Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
2. This communication is responsive to the amendment filed on 10/29/2025.
3. Claims 1-2, 4-6, 8-10 and 12 are currently pending in this Office action. This action is made Final.
Information Disclosure Statement
4. The information disclosure statement (IDS) filed on 01/13/2026 is being considered by the examiner.
Claim Rejections - 35 USC § 112
5. The 35 U.S.C. 112 second paragraph rejections made in the prior Office action are withdrawn. However, new 112 rejections are presented as shown below:
6. 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.
7. Claims 2-7, 9-14 and 16-20 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claims 1, 5 and 9, claim 1 recites the phrase of “a set of codon bitmaps corresponding to the one or more codons associated with the each amino acid” [emphasis added] in lines 19-20. However, it is unclear how the phrase of “a set of codon bitmaps” is related to the phrase of “a plurality of codon bitmaps” in line 9 and/or “the set of codon bitmaps” in line 24. Clarification is required. Additionally, claim 1 recites the limitation of “each correspondence indicating a respective amino acid of a plurality of amino acids in association with one or more codons correspondence between amino acids and codons” in lines 6-8. However, it is unclear how the phrase of “amino acids and codons” is related to the phrases of “a plurality of amino acids” or “one or more codons.” Again, it is unclear how they are related to each other. Clarification is required. Furthermore, claim 1 recites the limitation of “generating, for each amino acid of the plurality of amino acids” in line 14. However, it is unclear how the phrase of “each amino acid” is related to the phrase of “a respective amino acid of a plurality of amino acids” in line 7 and/or “between amino acids and codons” in line 8. It is unclear how they are related to each other. Clarification is required. In addition, claim 1 recites the phrase of “the amino acid bit map” in line 25. It is unclear if this phrase is referring to the phrase of “an amino acid bitmap” in lines 14-15. Clarification is required. Claim 1 also recites the phrase of “a position of an amino acid on the codon file” in lines 28-29. However, it is unclear how the phrase of “a position” is related to the phrases of “positions of each amino acid” in line 29 and/or “a position of each of the amino acid sequences” in lines 34-35. It is unclear how they are related to each other. Clarification is required. It is noted that claims 5 and 9 recite the similar limitations of claim 1. Thus, claims 5 and 9 are rejected due to the similar reasons set forth regarding claim 1.
Regarding claims 4, 8 and 12, claim 4 recites the limitation "the calculating includes calculating a bitmap of the amino acid transposition index of one amino acid" in lines 2-3. There is insufficient antecedent basis for this limitation [“the calculating”] in the claim. Clarification/correction is required. Additionally, it is unclear how the phrase of “calculating a bitmap of the amino acid transposition index” is related to the phrase of “the generated amino acid bitmaps” in lines 26-27 of claim 1. Clarification is required. It is noted that claims 8 and 12 recite the similar limitations of claim 4. Thus, claims 8 and 12 are rejected due to the similar reasons set forth regarding claim 4.
Though a claim is read in view of the specification, the specification does not shed any light as to the meaning of these phrases. Therefore, the examiner finds it unclear as to what the language of claims 1, 5 and 9 is directed. When the claims become so ambiguous that one of ordinary skill in the art cannot determine their scope absent speculation, such claims are invalid for indefiniteness. Because the examiner concludes that there are significant ambiguities with respect to the independent claims and thus to each of the claims depending therefrom, no patentability based on art against claims 1-2, 4-6, 8-10 and 12 will be applied at this time.
Claims not specifically mentioned above are also rejected in virtue of their dependency on a rejected claim.
Claim Rejections - 35 USC § 101
8. Applicant’s arguments [pages 9-14 of Remarks filed on 10/29/2026] are not persuasive. Again, when the claims are considered as a whole, they do not integrate the abstract idea into a practical application; they do not confine the use of the abstract idea to a particular technology; they do not solve a problem rooted in or arising from the use of a particular technology; they do not improve a technology by allowing the technology to perform a function that it previously was not capable of performing; and they do not provide any limitations beyond generally linking the use of the abstract idea to a particular technological environment and/or field of use. More specifically, the claims do not disclose any specific computational steps by which a computer performs or carries out the abstract idea, nor do they provide any details of how specific structures of a computer are used to implement these functions. Thus, the examiner maintains the rejection as set forth below:
9. Claims 1-2, 4-6, 8-10 and 12 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The judicial exception is not integrated into a practical application. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception. The eligibility analysis in support of these findings is provided below, in accordance with the 2019 Revised Patent Subject Matter Eligibility Guidance, hereinafter 2019 PEG.
Step 1. In accordance with Step 1 of the eligibility inquiry (as explained in MPEP 2106), it is noted that the method(s) of claims 1-2, 4-6, 8-10 and 12 are directed to one of the eligible categories of subject matter and therefore satisfy Step 1.
Step 2A. In accordance with Step 2A, prog one of the 2019 PEG:
In claim 1-2 and 4, the limitations directed to additional elements include: a non-transitory computer-readable medium; in claims 9-10 and 12, the limitations directed to additional elements include: an apparatus, one or more memories.
In exemplary claims 1, 5 or 9, limitations reciting the abstract idea are as follows:
(1) generating a codon transposition index based on the codon file and definition table; (2) generating, for each amino acid of the plurality of amino acids, an amino acid bitmap; (3) obtaining a correspondence associated with the each amino acid, identifying a set of codon bitmaps corresponding to the one or more codons associated with the ach amino acid, performing a logical or operation on the set of codon bitmaps to generate the amino acid bit map of the each amino acid; (3) generating an amino acid transposition index by collecting the generated amino acid bitmaps for the plurality of amino acids; (5) identifying positions of amino acid sequences repeatedly expressed in the codon file; (6) specifying each codon sequence corresponding to a position of each of the amino acid sequences; and (7) specifying a symmetrical amino acid sequence in which an arrangement is reversed and specifying each codon sequence corresponding to a position of the specified symmetrical amino acid sequence.
These limitations, under the broadest reasonable interpretation, recite mental processes because these limitations can be performed in the human mind or using pen and paper. The examiner believes that the steps disclosed in claim 1 [calculating, identifying, specifying] can be performed by a human, using observation, evaluation, and judgment, because the steps involve making identifications and determinations, which are mental tasks humans routinely perform in the course of producing and performing queries.
A claim recites a mental process when the claim encompasses acts the person can perform using the mind or pen and paper [determining that a claim whose ‘steps can be performed in the human mind, or by a human using a pen and paper’ is directed to an unpatentable mental process]. This is true even if the claim recites, as they do here, that a generic computer component performs the acts.
For example, a person can perform the “generating” step by simply gathering the codon and amino acid data in a table. A person can perform the “calculating” step by simply looking at and reading the position of an amino acid on a file. A person can also perform the “identifying” step by evaluating the positions expressed in the codon file, evaluate the second index. Finally, a person can perform the “specifying” step by manually evaluating each codon sequence comparing to a position of each amino acid; evaluating the arrangement order and evaluating the specified symmetrical amino acid sequence.
As noted above, if a claim, under its broadest reasonable interpretation, covers performance in the mind but for the recitation of generic computer components, then it is still in the mental processes category unless the claim cannot practically be performed in the mind. Here, the examiner is not persuaded that the aforementioned steps in claims 1, 5 or 9 cannot practically be performed in the human minds, or using pen and paper, but for the generic computing device.
Step 2A. In accordance with Step 2A, prog two of the 2019 PEG:
With respect to Step 2A, prog two, the judicial exception is not integrated into a practical application. The additional elements are directed to a non-transitory computer-readable medium, a computer an apparatus, one or more memories. However, these elements do not (1) improve the functioning of a computer or other technology; (2) are not applied with any particular machine (except for a generic computer); (3) do not effect a transformation of a particular article to a different state; and (4) are not applied in any meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception. In other words, the aforementioned additional element (or combination of elements) recited in the claims do not integrate the judicial exception into a practical application.
In other words, the claimed processes fail to improve the functioning of either the non-transitory computer-readable medium; an apparatus, one or more memories. Rather, these additional elements merely link the underlying abstract idea (i.e., mental processes or using pen and paper) to a particular technological environment, i.e., analyzing data. Thus, the claimed process uses conventional computers to automate tasks that would have otherwise been very labor intensive by a human searcher. Such claims are not patent eligible. See OIP Techs., Inc., v. Amazon.com, Inc., 788 F.3d 1359, 1363 (Fed. Cir. 2015) (“relying on a computer to perform routine tasks more quickly or more accurately is insufficient to render a claim patent eligible”).
Since the analysis of Step 2A prong one and prong two results in the conclusion that the claims are directed to an abstract idea, additional analysis under Step 2B of the eligibility inquiry must be conducted in order to determine whether any claim element or combination of elements amount to significantly more than the judicial exception.
Step 2B. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception. The additional limitations are directed to a non-transitory computer-readable medium, an apparatus, one or more memories at a very high level of generality and without imposing meaningful limitations on the scope of the claim. Such general-purpose computing device, high-level, and nominal involvement of a computer or computer-based elements for carrying out the invention merely serves to tie the abstract idea to a particular technological environment, which is not enough to render the claims patent-eligible.
The additional elements are broadly applied to the abstract idea at a high level of generality and they operate in a well-understood, routine, and conventional manner. Courts have held computer-implemented processes not to be significantly more than an abstract idea (and thus ineligible) where the claim as a whole amount to nothing more than generic computer functions merely used to implement an abstract idea, such as an idea that could be done by a human analog.
The dependent claims have been fully considered, however, similar to the findings for claims above, these claims are similarly directed to the “Mental Processes” grouping of abstract ideas set forth in the 2019 PEG, without integrating it into a practical application and with, at most, a general-purpose computer that serves to tie the idea to a particular technological environment, which does not add significantly more to the claims. The ordered combination of elements in the dependent claims (including the limitations inherited from the parent claim(s)) add nothing that is not already present as when the elements are taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. The collective functions merely provide conventional computer implementation. Accordingly, the subject matter encompassed by the dependent claims fail to amount to significantly more than the abstract idea.
Conclusion
10. 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MONICA M PYO whose telephone number is (571)272-8192. The examiner can normally be reached Monday-Friday 8am-4pm.
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/MONICA M PYO/Primary Examiner, Art Unit 2161