations of the identified, common and non-common BFs which, when inserted into the virtual n-dimensional array, results in a placement within the target node, using a coded form generator module which comprises code executing in the processor.
Brogle teaches generating at least one new coded form based on combinations of the identified, common CFs which, when inserted into the virtual n-dimensional array, results in a placement within the target node, using a coded form generator module which comprises code executing in the processor; and outputting a chemical identifier corresponding to the new coded form (col. 32, lines 23-28) and biologic identifiers (col. 5, line 53).
Claim 3 recites outputting a biological identifier corresponding to the new coded form.
Blake teaches outputting a chemical identifier corresponding to the new coded form (col. 32, lines 29-30) and biologic identifiers (col. 5, line 53).
Claim 4 recites selecting a first node among the nodes within the virtual n-dimensional array.
Brogle teaches selecting a first node among the nodes within the virtual n-dimensional array” (col. 32, lines 32-33).
Claim 4 recites comparing, using a biological feature (“BF”) module which comprises code executing in the processor, at least one BF corresponding to the coded form contained within the first node adjacent to at least one BF corresponding to the coded form contained in at least a second, adjacent node, the second node sharing a border with the first node in the virtual n-dimensional array.
Brogle teaches comparing, using a chemical feature ("CF") module which comprises code executing in the processor, at least one CF corresponding to the coded form contained within the first node adjacent to at least one CF corresponding to the coded form contained in at least a second, adjacent node, the second node sharing a border with the first node in the virtual n-dimensional array (col. 32, lines 34-41) and biologic identifiers (col. 5, line 53)..
Claim 4 recites identifying common and non-common CFs between the first and second nodes using a commonality module which comprises code executing in the processor.
Brogle teaches identifying common CFs between the first and second nodes using a commonality module which comprises code executing in the processor (col. 32, lines 42-44).
Claim 4 recites generating at least one new coded form based on combinations of the common and non-common BFs identified, which when inserted into the virtual n-dimensional array, results in a placement within the first or second node using a coded form generator module which comprises code executing in the processor; and outputting a biological identifier corresponding to the new coded form.
Brogle teaches generating at least one new coded form based on combinations of the identified, common BFs, which when inserted into the virtual n-dimensional array, results in a placement within the first or second node using a coded form generator module which comprises code executing in the processor; and outputting a chemical identifier corresponding to the new coded form (col. 32, lines 45-50).
Claim 5 recites selecting a first node among the nodes within the virtual n-dimensional array.
Brogle teaches selecting a first node among the nodes within the virtual n-dimensional array (col. 32, lines 32-33).
Claim 5 recites comparing, using a biological feature ("BF") module which comprises code executing in the processor, at least one BF corresponding to the coded form contained within the first node adjacent to at least one BF corresponding to the coded form contained in at least a second node, the second node sharing a border with the first node in the virtual n-dimensional array.
Brogle teaches comparing, using a chemical feature ("CF") module which comprises code executing in the processor, at least one CF corresponding to the coded form contained within the first node adjacent to at least one CF corresponding to the coded form contained in at least a second node, the second node sharing a border with the first node in the virtual n-dimensional array (col. 32, lines 34-41) and biologic identifiers (col. 5, line 53).
Claim 5 recites identifying common and non-common BFs between the first and second nodes using a commonality module which comprises code executing in the processor.
Brogle teaches identifying common CFs between the first and second nodes using a commonality module which comprises code executing in the processor (col. 32, lines 42-44) and biologic identifiers (col. 5, line 53).
Claim 5 recites generating at least one new coded form based on combinations of the identified, common and non-common BFs.
Brogle teaches generating at least one new coded form based on combinations of the identified, common CFs (col. 32, lines 45-46).
Claim 5 recites regenerating the n-dimensional node array to encompass the range of values stored in the second array including the new coded form such that, when inserted into the regenerated virtual n-dimensional array, the new coded form is placed in a node situated between the first and second nodes, using a coded form generator module which comprises code executing in the processor.
Brogle teaches regenerating the n-dimensional node array to encompass the range of values stored in the second array including the new coded form such that, when inserted into the regenerated virtual n-dimensional array, the new coded form is placed in a node situated between the first and second nodes, using a coded form generator module which comprises code executing in the processor (col. 33, lines 1-7).
Claim 5 recites outputting a biological identifier corresponding to the new coded form.
Brogle teaches outputting a chemical identifier corresponding to the new coded form (col. 33, lines 8-9-62) and biologic identifiers (col. 5, line 53).
Claim 6 recites generating a visual display indicating the addition of numerical forms to virtual n-dimensional array of nodes in the memory, wherein the addition of numerical forms concerns a common owner of the patent documents returned from the search, wherein the generating uses a time-series module comprising code executing in the processor.
Brogle teaches generating a visual display indicating the addition of numerical forms to virtual n-dimensional array of nodes in the memory, wherein the addition of numerical forms concerns a common owner of the patent documents returned from the search, wherein the generating uses a time-series module comprising code executing in the processor (col. 35, lines 14-20).
Claim 6 recites generating, using a time series plotting module comprising code executing in the processor, a time series plot indicating the publication of the patent documents over time.
Brogle teaches generating, using a time series plotting module comprising code executing in the processor, a time series plot indicating the publication of the patent documents over time (col. 35, lines 21-24).
Claim 6 recites extrapolating, with an extrapolating module comprising code executing in the
processor and based on the rate of publication of the patent documents and biologic identifiers extracted from the patent documents, a development path for an inventor or assignee; common to the patent documents returned from the search.
Brogle teaches extrapolating, with an extrapolating module comprising code executing in the processor and based on the rate of publication of the patent documents and chemical identifiers extracted from the patent documents, a development path for an inventor or assignee; common to the patent documents returned from the search (col. 35, lines 25-30).
Claim 6 recites generating a new biologic entity that when placed in virtual n-dimensional array of nodes occupies a node in the development path.
Brogle teaches generating a new chemical entity that when placed in virtual n-dimensional array of nodes occupies a node in the development path (col. 35, lines 31-33) and biologic identifiers (col. 5, line 53).
Claim 6 recites outputting a chemical formula corresponding to the new numerical value.
Brogle teaches outputting a chemical formula corresponding to the new numerical value (col. 35, lines 34-35).
Claim 7 recites generating, with a synthesis design module configured as code executing on the
processor to generate, based on the new biologic identifier, a synthesis strategy for synthesizing a biologic described by the biologic identifier.
Brogle teaches generating, with a synthesis design module configured as code executing on the processor to generate, based on the chemical identifier, a synthesis strategy for synthesizing a compound described by the chemical identifier (col. 34, lines 11-16) and that a biologic identifier “means a specific peptide, protein or nucleic acid or any amino acid, DNA or RNA sequences, or portions thereof” (col. 5, lines 53-57).
Claim 8 recites synthesizing a biopharmaceutical corresponding to the new biologic identifier
generated according to the synthesis strategy.
Brogle teaches synthesizing a biopharmaceutical corresponding to the new nucleotide biologic identifier generated according to the synthesis strategy (col. 4, lines 2-3).
Claim 9 recites the biologic identifiers are peptides, polypeptides, proteins, nucleotides, nucleotide sequences, or amino acid sequences.
Brogle teaches biological identifiers “means any schema used to identify a specific biologic entity or any portion thereof. For example a biologic identifier also means a specific peptide, protein or nucleic acid or any amino acid, DNA or RNA sequences, or portions thereof” (col. 5, lines 53-57).
Claim 10 recites biologic target is a protein, receptor, enzyme, or nucleic acid sequence that is associated with a form of cancer.
Brogle teaches the “biological target is selected from any type of cancer” (col. 12, line 20) and “nucleic molecules or residues, carbohydrates, fatty acids, peptides, monoclonal antibodies, polypeptides, proteins, natural and non-natural amino acids, and portions or fragments thereof” (col. 5, lines 49-52).
Claim 11 recites the biologic target is protein, receptor, enzyme, or nucleic acid sequence that is associated with a form of auto-immune disease.
Brogle teaches “the biological target is an autoimmune disorder” (col. 12, lines 22-23) and “nucleic molecules or residues, carbohydrates, fatty acids, peptides, monoclonal antibodies, polypeptides, proteins, natural and non-natural amino acids, and portions or fragments thereof” (col. 5, lines 49-52).
Regarding claims 1-13, the claimed invention by Brogle uses chemical identifiers as data being converted and input into the arrays. However, Brogle also discloses a broader “representational identifier” for representation of particular subject matter including nucleotide sequences and amino acid sequences (col. 5, lines 22-26) and specifically biologic identifiers (col. 5, lines 53-61). As the chemical and biologic identifiers are taught as interchangeable under the umbrella of representational identifiers, it is considered a simple substitution to substitute the claimed chemical identifiers with the disclosed biologic identifiers (MPEP 2143(I)(B)) and thus prima facie obvious to one having ordinary skill in the art.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4, 13-14, and 17-18 of U.S. Patent No. 10,013,467 in view of the disclosure of the U.S. Patent No. 10,013,467. Claims 1-4, 13-14, and 17-18 of U.S. Patent No. 10,013,467 disclose the limitations of claims 1-11 except for "chemical identifiers as data being converted and input into the arrays". However, Brogle also discloses a broader “representational identifier” for representation of particular subject matter including nucleotide sequences and amino acid sequences (col. 5, lines 22-26) and specifically biologic identifiers (col. 5, lines 53-61). The chemical and biologic identifiers are taught as interchangeable under the umbrella of representational identifiers. Once in their numerical form, there is not a difference in the data being chemical or biological. Therefore, one of ordinary skill in the art would be able to carry out such a substitution, and thus the invention is prima facie obvious.
Claims 1-11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10 of U.S. Patent No. 11,609,917 in view of the disclosure of U.S. Patent No. 11,609,917. The claimed invention by Blake uses identifiers as data being converted and input into the arrays. However, Blake also discloses a broader “representational identifier” for representation of particular subject matter including nucleotide sequences and amino acid sequences (col. 8, lines 44-48) and specifically biologic identifiers (col. 9, lines 7-15). The chemical and biologic identifiers are taught as interchangeable under the umbrella of representational identifiers. Once in their numerical form, there is not a difference in the data being chemical or biological. Therefore, one of ordinary skill in the art would be able to carry out such a substitution, and thus the invention is prima facie obvious.
Instant claim 1 is rejected in view of reference claim 1.
Instant claim 2 is rejected in view of Blake, where Blake teaches using the processor to align the sequences for optimal comparison purposes (col. 34, lines 38-39) and conversion using a substitution matrix for generating a numerical sequence (col. 28, lines 3-8).
Instant claim 3 is rejected in view of reference claim 2 and the disclosure of Blake.
Instant claim 4 is rejected in view of reference claim 3 and the disclosure of Blake.
Instant claim 5 is rejected in view of reference claim 4 and the disclosure of Blake.
Instant claim 6 is rejected in view of reference claim 5 and the disclosure of Blake.
Instant claim 7 is rejected in view of reference claim 6 and Blake, where Blake teaches generating, with a synthesis design module configured as code executing on the processor to generate, based on the new nucleotide identifier, a synthesis strategy for synthesizing a biologic described by the biologic identifier (col. 50, lines 2-6) and that a biologic identifier “means a specific peptide, protein or nucleic acid or any amino acid, DNA or RNA sequences, or portions thereof” (col. 9, lines 9-11).
Instant claim 8 is rejected in view of reference claim 7 and Blake, where Blake teaches synthesizing a biopharmaceutical corresponding to the new nucleotide biologic identifier generated according to the synthesis strategy (col. 50, lines 8-10).
Instant claim 9 is rejected in view of reference claim 8 and Blake, where Blake teaches the nucleotide identifiers are, nucleotide sequences, or amino acid sequences (col. 50, lines 12-13), and that a biologic identifier “means a specific peptide, protein or nucleic acid or any amino acid, DNA or RNA sequences, or portions thereof” (col. 9, lines 9-11).
Instant claim 10 is rejected in view of reference claim 9 and Blake, where Blake teaches the particular subject matter is a form of cancer (col. 50, lines 13-14).
Instant claim 11 is rejected in view of reference claim 10 and Blake, where Blake teaches the particular subject matter is a form of auto-immune disease (col. 50, lines 16-17).
Claims 1-11 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2 of copending Application No. 19/066,933 in view of Brogle (US 10,013,467 B1; previously cited on the 01 August 2022 IDS form).
This is a provisional nonstatutory double patenting rejection.
Instant claims 1-2 are taught by reference claims 1, where claim 1 teaches generating a new coded form based on common features and mapping in a virtual n-dimensional array, outputting an identifier, and generating a structured text document, and claim 2 teaches submitting a search to a database, extrapolating to a first array, transforming each biologic identifier, populating the respective coded forms, generating a virtual n-dimensional array, and placing the coded forms in a second array. The reference claims do not teach outputting a visual representation of the virtual n-dimensional array, which is taught by Brogle (col. 32, lines 6-7).
Claim 3 recites selecting a target node among the nodes within the virtual n-dimensional array.
Brogle teaches selecting a target node among the nodes within the virtual n-dimensional array (col. 32, lines 8-9).
Claim 3 recites comparing, using a biologic feature (“BF”) module which comprises code executing in the processor, at least one BF corresponding to the coded form contained within a first node adjacent to the target node to at least one BF corresponding to the coded form contained in at least a second node adjacent to the target node, the first and second nodes sharing a border with the target node in the virtual n-dimensional array.
Brogle teaches comparing, using a chemical feature ("CF") module which comprises code executing in the processor, at least one CF corresponding to the coded form contained within a first node adjacent to the target node to at least one CF corresponding to the coded form contained in at least a second node adjacent to the target node, the first and second nodes sharing a border with the target node in the virtual n-dimensional array (col. 32, lines 11-19) and biologic identifiers (col. 5, line 53).
Claim 3 recites identifying common and non-common BFs between the target and second nodes using a commonality module which comprises code executing in the processor.
Brogle teaches identifying common CFs between the target and second nodes using a commonality module which comprises code executing in the processor (col. 32, lines 20-22) and biologic identifiers (col. 5, line 53).
Claim 3 recites generating at least one new coded form based on combinations of the identified, common and non-common BFs which, when inserted into the virtual n-dimensional array, results in a placement within the target node, using a coded form generator module which comprises code executing in the processor.
Brogle teaches generating at least one new coded form based on combinations of the identified, common CFs which, when inserted into the virtual n-dimensional array, results in a placement within the target node, using a coded form generator module which comprises code executing in the processor; and outputting a chemical identifier corresponding to the new coded form (col. 32, lines 23-28) and biologic identifiers (col. 5, line 53).
Claim 3 recites outputting a biological identifier corresponding to the new coded form.
Blake teaches outputting a chemical identifier corresponding to the new coded form (col. 32, lines 29-30) and biologic identifiers (col. 5, line 53).
Claim 4 recites selecting a first node among the nodes within the virtual n-dimensional array.
Brogle teaches selecting a first node among the nodes within the virtual n-dimensional array” (col. 32, lines 32-33).
Claim 4 recites comparing, using a biological feature (“BF”) module which comprises code executing in the processor, at least one BF corresponding to the coded form contained within the first node adjacent to at least one BF corresponding to the coded form contained in at least a second, adjacent node, the second node sharing a border with the first node in the virtual n-dimensional array.
Brogle teaches comparing, using a chemical feature ("CF") module which comprises code executing in the processor, at least one CF corresponding to the coded form contained within the first node adjacent to at least one CF corresponding to the coded form contained in at least a second, adjacent node, the second node sharing a border with the first node in the virtual n-dimensional array (col. 32, lines 34-41) and biologic identifiers (col. 5, line 53)..
Claim 4 recites identifying common and non-common CFs between the first and second nodes using a commonality module which comprises code executing in the processor.
Brogle teaches identifying common CFs between the first and second nodes using a commonality module which comprises code executing in the processor (col. 32, lines 42-44).
Claim 4 recites generating at least one new coded form based on combinations of the common and non-common BFs identified, which when inserted into the virtual n-dimensional array, results in a placement within the first or second node using a coded form generator module which comprises code executing in the processor; and outputting a biological identifier corresponding to the new coded form.
Brogle teaches generating at least one new coded form based on combinations of the identified, common BFs, which when inserted into the virtual n-dimensional array, results in a placement within the first or second node using a coded form generator module which comprises code executing in the processor; and outputting a chemical identifier corresponding to the new coded form (col. 32, lines 45-50).
Claim 5 recites selecting a first node among the nodes within the virtual n-dimensional array.
Brogle teaches selecting a first node among the nodes within the virtual n-dimensional array (col. 32, lines 32-33).
Claim 5 recites comparing, using a biological feature ("BF") module which comprises code executing in the processor, at least one BF corresponding to the coded form contained within the first node adjacent to at least one BF corresponding to the coded form contained in at least a second node, the second node sharing a border with the first node in the virtual n-dimensional array.
Brogle teaches comparing, using a chemical feature ("CF") module which comprises code executing in the processor, at least one CF corresponding to the coded form contained within the first node adjacent to at least one CF corresponding to the coded form contained in at least a second node, the second node sharing a border with the first node in the virtual n-dimensional array (col. 32, lines 34-41) and biologic identifiers (col. 5, line 53).
Claim 5 recites identifying common and non-common BFs between the first and second nodes using a commonality module which comprises code executing in the processor.
Brogle teaches identifying common CFs between the first and second nodes using a commonality module which comprises code executing in the processor (col. 32, lines 42-44) and biologic identifiers (col. 5, line 53).
Claim 5 recites generating at least one new coded form based on combinations of the identified, common and non-common BFs.
Brogle teaches generating at least one new coded form based on combinations of the identified, common CFs (col. 32, lines 45-46).
Claim 5 recites regenerating the n-dimensional node array to encompass the range of values stored in the second array including the new coded form such that, when inserted into the regenerated virtual n-dimensional array, the new coded form is placed in a node situated between the first and second nodes, using a coded form generator module which comprises code executing in the processor.
Brogle teaches regenerating the n-dimensional node array to encompass the range of values stored in the second array including the new coded form such that, when inserted into the regenerated virtual n-dimensional array, the new coded form is placed in a node situated between the first and second nodes, using a coded form generator module which comprises code executing in the processor (col. 33, lines 1-7).
Claim 5 recites outputting a biological identifier corresponding to the new coded form.
Brogle teaches outputting a chemical identifier corresponding to the new coded form (col. 33, lines 8-9-62) and biologic identifiers (col. 5, line 53).
Claim 6 recites generating a visual display indicating the addition of numerical forms to virtual n-dimensional array of nodes in the memory, wherein the addition of numerical forms concerns a common owner of the patent documents returned from the search, wherein the generating uses a time-series module comprising code executing in the processor.
Brogle teaches generating a visual display indicating the addition of numerical forms to virtual n-dimensional array of nodes in the memory, wherein the addition of numerical forms concerns a common owner of the patent documents returned from the search, wherein the generating uses a time-series module comprising code executing in the processor (col. 35, lines 14-20).
Claim 6 recites generating, using a time series plotting module comprising code executing in the processor, a time series plot indicating the publication of the patent documents over time.
Brogle teaches generating, using a time series plotting module comprising code executing in the processor, a time series plot indicating the publication of the patent documents over time (col. 35, lines 21-24).
Claim 6 recites extrapolating, with an extrapolating module comprising code executing in the
processor and based on the rate of publication of the patent documents and biologic identifiers extracted from the patent documents, a development path for an inventor or assignee; common to the patent documents returned from the search.
Brogle teaches extrapolating, with an extrapolating module comprising code executing in the processor and based on the rate of publication of the patent documents and chemical identifiers extracted from the patent documents, a development path for an inventor or assignee; common to the patent documents returned from the search (col. 35, lines 25-30).
Claim 6 recites generating a new biologic entity that when placed in virtual n-dimensional array of nodes occupies a node in the development path.
Brogle teaches generating a new chemical entity that when placed in virtual n-dimensional array of nodes occupies a node in the development path (col. 35, lines 31-33) and biologic identifiers (col. 5, line 53).
Claim 6 recites outputting a chemical formula corresponding to the new numerical value.
Brogle teaches outputting a chemical formula corresponding to the new numerical value (col. 35, lines 34-35).
Claim 7 recites generating, with a synthesis design module configured as code executing on the
processor to generate, based on the new biologic identifier, a synthesis strategy for synthesizing a biologic described by the biologic identifier.
Brogle teaches generating, with a synthesis design module configured as code executing on the processor to generate, based on the chemical identifier, a synthesis strategy for synthesizing a compound described by the chemical identifier (col. 34, lines 11-16) and that a biologic identifier “means a specific peptide, protein or nucleic acid or any amino acid, DNA or RNA sequences, or portions thereof” (col. 5, lines 53-57).
Claim 8 recites synthesizing a biopharmaceutical corresponding to the new biologic identifier
generated according to the synthesis strategy.
Brogle teaches synthesizing a biopharmaceutical corresponding to the new nucleotide biologic identifier generated according to the synthesis strategy (col. 4, lines 2-3).
Claim 9 recites the biologic identifiers are peptides, polypeptides, proteins, nucleotides, nucleotide sequences, or amino acid sequences.
Brogle teaches biological identifiers “means any schema used to identify a specific biologic entity or any portion thereof. For example a biologic identifier also means a specific peptide, protein or nucleic acid or any amino acid, DNA or RNA sequences, or portions thereof” (col. 5, lines 53-57).
Claim 10 recites biologic target is a protein, receptor, enzyme, or nucleic acid sequence that is associated with a form of cancer.
Brogle teaches the “biological target is selected from any type of cancer” (col. 12, line 20) and “nucleic molecules or residues, carbohydrates, fatty acids, peptides, monoclonal antibodies, polypeptides, proteins, natural and non-natural amino acids, and portions or fragments thereof” (col. 5, lines 49-52).
Claim 11 recites the biologic target is protein, receptor, enzyme, or nucleic acid sequence that is associated with a form of auto-immune disease.
Brogle teaches “the biological target is an autoimmune disorder” (col. 12, lines 22-23) and “nucleic molecules or residues, carbohydrates, fatty acids, peptides, monoclonal antibodies, polypeptides, proteins, natural and non-natural amino acids, and portions or fragments thereof” (col. 5, lines 49-52).
Regarding claims 1-11, the combination of the reference application and Brogle would be obvious because Brogle teaches the same visualization and its benefit, which is taught as commercially available (col. 17, fifth paragraph). The prior art are drawn to the shared field of endeavor of generating and populating an n-dimensional array and as such their combination is prima facie obvious.
Conclusion
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/R.J.K./Examiner, Art Unit 1685
/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685